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@article{Miller2006,
abstract = {The first step in the encounter between a host and a pathogen is attachment to the host epithelium. For uropathogenic Escherichia coli, these interactions are mediated by type 1 and P adhesive pili, which are long (approximately 1 microm) rods composed of more than 1000 protein subunits arranged in a helical structure. Here we used single-molecule atomic force microscopy to study the mechanical properties of type 1 pili. We found that type 1 pili readily extend under an applied force and that this extensibility is the result of unwinding the pilus rod's helical quaternary structure. The forced unraveling is also reversible, with helical rewinding taking place under considerable forces (approximately 60 pN). These data are similar to those obtained on P pili using optical tweezers, indicating that these are conserved properties of uropathogenic E. coli pili. We also show that our data can readily be reproduced using Monte Carlo simulation techniques based on a two-state kinetic model. This model provides a simple way to extrapolate the mechanical behavior of pili under a wide range of forces. We propose that type 1 pilus unraveling is an essential mechanism for absorbing physiological shear forces encountered during urinary tract infections and probably essential for adhesion and colonization of the bladder epithelium.},
author = {Miller, Eric and Garcia, Tzintzuni and Hultgren, Scott J and Oberhauser, Andres F},
doi = {10.1529/biophysj.106.088989},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Miller et al. - The mechanical properties of E. coli type 1 pili measured by atomic force microscopy techniques. - 2006.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Atomic Force,Atomic Force: methods,Bacterial,Bacterial: physiology,Biological,Biomechanics,Computer Simulation,Elasticity,Escherichia coli,Escherichia coli: physiology,Fimbriae,Mechanical,Microscopy,Models,Shear Strength,Stress},
month = {nov},
number = {10},
pages = {3848--56},
pmid = {16950852},
title = {{The mechanical properties of E. coli type 1 pili measured by atomic force microscopy techniques.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1630485{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {91},
year = {2006}
}
@article{Manuscript2013,
author = {Manuscript, Author},
doi = {10.1038/mi.2011.41.Secretory},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Manuscript - NIH Public Access - 2013.pdf:pdf},
number = {6},
pages = {603--611},
title = {{NIH Public Access}},
volume = {4},
year = {2013}
}
@article{Bjornham2010,
author = {Bj{\"{o}}rnham, Oscar and Axner, Ove},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bj{\"{o}}rnham, Axner - Catch-Bond Behavior of Bacteria Binding by Slip Bonds - 2010.pdf:pdf},
journal = {Biophysical journal},
number = {5},
pages = {1331--1341},
title = {{Catch-Bond Behavior of Bacteria Binding by Slip Bonds}},
volume = {99},
year = {2010}
}
@article{Hahn2002a,
annote = {From Duplicate 2 ( Exploring the 3D Molecular Architecture of Escherichia coli Type 1 Pili - Hahn, Erik; Wild, Peter; Hermanns, Uta; Sebbel, Peter; Glockshuber, Rudi; H{\"{a}}ner, Marcus; Taschner, Nicole; Burkhard, Peter; Aebi, Ueli; M{\"{u}}ller, Shirley a. )
},
author = {Hahn, Erik and Wild, Peter and Hermanns, Uta and Sebbel, Peter and Glockshuber, Rudi and H{\"{a}}ner, Marcus and Taschner, Nicole and Burkhard, Peter and Aebi, Ueli and M{\"{u}}ller, Shirley a.},
doi = {10.1016/S0022-2836(02)01005-7},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hahn et al. - Exploring the 3D Molecular Architecture of Escherichia coli Type 1 Pili - 2002.pdf:pdf},
issn = {00222836},
journal = {Journal of Molecular Biology},
keywords = {3d model,electron microscopy,fimh,immuno-gold labeling,pilus,scanning transmission},
month = {nov},
number = {5},
pages = {845--857},
title = {{Exploring the 3D Molecular Architecture of Escherichia coli Type 1 Pili}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0022283602010057},
volume = {323},
year = {2002}
}
@article{Polikanov2007,
abstract = {Numerous biological processes are regulated by DNA elements that communicate with their targets over a distance via formation of protein-bridged DNA loops. One of the first questions arising in studies of DNA looping is whether the rate of loop formation is limited by diffusion of the DNA sites. We addressed this question by comparing the in vitro measured rates of transcription initiation in the NtrC-glnAp2 enhancer-dependent transcription initiation system with predictions of two different theoretical models. The promoter and enhancer were in a 7.6-kb plasmid and separated by 2.5 kb. The measurements were performed for different values of the plasmid superhelix density, from 0 to -0.07. Earlier theoretical analysis, based on the Monte Carlo simulation of DNA conformations, showed that if the rate of loop formation is determined by the equilibrium probability of juxtaposition of the DNA sites, the rate should be approximately 100 times higher in supercoiled than in relaxed DNA. On the other hand, Brownian dynamics simulation showed that if the rate of loop formation is limited by the site diffusion, it should be nearly independent of DNA supercoiling. We found that efficiency of the transcription initiation increases by nearly two orders of magnitude as a result of the corresponding increase of the template supercoiling. This clearly shows that the rate of bridging in the enhancer-promoter system is not limited by diffusion of the DNA sites to one another. We argue that this conclusion derived for the specific system is likely to be valid for the great majority of biological processes involving protein-mediated DNA looping.},
author = {Polikanov, Yury S and Bondarenko, Vladimir a and Tchernaenko, Vladimir and Jiang, Yong I and Lutter, Leonard C and Vologodskii, Alexander and Studitsky, Vasily M},
doi = {10.1529/biophysj.107.111245},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Polikanov et al. - Probability of the site juxtaposition determines the rate of protein-mediated DNA looping. - 2007.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Binding Sites,Computer Simulation,DNA,DNA-Binding Proteins,DNA-Binding Proteins: chemistry,DNA-Binding Proteins: ultrastructure,DNA: chemistry,DNA: ultrastructure,Models, Chemical,Models, Molecular,Models, Statistical,Nucleic Acid Conformation,Protein Binding,Protein Conformation},
month = {oct},
number = {8},
pages = {2726--31},
pmid = {17573434},
publisher = {Elsevier},
title = {{Probability of the site juxtaposition determines the rate of protein-mediated DNA looping.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1989718{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {93},
year = {2007}
}
@article{Etec1996,
author = {Etec, Eschericbia},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Etec - Colonization factors of - 1996.pdf:pdf},
number = {11},
title = {{Colonization factors of}},
year = {1996}
}
@article{VanDerWoude2006,
abstract = {Phase variation in bacteria is often considered a random process that has evolved to facilitate immune evasion in a host. Here, alternative biological roles for this process are presented and discussed, incorporating recent studies on nonpathogenic and commensal bacterial species. Furthermore, the integration of phase variation into bacterial regulatory networks and the relevance of this for considering phase variation as a random process are reviewed. Novel approaches are needed to study phase variation and its biological roles, but the insights obtained can contribute significantly to our understanding of the dynamic behaviour of bacterial populations and their interactions with the environment.},
author = {{Van Der Woude}, Marjan W.},
doi = {10.1111/j.1574-6968.2005.00038.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Van Der Woude - Re-examining the role and random nature of phase variation - 2006.pdf:pdf},
isbn = {0378-1097 (Print)$\backslash$r0378-1097 (Linking)},
issn = {03781097},
journal = {FEMS Microbiology Letters},
keywords = {Adhesion,Biofilm,Gene regulation,Immune evasion,Phase variation,Review},
number = {2},
pages = {190--197},
pmid = {16445745},
title = {{Re-examining the role and random nature of phase variation}},
volume = {254},
year = {2006}
}
@article{Pan2011,
author = {Pan, Lili and Chu, Wen-sheng and Saragih, Jason M and Torre, Fernando De and Xie, Mei},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Pan et al. - With Probabilistic Pairwise Voting - 2011.pdf:pdf},
number = {11},
pages = {639--642},
title = {{With Probabilistic Pairwise Voting}},
volume = {18},
year = {2011}
}
@article{Evans1975,
abstract = {k88, colonization,},
author = {Evans, D G and Silver, R P and Evans jr, D J and Chase, D G and Gorbach, S L},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans et al. - Plasmid-controlled colonization factor associated with virulence in Escherichia coli entrotoxigenic for humans. - 1975.pdf:pdf},
journal = {Infect. Immun.},
number = {3},
pages = {656--667},
title = {{Plasmid-controlled colonization factor associated with virulence in Escherichia coli entrotoxigenic for humans.}},
volume = {12},
year = {1975}
}
@article{King2001,
abstract = {A novel numerical simulation of adhesive particles (cells) reversibly interacting with an adhesive surface under flow is presented. Particle--particle and particle--wall hydrodynamic interactions in low Reynolds number Couette flow are calculated using a boundary element method that solves an integral representation of the Stokes equation. Molecular bonds between surfaces are modeled as linear springs and stochastically formed and broken according to postulated descriptions of force-dependent kinetics. The resulting simulation, Multiparticle Adhesive Dynamics, is applied to the problem of selectin-mediated rolling of hard spheres coated with leukocyte adhesion molecules (cell-free system). Simulation results are compared to flow chamber experiments performed with carbohydrate-coated spherical beads rolling on P-selectin. Good agreement is found between theory and experiment, with the main observation being a decrease in rolling velocity with increasing concentration of rolling cells or increasing proximity between rolling cells. Pause times are found to increase and deviation motion is found to decrease as pairs of rolling cells become closer together or align with the flow.},
annote = {        From Duplicate 1 (                           Multiparticle adhesive dynamics. Interactions between stably rolling cells.                         - King, M R; Hammer, D a )
                
        
        
      },
author = {King, M R and Hammer, D a},
doi = {10.1016/S0006-3495(01)75742-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley//King, Hammer - Multiparticle adhesive dynamics. Interactions between stably rolling cells. - 2001.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//King, Hammer - Multiparticle adhesive dynamics. Interactions between stably rolling cells. - 2001.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Algorithms,Biological,Cell Adhesion,Cell Movement,Cell-Free System,Computer Simulation,Flow,Leukocytes,Leukocytes: cytology,Leukocytes: metabolism,Microspheres,Models,Simulation,shear force,stokes},
mendeley-tags = {Flow,Simulation,shear force,stokes},
month = {aug},
number = {2},
pages = {799--813},
pmid = {11463626},
publisher = {Elsevier},
title = {{Multiparticle adhesive dynamics. Interactions between stably rolling cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1301554{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {81},
year = {2001}
}
@article{Koster2003,
abstract = {The tubular morphology of intracellular membranous compartments is actively maintained through interactions with motor proteins and the cytoskeleton. Moving along cytoskeletal elements, motor proteins exert forces on the membranes to which they are attached, resulting in the formation of membrane tubes and tubular networks. To study the formation of membrane tubes by motor proteins, we developed an in vitro assay consisting of purified kinesin proteins directly linked to the lipids of giant unilamellar vesicles. When the vesicles are brought into contact with a network of immobilized microtubules, membrane tubes and tubular networks are formed. Through systematic variation of the kinesin concentration and membrane composition we study the mechanism involved. We show that a threshold concentration of motor proteins is needed and that a low membrane tension facilitates tube formation. Forces involved in tube formation were measured directly with optical tweezers and are shown to depend only on the tension and bending rigidity of the membrane. The forces were found to be higher than can be generated by individual motor proteins, indicating that multiple motors were working together to pull tubes. We propose a simple mechanism by which individual motor proteins can dynamically associate into clusters that provide the force needed for the formation of tubes, explaining why, in contrast to earlier findings [Roux, A., Cappello, G., Cartaud, J., Prost, J., Goud, B. {\&} Bassereau, P. (2002) Proc. Natl. Acad. Sci. USA 99, 5394-5399], motor proteins do not need to be physically linked to each other to be able to pull tubes.},
author = {Koster, Gerbrand and Vanduijn, Martijn and Hofs, Bas and Dogterom, Marileen},
doi = {10.1073/pnas.2531786100},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Koster et al. - Membrane tube formation from giant vesicles by dynamic association of motor proteins. - 2003.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Biological,Cell Membrane,Cell Membrane: ultrastructure,Cytoskeleton,Cytoskeleton: physiology,Cytoskeleton: ultrastructure,Lipid Bilayers,Lipid Bilayers: chemistry,Mechanical,Models,Organelles,Organelles: ultrastructure,Stress,Tubulin,Tubulin: chemistry,Tubulin: ultrastructure},
month = {dec},
number = {26},
pages = {15583--8},
pmid = {14663143},
title = {{Membrane tube formation from giant vesicles by dynamic association of motor proteins.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=307611{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {100},
year = {2003}
}
@article{Ryu2010,
abstract = {Contraction of Vortlcella convallaria, a sessile ciliated protozoan, is completed within a few milliseconds and results in a retraction of its cell body toward the substratum by coiling its stalk. Previous studies have modeled the cell body as a sphere and assumed a drag force that satisfies Stokes' law. However, the contraction-induced flow of the medium is transient and bounded by the substrate, and the maximum Reynolds number is larger than unity. Thus, calculations of contractile force from the drag force are incomplete. In this study, we analyzed fluid flow during contraction by the particle tracking velocimetry and computational fluid dynamics simulations to estimate the contractile force. Particle paths show that the induced flow is limited by the substrate. Simulation-based force estimates suggest that the combined effect of the flow unsteadiness, the finite Reynolds number, and the substrate comprises 35{\%} of the total force. The work done in the early stage of contraction and the maximum power output are similar regardless of the medium viscosity. These results suggest that, during the initial development of force, V. convallaria uses a common mechanism for performing mechanical work irrespective of viscous loading conditions. ?? 2010 by the Biophysical Society.},
author = {Ryu, Sangjin and Matsudaira, Paul},
doi = {10.1016/j.bpj.2010.02.025},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ryu, Matsudaira - Unsteady motion, finite Reynolds numbers, and wall effect on Vorticella convallaria contribute contraction force great.pdf:pdf},
issn = {00063495},
journal = {Biophysical Journal},
number = {11},
pages = {2574--2581},
pmid = {20513401},
publisher = {Biophysical Society},
title = {{Unsteady motion, finite Reynolds numbers, and wall effect on Vorticella convallaria contribute contraction force greater than the Stokes drag}},
url = {http://dx.doi.org/10.1016/j.bpj.2010.02.025},
volume = {98},
year = {2010}
}
@article{Ochoa2010,
author = {Ochoa, Theresa J. and Rivera, Fulton P. and Bernal, Maria and Meza, Rina and Ecker, Lucie and Gil, Ana I. and Cepeda, David and Mosquito, Susan and Mercado, Erik and Maves, Ryan C. and Hall, Eric R. and Svennerholm, Ann-Mari and McVeigh, Annette and Savarino, Stephen J and Lanata, Claudio F.},
doi = {10.1111/j.1574-695X.2010.00730.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ochoa et al. - Detection of the CS20 colonization factor antigen in diffuse-adhering Escherichia coli strains - 2010.pdf:pdf},
issn = {09288244},
journal = {FEMS Immunology {\&} Medical Microbiology},
keywords = {colonization factor antigens,diarrhea,diarrheagenic escherichia coli,diffusely adherent escherichia coli,enterotoxigenic,escherichia coli},
month = {nov},
number = {2},
pages = {186--189},
title = {{Detection of the CS20 colonization factor antigen in diffuse-adhering Escherichia coli strains}},
url = {http://doi.wiley.com/10.1111/j.1574-695X.2010.00730.x},
volume = {60},
year = {2010}
}
@article{Wright2007,
abstract = {Abstract{\&}nbsp;{\&}nbsp;A short review of the use of optical tweezers in fungal cell biological research is provided. First, we describe how optical tweezers work. Second, we review how they have been used in various experimental live-cell studies to manipulate intracellular organelles, hyphal growth and branching, and whole cells. Third, we indicate how optically trapped microbeads can be used for the localized delivery of chemicals or mechanical stimulation to cells, as well as permitting measurements of the growth forces generated by germ tubes. Finally, the effects of optical trapping on fungal cell viability and growth are assessed.},
author = {Wright, Graham D. and Arlt, Jochen and Poon, W. C K and Read, Nick D.},
doi = {10.1007/s10267-006-0326-4},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wright et al. - Experimentally manipulating fungi with optical tweezers - 2007.pdf:pdf},
issn = {13403540},
journal = {Mycoscience},
keywords = {Germ tubes,Hyphal tip growth,Neurospora crassa,Optical tweezers,Spitzenk??rper},
number = {1},
pages = {15--19},
title = {{Experimentally manipulating fungi with optical tweezers}},
url = {http://dx.doi.org/10.1007/S10267-006-0326-4},
volume = {48},
year = {2007}
}
@article{Stamm2001,
author = {Stamm, W E and Norrby, S R},
doi = {10.1086/318850},
isbn = {0022-1899 (Print)$\backslash$n0022-1899 (Linking)},
issn = {0022-1899},
journal = {The Journal of infectious diseases},
pages = {S1--S4},
pmid = {11171002},
title = {{Urinary tract infections: disease panorama and challenges.}},
volume = {183 Suppl },
year = {2001}
}
@article{Han,
author = {Han, L I N and Lui, Bertrand and Blumberg, Seth and Beausang, John F and Nelson, Philip C and Phillips, R O B},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Han et al. - Calibration of tethered particle motion experiments - Unknown.pdf:pdf},
journal = {Idea},
keywords = {91125,92c37,ams,brownian motion,calibration,california institute of technology,department of applied physics,dna,keck foundation,mos,national science foundation grants,partially supported by the,pasadena ca,primary 92c05,secondary 92c40,single molecule,subject classifications,tethered particle},
pages = {1--16},
title = {{Calibration of tethered particle motion experiments}}
}
@article{Kaibuchi1999,
author = {Kaibuchi, K and Kuroda, S and Amano, M},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kaibuchi, Kuroda, Amano - R Egulation of the C Ytoskeleton and C Ell a Dhesion By the R Ho F Amily Gtp Ases in M Ammalian C Ells - 1999.pdf:pdf},
keywords = {a variety of signaling,actin,and differentiation,and with neighbor-,cell adhesion,events including those involved,in mitogenesis,ing cells profoundly influence,insights,integrins,recent advances have provided,receptors,s abstract cellular interactions,signaling,survival,with the extracellular matrix},
pages = {459--486},
title = {{R Egulation of the C Ytoskeleton and C Ell a Dhesion By the R Ho F Amily Gtp Ases in M Ammalian C Ells}},
year = {1999}
}
@article{Zeng2005,
author = {Zeng, Lanying and Balachandar, S. and Fischer, Paul},
doi = {10.1017/S0022112005004738},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zeng, Balachandar, Fischer - Wall-induced forces on a rigid sphere at finite Reynolds number - 2005.pdf:pdf},
issn = {0022-1120},
journal = {Journal of Fluid Mechanics},
month = {jul},
pages = {1--25},
title = {{Wall-induced forces on a rigid sphere at finite Reynolds number}},
url = {http://www.journals.cambridge.org/abstract{\_}S0022112005004738},
volume = {536},
year = {2005}
}
@article{Lee2007,
abstract = {The application of optical traps has come to the fore in the last three decades. They provide a powerful, sterile and noninvasive tool for the manipulation of cells, single biological macromolecules, colloidal microparticles and nanoparticles. An optically trapped microsphere may act as a force transducer that is used to measure forces in the piconewton regime. By setting up a well-calibrated single-beam optical trap within a fluorescence microscope system, one can measure forces and collect fluorescence signals upon biological systems simultaneously. In this protocol, we aim to provide a clear exposition of the methodology of assembling and operating a single-beam gradient force trap (optical tweezers) on an inverted fluorescence microscope. A step-by-step guide is given for alignment and operation, with discussion of common pitfalls.},
author = {Lee, Woei Ming and Reece, Peter J and Marchington, Robert F and Metzger, Nikolaus K and Dholakia, Kishan},
doi = {10.1038/nprot.2007.446},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lee et al. - Construction and calibration of an optical trap on a fluorescence optical microscope. - 2007.pdf:pdf},
issn = {1750-2799},
journal = {Nature protocols},
keywords = {Micromanipulation,Micromanipulation: instrumentation,Microscopy, Fluorescence,Microscopy, Fluorescence: instrumentation,Microspheres,Optical Tweezers,Optics and Photonics,Optics and Photonics: instrumentation,Particle Size},
month = {jan},
number = {12},
pages = {3226--38},
pmid = {18079723},
title = {{Construction and calibration of an optical trap on a fluorescence optical microscope.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18079723},
volume = {2},
year = {2007}
}
@article{Vetsch2006,
abstract = {The chaperone-usher pathway directs the formation of adhesive surface fibres in numerous pathogenic Gram-negative bacteria. The fibres or pili consist exclusively of protein subunits that, before assembly, form transient complexes with a chaperone in the periplasm. In these chaperone:subunit complexes, the chaperone donates one beta-strand to complete the imperfect immunoglobulin-like fold of the subunit. During pilus assembly, the chaperone is replaced by a polypeptide extension of another subunit in a process termed 'donor strand exchange' (DSE). Here we show that DSE occurs in a concerted reaction in which a chaperone-bound acceptor subunit is attacked by another chaperone-bound donor subunit. We provide evidence that efficient DSE requires interactions between the reacting subunits in addition to those involving the attacking donor strand. Our results indicate that the pilus assembly platforms in the outer membrane, referred to as ushers, catalyse fibre formation by increasing the effective concentrations of donor and acceptor subunits.},
author = {Vetsch, Michael and Erilov, Denis and Moli{\`{e}}re, No{\"{e}}l and Nishiyama, Mireille and Ignatov, Oleksandr and Glockshuber, Rudi},
doi = {10.1038/sj.embor.7400722},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Vetsch et al. - Mechanism of fibre assembly through the chaperone-usher pathway. - 2006.pdf:pdf},
issn = {1469-221X},
journal = {EMBO reports},
keywords = {Bacterial Adhesion,Bacterial Adhesion: physiology,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: physiology,Escherichia coli: pathogenicity,Escherichia coli: physiology,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: physiology,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Models, Biological,Molecular Chaperones,Molecular Chaperones: chemistry,Molecular Chaperones: physiology,Protein Structure, Tertiary},
month = {jul},
number = {7},
pages = {734--8},
pmid = {16767077},
title = {{Mechanism of fibre assembly through the chaperone-usher pathway.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1500831{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {7},
year = {2006}
}
@book{Reif1965,
address = {Tokyo},
author = {Reif, F},
pages = {651},
publisher = {McGraw-Hill Book comapny},
title = {{Fundamentals of statistical and thermal physics}},
year = {1965}
}
@article{Liu2014,
abstract = {In this paper, we propose a robust and efficient circle detector, which achieves accurate results with a controlled number of false detections and requires no parameter tuning. The proposed algorithm consists of three steps as follows. First, we propose a novel edge point chaining method to extract Canny edge segments (i.e., contiguous and sequential chains of Canny edge points). Second, we split each edge segment into several smooth sub-segments, and detect candidate circles within each obtained sub-segment based on top-down least-square fitting analysis. Third, we employ Desolneux et al.'s method to reject the false detections. Experimental results demonstrate that the proposed method is efficient and more robust than the state-of-the-art algorithm EDCircles. © 2013 Elsevier Ltd. All rights reserved.},
author = {Liu, Dong and Wang, Yongtao and Tang, Zhi and Lu, Xiaoqing},
doi = {10.1016/j.compeleceng.2014.03.011},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Liu et al. - A robust circle detection algorithm based on top-down least-square fitting analysis - 2014.pdf:pdf},
issn = {00457906},
journal = {Computers and Electrical Engineering},
month = {may},
number = {4},
pages = {1415--1428},
publisher = {Elsevier Ltd},
title = {{A robust circle detection algorithm based on top-down least-square fitting analysis}},
volume = {40},
year = {2014}
}
@article{Roux1998,
abstract = {Various native and hinge-modified forms of Ig with identical Ids were reacted with an anti-Id mAb, and the resultant immune complexes were analyzed by negative stain immunoelectron microscopy. Complexes were scored for their geometry (linear versus ring complexes) and size (dimer, trimer, etc.). Ring dimers are the thermodynamically most favorable configuration, unless inhibited by steric and/or flexibility constraints. We found ring dimerization to correlate with the length of the upper, but not middle or lower, hinge. In contrast, the geometry and size of complexes of those molecules lacking formal hinges were unpredictable. A hingeless IgG mutant and native IgE readily formed ring dimers. Remarkably, monomeric IgM formed more ring dimers than any of the other Igs tested, including IgG3. We also tagged the Fab arms and measured the mean Fab-Fab angles and the degree of angular variation for each type of Ig. Surprisingly, IgM proved the most flexible by this assay. In hinged Igs, there was a correlation between length of the upper hinge and Fab-Fab flexibility. In contrast, we found no correlation between the mean Fab-Fab angle in uncomplexed Igs and their ability to dimerize with anti-Id mAb. These data suggest that the physicochemical methods typically used to evaluate molecular flexibility are often of low predictive value when tested in a functional assay.},
author = {Roux, K H and Strelets, L and Brekke, O H and Sandlie, I and Michaelsen, T E},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Roux et al. - Comparisons of the ability of human IgG3 hinge mutants, IgM, IgE, and IgA2, to form small immune complexes a role for flex.pdf:pdf},
issn = {0022-1767},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
keywords = {Amino Acid Sequence,Antigen-Antibody Complex,Antigen-Antibody Complex: chemistry,Antigen-Antibody Complex: genetics,Humans,Immunoelectron,Immunoglobulin A,Immunoglobulin A: chemistry,Immunoglobulin A: immunology,Immunoglobulin E,Immunoglobulin E: chemistry,Immunoglobulin E: immunology,Immunoglobulin G,Immunoglobulin G: genetics,Immunoglobulin G: immunology,Immunoglobulin M,Immunoglobulin M: chemistry,Immunoglobulin M: immunology,Microscopy,Molecular Sequence Data,Mutation,Structure-Activity Relationship,antibodies},
mendeley-tags = {antibodies},
month = {oct},
number = {8},
pages = {4083--90},
pmid = {9780179},
title = {{Comparisons of the ability of human IgG3 hinge mutants, IgM, IgE, and IgA2, to form small immune complexes: a role for flexibility and geometry.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9780179},
volume = {161},
year = {1998}
}
@article{Jager2001,
abstract = {The deformation behavior of certain biologic macromolecules is modeled by the "sticky chain," a freely jointed chain with weak bonds between subsequent joints. Straining the chain leads to thermally assisted breaking of the weak bonds, yielding a characteristic shape of the force-elongation curve, usually with a pronounced plateau, but sometimes displaying a pseudo-Hookean behavior over a wide range of deformations. The number of individual links is assumed to be large, so the stochastic time evolution of the individual events can be approximated by a differential equation. The cases of individual and collective bond breaking are treated and formulae given for various measurable quantities. A threshold strain rate is found, below which the deformation force no longer depends on the deformation velocity. The method is applied to experimental results for the deformation of single molecules like titin or DNA and the results agree with the parameters deduced from the same experiments by the original authors using Monte Carlo (MC) calculations. Despite its intrinsic continuous character, the model, therefore, is applicable even for the deformation of macromolecules with only a few discrete unfolding elements, yielding physical quantities from experimental results using simple formulae instead of a host of MC computations.},
author = {J{\"{a}}ger, I L},
doi = {10.1016/S0006-3495(01)75841-9},
file = {:E$\backslash$:/Mina Dokument/Mendeley/J{\"{a}}ger - The sticky chain a kinetic model for the deformation of biological macromolecules. - 2001.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {DNA,DNA: chemistry,Kinetics,Macromolecular Substances,Models, Chemical,Molecular Conformation,Monte Carlo Method,Muscle Proteins,Muscle Proteins: chemistry,Protein Kinases,Protein Kinases: chemistry,Spectrin,Spectrin: chemistry,Tenascin,Tenascin: chemistry},
month = {oct},
number = {4},
pages = {1897--906},
pmid = {11566764},
title = {{The "sticky chain": a kinetic model for the deformation of biological macromolecules.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1301665{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {81},
year = {2001}
}
@article{Bebbington2008,
abstract = {Antibodies can be used for the prevention and treatment of bacterial infections in animal models of disease. Current antibody technology allows the generation of high affinity human/humanized antibodies that can be optimized for antibacterial activity and in vivo biodistribution and pharmacokinetics. Such antibodies have exquisite selectivity for their bacterial target antigen and promise efficacy and safety. Why are there no monoclonal antibody products approved for the treatment or prevention of bacterial infections? Can antibodies succeed where antibiotics are failing? Some antibody therapies are currently being evaluated in clinical trials but several have failed despite positive data in animal disease models. This review will discuss the pros and cons of antibody therapeutics targeted at bacterial infections.},
author = {Bebbington, Christopher and Yarranton, Geoffrey},
doi = {10.1016/j.copbio.2008.10.002},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bebbington, Yarranton - Antibodies for the treatment of bacterial infections current experience and future prospects. - 2008.pdf:pdf},
issn = {1879-0429},
journal = {Current opinion in biotechnology},
keywords = {Antibodies, Monoclonal,Antibodies, Monoclonal: therapeutic use,Antigens, Bacterial,Antigens, Bacterial: immunology,Bacteria,Bacteria: immunology,Bacteria: pathogenicity,Bacterial Infections,Bacterial Infections: microbiology,Bacterial Infections: therapy,Neutralization Tests},
month = {dec},
number = {6},
pages = {613--9},
pmid = {19000762},
title = {{Antibodies for the treatment of bacterial infections: current experience and future prospects.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19000762},
volume = {19},
year = {2008}
}
@article{Tchesnokova2008,
abstract = {FimH is the adhesive subunit of type 1 fimbriae of the Escherichia coli that is composed of a mannose-binding lectin domain and a fimbria-incorporating pilin domain. FimH is able to interact with mannosylated surface via a shear-enhanced catch bond mechanism. We show that the FimH lectin domain possesses a ligand-induced binding site (LIBS), a type of allosterically regulated epitopes characterized in integrins. Analogous to integrins, in FimH the LIBS epitope becomes exposed in the presence of the ligand (or "activating" mutations) and is located far from the ligand-binding site, close to the interdomain interface. Also, the antibody binding to the LIBS shifts adhesin from the low to high affinity state. Binding of streptavidin to the biotinylated residue within the LIBS also locks FimH in the high affinity state, suggesting that the allosteric perturbations in FimH are sustained by the interdomain wedging. In the presence of antibodies, the strength of bacterial adhesion to mannose is increased similar to the increase observed under shear force, suggesting the same allosteric mechanism, a shift in the interdomain configuration. Thus, an integrin-like allosteric link between the binding pocket and the interdomain conformation can serve as the basis for the catch bond property of FimH and, possibly, other adhesive proteins.},
author = {Tchesnokova, Veronika and Aprikian, Pavel and Yakovenko, Olga and Larock, Christopher and Kidd, Brian and Vogel, Viola and Thomas, Wendy E and Sokurenko, Evgeni V},
doi = {10.1074/jbc.M707804200},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tchesnokova et al. - Integrin-like allosteric properties of the catch bond-forming FimH adhesin of Escherichia coli. - 2008.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Adhesins,Allosteric Regulation,Allosteric Regulation: drug effects,Allosteric Regulation: physiology,Antibodies,Bacterial,Bacterial Adhesion,Bacterial Adhesion: drug effects,Bacterial Adhesion: physiology,Bacterial: chemistry,Bacterial: pharmacology,Binding Sites,Binding Sites: physiology,Epitopes,Epitopes: genetics,Epitopes: metabolism,Escherichia coli,Escherichia coli K12,Escherichia coli K12: genetics,Escherichia coli K12: metabolism,Escherichia coli: genetics,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: genetics,Fimbriae Proteins: metabolism,Ligands,Mannose-Binding Lectin,Mannose-Binding Lectin: genetics,Mannose-Binding Lectin: metabolism,Monoclonal,Monoclonal: chemistry,Monoclonal: pharmacology,Mutation,Protein Structure,Tertiary,Tertiary: physiology},
month = {mar},
number = {12},
pages = {7823--33},
pmid = {18174167},
title = {{Integrin-like allosteric properties of the catch bond-forming FimH adhesin of Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18174167},
volume = {283},
year = {2008}
}
@article{Giuliano2014,
author = {Giuliano, Camila B. and Zhang, Rongjing and Wilson, Laurence G.},
doi = {10.3791/50488},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Giuliano, Zhang, Wilson - Digital Inline Holographic Microscopy (DIHM) of Weakly-scattering Subjects - 2014.pdf:pdf},
issn = {1940-087X},
journal = {Journal of Visualized Experiments},
keywords = {3d imaging,basic protocol,digital inline holographic microscopy,dihm,holography,issue 84,microbiology,microscopy,streptococcus},
number = {84},
pages = {1--8},
title = {{Digital Inline Holographic Microscopy (DIHM) of Weakly-scattering Subjects}},
url = {http://www.jove.com/video/50488/digital-inline-holographic-microscopy-dihm-weakly-scattering},
year = {2014}
}
@article{Arce2009,
abstract = {Nontypeable Haemophilus influenzae (NTHI) bacteria are commensals in the human nasopharynx, as well as pathogens associated with a spectrum of acute and chronic infections. Two important factors that influence NTHI pathogenicity are their ability to adhere to human tissue and their ability to form biofilms. Extracellular polymeric substances (EPS) and bacterial appendages such as pili critically influence cell adhesion and intercellular cohesion during biofilm formation. Structural components in the outer cell membrane, such as lipopolysaccharides, also play a fundamental role in infection of the host organism. In spite of their importance, these pathogenic factors are not yet well characterized at the nanoscale. Here, atomic force microscopy (AFM) was used in aqueous environments to visualize structural details, including probable Hif-type pili, of live NTHI bacteria at the early stages of biofilm formation. Using single-molecule AFM-based spectroscopy, the molecular elasticities of lipooligosaccharides present on NTHI cell surfaces were analyzed and compared between two strains (PittEE and PittGG) with very different pathogenicity profiles. Furthermore, the stiffness of single cells of both strains was measured and subsequently their turgor pressure was estimated.},
author = {Arce, Fernando Ter{\'{a}}n and Carlson, Ross and Monds, James and Veeh, Richard and Hu, Fen Z and Stewart, Philip S and Lal, Ratnesh and Ehrlich, Garth D and Avci, Recep},
doi = {10.1128/JB.01596-08},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Arce et al. - Nanoscale structural and mechanical properties of nontypeable Haemophilus influenzae biofilms. - 2009.pdf:pdf},
issn = {1098-5530},
journal = {Journal of bacteriology},
keywords = {Biofilms,Elasticity,Fimbriae, Bacterial,Fimbriae, Bacterial: ultrastructure,Haemophilus influenzae,Haemophilus influenzae: chemistry,Haemophilus influenzae: physiology,Haemophilus influenzae: ultrastructure,Lipopolysaccharides,Lipopolysaccharides: chemistry,Microscopy, Atomic Force},
month = {apr},
number = {8},
pages = {2512--20},
pmid = {19218382},
title = {{Nanoscale structural and mechanical properties of nontypeable Haemophilus influenzae biofilms.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2668387{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {191},
year = {2009}
}
@article{Mortezaei2015a,
abstract = {Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrhea worldwide, and infection of children in underdeveloped countries often leads to high mortality rates. Isolated ETEC express a plethora of colonization factors (fimbriae/pili), of which CFA/I and CFA/II that are assembled via the alternate chaperone pathway (ACP), are amongst the most common. Fimbriae are filamentous structures, whose shafts are primarily composed of helically arranged single pilin-protein subunits, with a unique biomechanical capability allowing them to unwind and rewind. A sustained ETEC infection, under adverse conditions of dynamic shear forces, is primarily attributed to this biomechanical feature of ETEC fimbriae. Recent understandings about the role of fimbriae as virulence factors are pointing to an evolutionary adaptation of their structural and biomechanical features. In this work, we investigated the biophysical properties of CS2 fimbriae from the CFA/II group. Homology modelling its major structural subunit CotA reveals structural clues and these are related to the niche in which they are expressed. Using optical tweezers force spectroscopy we found that CS2 fimbriae unwind at a constant force of 10 pN and have a corner velocity of 1300 nm/s, i.e., the velocity at which the force required for unwinding rises exponentially with increased speed. The biophysical properties of CS2 fimbriae assessed in this work classify them into a low-force unwinding group of fimbriae together with the CFA/I and CS20 fimbriae expressed by ETEC strains. The three fimbriae are expressed by ETEC, colonize in similar gut environments, and exhibit similar biophysical features, but differ in their biogenesis. Our observation suggests that the environment has a strong impact on the biophysical characteristics of fimbriae expressed by ETEC.},
author = {Mortezaei, Narges and Singh, Bhupender and Zakrisson, Johan and Bullitt, Esther and Andersson, Magnus},
doi = {10.1016/j.bpj.2015.05.022},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Mortezaei et al. - Biomechanical and Structural features of CS2 fimbriae of Enterotoxigenic Escherichia coli - 2015.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Mortezaei et al. - Biomechanical and Structural features of CS2 fimbriae of Enterotoxigenic Escherichia coli - 2015(2).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Mortezaei et al. - Biomechanical and Structural features of CS2 fimbriae of Enterotoxigenic Escherichia coli - 2015(3).pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {bacteria,optical tweezers,pathogenesis,pili,virulence factors},
number = {1},
pages = {49--56},
publisher = {Biophysical Society},
title = {{Biomechanical and Structural features of CS2 fimbriae of Enterotoxigenic Escherichia coli}},
url = {http://dx.doi.org/10.1016/j.bpj.2015.05.022},
volume = {109},
year = {2015}
}
@article{Ashok2011c,
author = {Ashok, Praveen C and {De Luca}, Anna Chiara and Mazilu, Michael and Dholakia, Kishan},
doi = {10.1002/jbio.201000107},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ashok et al. - Enhanced bioanalyte detection in waveguide confined Raman spectroscopy using wavelength modulation - 2011.pdf:pdf},
issn = {1864063X},
journal = {Journal of Biophotonics},
keywords = {a,bioanalyte detection,corporates a fibre based,fluorescent suppression,in-,microfluidic platform enabling the,microfluidics,raman detection system in,raman spectroscopy,spectroscopic detec-,waveguide confined raman spectroscopy,wcrs},
month = {jan},
pages = {n/a--n/a},
title = {{Enhanced bioanalyte detection in waveguide confined Raman spectroscopy using wavelength modulation}},
url = {http://doi.wiley.com/10.1002/jbio.201000107},
volume = {5},
year = {2011}
}
@article{Marshall2003,
author = {Marshall, Bryan T and Long, Mian and Piper, James W and Yago, Tadayuki and Mcever, Rodger P and Zhu, Cheng},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Marshall et al. - Direct observation of catch bonds involving cell-adhesion molecules - 2003.pdf:pdf},
number = {May},
pages = {8--11},
title = {{Direct observation of catch bonds involving cell-adhesion molecules}},
volume = {423},
year = {2003}
}
@article{Merkel1999,
abstract = {Atomic force microscopy (AFM) has been used to measure the strength of bonds between biological receptor molecules and their ligands. But for weak noncovalent bonds, a dynamic spectrum of bond strengths is predicted as the loading rate is altered, with the measured strength being governed by the prominent barriers traversed in the energy landscape along the force-driven bond-dissociation pathway. In other words, the pioneering early AFM measurements represent only a single point in a continuous spectrum of bond strengths, because theory predicts that these will depend on the rate at which the load is applied. Here we report the strength spectra for the bonds between streptavidin (or avidin) and biotins-the prototype of receptor-ligand interactions used in earlier AFM studies, and which have been modelled by molecular dynamics. We have probed bond formation over six orders of magnitude in loading rate, and find that the bond survival time diminished from about 1 min to 0.001 s with increasing loading rate over this range. The bond strength, meanwhile, increased from about 5 pN to 170 pN. Thus, although they are among the strongest noncovalent linkages in biology (affinity of 10(13) to 10(15) M(-1)), these bonds in fact appear strong or weak depending on how fast they are loaded. We are also able to relate the activation barriers derived from our strength spectra to the shape of the energy landscape derived from simulations of the biotin-avidin complex.},
author = {Merkel, R and Nassoy, P and Leung, A and Ritchie, K and Evans, Evan},
doi = {10.1038/16219},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Merkel et al. - Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy. - 1999.pdf:pdf},
isbn = {0028-0836},
issn = {0028-0836},
journal = {Nature},
number = {6714},
pages = {50--53},
pmid = {9892352},
title = {{Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy.}},
volume = {397},
year = {1999}
}
@article{Ashkin1987a,
abstract = {Use of optical traps for the manipulation of biological particles was recently proposed, and initial observations of laser trapping of bacteria and viruses with visible argon-laser light were reported. We report here the use of infrared (IR) light to make much improved laser traps with significantly less optical damage to a variety of living cells. Using IR light we have observed the reproduction of Escherichia coli within optical traps at power levels sufficient to give manipulation at velocities up to approximately 500 micron s-1. Reproduction of yeast cells by budding was also achieved in IR traps capable of manipulating individual cells and clumps of cells at velocities of approximately micron s-1. Damage-free trapping and manipulation of suspensions of red blood cells of humans and of organelles located within individual living cells of spirogyra was also achieved, largely as a result of the reduced absorption of haemoglobin and chlorophyll in the IR. Trapping of many types of small protozoa and manipulation of organelles within protozoa is also possible. The manipulative capabilities of optical techniques were exploited in experiments showing separation of individual bacteria from one sample and their introduction into another sample. Optical orientation of individual bacterial cells in space was also achieved using a pair of laser-beam traps. These new manipulative techniques using IR light are capable of producing large forces under damage-free conditions and improve the prospects for wider use of optical manipulation techniques in microbiology.},
author = {Ashkin, A and Dziedzic, J M and Yamane, T},
doi = {10.1038/330769a0},
journal = {Nature},
keywords = {Animals,Cell Division,Cell Separation,Erythrocytes,Escherichia coli,Humans,Infrared Rays,Lasers,Protozoa,Saccharomyces cerevisiae,optical tweezers},
mendeley-tags = {optical tweezers},
number = {6150},
pages = {769--771},
title = {{Optical trapping and manipulation of single cells using infrared laser beams}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=3320757 http://www.nature.com/doifinder/10.1038/330769a0},
volume = {330},
year = {1987}
}
@article{Hammer1992,
abstract = {The receptor-mediated adhesion of cells to ligand-coated surfaces in viscous shear flow is an important step in many physiological processes, such as the neutrophil-mediated inflammatory response, lymphocyte homing, and tumor cell metastasis. This paper describes a calculational method which simulates the interaction of a single cell with a ligand-coated surface under flow. The cell is idealized as a microvilli-coated hard sphere covered with adhesive springs. The distribution of microvilli on the cell surface, the distribution of receptors on microvilli tips, and the forward and reverse reaction between receptor and ligand are all simulated using random number sampling of appropriate probability functions. The velocity of the cell at each time step in the simulation results from a balance of hydrodynamic, colloidal and bonding forces; the bonding force is derived by summing the individual contributions of each receptor-ligand tether. The model can simulate the effect of many parameters on adhesion, such as the number of receptors on microvilli tips, the density of ligand, the rates of reaction between receptor and ligand, the stiffness of the resulting receptor-ligand springs, the response of springs to strain, and the magnitude of the bulk hydrodynamic stresses. The model can successfully recreate the entire range of expected and observed adhesive phenomena, from completely unencumbered motion, to rolling, to transient attachment, to firm adhesion. Also, the method can generate meaningful statistical measures of adhesion, including the mean and variance in velocity, rate constants for cell attachment and detachment, and the frequency of adhesion. We find a critical modulating parameter of adhesion is the fractional spring slippage, which relates the strain of a bond to its rate of breakage; the higher the slippage, the faster the breakage for the same strain. Our analysis of neutrophil adhesive behavior on selectin-coated (CD62-coated) surfaces in viscous shear flow reported by Lawrence and Springer (Lawrence, M.B., and T.A. Springer 1991. Cell. 65:859-874) shows the fractional spring slippage of the CD62-LECAM-1 bond is likely below 0.01. We conclude the unique ability of this selectin bond to cause neutrophil rolling under flow is a result of its unique response to strain. Furthermore, our model can successfully recreate data on neutrophil rolling as function of CD62 surface density.},
author = {Hammer, D a and Apte, S M},
doi = {10.1016/S0006-3495(92)81577-1},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hammer, Apte - Simulation of cell rolling and adhesion on surfaces in shear flow general results and analysis of selectin-mediated neutr.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Animals,Biological,Biomechanics,Biophysical Phenomena,Biophysics,Cell Adhesion,Cell Adhesion Molecules,Cell Adhesion Molecules: physiology,Cell Adhesion: physiology,Cell Movement,Cell Movement: physiology,Microvilli,Microvilli: physiology,Models,Neutrophils,Neutrophils: physiology,P-Selectin,Platelet Membrane Glycoproteins,Platelet Membrane Glycoproteins: physiology},
month = {jul},
number = {1},
pages = {35--57},
pmid = {1384734},
title = {{Simulation of cell rolling and adhesion on surfaces in shear flow: general results and analysis of selectin-mediated neutrophil adhesion.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1262123{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {63},
year = {1992}
}
@article{Babcock2004,
abstract = {The question of how genetic materials are trafficked in and out of the cell nucleus is a problem of great importance not only for understanding viral infections but also for advancing gene-delivery technology. Here we demonstrate a physical technique that allows gene trafficking to be studied at the single-gene level by combining sensitive fluorescence microscopy with microinjection. As a model system, we investigate the nuclear import of influenza genes, in the form of ribonucleoproteins (vRNPs), by imaging single vRNPs in living cells in real time. Our single-particle trajectories show that vRNPs are transported to the nuclear envelope by diffusion. We have observed heterogeneous interactions between the vRNPs and nuclear pore complexes with dissociation rate constants spanning two orders of magnitude. Our single-particle tracking experiments also provided new insights into the regulation mechanisms for the nuclear import of vRNPs: the influenza M1 protein, a regulatory protein for the import process, downregulates the nuclear import of vRNPs by inhibiting the interactions between vRNPs and nuclear pore complexes but has no significant effect on the transport properties of vRNPs. We expect this single-particle tracking approach to find broad application in investigations of genetic trafficking.},
author = {Babcock, Hazen P and Chen, Chen and Zhuang, Xiaowei},
doi = {10.1529/biophysj.104.042234},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Babcock, Chen, Zhuang - Using single-particle tracking to study nuclear trafficking of viral genes. - 2004.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Active Transport, Cell Nucleus,Active Transport, Cell Nucleus: physiology,Cell Nucleus,Cell Nucleus: metabolism,Cell Nucleus: ultrastructure,Flow Cytometry,Flow Cytometry: methods,Flow Injection Analysis,Flow Injection Analysis: methods,Genes, Viral,Genes, Viral: physiology,Image Interpretation, Computer-Assisted,Image Interpretation, Computer-Assisted: methods,Microscopy, Fluorescence,Microscopy, Fluorescence: methods,Microscopy, Video,Ribonucleoproteins,Ribonucleoproteins: metabolism,Ribonucleoproteins: ultrastructure},
month = {oct},
number = {4},
pages = {2749--58},
pmid = {15454466},
title = {{Using single-particle tracking to study nuclear trafficking of viral genes.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1304693{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {87},
year = {2004}
}
@article{Sarshar2014,
author = {Sarshar, Mohammad and Wong, Winson T and Anvari, Bahman},
doi = {10.1117/1.JBO.19.11.115001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sarshar, Wong, Anvari - Comparative study of methods to calibrate the stiffness of a single-beam gradient-force optical tweezers over va.pdf:pdf},
issn = {1560-2281},
journal = {Journal of biomedical optics},
keywords = {boltzmann statistics,charge-coupled diode camera,equipartition theorem,power spectral density,quadrant,viscous drag},
month = {nov},
number = {11},
pages = {115001},
pmid = {25375348},
title = {{Comparative study of methods to calibrate the stiffness of a single-beam gradient-force optical tweezers over various laser trapping powers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25375348},
volume = {19},
year = {2014}
}
@article{Tjarnhage2013,
author = {Tj{\"{a}}rnhage, Torbj{\"{o}}rn and Gradmark, Per-{\AA}ke and Larsson, Anders and Mohammed, Abdelsalam and Landstr{\"{o}}m, Lars and Sagerfors, Eva and Jonsson, Per and Kullander, Fredrik and Andersson, Magnus},
doi = {10.1016/j.optcom.2013.01.044},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tj{\"{a}}rnhage et al. - Development of a laser-induced breakdown spectroscopy instrument for detection and classification of single-particle.pdf:pdf},
issn = {00304018},
journal = {Optics Communications},
month = {feb},
pages = {106--108},
title = {{Development of a laser-induced breakdown spectroscopy instrument for detection and classification of single-particle aerosols in real-time}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0030401813001260},
volume = {296},
year = {2013}
}
@article{Zbelev1994,
author = {Zbelev, Doncho V and Needham, David and Hochmuth, Robert M},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zbelev, Needham, Hochmuth - Vesicle Membranes - 1994.pdf:pdf},
number = {August},
pages = {720--727},
title = {{Vesicle Membranes}},
year = {1994}
}
@book{Happel1983a,
address = {Dordrecht},
author = {Happel, J and Brenner, H},
isbn = {9789024728770},
pages = {572},
publisher = {Kluwer Academic Publishers},
title = {{Low Reynolds Number Hydrodynamics}},
year = {1983}
}
@article{Petrov2010a,
author = {Petrov, Dmitri},
doi = {10.1117/1.3515371},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Petrov - Commentary Raman nanospectroscopy of single DNA molecules - 2010.pdf:pdf},
issn = {19342608},
journal = {Journal of Nanophotonics},
number = {1},
pages = {040306},
title = {{Commentary: Raman nanospectroscopy of single DNA molecules}},
url = {http://link.aip.org/link/JNOACQ/v4/i1/p040306/s1{\&}Agg=doi},
volume = {4},
year = {2010}
}
@article{Kantsler2014,
abstract = {A major puzzle in biology is how mammalian sperm maintain the correct swimming direction during various phases of the sexual reproduction process. Whilst chemotaxis may dominate near the ovum, it is unclear which cues guide spermatozoa on their long journey towards the egg. Hypothesized mechanisms range from peristaltic pumping to temperature sensing and response to fluid flow variations (rheotaxis), but little is known quantitatively about them. We report the first quantitative study of mammalian sperm rheotaxis, using microfluidic devices to investigate systematically swimming of human and bull sperm over a range of physiologically relevant shear rates and viscosities. Our measurements show that the interplay of fluid shear, steric surface-interactions, and chirality of the flagellar beat leads to stable upstream spiralling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilisation. A minimal mathematical model is presented that accounts quantitatively for the experimental observations.DOI: http://dx.doi.org/10.7554/eLife.02403.001.},
archivePrefix = {arXiv},
arxivId = {1405.6489},
author = {Kantsler, Vasily and Dunkel, J{\"{o}}rn and Blayney, Martyn and Goldstein, Raymond E},
doi = {10.7554/eLife.02403},
eprint = {1405.6489},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kantsler et al. - Rheotaxis facilitates upstream navigation of mammalian sperm cells. - 2014.pdf:pdf},
isbn = {2050-084X (Electronic)},
issn = {2050-084X},
journal = {eLife},
pages = {e02403},
pmid = {24867640},
title = {{Rheotaxis facilitates upstream navigation of mammalian sperm cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4031982{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {3},
year = {2014}
}
@article{Sheng2003,
author = {Sheng, Jian and Malkiel, Edwin and Katz, Joseph},
journal = {Applied optics},
pages = {235--50},
title = {{Single beam two-views holographic particle image velocimetry}},
volume = {42},
year = {2003}
}
@article{Rodas2011,
abstract = {Enterotoxigenic Escherichia coli (ETEC) is recognized as the main cause of bacterial diarrhoea among children in Asia, Africa and Latin America but less investigated in Bolivia. Objective: To determine the relation between enterotoxins, CFs and serotypes as well as the antimicrobial resistance patterns in a set of ETEC isolates collected from hospitalized children with acute diarrhea. In the present study we characterized 43 ETEC strains isolated from 2002 to 2006 from hospitalized children (0-5 years) with acute diarrhea in Bolivia. The strains were analyzed for heat-labile (LT) and heat-stable (ST) enterotoxins and colonization factor (CF) profiles, as well as for serogroups and antimicrobial resistance using phenotypic (ELISA, dot blot, slide agglutination and disc difusion) and genotypic (Multiplex PCR) methods. Among the ETEC isolates tested, 30 were positive for LT, 3 for ST and 10 for LT/ST. Sixty-five percent (28/43) of the strains expressed one or more CF. The most common CFs were CS17 (n = 8) and CFA/I (n = 8). The phenotypical and genotypical results for toxins and CFs were congruent except for CS21 that was amplifed in 10 of the strains by multiplex PCR, but CS21 pili was only detected phenotypically in four of these strains. The ETEC strains had diverse O and H antigens and the most common types were O8:H9 LT CS17 (n = 6; 14{\%}) and O78:HNM LT-ST CFA/I (n = 4; 9{\%}). The analysis of antibiotic resistance showed that 67{\%} (n = 29/43) of the strains were resistant to one or several of the antimicrobial agents tested. Presence of CFs was associated with antibiotic resistance. Conclusion: The most common toxin profile was LT 70{\%}, LT/ST 23{\%} and ST 7{\%}. High antimicrobial resistance to ampicillin among serogroups O6, O8 and O78 were the most common. © Elsevier Editora Ltda.},
author = {Rodas, Claudia and Mamani, Rosal{\'{\i}}a and Blanco, Jorge and Blanco, Jesus Eulogio and Wiklund, Gudrun and Svennerholm, Ann-Mari and Sj{\"{o}}ling, {\AA}sa and Iniguez, Volga},
doi = {10.1016/S1413-8670(11)70158-1},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rodas et al. - Enterotoxins, colonization factors, serotypes and antimicrobial resistance of enterotoxigenic Escherichia coli (ETEC) str.pdf:pdf},
isbn = {4631786620},
issn = {14138670},
journal = {Brazilian Journal of Infectious Diseases},
keywords = {Bolivia,Drug resistance,Enterotoxigenic escherichia coli,Enterotoxins},
pages = {132--137},
pmid = {21503399},
title = {{Enterotoxins, colonization factors, serotypes and antimicrobial resistance of enterotoxigenic Escherichia coli (ETEC) strains isolated from hospitalized children with diarrhea in Bolivia}},
volume = {15},
year = {2011}
}
@article{Roichman2008,
abstract = {We demonstrate both theoretically and experimentally that phase gradients in a light field can be used to create a new category of optical traps complementary to the more familiar intensity-gradient traps known as optical tweezers. We further show that the work done by phase-gradient forces is path dependent and briefly discuss some ramifications of this nonconservativity.},
author = {Roichman, Yohai and Sun, Bo and Roichman, Yael and Amato-Grill, Jesse and Grier, David G},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Roichman et al. - Optical forces arising from phase gradients. - 2008.pdf:pdf},
issn = {0031-9007},
journal = {Physical review letters},
month = {jan},
number = {1},
pages = {013602},
pmid = {18232759},
title = {{Optical forces arising from phase gradients.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18232759},
volume = {100},
year = {2008}
}
@article{Sekatskii2013,
author = {Sekatskii, S. K. and Benedetti, F. and Dietler, G.},
doi = {10.1063/1.4815869},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sekatskii, Benedetti, Dietler - Dependence of the most probable and average bond rupture force on the force loading rate First order cor.pdf:pdf},
issn = {00218979},
journal = {Journal of Applied Physics},
number = {3},
pages = {034701},
title = {{Dependence of the most probable and average bond rupture force on the force loading rate: First order correction to the Bell–Evans model}},
url = {http://link.aip.org/link/JAPIAU/v114/i3/p034701/s1{\&}Agg=doi},
volume = {114},
year = {2013}
}
@article{Paracuellos2012,
abstract = {Pathogenic Escherichia coli strains commonly harbor genes involved in formation of fimbriae, such as the sfa(II) fimbrial gene cluster found in uropathogenic and newborn meningitis isolates. The sfaX(II) gene, located at the distal end of the sfa(II) operon, was recently shown to play a role in controlling virulence-related gene expression in extraintestinal pathogenic E. coli (ExPEC). Until now, detailed characterization of the SfaX(II) protein has been hampered by difficulties in obtaining large quantities of soluble protein. By a rational modeling approach, we engineered a Cys70Ser mutation, which successfully improved solubility of the protein. Here, we present the expression, purification, and initial characterization of the recombinant SfaX(IIC70S) mutant. The protein was produced in E. coli BL21 (DE3) cells grown in autoinduction culture media. The plasmid vector harbored DNA encoding the SfaX(IIC70S) protein N-terminally fused with a six histidine (H6) sequence followed by a ZZ tag (a derivative of the Staphylococcus protein A) (H6-ZZ tag). The H6-ZZ tag was cleaved off with Tobacco Etch Virus (TEV) protease and the 166 amino acid full-length homo-dimeric protein was purified using affinity and size-exclusion chromatography. Electrophoretic mobility gel shift assays and atomic force microscopy demonstrated that the protein possesses DNA-binding properties, suggesting that the transcriptional regulatory activity of SfaX(II) can be mediated via direct binding to DNA.},
author = {Paracuellos, Patricia and Ohman, Anders and Sauer-Eriksson, a Elisabeth and Uhlin, Bernt Eric},
doi = {10.1016/j.pep.2012.09.006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Paracuellos et al. - Expression and purification of SfaX(II), a protein involved in regulating adhesion and motility genes in extraintes.pdf:pdf},
issn = {1096-0279},
journal = {Protein expression and purification},
month = {dec},
number = {2},
pages = {127--34},
pmid = {23022032},
publisher = {Elsevier Inc.},
title = {{Expression and purification of SfaX(II), a protein involved in regulating adhesion and motility genes in extraintestinal pathogenic Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23022032},
volume = {86},
year = {2012}
}
@article{Thomas2007b,
author = {Thomas, Wendy E},
doi = {10.2174/157341307779940544},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Thomas - Understanding the Counterintuitive Phenomenon of Catch Bonds - 2007.pdf:pdf},
issn = {15734137},
journal = {Current Nanoscience},
month = {feb},
number = {1},
pages = {63--77},
title = {{Understanding the Counterintuitive Phenomenon of Catch Bonds}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=1573-4137{\&}volume=3{\&}issue=1{\&}spage=63},
volume = {3},
year = {2007}
}
@article{Baga1984,
abstract = {The papA gene of the uropathogenic strain Escherichia coli J96, coding for the Pap pili subunit, was subjected to DNA sequencing, and found to code for an 185-amino acid-long polypeptide with a 22-amino acid-long signal peptide. Here we present the primary sequence, the hydrophilicity profile, and the predicted polypeptide secondary structure of the Pap pili subunit.},
author = {B{\aa}ga, M and Normark, S and Hardy, J and O'Hanley, P and Lark, D and Olsson, O and Schoolnik, G and Falkow, S},
file = {:E$\backslash$:/Mina Dokument/Mendeley//B{\aa}ga et al. - Nucleotide sequence of the papA gene encoding the Pap pilus subunit of human uropathogenic Escherichia coli. - 1984.pdf:pdf},
issn = {0021-9193},
journal = {Journal of bacteriology},
keywords = {Amino Acid Sequence,Base Sequence,DNA, Bacterial,DNA, Bacterial: genetics,Escherichia coli,Escherichia coli: genetics,Escherichia coli: ultrastructure,Fimbriae, Bacterial,Fimbriae, Bacterial: ultrastructure,Genes, Bacterial,Genetic Code,Humans,Peptides,Peptides: genetics,Protein Conformation,Urologic Diseases,Urologic Diseases: microbiology},
month = {jan},
number = {1},
pages = {330--3},
pmid = {6140260},
title = {{Nucleotide sequence of the papA gene encoding the Pap pilus subunit of human uropathogenic Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=215181{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {157},
year = {1984}
}
@article{Ashkin1971,
abstract = {Stable optical levitation of transparent hollow dielectric spheres has been demonstrated using TEM01 mode laser beams. The levitation of solid dielectric spheres has been made much more stable using highly convergent TEM00 mode beams. We have discovered the existence of two distinct stable regimes of levitation for solid spheres, one located above the beam focus, the other below it. A particle can be switched back and forth between these regimes. Three separate stable regimes are also possible.},
author = {Ashkin, A and Dziedzic, J. M.},
doi = {10.1063/1.1653919},
isbn = {0003-6951},
issn = {00036951},
journal = {Applied Physics Letters},
number = {8},
pages = {283--285},
pmid = {22635303},
title = {{Optical levitation by radiation pressure}},
volume = {19},
year = {1971}
}
@article{Klein2007a,
abstract = {High-resolution long-time force measurements by optical tweezers are often limited by low-frequency (1/f) noise. A dual-trap technique is presented that can reduce such noise in the force signal. It incorporates a second trap (a reference trap) that probes the noise in the system and it is based upon the assumption that the low-frequency parts of the noise from the two traps are correlated. A subtraction of the low-frequency signal from the reference trap from the signal from the force measuring trap will therefore yield a net signal that is significantly less influenced by noise. It is shown that this dual-trap technique can reduce the noise in the force signal up to 60{\%} depending on detection bandwidth.},
author = {Klein, Markus and Andersson, Magnus and Axner, Ove and F{\"{a}}llman, Erik},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Klein et al. - Dual-trap technique for reduction of low-frequency noise in force measuring optical tweezers. - 2007.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
keywords = {Adhesion,Bonds,Coli P-Pili,Design,Equipment Design,Escherichia-Coli,Lasers,Micromanipulation,Micromanipulation: instrumentation,Micromanipulation: methods,Models,Motion,Optics and Photonics,Particle Size,Resolution,Rna-Polymerase,Single-Molecule,Spectroscopy,Statistical,Stress,Theoretical,Time Factors,dual trap,optical tweezers},
mendeley-tags = {dual trap,optical tweezers},
month = {jan},
number = {3},
pages = {405--12},
pmid = {17228388},
title = {{Dual-trap technique for reduction of low-frequency noise in force measuring optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=000243551000020 http://www.ncbi.nlm.nih.gov/pubmed/17228388},
volume = {46},
year = {2007}
}
@article{Schwesinger2000,
author = {Schwesinger, Falk and Ros, Robert and Strunz, Torsten and Anselmetti, Dario and Gu, Hans-joachim and Honegger, Annemarie and Jermutus, Lutz and Tiefenauer, Louis and Plu, Andreas},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schwesinger et al. - Unbinding forces of single antibody-antigen complexes correlate with their thermal - 2000.pdf:pdf},
title = {{Unbinding forces of single antibody-antigen complexes correlate with their thermal}},
year = {2000}
}
@article{Weiße2012,
abstract = {We present a quantitative 3D analysis of the motility of the blood parasite Trypanosoma brucei. Digital in-line holographic microscopy has been used to track single cells with high temporal and spatial accuracy to obtain quantitative data on their behavior. Comparing bloodstream form and insect form trypanosomes as well as mutant and wildtype cells under varying external conditions we were able to derive a general two-state-run-and-tumble-model for trypanosome motility. Differences in the motility of distinct strains indicate that adaption of the trypanosomes to their natural environments involves a change in their mode of swimming.},
author = {Wei{\ss}e, Sebastian and Heddergott, Niko and Heydt, Matthias and Pfl{\"{a}}sterer, Daniel and Maier, Timo and Haraszti, Tam{\'{a}}s and Grunze, Michael and Engstler, Markus and Rosenhahn, Axel},
doi = {10.1371/journal.pone.0037296},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wei{\ss}e et al. - A quantitative 3D motility analysis of Trypanosoma brucei by use of digital in-line holographic microscopy. - 2012.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Cell Movement,Holography,Microscopy,Trypanosoma brucei brucei,Trypanosoma brucei brucei: cytology},
month = {jan},
number = {5},
pages = {e37296},
pmid = {22629379},
title = {{A quantitative 3D motility analysis of Trypanosoma brucei by use of digital in-line holographic microscopy.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3358310{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {7},
year = {2012}
}
@article{Bustamante2004,
abstract = {Mechanical processes are involved in nearly every facet of the cell cycle. Mechanical forces are generated in the cell during processes as diverse as chromosomal segregation, replication, transcription, translation, translocation of proteins across membranes, cell locomotion, and catalyzed protein and nucleic acid folding and unfolding, among others. Because force is a product of all these reactions, biochemists are beginning to directly apply external forces to these processes to alter the extent or even the fate of these reactions hoping to reveal their underlying molecular mechanisms. This review provides the conceptual framework to understand the role of mechanical force in biochemistry.},
author = {Bustamante, Carlos and Chemla, Yann R and Forde, Nancy R and Izhaky, David},
doi = {10.1146/annurev.biochem.72.121801.161542},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bustamante et al. - Mechanical processes in biochemistry. - 2004.pdf:pdf},
issn = {0066-4154},
journal = {Annual review of biochemistry},
keywords = {Animals,Biochemical Phenomena,Biochemistry,Biomechanics,Catalysis,Enzymes,Enzymes: chemistry,Kinetics,Molecular Conformation,Molecular Motor Proteins,Molecular Motor Proteins: chemistry,Thermodynamics},
month = {jan},
pages = {705--48},
pmid = {15189157},
title = {{Mechanical processes in biochemistry.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15189157},
volume = {73},
year = {2004}
}
@article{Ludi2006,
abstract = {Infections with enterotoxigenic Escherichia coli (ETEC) are a major cause of travelers' diarrhea worldwide. Colonization of the small intestine mucosa is dependent on specific colonization factor antigens (CFA) and coli surface (CS) antigens. CFA/1, CS3, and CS6 are the most prevalent fimbrial antigens found in clinical isolates. The goal of our study was to visualize the morphology of CS3 and CS6 fimbriae in wild-type and recombinant E. coli strains by means of transmission electron microscopy in conjunction with negative staining and immunolabeling. Corresponding ETEC genes were cloned into E. coli K12 strain DH10B. Expression of fimbriae was dependent on culture conditions and sample handling. Specific immunolabeling of fimbriae unequivocally demonstrated the presence of all types of surface antigens investigated. Negative staining was effective in revealing CS3 but not CS6. In addition, this technique clearly demonstrated differences in the morphology of genetically and immunologically identical CS3 surface antigens in wild-type and recombinant strains. This paper provides a basis for the assessment of recombinant vaccines.},
author = {L{\"{u}}di, Stefan and Frey, Joachim and Favre, Didier and Stoffel, Michael H},
doi = {10.1369/jhc.5A6794.2005},
file = {:E$\backslash$:/Mina Dokument/Mendeley/L{\"{u}}di et al. - Assessing the expression of enterotoxigenic Escherichia coli-specific surface antigens in recombinant strains by transmiss.pdf:pdf},
issn = {0022-1554},
journal = {The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society},
number = {4},
pages = {473--477},
pmid = {16344328},
title = {{Assessing the expression of enterotoxigenic Escherichia coli-specific surface antigens in recombinant strains by transmission electron microscopy and immunolabeling.}},
volume = {54},
year = {2006}
}
@article{Tobias2010a,
abstract = {Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrheal disease and deaths among children in developing countries and the major cause of traveller's diarrhea. Since surface protein colonization factors (CFs) of ETEC are important for pathogenicity and immune protection is mainly mediated by locally produced IgA antibodies in the gut, much effort has focused on the development of an oral CF-based vaccine. We have recently described the development of recombinant strains over-expressing CFA/I; the most prevalent CF among human clinical ETEC isolates. Here, non-toxigenic recombinant E. coli strains over-expressing Coli surface antigen 2 (CS2), CS4, CS5, and CS6, either alone, or each in combination with CFA/I were constructed by cloning the genes required for expression and assembly of each CF into expression vectors harboring a strong promoter. Immunological assays showed that recombinant strains expressing single CFs produced those in significantly larger amounts than did corresponding naturally high producing reference strains. Recombinant strains co-expressing CFA/I together with another CF also expressed significantly larger amounts of both CFs compared with the corresponding references strains. Further, when tested in mice, oral immunization with formalin-killed recombinant bacteria co-expressing one such double-expression CF pair, CFA/I. +. CS2, induced specific serum IgG. +. IgM and fecal IgA antibody responses against both CFs exceeding the responses induced by immunizations with natural reference strains expressing CFA/I and CS2, respectively. We conclude that the described type of recombinant bacteria over-expressing major CFs of ETEC, alone or in combination, may be useful as candidate strains for use in an oral whole-cell CF-ETEC vaccine. ?? 2010 Elsevier Ltd.},
author = {Tobias, Joshua and Holmgren, Jan and Hellman, Maria and Nygren, Erik and Lebens, Michael and Svennerholm, Ann-Mari},
doi = {10.1016/j.vaccine.2010.08.047},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tobias et al. - Over-expression of major colonization factors of enterotoxigenic Escherichia coli, alone or together, on non-toxigenic E.pdf:pdf},
issn = {0264410X},
journal = {Vaccine},
keywords = {Anti-colonization immunity,Co-expression,Colonization factors,ETEC,ETEC vaccine,Over-expression},
number = {43},
pages = {6977--6984},
pmid = {20728524},
publisher = {Elsevier Ltd},
title = {{Over-expression of major colonization factors of enterotoxigenic Escherichia coli, alone or together, on non-toxigenic E. coli bacteria}},
url = {http://dx.doi.org/10.1016/j.vaccine.2010.08.047},
volume = {28},
year = {2010}
}
@article{Ashkin1986,
abstract = {Optical trapping of dielectric particles by a single-beam gradient force trap was demonstrated for the first reported time. This confirms the concept of negative light pressure due to the gradient force. Trapping was observed over the entire range of particle size from 10 µm to {\~{}}25 nm in water. Use of the new trap extends the size range of macroscopic particles accessible to optical trapping and manipulation well into the Rayleigh size regime. Application of this trapping principle to atom trapping is considered.},
author = {Ashkin, A and Dziedzic, J M and Bjorkholm, J E and Chu, S},
doi = {10.1364/OL.11.000288},
isbn = {0750309016},
issn = {0146-9592},
journal = {Optics letters},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
number = {5},
pages = {288},
pmid = {19730608},
title = {{Observation of a single-beam gradient force optical trap for dielectric particles.}},
volume = {11},
year = {1986}
}
@article{Maxey1983,
abstract = {The forces on a small rigid sphere in a nonuniform flow are considered from first prinicples in order to resolve the errors in Tchens equation and the subsequent modified versions that have since appeared. Forces from the undisturbed flow and the disturbance flow created by the presence of the sphere are treated separately. Proper account is taken of the effect of spatial variations of the undisturbed flow on both forces. In particular the appropriate Faxen correction for unsteady Stokes flow is derived and included as part of the consistent approximation for the equation of motion.},
author = {Maxey, Mr R and Riley, Jj J},
doi = {10.1063/1.864230},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Maxey, Riley - Equation of motion for a small rigid sphere in a nonuniform flow - 1983.pdf:pdf},
isbn = {00319171 (ISSN)},
issn = {00319171},
journal = {Physics of Fluids},
number = {1983},
pages = {883},
title = {{Equation of motion for a small rigid sphere in a nonuniform flow}},
url = {http://scitation.aip.org/content/aip/journal/pof1/26/4/10.1063/1.864230$\backslash$nhttp://link.aip.org/link/PFLDAS/v26/i4/p883/s1{\&}Agg=doi},
volume = {26},
year = {1983}
}
@article{Giamarellou1984,
author = {Giamarellou, Helen},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Giamarellou - Antibody-coated bacteria in urine when, where and why - 1984.pdf:pdf},
journal = {Journal of Antimicrobial Chemotherapy},
pages = {95--99},
title = {{Antibody-coated bacteria in urine: when, where and why?}},
volume = {13},
year = {1984}
}
@article{Kalkbrenner2009,
abstract = {The intramolecular diffusive motion within supercoiled DNA molecules is of central importance for a wide array of gene regulation processes. It has recently been shown, using fluorescence correlation spectroscopy, that plasmid DNA exhibits unexpected acceleration of its internal diffusive motion upon supercoiling to intermediate density. Here, we present an independent study that shows a similar acceleration for fully supercoiled plasmid DNA. We have developed a method that allows fluorescent labeling of a 200-bp region, as well as efficient supercoiling by Escherichia coli gyrase. Compared to plain circular or linear DNA, the submicrosecond motion within the supercoiled molecules appears faster by up to an order of magnitude. The mean-square displacement as a function of time reveals an additional intermediate regime with a lowered scaling exponent compared to that of circular DNA. Although this unexpected behavior is not fully understood, it could be explained by conformational constraints of the DNA strand within the supercoiled topology in combination with an increased apparent persistence length.},
author = {Kalkbrenner, Thomas and Arnold, Axel and Tans, Sander J},
doi = {10.1016/j.bpj.2009.03.056},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kalkbrenner, Arnold, Tans - Internal dynamics of supercoiled DNA molecules. - 2009.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {DNA Gyrase,DNA Gyrase: metabolism,DNA, Superhelical,DNA, Superhelical: chemistry,DNA, Superhelical: genetics,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: enzymology,Escherichia coli: genetics,Fluorescent Dyes,Fluorescent Dyes: analysis,Fluorescent Dyes: chemistry,Plasmids,Plasmids: chemistry,Plasmids: genetics},
month = {jun},
number = {12},
pages = {4951--5},
pmid = {19527654},
publisher = {Biophysical Society},
title = {{Internal dynamics of supercoiled DNA molecules.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2712042{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {96},
year = {2009}
}
@article{Taylor2013,
author = {Taylor, Michael a and Bowen, Warwick P},
doi = {10.1088/2040-8978/15/8/085701},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Taylor, Bowen - A computational tool to characterize particle tracking measurements in optical tweezers - 2013.pdf:pdf},
issn = {2040-8978},
journal = {Journal of Optics},
keywords = {085701,15,available from stacks,computational tool,in colour only in,iop,jopt,mmedia,optical tweezers,org,particle tracking,s online supplementary data,shot-noise limit,some figures may appear,the online journal},
month = {aug},
number = {8},
pages = {085701},
title = {{A computational tool to characterize particle tracking measurements in optical tweezers}},
url = {http://stacks.iop.org/2040-8986/15/i=8/a=085701?key=crossref.ddf40bf53ee3c6bde2ae0723037b45b6},
volume = {15},
year = {2013}
}
@article{Dufrene2014,
author = {Dufr{\^{e}}ne, Yves F},
doi = {10.1128/mBio.01363-14.Updated},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dufr{\^{e}}ne - Atomic Force Microscopy in Microbiology New Structural and Functional Insights into the Microbial Cell Surface - 2014.pdf:pdf},
number = {4},
pages = {1--14},
title = {{Atomic Force Microscopy in Microbiology : New Structural and Functional Insights into the Microbial Cell Surface}},
volume = {5},
year = {2014}
}
@book{Ponce2012,
abstract = {The accessible presentation of this book gives both a general view of the entire computer vision enterprise and also offers sufficient detail to be able to build useful applications. Users learn techniques that have proven to be useful by first-hand experience and a wide range of mathematical methods. A CD-ROM with every copy of the text contains source code for programming practice, color images, and illustrative movies. Comprehensive and up-to-date, this book includes essential topics that either reflect practical significance or are of theoretical importance. Topics are discussed in substantial and increasing depth. Application surveys describe numerous important application areas such as image based rendering and digital libraries. Many important algorithms broken down and illustrated in pseudo code. Appropriate for use by engineers as a comprehensive reference to the computer vision enterprise.},
author = {Ponce, J and Forsyth, D},
booktitle = {Computer},
doi = {10.1016/j.cbi.2010.05.017},
isbn = {9780136085928},
issn = {18727786},
pages = {793},
pmid = {20595049},
title = {{Computer vision: a modern approach}},
year = {2012}
}
@article{Barbey2009,
author = {Barbey, Raphael and Lavanant, Laurent and Paripovic, Dusko and Schu, Nicolas and Sugnaux, Caroline and Tugulu, Stefano and Klok, Harm-anton},
journal = {Chemical Reviews},
pages = {5437--5527},
title = {{Polymer Brushes via Surface-Initiated Controlled Radical Polymerization : Synthesis , Characterization , Properties , and Applications}},
volume = {109},
year = {2009}
}
@article{Jian1998b,
abstract = {Thermal motions in supercoiled DNA are studied by Brownian dynamics (BD) simulations with a focus on the site juxtaposition process. It had been shown in the last decade that the BD approach is capable of describing actual times of large-scale DNA motion. The bead model of DNA used here accounts for bending and torsional elasticity as well as the electrostatic repulsion among DNA segments. The hydrodynamic interaction among the beads of the model chain and the aqueous solution is incorporated through the Rotne-Prager tensor. All simulations were performed for the sodium ion concentration of 0.01 M. We first showed, to test our BD procedure, that the same distributions of equilibrium conformational properties are obtained as by Monte Carlo simulations for the corresponding DNA model. The BD simulations also predict with accuracy published experimental values of the diffusion coefficients of supercoiled DNA. To describe the rate of conformational changes, we also calculated the autocorrelation functions for the writhe and radius of gyration for the supercoiled molecules. The rate of site juxtaposition was then studied for DNA molecules up to 3000 bp in length. We find that site juxtaposition is a very slow process: although accelerated by a factor of more than 100 by DNA supercoiling, the times of juxtaposition are in the range of ms even for highly supercoiled DNA, about two orders of magnitude higher than the relaxation times of writhe and the radius of gyration for the same molecules. By inspecting successive simulated conformations of supercoiled DNA, we conclude that slithering of opposing segments of the interwound superhelix is not an efficient mechanism to accomplish site juxtaposition, at least for conditions of low salt concentration. Instead, transient distortions of the interwound superhelix, followed by continuous reshaping of the molecule, contribute more significantly to site juxtaposition kinetics.},
author = {Jian, H and Schlick, T and Vologodskii, a},
doi = {10.1006/jmbi.1998.2170},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jian, Schlick, Vologodskii - Internal motion of supercoiled DNA brownian dynamics simulations of site juxtaposition. - 1998(2).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Jian, Schlick, Vologodskii - Internal motion of supercoiled DNA brownian dynamics simulations of site juxtaposition. - 1998.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Algorithms,Chemical,Computer Simulation,DNA,Kinetics,Models,Molecular,Motion,Nucleic Acid Conformation,Static Electricity,Superhelical,Superhelical: chemistry},
month = {nov},
number = {2},
pages = {287--96},
pmid = {9813118},
title = {{Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9813118},
volume = {284},
year = {1998}
}
@article{Saffman1965a,
annote = {        From Duplicate 1 (                   Lift on a small sphere in a slow shear flow                 - Saffman, P G )
                
ISI Document Delivery No.: 65713
Times Cited: 1055
Cited Reference Count: 16
Saffman, pg
Cambridge univ press
New york
Part 2
        
        From Duplicate 2 (                   The lift on a small sphere in a slow shear flow                 - Saffman, P. G. )
                
        
        
      },
author = {Saffman, P. G.},
doi = {10.1017/S0022112065000824},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Saffman - The lift on a small sphere in a slow shear flow - 1965.pdf:pdf},
isbn = {0022-1120},
issn = {0022-1120},
journal = {Journal of Fluid Mechanics},
language = {English},
month = {mar},
number = {02},
pages = {385--400},
title = {{The lift on a small sphere in a slow shear flow}},
url = {<Go to ISI>://WOS:A19656571300015 http://www.journals.cambridge.org/abstract{\_}S0022112065000824},
volume = {22},
year = {1965}
}
@article{Theofanidou2004,
author = {Theofanidou, Eirini and Wilson, Laurence and Hossack, William J and Arlt, Jochen},
doi = {10.1016/j.optcom.2004.03.009},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Theofanidou et al. - Spherical aberration correction for optical tweezers - 2004.pdf:pdf},
journal = {Optics Communications},
number = {December 2003},
pages = {145--150},
title = {{Spherical aberration correction for optical tweezers}},
volume = {236},
year = {2004}
}
@article{Kemper2007,
abstract = {Digital holographic microscopy provides quantitative phase contrast im- aging that is suitable for high resolving investigations on reflective surfaces as well as for marker-free analysis of living cells. Results from engineered surfaces and living cells demonstrate applications of digital holographic microscopy for technical inspection and life cell imaging.},
author = {Kemper, Bj{\"{o}}rn and Langehanenberg, Patrik and von Bally, Gert},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kemper, Langehanenberg, von Bally - Digital Holographic Microscopy A new Method for surface Analysis and Marker-Free Dynamic Life cell i.pdf:pdf},
journal = {Optik {\&} Photonik},
keywords = {digital holographic microscopy},
pages = {41--44},
title = {{Digital Holographic Microscopy A new Method for surface Analysis and Marker-Free Dynamic Life cell imaging}},
volume = {1394},
year = {2007}
}
@article{Mirsaidov2008,
abstract = {Optical trapping is a powerful tool for the micromanipulation of living cells--especially bacteria--but photodamage induced by the laser beam can adversely affect viability. We have explored optical trapping conditions in the near infrared (840-930 nm) that preserve the viability of E. coli, as measured by gene expression of green fluorescent protein. We have found that time-sharing the optical traps, i.e., dwelling only 10 micros-1 ms on the cell, improves viability relative to continuous wave (CW) exposure for the same exposure time. We have also observed that similar to CW traps the photodamage in a time-shared trap depends weakly on wavelength, but linearly on peak power, implying an effect induced by single photon absorption. Taken altogether, integrating the exposure time and peak power, the data indicate that there is a lethal energy dose of about 5 J for E. coli. Thus a single parameter--the energy--can be used to describe the limitation on viability.},
author = {Mirsaidov, Utkur and Timp, Winston and Timp, Kaethe and Mir, Mustafa and Matsudaira, Paul and Timp, Gregory},
doi = {10.1103/PhysRevE.78.021910},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mirsaidov et al. - Optimal optical trap for bacterial viability - 2008(2).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Mirsaidov et al. - Optimal optical trap for bacterial viability - 2008.pdf:pdf},
isbn = {1539-3755 (Print)$\backslash$r1539-3755 (Linking)},
issn = {15393755},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
month = {aug},
number = {2},
pages = {1--7},
pmid = {18850868},
title = {{Optimal optical trap for bacterial viability}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.78.021910},
volume = {78},
year = {2008}
}
@article{Isberg2002,
abstract = {Most bacteria that colonize eukaryotes must bind directly to host cells to establish a replicative niche. In enteric bacteria, adhesion to host cells is often promoted by a lectin found on surface-localized pili. Some pili promote efficient adhesion only when they are subjected to shear stress, as found during the flow of blood over endothelium or mucous over the surface of the epithelium.},
author = {Isberg, Ralph R and Barnes, Penelope},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Isberg, Barnes - Dancing with the host flow-dependent bacterial adhesion. - 2002.pdf:pdf},
issn = {0092-8674},
journal = {Cell},
keywords = {Adhesins, Bacterial,Adhesins, Bacterial: metabolism,Adhesins, Escherichia coli,Animals,Bacterial Adhesion,Bacterial Adhesion: physiology,Fimbriae Proteins,Fimbriae, Bacterial,Fimbriae, Bacterial: metabolism,Fimbriae, Bacterial: physiology,Humans,Models, Biological,Receptors, Cell Surface,Receptors, Cell Surface: metabolism,Receptors, Cell Surface: physiology,Rheology},
month = {jul},
number = {1},
pages = {1--4},
pmid = {12150990},
title = {{Dancing with the host; flow-dependent bacterial adhesion.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12150990},
volume = {110},
year = {2002}
}
@article{Lin2001,
author = {Lin, Chiunhsiun and Fan, Kuo-chin},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lin, Fan - Triangle-based approach to the detection of human face - 2001.pdf:pdf},
keywords = {face detection,triangle-based segmentation,weighting mask function},
number = {August 1999},
pages = {1271--1284},
title = {{Triangle-based approach to the detection of human face}},
volume = {34},
year = {2001}
}
@article{Ruggeri2007,
abstract = {Platelet adhesion is an essential function in response to vascular injury and is generally viewed as the first step during which single platelets bind through specific membrane receptors to cellular and extracellular matrix constituents of the vessel wall and tissues. This response initiates thrombus formation that arrests hemorrhage and permits wound healing. Pathological conditions that cause vascular alterations and blood flow disturbances may turn this beneficial process into a disease mechanism that results in arterial occlusion, most frequently in atherosclerotic vessels of the heart and brain. Besides their relevant role in hemostasis and thrombosis, platelet adhesive properties are central to a variety of pathophysiological processes that extend from inflammation to immune-mediated host defense and pathogenic mechanisms as well as cancer metastasis. All of these activities depend on the ability of platelets to circulate in blood as sentinels of vascular integrity, adhere where alterations are detected, and signal the abnormality to other platelets and blood cells. In this respect, therefore, platelet adhesion to vascular wall structures, to one another (aggregation), or to other blood cells, represent different aspects of the same fundamental biological process. Detailed studies by many investigators over the past several years have been aimed to dissect the complexity of these functions, and the results obtained now permit an attempt to integrate all the available information into a picture that highlights the balanced diversity and synergy of distinct platelet adhesive interactions.},
author = {Ruggeri, Zaverio M and Mendolicchio, G Loredana},
doi = {10.1161/01.RES.0000267878.97021.ab},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ruggeri, Mendolicchio - Adhesion mechanisms in platelet function. - 2007.pdf:pdf},
issn = {1524-4571},
journal = {Circulation research},
keywords = {Animals,Atherosclerosis,Atherosclerosis: physiopathology,Blood Platelets,Blood Platelets: physiology,Cell Adhesion Molecules,Cell Adhesion Molecules: physiology,Collagen,Collagen: physiology,Extracellular Matrix,Extracellular Matrix: physiology,Flow,Hemostasis,Hemostasis: physiology,Humans,Inflammation,Inflammation: physiopathology,Platelet Adhesiveness,Platelet Adhesiveness: physiology,Platelet Aggregation,Platelet Aggregation: physiology,Receptors,Simulation,Thrombosis,Thrombosis: physiopathology,paper3,shear rate},
mendeley-tags = {Flow,Simulation,paper3,shear rate},
month = {jun},
number = {12},
pages = {1673--85},
pmid = {17585075},
title = {{Adhesion mechanisms in platelet function.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17585075},
volume = {100},
year = {2007}
}
@phdthesis{Chattopadhyay2008,
abstract = {Bacteria are arguably the simplest of known microorganisms, forming a fundamental part of the world we live in. Many functions they perform are found in scaled-up versions in higher organisms. Among many advanced functions, bacteria possess the ability to move in search for nutrients and favorable growth conditions. Measurement of the dynamical variables associated with bacterial swimming has proven to be difﬁcult due to the lack of an accurate and convenient tool. In the past optical traps have been used for the manipulation of microscopic objects and measurement of minute forces. Herein, I have devised techniques for use of optical traps for direct measurement of the dynamics of bacterial swimming and chemotaxis, shedding light on the propulsion apparatus and sensory systems. A detailed analysis is performed to explore the effects of non-local hydrodynamic interactions on the swimming of single cells. Due to the lack of reliable measurement techniques, experimentalists often use theoretical models to estimate bacterial dynamics, the validity of which are tested. I emphasize the shortcomings of the very popular Resistive Force Theory (RFT) and indicate how the more rigorous Slender Body Theory (SBT) is able to overcome the limitations. In addition the chemotaxis of the marine bacterial strain Vibrio alginolyticus is studied with the revelation of a previously unknown chemotactic mechanism. Direct observations showed that these cells are able to bend their ﬂagella to impart direction changes, which is paramount for an effective search strategy. This interesting ﬁnd opens several intriguing questions pertaining to chemotaxis.},
author = {Chattopadhyay, Suddhashil},
booktitle = {Astronomy},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chattopadhyay - Study of bacterial motility using optical tweezers - 2008.pdf:pdf},
keywords = {bacteria,flagella,optical tweezers,rotation},
school = {University of Pittsburgh},
title = {{Study of bacterial motility using optical tweezers}},
type = {PhD thesis},
url = {http://etd.library.pitt.edu/ETD/available/etd-11022008-104451/unrestricted/Chattopadhyay{\_}Suddhashil{\_}ETD2008.pdf},
year = {2008}
}
@article{Lee1994,
abstract = {Molecular recognition forms the basis for assembly and regulation in living organisms. We have used the atomic force microscope (AFM) to study the interaction of a model receptor streptavidin with its ligand biotin under physiological conditions. Surfaces functionalized with biotin and streptavidin exhibited adhesive forces 3-8 times greater than the nonspecific interactions observed between blocked streptavidin and biotinylated surfaces. The magnitude and distribution of the observed adhesive forces suggest they result from individual streptavidin-biotin interactions. This technique provides a means to directly study molecular recognition interactions at the molecular level.},
author = {Lee, G U and Kidwell, D A and Colton, R J},
doi = {10.1021/la00014a003},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lee, Kidwell, Colton - Sensing Discrete Streptavidin Biotin Interactions With Atomic-Force Microscopy - 1994.pdf:pdf},
isbn = {0743-7463},
issn = {0743-7463},
journal = {Langmuir},
number = {2},
pages = {354--357},
pmid = {128},
title = {{Sensing Discrete Streptavidin Biotin Interactions With Atomic-Force Microscopy}},
url = {papers2://publication/uuid/F41F0F29-0794-4EB5-A20C-B2FC7CC52A3A},
volume = {10},
year = {1994}
}
@article{Kucheria2005a,
abstract = {This review discusses recent advances in the understanding of how the common pathogen, uropathogenic Escherichia coli, interacts with the host to lead to infection.},
author = {Kucheria, R and Dasgupta, P and Sacks, S H and Khan, M S and Sheerin, N S},
doi = {10.1136/pgmj.2004.023036},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kucheria et al. - Urinary tract infections new insights into a common problem. - 2005.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Kucheria et al. - Urinary tract infections new insights into a common problem. - 2005(2).pdf:pdf},
issn = {0032-5473},
journal = {Postgraduate medical journal},
keywords = {Bacterial,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli Infections: microbiology,Escherichia coli: immunology,Escherichia coli: pathogenicity,Female,Fimbriae,Humans,Immunity,Innate,Urinary Tract Infections,Urinary Tract Infections: immunology,Urinary Tract Infections: microbiology,Virulence},
month = {feb},
number = {952},
pages = {83--6},
pmid = {15701738},
title = {{Urinary tract infections: new insights into a common problem.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1743204{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {81},
year = {2005}
}
@article{Czerwinski2009,
abstract = {One limitation on the performance of optical traps is the noise inherently present in every setup. Therefore, it is the desire of most experimentalists to minimize and possibly eliminate noise from their optical trapping experiments. A step in this direction is to quantify the actual noise in the system and to evaluate how much each particular component contributes to the overall noise. For this purpose we present Allan variance analysis as a straightforward method. In particular, it allows for judging the impact of drift which gives rise to low-frequency noise, which is extremely difficult to pinpoint by other methods. We show how to determine the optimal sampling time for calibration, the optimal number of data points for a desired experiment, and we provide measurements of how much accuracy is gained by acquiring additional data points. Allan variances of both micrometer-sized spheres and asymmetric nanometer-sized rods are considered.},
annote = {Published in: Proc. SPIE, Vol. 7400, 740004 (2009)

14 pages, 6 figures, presented at SPIE Optics+Photonics 2009 in San
Diego, CA, USA},
author = {Czerwinski, Fabian and Richardson, Andrew C and Selhuber-Unkel, Christine and Oddershede, Lene B.},
doi = {10.1117/12.827975},
journal = {arXiv},
keywords = {physics.data-an,physics.optics},
title = {{Allan Variance Analysis as Useful Tool to Determine Noise in Various Single-Molecule Setups}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=0908.4484v1 http://arxiv.org/abs/0908.4484v1},
volume = {physics.da},
year = {2009}
}
@article{Wang2011,
abstract = {The quantitative study of the cell growth [1-5] has led to many fundamental insights in our understanding of a wide range of subjects from cell cycle [6-9] to senescence [10]. Of particular importance is the growth rate, whose constancy represents a physiological steady state of an organism. Recent studies, however, suggest that the rate of elongation during exponential growth of bacterial cells decreases cumulatively with replicative age for both asymmetrically [11] and symmetrically [12,13] dividing organisms, implying that a “steady-state” population consists of individual cells that are never in a steady state of growth. To resolve this seeming paradoxical observation, we studied the long-term growth and division patterns of Escherichia coli cells by employing a microfluidic device designed to follow steady state growth and division of a large number of cells at a defined reproductive age. Our analysis of {\~{}}105 individual cells reveals a remarkable stability of growth of the mother cell inheriting the same pole for hundreds of generations. We further show that death of E. coli is not purely stochastic but is the result of accumulating damages. We conclude that E. coli, unlike all other aging model systems studied to date, has a robust mechanism of growth that is decoupled from cell death.},
author = {Wang, Ping and Robert, Lydia and Pelletier, James and Dang, Wei Lien and Taddei, Francois and Wright, Andrew and Jun, Suckjoon},
doi = {10.1016/j.cub.2010.04.045.Robust},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wang et al. - Robust growth of Escherichia coli - 2011.pdf:pdf},
journal = {Current Biology},
number = {12},
pages = {1099--1103},
title = {{Robust growth of Escherichia coli}},
volume = {20},
year = {2011}
}
@article{Kotloff2013,
abstract = {BACKGROUND: Diarrhoeal diseases cause illness and death among children younger than 5 years in low-income countries. We designed the Global Enteric Multicenter Study (GEMS) to identify the aetiology and population-based burden of paediatric diarrhoeal disease in sub-Saharan Africa and south Asia.

METHODS: The GEMS is a 3-year, prospective, age-stratified, matched case-control study of moderate-to-severe diarrhoea in children aged 0-59 months residing in censused populations at four sites in Africa and three in Asia. We recruited children with moderate-to-severe diarrhoea seeking care at health centres along with one to three randomly selected matched community control children without diarrhoea. From patients with moderate-to-severe diarrhoea and controls, we obtained clinical and epidemiological data, anthropometric measurements, and a faecal sample to identify enteropathogens at enrolment; one follow-up home visit was made about 60 days later to ascertain vital status, clinical outcome, and interval growth.

FINDINGS: We enrolled 9439 children with moderate-to-severe diarrhoea and 13,129 control children without diarrhoea. By analysing adjusted population attributable fractions, most attributable cases of moderate-to-severe diarrhoea were due to four pathogens: rotavirus, Cryptosporidium, enterotoxigenic Escherichia coli producing heat-stable toxin (ST-ETEC; with or without co-expression of heat-labile enterotoxin), and Shigella. Other pathogens were important in selected sites (eg, Aeromonas, Vibrio cholerae O1, Campylobacter jejuni). Odds of dying during follow-up were 8·5-fold higher in patients with moderate-to-severe diarrhoea than in controls (odd ratio 8·5, 95{\%} CI 5·8-12·5, p<0·0001); most deaths (167 [87·9{\%}]) occurred during the first 2 years of life. Pathogens associated with increased risk of case death were ST-ETEC (hazard ratio [HR] 1·9; 0·99-3·5) and typical enteropathogenic E coli (HR 2·6; 1·6-4·1) in infants aged 0-11 months, and Cryptosporidium (HR 2·3; 1·3-4·3) in toddlers aged 12-23 months.

INTERPRETATION: Interventions targeting five pathogens (rotavirus, Shigella, ST-ETEC, Cryptosporidium, typical enteropathogenic E coli) can substantially reduce the burden of moderate-to-severe diarrhoea. New methods and accelerated implementation of existing interventions (rotavirus vaccine and zinc) are needed to prevent disease and improve outcomes.

FUNDING: The Bill {\&} Melinda Gates Foundation.},
author = {Kotloff, Karen L and Nataro, James P and Blackwelder, William C and Nasrin, Dilruba and Farag, Tamer H and Panchalingam, Sandra and Wu, Yukun and Sow, Samba O and Sur, Dipika and Breiman, Robert F and Faruque, Abu Sg and Zaidi, Anita Km and Saha, Debasish and Alonso, Pedro L and Tamboura, Boubou and Sanogo, Doh and Onwuchekwa, Uma and Manna, Byomkesh and Ramamurthy, Thandavarayan and Kanungo, Suman and Ochieng, John B and Omore, Richard and Oundo, Joseph O and Hossain, Anowar and Das, Sumon K and Ahmed, Shahnawaz and Qureshi, Shahida and Quadri, Farheen and Adegbola, Richard a and Antonio, Martin and Hossain, M Jahangir and Akinsola, Adebayo and Mandomando, Inacio and Nhampossa, Tacilta and Ac{\'{a}}cio, Sozinho and Biswas, Kousick and O'Reilly, Ciara E and Mintz, Eric D and Berkeley, Lynette Y and Muhsen, Khitam and Sommerfelt, Halvor and Robins-Browne, Roy M and Levine, Myron M},
doi = {10.1016/S0140-6736(13)60844-2},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kotloff et al. - Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Mu.pdf:pdf},
issn = {1474-547X},
journal = {Lancet},
keywords = {Africa South of the Sahara,Asia, Western,Asia, Western: epidemiology,Bacterial Infections,Bacterial Infections: mortality,Case-Control Studies,Child, Preschool,Cost of Illness,Developing Countries,Diarrhea,Diarrhea, Infantile,Diarrhea, Infantile: microbiology,Diarrhea, Infantile: mortality,Diarrhea: microbiology,Diarrhea: mortality,Female,Humans,Infant,Male,Prospective Studies,Rotavirus Infections,Rotavirus Infections: mortality},
month = {jul},
number = {9888},
pages = {209--22},
pmid = {23680352},
title = {{Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23680352},
volume = {382},
year = {2013}
}
@article{Aprikian2007,
abstract = {FimH is a mannose-specific adhesin located on the tip of type 1 fimbriae of Escherichia coli that is capable of mediating shear-enhanced bacterial adhesion. FimH consists of a fimbria-associated pilin domain and a mannose-binding lectin domain, with the binding pocket positioned opposite the interdomain interface. By using the yeast two-hybrid system, purified lectin and pilin domains, and docking simulations, we show here that the FimH domains interact with one another. The affinity for mannose is greatly enhanced (up to 300-fold) in FimH variants in which the interdomain interaction is disrupted by structural mutations in either the pilin or lectin domains. Also, affinity to mannose is dramatically enhanced in isolated lectin domains or in FimH complexed with the chaperone molecule that is wedged between the domains. Furthermore, FimH with native structure mediates weak binding at low shear stress but shifts to strong binding at high shear, whereas FimH with disrupted interdomain contacts (or the isolated lectin domain) mediates strong binding to mannose-coated surfaces even under low shear. We propose that interactions between lectin and pilin domains decrease the affinity of the mannose-binding pocket via an allosteric mechanism. We further suggest that mechanical force at high shear stress separates the two domains, allowing the lectin domain to switch from a low affinity to a high affinity state. This shift provides a mechanism for FimH-mediated shear-enhanced adhesion by enabling the adhesin to form catch bond-like interactions that are longer lived at high tensile force.},
author = {Aprikian, Pavel and Tchesnokova, Veronika and Kidd, Brian and Yakovenko, Olga and Yarov-Yarovoy, Vladimir and Trinchina, Elena and Vogel, Viola and Thomas, Wendy E and Sokurenko, Evgeni V},
doi = {10.1074/jbc.M702037200},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Aprikian et al. - Interdomain interaction in the FimH adhesin of Escherichia coli regulates the affinity to mannose. - 2007.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Adhesins,Cell Adhesion,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: genetics,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Genetic Variation,Lectins,Lectins: chemistry,Mannose,Mannose: chemistry,Mechanical,Molecular Conformation,Mutagenesis,Protein Binding,Protein Conformation,Protein Structure,Saccharomyces cerevisiae,Saccharomyces cerevisiae: metabolism,Site-Directed,Stress,Tensile Strength,Tertiary},
month = {aug},
number = {32},
pages = {23437--46},
pmid = {17567583},
title = {{Interdomain interaction in the FimH adhesin of Escherichia coli regulates the affinity to mannose.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17567583},
volume = {282},
year = {2007}
}
@article{Leijnse2015,
abstract = {SignificanceFilopodia are essential membrane protrusions that facilitate cellular sensing and interaction with the environment. The mechanical properties of filopodia are crucial for their ability to push and pull on external objects and are attributed to actin dynamics. We confirm the presence of F-actin inside extended filopodia and reveal a new mechanism by which actin can exert traction forces on external objects. This mechanism is mediated by rotation and helical buckling, which cause shortening and retraction of the actin shaft. By imaging of F-actin and simultaneous force spectroscopy, we reveal and detail how force propagates through this spiral actin structure and show how torsional twist of the actin shaft is translated into a traction force at the filopodial tip. Cells can interact with their surroundings via filopodia, which are membrane protrusions that extend beyond the cell body. Filopodia are essential during dynamic cellular processes like motility, invasion, and cell-cell communication. Filopodia contain cross-linked actin filaments, attached to the surrounding cell membrane via protein linkers such as integrins. These actin filaments are thought to play a pivotal role in force transduction, bending, and rotation. We investigated whether, and how, actin within filopodia is responsible for filopodia dynamics by conducting simultaneous force spectroscopy and confocal imaging of F-actin in membrane protrusions. The actin shaft was observed to periodically undergo helical coiling and rotational motion, which occurred simultaneously with retrograde movement of actin inside the filopodium. The cells were found to retract beads attached to the filopodial tip, and retraction was found to correlate with rotation and coiling of the actin shaft. These results suggest a previously unidentified mechanism by which a cell can use rotation of the filopodial actin shaft to induce coiling and hence axial shortening of the filopodial actin bundle.},
author = {Leijnse, Natascha and Oddershede, Lene B. and Bendix, Poul M.},
doi = {10.1073/pnas.1411761112},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Leijnse, Oddershede, Bendix - Helical buckling of actin inside filopodia generates traction - 2015.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {Vesicle},
mendeley-tags = {Vesicle},
number = {1},
pages = {136--141},
pmid = {25535347},
title = {{Helical buckling of actin inside filopodia generates traction}},
url = {http://www.pnas.org/content/112/1/136},
volume = {112},
year = {2015}
}
@article{Nishimura2002,
author = {Nishimura, L.S. and Giron, J.A. and Nunes, S.L. and Guth, B.E.C.},
doi = {10.1128/JCM.40.7.2606},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nishimura et al. - Prevalence of enterotoxigenic Escherichia coli strains harboring the longus pilus gene in Brazil - 2002.pdf:pdf},
journal = {Journal of clinical microbiology},
number = {7},
pages = {2606},
publisher = {American Society for Microbiology (ASM)},
title = {{Prevalence of enterotoxigenic Escherichia coli strains harboring the longus pilus gene in Brazil}},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC120555/},
volume = {40},
year = {2002}
}
@article{Sheng2007,
abstract = {The shallow depth of field of conventional microscopy hampers analyses of 3D swimming behavior of fast dinoflagellates, whose motility influences macroassemblages of these cells into often-observed dense "blooms." The present analysis of cinematic digital holographic microscopy data enables simultaneous tracking and characterization of swimming of thousands of cells within dense suspensions. We focus on Karlodinium veneficum and Pfiesteria piscicida, mixotrophic and heterotrophic dinoflagellates, respectively, and their preys. Nearest-neighbor distance analysis shows that predator and prey cells are randomly distributed relative to themselves, but, in mixed culture, each predator clusters around its respective prey. Both dinoflagellate species exhibit complex highly variable swimming behavior as characterized by radius and pitch of helical swimming trajectories and by translational and angular velocity. K. veneficum moves in both left- and right-hand helices, whereas P. piscicida swims only in right-hand helices. When presented with its prey (Storeatula major), the slower K. veneficum reduces its velocity, radius, and pitch but increases its angular velocity, changes that reduce its hydrodynamic signature while still scanning its environment as "a spinning antenna." Conversely, the faster P. piscicida increases its speed, radius, and angular velocity but slightly reduces its pitch when exposed to prey (Rhodomonas sp.), suggesting the preferred predation tactics of an "active hunter."},
author = {Sheng, Jian and Malkiel, Edwin and Katz, Joseph and Adolf, Jason and Belas, Robert and Place, Allen R},
doi = {10.1073/pnas.0704658104},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sheng et al. - Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates. - 2007.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {44},
pages = {17512--17517},
pmid = {17959778},
title = {{Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates.}},
volume = {104},
year = {2007}
}
@article{Kantele2008,
abstract = {Vaccines are needed against urinary tract infections (UTIs) in children, as episodes of pyelonephritis (PN) may cause renal scarring. Local immune mechanisms are regarded to confer protection, yet they have been poorly characterized for children. This study explores the local immune response in children by looking for newly activated pathogen-specific antibody-secreting cells (ASC), expected to appear transiently in the circulation as a response to UTI. Urinary tract-originating ASC specific to each patient's own pathogen or P fimbria were studied in 37 children with PN. The children were examined for recidivism and renal scarring in a 6-month follow-up study. Pathogen-specific ASC were found in 33/37 children, with the magnitude increasing with age. In contrast to the case for adults, with immunoglobulin A (IgA) dominance, in 18/33 cases IgM dominated the response, and this occurred more frequently in infants (63{\%}) than in older children (30{\%}). The most vigorous response was found to whole Escherichia coli bacteria (geometric mean, 63 +/- 2,135 ASC/10(6) peripheral blood mononuclear cells [PBMC]), yet responses were found to P fimbriae (13 +/- 33 ASC/10(6) PBMC), too. The response peaked at 1 to 2 weeks and was low/negligible 3 to 7 weeks after the beginning of symptoms. Recidivism was seen in seven patients, and renal scarring was seen in nine patients. In conclusion, a response of circulating ASC was found in children with UTIs, with the magnitude increasing with age. Since IgM is not present in urine, the IgM dominance of the response suggests that systemic immune mechanisms are more important in the immune defense in children than in adults. In 81{\%} of patients, no recidivism was seen, suggesting a successful immune defense.},
author = {Kantele, Anu and Palkola, Nina and Arvilommi, Heikki and Honkinen, Olli and Jahnukainen, Timo and Mertsola, Jussi and Kantele, Jussi M},
doi = {10.1128/CVI.00373-07},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kantele et al. - Local immune response to upper urinary tract infections in children. - 2008.pdf:pdf},
issn = {1556-679X},
journal = {Clinical and vaccine immunology : CVI},
keywords = {Adolescent,Adult,Antibodies, Bacterial,Antibodies, Bacterial: blood,Antibody-Producing Cells,Antibody-Producing Cells: immunology,Child,Child, Preschool,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli Infections: microbiology,Escherichia coli: immunology,Female,Fimbriae, Bacterial,Fimbriae, Bacterial: immunology,Humans,Immunoglobulin M,Immunoglobulin M: blood,Infant,Infant, Newborn,Male,Pyelonephritis,Pyelonephritis: diagnosis,Pyelonephritis: immunology,Pyelonephritis: microbiology,Urinary Tract Infections,Urinary Tract Infections: diagnosis,Urinary Tract Infections: immunology,Urinary Tract Infections: microbiology},
month = {mar},
number = {3},
pages = {412--7},
pmid = {18184820},
title = {{Local immune response to upper urinary tract infections in children.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2268270{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {15},
year = {2008}
}
@article{Otto2008a,
abstract = {Recent applications of biophysical techniques to the study of adhesion and biofilm formation are playing an important role in broadening our understanding of bacterial interactions. While non-invasive methods enable measurement of adhesion kinetics in real time, single-cell approaches provide information about adhesion forces mediated by specific cell surface structures. Promising approaches are presented in this review. ?? 2008 Elsevier Masson SAS. All rights reserved.},
author = {Otto, Karen},
doi = {10.1016/j.resmic.2008.04.007},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Otto - Biophysical approaches to study the dynamic process of bacterial adhesion - 2008.pdf:pdf},
isbn = {0923-2508},
issn = {09232508},
journal = {Research in Microbiology},
keywords = {Adhesion kinetics,Adhesive strength,Atomic force microscopy,Bacterial adhesion,Biofilm formation,Inhibition of adhesion,Micromanipulation,Optical tweezers,Quartz crystal microbalance,Surface plasmon resonance},
number = {6},
pages = {415--422},
pmid = {18550342},
title = {{Biophysical approaches to study the dynamic process of bacterial adhesion}},
volume = {159},
year = {2008}
}
@article{Czerwinski2011,
author = {Czerwinski, Fabian and Oddershede, Lene B.},
doi = {10.1016/j.cpc.2010.10.019},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Czerwinski, Oddershede - TimeSeriesStreaming.vi LabVIEW program for reliable data streaming of large analog time series - 2011.pdf:pdf},
issn = {00104655},
journal = {Computer Physics Communications},
month = {feb},
number = {2},
pages = {485--489},
publisher = {Elsevier B.V.},
title = {{TimeSeriesStreaming.vi: LabVIEW program for reliable data streaming of large analog time series}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0010465510004200},
volume = {182},
year = {2011}
}
@inproceedings{Kidney2004,
author = {Kidney, Artificial},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kidney - BIOFLUID DYNAMICS OF THE HUMAN KIDNEY SYSTEM AND D-1 D-2 - 2004.pdf:pdf},
keywords = {artificial kidney,dialysis,hemodialysis,kidney,peritoneal},
pages = {1--31},
title = {{BIOFLUID DYNAMICS OF THE HUMAN KIDNEY SYSTEM AND D-1 D-2}},
year = {2004}
}
@article{Tolic-Nørrelykke2006a,
author = {Tolić-N{\o}rrelykke, Simon F. and Schäffer, Erik and Howard, Jonathon and Pavone, Francesco S. and Jülicher, Frank and Flyvbjerg, Henrik},
doi = {10.1063/1.2356852},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tolić-N{\o}rrelykke et al. - Calibration of optical tweezers with positional detection in the back focal plane - 2006.pdf:pdf},
issn = {00346748},
journal = {Review of Scientific Instruments},
number = {10},
pages = {103101},
title = {{Calibration of optical tweezers with positional detection in the back focal plane}},
url = {http://link.aip.org/link/RSINAK/v77/i10/p103101/s1{\&}Agg=doi},
volume = {77},
year = {2006}
}
@article{Lipowsky1991,
author = {Lipowsky, Reinhard},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Lipowsky - Adhesion of vesicles and membranes - 1991.pdf:pdf},
journal = {Molecular Crystals and Liquid Crystals},
keywords = {shape transformation,unbinding phenomena,vesicle,vesicle fusion},
number = {September 1990},
pages = {17--25},
title = {{Adhesion of vesicles and membranes}},
url = {http://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:Adhesion+of+Vesicles+and+Membranes{\#}0},
volume = {202},
year = {1991}
}
@article{Kim2013,
author = {Kim, M-S and Naqavi, a and Scharf, T and Weible, K J and V{\"{o}}lkel, R and Rockstuhl, C and Herzig, H P},
doi = {10.1088/2040-8978/15/10/105708},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kim et al. - Experimental and theoretical study of the Gouy phase anomaly of light in the focus of microlenses - 2013.pdf:pdf},
issn = {2040-8978},
journal = {Journal of Optics},
month = {oct},
number = {10},
pages = {105708},
title = {{Experimental and theoretical study of the Gouy phase anomaly of light in the focus of microlenses}},
url = {http://stacks.iop.org/2040-8986/15/i=10/a=105708?key=crossref.4c9b25f0f71c2fad1777e7e7f22305db},
volume = {15},
year = {2013}
}
@article{Frolov2003,
abstract = {Shape dynamics and permeability of a membrane neck connecting a vesicle and plasma membrane are considered. The neck is modeled by a lipid membrane tubule extended between two parallel axisymmetric rings. Within a range of lengths, defined by system geometry and mechanical properties of the membrane, the tubule has two stable shapes: catenoidal microtubule and cylindrical nanotubule. The permeabilities of these two shapes, measured as ionic conductivity of the tubule interior, differ by up to four orders of magnitude. Near the critical length the transitions between the shapes occur within less than a millisecond. Theoretical estimates show that the shape switching is controlled by a single parameter, the tubule length. Thus the tubule connection can operate as a conductivity microswitch, toggling the release of vesicle content in such cellular processes as "kiss-and-run" exocytosis. In support of this notion, bistable behavior of membrane connections between vesicles and the cell plasma membrane in macrophages is demonstrated.},
author = {Frolov, Vadim A and Lizunov, Vladimir a and Dunina-Barkovskaya, Antonina Ya and Samsonov, Andrey V and Zimmerberg, Joshua},
doi = {10.1073/pnas.1432962100},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Frolov et al. - Shape bistability of a membrane neck a toggle switch to control vesicle content release - 2003.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Artificial,Biological,Biophysical Phenomena,Biophysics,Cell Membrane,Cell Membrane: chemistry,Electric Conductivity,Electrochemistry,Lipid Bilayers,Lipid Bilayers: chemistry,Membranes,Models,Molecular,Surface Properties},
month = {jul},
number = {15},
pages = {8698--703},
pmid = {12857952},
title = {{Shape bistability of a membrane neck: a toggle switch to control vesicle content release}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=166375{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {100},
year = {2003}
}
@article{Mortezaei2013,
abstract = {Uropathogenic strains of Escherichia coli establish urinary tract infections by attaching to host epithelial cells using adhesive organelles called fimbriae. Fimbriae are helix-like structures with a remarkable adaptability, offering safeguarding for bacteria exposed to changing fluid forces in the urinary tract. We challenged this property of P-fimbriae by cross-linking their subunits with shaft-specific antibodies and measuring the corresponding force response at a single organelle level. Our data show compromised extension and rewinding of P-fimbriae in the presence of antibodies and reduced fimbrial elasticity, which are important properties of fimbriae contributing to the ability of bacteria to cause urinary tract infections. The reduced elasticity found by cross-linking fimbrial subunits could thus be another assignment for antibodies; in addition to marking bacteria as foreign, antibodies physically compromise fimbrial function. We suggest that our assay and results will be a starting point for further investigations aimed at inhibiting sustained bacterial adhesion by antibodies.},
author = {Mortezaei, Narges and Singh, Bhupender and Bullitt, Esther and Uhlin, Bernt Eric and Andersson, Magnus},
doi = {10.1038/srep03393},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Mortezaei et al. - P-fimbriae in the presence of anti-PapA antibodies new insight of antibodies action against pathogens. - 2013.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Mortezaei et al. - P-fimbriae in the presence of anti-PapA antibodies new insight of antibodies action against pathogens. - 2013.doc:doc},
issn = {2045-2322},
journal = {Scientific reports},
month = {jan},
pages = {3393},
pmid = {24292100},
title = {{P-fimbriae in the presence of anti-PapA antibodies: new insight of antibodies action against pathogens.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3848023{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {3},
year = {2013}
}
@article{Saulino2000,
abstract = {Type 1 pilus biogenesis was used as a paradigm to investigate ordered macromolecular assembly at the outer cell membrane. The ability of Gram-negative bacteria to secrete proteins across their outer membrane and to assemble adhesive macromolecular structures on their surface is a defining event in pathogenesis. We elucidated genetic, biochemical, and biophysical requirements for assembly of functional type 1 pili. We discovered that the minor pilus protein FimG plays a critical role in nucleating the formation of the adhesive tip fibrillum. Genetic methods were used to trap pilus subunits during their translocation through the outer membrane usher protein, providing data on the structural interactions that occur between subunit components during type 1 pilus formation. Electron microscopic and biochemical analyses of these stepwise assembly intermediates demonstrated that translocation of pilus subunits occurs linearly through the usher's central channel, with formation of the pilus helix occurring extracellularly. Specialized pilin subunits play unique roles both in this multimerization and in the final ultrastructure of the adhesive pilus.},
author = {Saulino, E T and Bullitt, Esther and Hultgren, Scott J},
doi = {10.1073/pnas.160070497},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Saulino, Bullitt, Hultgren - Snapshots of usher-mediated protein secretion and ordered pilus assembly. - 2000.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Animals,Bacterial,Bacterial Proteins,Bacterial Proteins: secretion,Electron,Fimbriae,Guinea Pigs,Microscopy},
month = {aug},
number = {16},
pages = {9240--5},
pmid = {10908657},
title = {{Snapshots of usher-mediated protein secretion and ordered pilus assembly.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=16852{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {97},
year = {2000}
}
@article{Ashkin1980,
abstract = {Use of lasers has revolutionized the study and applications of radiation pressure. Light forces have been achieved which strongly affect the dynamics of individual small particles. It is now possible to optically accelerate, slow, stably trap, and manipulate micrometer-sized dielectric particles and atoms. This leads to a diversity of new scientific and practical applications in fields where small particles play a role, such as light scattering, cloud physics, aerosol science, atomic physics, quantum optics, and high-resolution spectroscopy.},
author = {Ashkin, A},
doi = {10.1126/science.210.4474.1081},
issn = {0036-8075},
journal = {Science (New York, N.Y.)},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
number = {4474},
pages = {1081--1088},
pmid = {17831450},
title = {{Applications of laser radiation pressure.}},
volume = {210},
year = {1980}
}
@article{Leckband2000,
author = {Leckband, Deborah},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Leckband - Measuring the forces that control protein interactions - 2000.pdf:pdf},
journal = {Annual review of biophysics},
keywords = {Dynamic force spectroscopy,force probes,intermolecular,intermolecular potentials,molecular forces,receptor},
mendeley-tags = {Dynamic force spectroscopy,intermolecular},
number = {29},
pages = {1--26},
title = {{Measuring the forces that control protein interactions}},
year = {2000}
}
@article{Forero2006a,
abstract = {We determined whether the molecular structures through which force is applied to receptor-ligand pairs are tuned to optimize cell adhesion under flow. The adhesive tethers of our model system, Escherichia coli, are type I fimbriae, which are anchored to the outer membrane of most E. coli strains. They consist of a fimbrial rod (0.3-1.5 microm in length) built from a helically coiled structural subunit, FimA, and an adhesive subunit, FimH, incorporated at the fimbrial tip. Previously reported data suggest that FimH binds to mannosylated ligands on the surfaces of host cells via catch bonds that are enhanced by the shear-originated tensile force. To understand whether the mechanical properties of the fimbrial rod regulate the stability of the FimH-mannose bond, we pulled the fimbriae via a mannosylated tip of an atomic force microscope. Individual fimbriae rapidly elongate for up to 10 microm at forces above 60 pN and rapidly contract again at forces below 25 pN. At intermediate forces, fimbriae change length more slowly, and discrete 5.0 +/- 0.3-nm changes in length can be observed, consistent with uncoiling and coiling of the helical quaternary structure of one FimA subunit at a time. The force range at which fimbriae are relatively stable in length is the same as the optimal force range at which FimH-mannose bonds are longest lived. Higher or lower forces, which cause shorter bond lifetimes, cause rapid length changes in the fimbria that help maintain force at the optimal range for sustaining the FimH-mannose interaction. The modulation of force and the rate at which it is transmitted from the bacterial cell to the adhesive catch bond present a novel physiological role for the fimbrial rod in bacterial host cell adhesion. This suggests that the mechanical properties of the fimbrial shaft have codeveloped to optimize the stability of the terminal adhesive under flow.},
author = {Forero, Manu and Yakovenko, Olga and Sokurenko, Evgeni V and Thomas, Wendy E and Vogel, Viola},
doi = {10.1371/journal.pbio.0040298},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Forero et al. - Uncoiling mechanics of Escherichia coli type I fimbriae are optimized for catch bonds. - 2006.pdf:pdf},
issn = {1545-7885},
journal = {PLoS biology},
keywords = {Adhesins,Atomic Force,Atomic Force: methods,Bacterial,Bacterial Adhesion,Bacterial: metabolism,Bacterial: physiology,Biological,Compressive Strength,Escherichia coli,Escherichia coli: metabolism,Escherichia coli: physiology,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: metabolism,Fimbriae Proteins: physiology,Ligands,Mannose,Mannose-Binding Lectin,Mannose-Binding Lectin: metabolism,Mannose: metabolism,Mechanical,Microscopy,Models,Protein Structure,Quaternary,Stress},
month = {sep},
number = {9},
pages = {1509--1516},
pmid = {16933977},
title = {{Uncoiling mechanics of Escherichia coli type I fimbriae are optimized for catch bonds.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16933977},
volume = {4},
year = {2006}
}
@article{Legendre2008,
abstract = {The three-dimensional flow around a hemispherical bubble sliding and growing on a wall in a viscous linear shear flow is studied numerically by solving the full Navier-Stokes equations in a boundary-fitted domain. The main goal of the present study is to provide a complete description of the forces experienced by the bubble (drag, lift and added mass) over a wide range of sliding and shear Reynolds numbers (0.01<or=R(eb), R(ealpha)<or=2000) and shear rate (0<or=Sr<or=5). The drag and lift forces are computed successively for the following situations: an immobile bubble in a linear shear flow; a bubble sliding on the wall in a fluid at rest; and a bubble sliding in a linear shear flow. The added-mass force is studied by considering an unsteady motion relative to the wall or a time-dependent radius.},
author = {Legendre, Dominique and Colin, Catherine and Coquard, Typhaine},
doi = {10.1098/rsta.2008.0009},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Legendre, Colin, Coquard - Lift, drag and added mass of a hemispherical bubble sliding and growing on a wall in a viscous linear shear f.pdf:pdf},
issn = {1364-503X},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
month = {jun},
number = {1873},
pages = {2233--48},
pmid = {18348971},
title = {{Lift, drag and added mass of a hemispherical bubble sliding and growing on a wall in a viscous linear shear flow.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18348971},
volume = {366},
year = {2008}
}
@inproceedings{Grip2009,
abstract = {Today there is no efficient and user friendly method to continuously register, quantify and evaluate human movements. Hip- and knee joint kinematics is an area that has a large clinical interest and a large need of evidence based documentation. There are advanced movement measurement systems, measuring three dimensional movements with a high degree of accuracy. Such systems suffer from limitations when it comes to measurements in a clinic or in a natural setting, for example in the home environment of the patient, since such systems demands a specialised laboratory environment. The systems are also expensive to buy and maintain. Another im- portant factor is the lack of good and easy-to-use tools to ana- lyse and evaluate movements for medical applications. The long term aim is to develop a portable and easy-to use measurement system to quantify movement ability in upper or lower limbs. and precision of a custom developed portable system based on gyroscopic sensors.},
author = {Grip, H and Gustavsson, O and Ohberg, F and Edstr{\"{o}}m, U and Hager-Ross, C and Lundstr{\"{o}}m, R},
booktitle = {World Congress on Medical Physics and Biomedical Engineering September 712 2009 Munich Germany},
keywords = {gyroscopic sensors,kine,movement analysis},
pages = {520--522},
publisher = {Springer},
title = {{Movement of Lower Extremity–Development of a Portable System for Movement Analysis}},
url = {http://www.springerlink.com/index/K7W6T51316783294.pdf},
year = {2009}
}
@article{Lentle2008b,
abstract = {The physical properties of digesta may influence mixing, efficiency of digestion, and absorption within the lumen of the intestine. We review how the physical properties of digesta change during transit through the various segments of the intestine, and how their influence on flow and mixing may be modulated by peristaltic activity. We examine how, in more fluid digesta, the solid and liquid phases interact to influence flow and mixing. Similarly, how in viscid digesta, shear strength, plasticity and elasticity of contained particulate material may influence the permeation of the fluid phase and secretions into and out of the digesta bolus. The manner in which the solid and liquid phases of digesta interact in a partly gaseous environment, such as the lower bowel, to influence bolus cohesion is also examined. Those mechanisms that promote the formation of a less viscous layer at the mucosal interface to promote plug flow are reviewed, and their effect on the efficiency of mixing and digestion discussed. It is recommended that in any future work investigating the character of mixing in the intestine, a wider range of appropriate digesta properties be measured and that, in investigations of intestinal movement, perfusates with similar characteristics to digesta be used.},
author = {Lentle, R G and Janssen, P W M},
doi = {10.1007/s00360-008-0264-x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lentle, Janssen - Physical characteristics of digesta and their influence on flow and mixing in the mammalian intestine a review. - 2008.pdf:pdf},
issn = {0174-1578},
journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology},
keywords = {Animal,Animals,Biological,Digestion,Digestion: physiology,Elasticity,Food,Gastrointestinal Contents,Gastrointestinal Contents: chemistry,Gastrointestinal Motility,Gastrointestinal Transit,Intestinal Absorption,Intestines,Intestines: physiology,Models,Particle Size,Peristalsis,Permeability,Rheology,Shear Strength,Viscosity},
month = {aug},
number = {6},
pages = {673--90},
pmid = {18401586},
title = {{Physical characteristics of digesta and their influence on flow and mixing in the mammalian intestine: a review.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18401586},
volume = {178},
year = {2008}
}
@article{Evans1990,
author = {Evans, Evan and Rawicz, W},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans, Rawicz - Entropy-Driven Tension and Bending Elasticity in Condensed-Fluid Membranes - 1990.pdf:pdf},
journal = {Physical Review Letters},
number = {17},
title = {{Entropy-Driven Tension and Bending Elasticity in Condensed-Fluid Membranes}},
volume = {64},
year = {1990}
}
@article{Chung2012,
abstract = {Circle detection is fundamental in pattern recognition and computer vision. The randomized approach has received much attention for its computational benefit when compared with the Hough transform. In this paper, a multiple-evidence-based sampling strategy is proposed to speed up the randomized approach. Next, an efficient refinement strategy is proposed to improve the accuracy. Based on different kinds of ten test images, experimental results demonstrate the computation-saving and accuracy effects when plugging the proposed strategies into three existing circle detection methods. ?? 2011 Elsevier Ltd. All rights reserved.},
author = {Chung, Kuo Liang and Huang, Yong Huai and Shen, Shi Ming and Krylov, Andrey S. and Yurin, Dmitry V. and Semeikina, Ekaterina V.},
doi = {10.1016/j.patcog.2011.07.004},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chung et al. - Efficient sampling strategy and refinement strategy for randomized circle detection - 2012.pdf:pdf},
issn = {00313203},
journal = {Pattern Recognition},
month = {jan},
number = {1},
pages = {252--263},
publisher = {Elsevier},
title = {{Efficient sampling strategy and refinement strategy for randomized circle detection}},
volume = {45},
year = {2012}
}
@article{Roux1997,
abstract = {A variable region (Id)-matched set of genetically engineered human IgG1, -2, -3, and -4 subclass molecules was analyzed by electron microscopy for hinge-mediated differences in flexibility. The hinge-mediated bending was studied, as was the ability of the subclasses to form immune complexes with two anti-Id mAbs. The data show that the rank order (most to least flexible) of the IgG subclasses for hinge-folding mode of flexibility between Fab arms is IgG3 > IgG1 > IgG4 > IgG2. The mean Fab-Fab angles for the subclasses are IgG3, 136 degrees; IgG4, 128 degrees; IgG2, 127 degrees; and IgG1, 117 degrees. Fab-Fc angles were similarly analyzed. By sampling of equimolar mixtures of Id-bearing IgGs and each of two anti-Id mAb after incubation over time (1.5 min to 3.5 h), different kinetic profiles of immune complex formation of defined geometry were documented. Both anti-Id mAbs displayed unique kinetic profiles when complexed with the four IgG subclass molecules but also shared important features. Most notable was the higher propensity to form closed bivalent ring Id-anti-Id dimers with IgG3 than with IgG2 and IgG4. IgG1 was intermediate in its ability to form such dimers.},
author = {Roux, K H and Strelets, L and Michaelsen, T E},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Roux, Strelets, Michaelsen - Flexibility of human IgG subclasses. - 1997.pdf:pdf},
issn = {0022-1767},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
keywords = {Animals,Anti-Idiotypic,Anti-Idiotypic: chemistry,Antibodies,Antigen-Antibody Complex,Antigen-Antibody Complex: chemistry,Cell Line,Humans,Immunoglobulin Fab Fragments,Immunoglobulin Fab Fragments: chemistry,Immunoglobulin G,Immunoglobulin G: chemistry,Immunoglobulin G: classification,Immunoglobulin G: genetics,Immunoglobulin G: immunology,Immunoglobulin Heavy Chains,Immunoglobulin Heavy Chains: chemistry,Immunoglobulin Idiotypes,Immunoglobulin Idiotypes: chemistry,Immunoglobulin Light Chains,Immunoglobulin Light Chains: chemistry,Immunoglobulin Variable Region,Immunoglobulin Variable Region: chemistry,Mice,Monoclonal,Monoclonal: chemistry,Protein Folding,Structure-Activity Relationship,antibodies},
mendeley-tags = {antibodies},
month = {oct},
number = {7},
pages = {3372--82},
pmid = {9317136},
title = {{Flexibility of human IgG subclasses.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9317136},
volume = {159},
year = {1997}
}
@article{Driskell2010a,
abstract = {Human enteric virus infections range from gastroenteritis to life threatening diseases such as myocarditis and aseptic meningitis. Rotavirus is one of the most common enteric agents and mortality associated with infection can be very significant in developing countries. Most enteric viruses produce diseases that are not distinct from other pathogens, and current diagnostics is limited in breadth and sensitivity required to advance virus detection schemes for disease intervention strategies. A spectroscopic assay based on surface enhanced Raman scattering (SERS) has been developed for rapid and sensitive detection of rotavirus. The SERS method relies on the fabrication of silver nanorod array substrates that are extremely SERS-active allowing for direct structural characterization of viruses. SERS spectra for eight rotavirus strains were analyzed to qualitatively identify rotaviruses and to classify each according to G and P genotype and strain with >96{\%} accuracy, and a quantitative model based on partial least squares regression analysis was evaluated. This novel SERS-based virus detection method shows that SERS can be used to identify spectral fingerprints of human rotaviruses, and suggests that this detection method can be used for pathogen detection central to human health care.},
author = {Driskell, Jeremy D and Zhu, Yu and Kirkwood, Carl D and Zhao, Yiping and Dluhy, Richard a and Tripp, Ralph a},
doi = {10.1371/journal.pone.0010222},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Driskell et al. - Rapid and sensitive detection of rotavirus molecular signatures using surface enhanced Raman spectroscopy. - 2010.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
month = {jan},
number = {4},
pages = {e10222},
pmid = {20419101},
title = {{Rapid and sensitive detection of rotavirus molecular signatures using surface enhanced Raman spectroscopy.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2856680{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {5},
year = {2010}
}
@article{Kaya2012,
abstract = {We provide an experimental demonstration of positive rheotaxis (rapid and continuous upstream motility) in wild-type Escherichia coli freely swimming over a surface. This hydrodynamic phenomenon is dominant below a critical shear rate and robust against Brownian motion and cell tumbling. We deduce that individual bacteria entering a flow system can rapidly migrate upstream (>20 ??m/s) much faster than a gradually advancing biofilm. Given a bacterial population with a distribution of sizes and swim speeds, local shear rate near the surface determines the dominant hydrodynamic mode for motility, i.e., circular or random trajectories for low shear rates, positive rheotaxis for moderate flow, and sideways swimming at higher shear rates. Faster swimmers can move upstream more rapidly and at higher shear rates, as expected. Interestingly, we also find on average that both swim speed and upstream motility are independent of cell aspect ratio. ?? 2012 Biophysical Society.},
author = {Kaya, Tolga and Koser, Hur},
doi = {10.1016/j.bpj.2012.03.001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kaya, Koser - Direct upstream motility in Escherichia coli - 2012.pdf:pdf},
issn = {00063495},
journal = {Biophysical Journal},
number = {7},
pages = {1514--1523},
pmid = {22500751},
publisher = {Biophysical Society},
title = {{Direct upstream motility in Escherichia coli}},
url = {http://dx.doi.org/10.1016/j.bpj.2012.03.001},
volume = {102},
year = {2012}
}
@article{Mulvey2002a,
author = {Mulvey, Matthew A},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mulvey - Microreview Adhesion and entry of uropathogenic Escherichia coli - 2002.pdf:pdf},
journal = {Cellular microbiology},
number = {5},
pages = {257--271},
title = {{Microreview Adhesion and entry of uropathogenic Escherichia coli}},
volume = {4},
year = {2002}
}
@article{Salminen2007,
abstract = {OBJECTIVES: Uropathogenic P-fimbriated Escherichia coli adheres to host cells by specific adhesins recognizing galabiose (Galalpha1-4Gal)-containing structures on cell surfaces. In search of agents inhibiting this first step of infection, the inhibition potency of a set of synthetic mono- and multivalent galabiose compounds was evaluated. In order to mimic the flow conditions of natural infections, a live-bacteria application of surface plasmon resonance (SPR) was established. METHODS AND RESULTS: For the measurement of the binding of E. coli to a surface containing galabiose, live bacteria were injected over the flow cell, and the inhibition of adhesion caused by the galabiose inhibitors was recorded. Quantitative binding data were recorded in real-time for each inhibitor. The results were compared with those of conventional static haemagglutination and ELISA-based cell adhesion assays. Compared with the Gram-positive Streptococcus suis bacteria, which also bind to galabiose and whose binding inhibition is strongly dependent on the multivalency of the inhibitor, E. coli inhibition was only moderately affected by the valency. However, a novel octavalent compound was found to be the most effective inhibitor of E. coli PapG(J96) adhesion, with an IC50 value of 2 microM. CONCLUSIONS: Measurement of bacterial adhesion by SPR is an efficient way to characterize the adhesion of whole bacterial cells and allows the characterization of the inhibitory potency of adhesion inhibitors under dynamic flow conditions. Under these conditions, multivalency increases the anti-adhesion potency of galabiose-based inhibitors of P-fimbriated E. coli adhesion and provides a promising approach for the design of high-affinity anti-adhesion agents.},
author = {Salminen, Annika and Loimaranta, Vuokko and Joosten, John a F and Khan, A. Salam and Hacker, J{\"{o}}rg and Pieters, Roland J and Finne, Jukka},
doi = {10.1093/jac/dkm251},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Salminen et al. - Inhibition of P-fimbriated Escherichia coli adhesion by multivalent galabiose derivatives studied by a live-bacteria a.pdf:pdf},
issn = {0305-7453},
journal = {The Journal of antimicrobial chemotherapy},
keywords = {Bacterial,Bacterial Adhesion,Bacterial Adhesion: drug effects,Bacterial: physiology,Bovine,Bovine: chemistry,Carbohydrates,Carbohydrates: chemistry,Disaccharides,Disaccharides: antagonists {\&} inhibitors,Disaccharides: pharmacology,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: drug effects,Escherichia coli: physiology,Fimbriae,Hemagglutination Tests,Serum Albumin,Streptococcus suis,Streptococcus suis: drug effects,Surface Plasmon Resonance},
month = {sep},
number = {3},
pages = {495--501},
pmid = {17623698},
title = {{Inhibition of P-fimbriated Escherichia coli adhesion by multivalent galabiose derivatives studied by a live-bacteria application of surface plasmon resonance.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17623698},
volume = {60},
year = {2007}
}
@article{Fedosov2011,
abstract = {Red blood cells (RBCs) infected by the Plasmodium falciparum (Pf-RBCs) parasite lose their membrane deformability and they also exhibit enhanced cytoadherence to vascular endothelium and other healthy and infected RBCs. The combined effect may lead to severe disruptions of normal blood circulation due to capillary occlusions. Here we extend the adhesion model to investigate the adhesive dynamics of Pf-RBCs as a function of wall shear stress (WSS) and other parameters using a three-dimensional, multiscale RBC model. Several types of adhesive behavior are identified, including firm adhesion, flipping dynamics, and slow slipping along the wall. In particular, the flipping dynamics of Pf-RBCs observed in experiments appears to be due to the increased stiffness of infected cells and the presence of the solid parasite inside the RBC, which may cause an irregular adhesion behavior. Specifically, a transition from crawling dynamics to flipping behavior occurs at a Young's modulus approximately three times larger than that of healthy RBCs. The simulated dynamics of Pf-RBCs is in excellent quantitative agreement with available microfluidic experiments if the force exerted on the receptors and ligands by an existing bond is modeled as a nonlinear function of WSS.},
author = {Fedosov, Dmitry a and Caswell, Bruce and Karniadakis, George Em},
doi = {10.1016/j.bpj.2011.03.027},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Fedosov, Caswell, Karniadakis - Wall shear stress-based model for adhesive dynamics of red blood cells in malaria. - 2011.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
month = {may},
number = {9},
pages = {2084--93},
pmid = {21539775},
publisher = {Biophysical Society},
title = {{Wall shear stress-based model for adhesive dynamics of red blood cells in malaria.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21539775},
volume = {100},
year = {2011}
}
@article{Alm2011,
abstract = {Digital holographic microscopy (DHM) is a novel high-resolution imaging technique that offers real-time imaging and quantitative measurements of physiological parameters. It has developed into a broad field, and one of many interesting applications is to study cells without staining or labeling them and without affecting them in any way. Digital holography makes it possible to easily measure cell properties that previously have been very difficult to study in living cells, such as cell thickness, volume, and cell refractive index (Marquet et al., 2005; Rappaz et al. 2005; M{\"{o}}lder et al., 2008; El-Schish et al., in press; Persson et al., in press). Living, dying or dead cells as well as fixed cells can be studied. The first DHM images showing living cells were published in 2003 and 2004 (You et al., 2003; Carl et al., 2004), making this field of research rather new. Two of the most interesting functions of DHM is 3-D imaging of objects and to make in-focus measurements over time. Digital holography has been used to study a wide range of cells, e.g. protozoa, bacteria and plant cells as well as several types of mammalian cells such as nerve cells and tumor cells (Emery et al., 2007; Kemper et al., 2006; Moon and Javidi 2007). It has also been applied for studies of cell proliferation, cell movement and cell morphology (Kemper et al., 2009; Yu et al., 2009). Movement in both 2-D and 3-D has been studied (Langehanenberg et al., 2009; Persson et al., in press). In addition, cell viability status can be determined using DHM (Kemper et al., 2006; Kemmler et al., 2007). Interestingly, it is possible to study both single cells and entire populations simultaneously, allowing for very detailed studies. In this chapter we will compare DHM with previously used techniques and discuss the benefits and drawbacks of digital holography cell measurements. We will also present cell studies made possible by},
author = {Alm, Kersti and Cirenajwis, Helena and Gisselsson, Lennart and Wingren, Anette Gj{\"{o}}rloff and Janicke, Birgit and M{\"{o}}lder, Anna and Oredsson, Stina and Persson, Johan},
doi = {10.5772/15364},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Alm et al. - Digital Holography and Cell Studies - 2011.pdf:pdf},
isbn = {978-953-307-227-2},
journal = {Holography, Research and Technology},
pages = {237--252},
title = {{Digital Holography and Cell Studies}},
year = {2011}
}
@article{Vig2012,
author = {Vig, Dhruv and Wolgemuth, Charles},
doi = {10.1103/PhysRevLett.109.218104},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Vig, Wolgemuth - Swimming Dynamics of the Lyme Disease Spirochete - 2012.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {nov},
number = {21},
pages = {218104},
title = {{Swimming Dynamics of the Lyme Disease Spirochete}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.109.218104},
volume = {109},
year = {2012}
}
@article{Verger2007,
abstract = {P pili are important adhesive fibres involved in kidney infection by uropathogenic Escherichia coli strains. P pili are assembled by the conserved chaperone-usher pathway, which involves the PapD chaperone and the PapC usher. During pilus assembly, subunits are incorporated into the growing fiber via the donor-strand exchange (DSE) mechanism, whereby the chaperone's G1 beta-strand that complements the incomplete immunoglobulin-fold of each subunit is displaced by the N-terminal extension (Nte) of an incoming subunit. P pili comprise a helical rod, a tip fibrillum, and an adhesin at the distal end. PapA is the rod subunit and is assembled into a superhelical right-handed structure. Here, we have solved the structure of a ternary complex of PapD bound to PapA through donor-strand complementation, itself bound to another PapA subunit through DSE. This structure provides insight into the structural basis of the DSE reaction involving this important pilus subunit. Using gel filtration chromatography and electron microscopy on a number of PapA Nte mutants, we establish that PapA differs in its mode of assembly compared with other Pap subunits, involving a much larger Nte that encompasses not only the DSE region of the Nte but also the region N-terminal to it.},
author = {Verger, Denis and Bullitt, Esther and Hultgren, Scott J and Waksman, Gabriel},
doi = {10.1371/journal.ppat.0030073},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Verger et al. - Crystal structure of the P pilus rod subunit PapA. - 2007.pdf:pdf},
issn = {1553-7374},
journal = {PLoS pathogens},
keywords = {Adhesins, Bacterial,Chromatography, Gel,Crystallography, X-Ray,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Fimbriae Proteins,Fimbriae Proteins: chemistry,Immunoglobulins,Microscopy, Electron,Molecular Chaperones,Molecular Chaperones: chemistry,Multiprotein Complexes,Multiprotein Complexes: chemistry,Periplasmic Proteins,Periplasmic Proteins: chemistry,Protein Conformation},
month = {may},
number = {5},
pages = {e73},
pmid = {17511517},
title = {{Crystal structure of the P pilus rod subunit PapA.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1868955{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {3},
year = {2007}
}
@article{Svennerholm2012,
abstract = {Enterotoxigenic Escherichia coli(ETEC) is the most common cause of bacterial diarrhea in children in Africa, Asia and Latin America and in travelers to these regions. Despite this, no effective vaccine for ETEC is available. ETEC causes disease by colonizing the small intestine with colonization factors, most of which are fimbriae, and production of heat-labile and/or heat-stable enterotoxins. Antibodies against heat-labile enterotoxin and the colonization factors have been shown to be protective, and local immunity in the gut seems to be of prime importance for protection. Hence, several inactivated and live candidate ETEC vaccines consisting of toxin antigens, alone or together with colonization factors, have been evaluated in clinical trials. In this review, the authors describe ETEC vaccine development in progress and the rationale for constructing different types of vaccines. They also discuss possibilities of enhancing immune responses to candidate ETEC vaccines, particularly in children.},
author = {Svennerholm, Ann-Mari and Lundgren, Anna},
doi = {10.1586/erv.12.12},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Svennerholm, Lundgren - Recent progress toward an enterotoxigenic Escherichia coli vaccine - 2012.pdf:pdf},
issn = {1744-8395},
journal = {Expert Rev Vaccines},
keywords = {Africa,Africa: epidemiology,Animals,Antibodies,Antigens,Asia,Asia: epidemiology,Attenuated,Attenuated: administration {\&} dosage,Attenuated: immunology,Bacterial,Bacterial: immunology,Child,Diarrhea,Diarrhea: epidemiology,Diarrhea: microbiology,Diarrhea: prevention {\&} control,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: immunology,Escherichia coli Infections,Escherichia coli Infections: epidemiology,Escherichia coli Infections: microbiology,Escherichia coli Infections: prevention {\&} control,Escherichia coli Vaccines,Escherichia coli Vaccines: administration {\&} dosage,Escherichia coli Vaccines: immunology,Humans,Inactivated,Inactivated: administration {\&} dosage,Inactivated: immunology,Latin America,Latin America: epidemiology,Preschool,Vaccines},
number = {4},
pages = {495--507},
pmid = {22551034},
title = {{Recent progress toward an enterotoxigenic Escherichia coli vaccine}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22551034},
volume = {11},
year = {2012}
}
@article{Strick2002,
abstract = {In this paper we review the biophysics revealed by stretching single biopolymers. During the last$\backslash$r decade various techniques have emerged allowing micromanipulation of single molecules and$\backslash$r simultaneous measurements of their elasticity. Using such techniques, it has been possible to$\backslash$r investigate some of the interactions playing a role in biology. We shall first review the simplest$\backslash$r case of a non-interacting polymer and then present the structural transitions in DNA, RNA and$\backslash$r proteins that have been studied by single-molecule techniques. We shall explain how these techniques$\backslash$r permit a new approach to the protein folding/unfolding transition.},
author = {Strick, T R and Dessinges, M-N and Charvin, G and Dekker, N H and Allemand, J-F and Bensimon, D and Croquette, V},
doi = {10.1088/0034-4885/66/1/201},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Strick et al. - Stretching of macromolecules and proteins - 2002.pdf:pdf},
isbn = {0034-4885},
issn = {0034-4885},
journal = {Reports on Progress in Physics},
number = {1},
pages = {1--45},
title = {{Stretching of macromolecules and proteins}},
volume = {66},
year = {2002}
}
@article{Valvatne2004,
abstract = {Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea among children living in developing countries and of travelers' diarrhea. Current ETEC vaccine designs aim to induce an anti-colonizing immunity by including the ETEC surface colonization factor antigens. We isolated and characterized the structural gene of the coli surface antigen 20 (CS20). CS20 has an N-terminal amino acid sequence similar to that of CS18. We therefore used a DNA fragment carrying the CS18 fotA gene as a probe in a hybridization assay to detect the corresponding gene in a CS20-positive strain isolated from an Indian child. Cross hybridizing DNA was isolated and found to contain an open reading frame encoding a polypeptide of 195 amino acids, including a 22 amino acid signal peptide. The gene, which we named csnA, shows a high degree of identity to the major fimbrial subunits of CS12, CS18 and F6 (also referred to as 987P), a CS of porcine ETEC. The coding region of csnA was inserted into an expression system to generate a polypeptide confirmed to be CS20 by Western blot. A CS20 colony hybridization assay using a DNA probe derived from csnA was developed.},
author = {Valvatne, H{\aa}vard and Steinsland, Hans and Grewal, Harleen M S and M{\o}lbak, K{\aa}re and Vuust, Jens and Sommerfelt, Halvor},
doi = {10.1016/j.femsle.2004.08.028},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Valvatne et al. - Identification and molecular characterization of the gene encoding coli surface antigen 20 of enterotoxigenic Escheric.pdf:pdf},
issn = {0378-1097},
journal = {FEMS microbiology letters},
keywords = {Antigens,Bacterial,Bacterial: chemistry,Bacterial: genetics,Bacterial: metabolism,Base Sequence,Cloning,DNA,Escherichia coli,Escherichia coli: genetics,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: genetics,Fimbriae Proteins: metabolism,Humans,Molecular,Molecular Sequence Data,Recombinant Proteins,Recombinant Proteins: genetics,Recombinant Proteins: metabolism,Sequence Alignment,Sequence Analysis,cs20},
mendeley-tags = {cs20},
month = {oct},
number = {1},
pages = {131--8},
pmid = {15451111},
title = {{Identification and molecular characterization of the gene encoding coli surface antigen 20 of enterotoxigenic Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15451111},
volume = {239},
year = {2004}
}
@article{Allan1966,
abstract = {Allan, D.W. Proceedings of the IEEE Volume 54, Issue 2, Feb. 1966 Page(s): 221 - 230 Digital Object Identifier Summary: A theoretical development is presented which results in a relationship between the expectation value of the standard deviation of the frequency fluctuations for any finite number of data samples and the infinite time average value of the standard deviation, which provides an invariant measure of an important quality factor of a frequency standard. A practical and straightforward method of determining the power spectral density of the frequency fluctuations from the variance of the frequency fluctuations, the sampling time, the number of samples taken, and the dependence on system bandwidth is also developed. Additional insight is also given into some of the problems that arise from the presence of "flicker noise" (spectrum proportional to |$\omega$|{\^{}}(-1)) modulation of the frequency of an oscillator. The theory is applied in classifying the types of noise on the signals of frequency standards made available at NBS, Boulder Laboratories, such as: masers (both H and N15H3), the cesium beam frequency standard employed as the U. S. Frequency Standard, and rubidium gas cells. "Flicker noise" frequency modulation was not observed on the signals of masers for sampling times ranging from 0.1 second to 4 hours. In a comparison between the NBS hydrogen maser and the NBS III cesium beam, uncorrelated random noise was observed on the frequency fluctuations for sampling times extending to 4 hours; the fractional standard deviations of the frequency fluctuations were as low as 5 parts in 10{\^{}}(14).},
author = {Allan, D W},
journal = {Proc IEEE},
keywords = {Allan variance},
mendeley-tags = {Allan variance},
number = {2},
pages = {221--230},
title = {{Statistics of atomic frequency standards}},
volume = {54},
year = {1966}
}
@article{Grange2001,
author = {Grange, Wilfried and Strunz, Torsten and Schumakovitch, Irina and G{\"{u}}ntherodt, Hans-Joachim and Hegner, Martin},
doi = {10.1002/1438-5171(200107)2:2<75::AID-SIMO75>3.0.CO;2-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Grange et al. - Molecular Recognition and Adhesion of Individual DNA Strands Studied by Dynamic Force Microscopy - 2001.pdf:pdf},
issn = {1438-5163},
journal = {Single Molecules},
month = {jul},
number = {2},
pages = {75--78},
publisher = {John Wiley {\&} Sons},
title = {{Molecular Recognition and Adhesion of Individual DNA Strands Studied by Dynamic Force Microscopy}},
url = {http://doi.wiley.com/10.1002/1438-5171{\%}28200107{\%}292{\%}3A2{\%}3C75{\%}3A{\%}3AAID-SIMO75{\%}3E3.0.CO{\%}3B2-8},
volume = {2},
year = {2001}
}
@article{Tripathi2013,
abstract = {Knowledge of the mechanisms by which bacterial pili adhere to host cells and withstand external forces is critical to our understanding of their functional roles and offers exciting avenues in biomedicine for controlling the adhesion of bacterial pathogens and probiotics. While much progress has been made in the nanoscale characterization of pili from Gram-negative bacteria, the adhesive and mechanical properties of Gram-positive bacterial pili remain largely unknown. Here, we use single-molecule atomic force microscopy to unravel the binding mechanism of pili from the probiotic Gram-positive bacterium Lactobacillus rhamnosus GG (LGG). First, we show that SpaC, the key adhesion protein of the LGG pilus, is a multifunctional adhesin with broad specificity. SpaC forms homophilic trans-interactions engaged in bacterial aggregation and specifically binds mucin and collagen, two major extracellular components of host epithelial layers. Homophilic and heterophilic interactions display similar binding strengths and dissociation rates. Next, pulling experiments on living bacteria demonstrate that LGG pili exhibit two unique mechanical responses, that is, zipper-like adhesion involving multiple SpaC molecules distributed along the pilus length and nanospring properties enabling pili to resist high force. These mechanical properties may represent a generic mechanism among Gram-positive bacterial pili for strengthening adhesion and withstanding shear stresses in the natural environment. The single-molecule experiments presented here may help us to design molecules capable of promoting or inhibiting bacterial-host interactions.},
author = {Tripathi, Prachi and Beaussart, Audrey and Alsteens, David and Dupres, Vincent and Claes, Ingmar and von Ossowski, Ingemar and de Vos, Willem M and Palva, Airi and Lebeer, Sarah and Vanderleyden, Jos and Dufr{\^{e}}ne, Yves F},
doi = {10.1021/nn400705u},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tripathi et al. - Adhesion and Nanomechanics of Pili from the Probiotic Lactobacillus rhamnosus GG. - 2013.pdf:pdf},
issn = {1936-086X},
journal = {ACS nano},
keywords = {adhesion,afm,bacterial pili,bute to human health,force spectroscopy,including competitive ex-,mechanisms,nanomechanics,probiotics,robiotic bacteria are thought,single-molecule manipulation,through several,to contri-},
month = {mar},
number = {4},
pages = {3685--3697},
pmid = {23531039},
title = {{Adhesion and Nanomechanics of Pili from the Probiotic Lactobacillus rhamnosus GG.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23531039},
volume = {7},
year = {2013}
}
@article{Bechhoefer2002,
author = {Bechhoefer, John and Wilson, Scott},
doi = {10.1119/1.1445403},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bechhoefer, Wilson - Faster, cheaper, safer optical tweezers for the undergraduate laboratory - 2002.pdf:pdf},
issn = {00029505},
journal = {American Journal of Physics},
number = {4},
pages = {393},
title = {{Faster, cheaper, safer optical tweezers for the undergraduate laboratory}},
url = {http://link.aip.org/link/AJPIAS/v70/i4/p393/s1{\&}Agg=doi},
volume = {70},
year = {2002}
}
@article{Thomas2010,
author = {Thomas, Wendy E and Discher, Dennis E and Shastri, V Prasad},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Thomas, Discher, Shastri - M echanical Regulation of Cells by Materials and Tissues Introduction Cells Feel Their - 2010.pdf:pdf},
number = {August},
title = {{M echanical Regulation of Cells by Materials and Tissues Introduction : Cells Feel Their}},
volume = {35},
year = {2010}
}
@article{Langehanenberg2008,
abstract = {Digital holography enables a multifocus quantitative phase microscopy for the investigation of reflective surfaces and for marker-free live cell imaging. For digital holographic long-term investigations of living cells an automated (subsequent) robust and reliable numerical focus adjustment is of particular importance. Four numerical methods for the determination of the optimal focus position in the numerical reconstruction and propagation of the complex object waves of pure phase objects are characterized, compared, and adapted to the requirements of digital holographic microscopy. Results from investigations of an engineered surface and human pancreas tumor cells demonstrate the applicability of Fourier-weighting- and gradient-operator-based methods for robust and reliable automated subsequent numerical digital holographic focusing.},
author = {Langehanenberg, Patrik and Kemper, Bj{\"{o}}rn and Dirksen, Dieter and von Bally, Gert},
doi = {10.1364/AO.47.00D176},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Langehanenberg et al. - Autofocusing in digital holographic phase contrast microscopy on pure phase objects for live cell imaging. - 200.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
number = {19},
pages = {D176--D182},
pmid = {18594573},
title = {{Autofocusing in digital holographic phase contrast microscopy on pure phase objects for live cell imaging.}},
volume = {47},
year = {2008}
}
@article{Ramser2010,
abstract = {In the last decade optical manipulation has evolved from a field of interest for physicists to a versatile tool widely used within life sciences. This has been made possible in particular due to the development of a large variety of imaging techniques that allow detailed information to be gained from investigations of single cells. The use of multiple optical traps has high potential within single-cell analysis since parallel measurements provide good statistics. Multifunctional optical tweezers are, for instance, used to study cell heterogeneity in an ensemble, and force measurements are used to investigate the mechanical properties of individual cells. Investigations of molecular motors and forces on the single-molecule level have led to discoveries that would have been difficult to make with other techniques. Optical manipulation has prospects within the field of cell signalling and tissue engineering. When combined with microfluidic systems the chemical environment of cells can be precisely controlled. Hence the influence of pH, salt concentration, drugs and temperature can be investigated in real time. Fast advancing technical developments of automated and user-friendly optical manipulation tools and cross-disciplinary collaboration will contribute to the routinely use of optical manipulation techniques within the life sciences.},
author = {Ramser, Kerstin and Hanstorp, Dag},
doi = {10.1002/jbio.200910050},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ramser, Hanstorp - Optical manipulation for single-cell studies. - 2010.pdf:pdf},
issn = {1864-0648},
journal = {Journal of biophotonics},
keywords = {Animals,Biomechanics,Cells,Cells: cytology,Cells: radiation effects,Humans,Lab-On-A-Chip Devices,Optical Tweezers},
month = {apr},
number = {4},
pages = {187--206},
pmid = {19718682},
title = {{Optical manipulation for single-cell studies.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19718682},
volume = {3},
year = {2010}
}
@article{Poole2007,
abstract = {Fimbrial filaments assembled by distinct chaperone pathways share a common mechanism of intersubunit interaction, as elucidated for colonization factor antigen I (CFA/I), archetype of enterotoxigenic Escherichia coli (ETEC) Class 5 fimbriae. We postulated that a highly conserved beta-strand at the major subunit N-terminus represents the donor strand, analogous to interactions within Class I pili. We show here that CFA/I fimbriae utilize donor strand complementation to promote proper folding of and interactions between CFA/I subunits. We constructed a series of genetic variants of CfaE, the CFA/I adhesin, incorporating a C-terminal extension comprising a flexible linker and 10-19 of the N-terminal residues of CfaB, the major subunit. Variants with a donor strand complement (dsc) of >or= 12 residues were recoverable from periplasmic fractions. Genetic disruption of the donor beta-strand reduced CfaE recovery. A hexahistidine-tagged variant of dsc19CfaE formed soluble monomers, folded into beta-sheet conformation, displayed adhesion characteristic of CFA/I, and elicited antibodies that inhibited mannose-resistant haemagglutination by ETEC expressing CFA/I, CS4 and CS14 fimbriae. Immunoelectron microscopy indicated that CfaE was confined to the distal fimbrial tip. Our findings provide the basis to elucidate structure and function of this class of fimbrial adhesins and assess the feasibility of an adhesin-based vaccine.},
author = {Poole, Steven T and McVeigh, Annette L and Anantha, Ravi P and Lee, Lanfong H and Akay, Yasemin M and Pontzer, Emily a and Scott, Daniel a and Bullitt, Esther and Savarino, Stephen J},
doi = {10.1111/j.1365-2958.2007.05612.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Poole et al. - Donor strand complementation governs intersubunit interaction of fimbriae of the alternate chaperone pathway. - 2007.pdf:pdf},
issn = {0950-382X},
journal = {Molecular microbiology},
keywords = {Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: genetics,Escherichia coli Proteins: metabolism,Escherichia coli: genetics,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: genetics,Fimbriae Proteins: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Hemagglutination Inhibition Tests,Microscopy, Immunoelectron,Protein Binding,Protein Folding,Protein Subunits,Protein Subunits: genetics,Protein Subunits: metabolism,Recombinant Proteins,Recombinant Proteins: genetics,Recombinant Proteins: metabolism},
month = {mar},
number = {5},
pages = {1372--84},
pmid = {17302815},
title = {{Donor strand complementation governs intersubunit interaction of fimbriae of the alternate chaperone pathway.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17302815},
volume = {63},
year = {2007}
}
@article{Ramstedt2007,
author = {Ramstedt, Madeleine and Cheng, Nan and Azzaroni, Omar and Mossialos, Dimitris and Mathieu, Hans J{\"{o}}rg and Huck, Wilhelm T S},
doi = {10.1021/la062670+},
journal = {Langmuir},
number = {6},
pages = {3314--3321},
title = {{Synthesis and Characterization of Poly(3-Sulfopropylmethacrylate) Brushes for Potential Antibacterial Applications}},
volume = {23},
year = {2007}
}
@article{Qadri2006,
abstract = {We have studied homologous (HoM) and cross-reacting (CR) immunoglobulin A (IgA) antibody responses to colonization factors (CFs) in Bangladeshi children with diarrhea due to enterotoxigenic E. coli (ETEC) strains of the CF antigen I (CFA/I) group (CFA/I, n = 25; coli surface antigen 4 [CS4], n = 8; CS14, n = 11) and the CS5 group (CS5, n = 15; CS7, n = 8), respectively. The responses to the HoM, CR, and heterologous (HeT) CF antigens in each group of patient were studied and compared to that seen in healthy children (n = 20). In the CFA/I group (CFA/I and CS14), patients responded with antibody-secreting cell (ASC) responses to HoM CFs (geometric mean, 156 to 329 ASCs/10(6) peripheral blood mononuclear cells [PBMCs]) and to CR CFs ( approximately 15 to 38 ASCs/10(6) PBMCs) but least of all to the HeT CS5 antigen (2 to 4 ASCs/10(6) PBMCs). For the CS5 group of patients with ETEC (CS5 and CS7), likewise, responses to HoM CFs (230 to 372 ASCs/10(6) PBMCs) and CR CFs (27 to 676 ASCs/10(6) PBMCs) were seen, along with lower responses to the HeT CFA/I antigen (9 to 38 ASCs/10(6) PBMCs). Both groups of patients responded with CF-specific IgA antibodies to HoM and CR antigens in plasma but responded less to the HeT CFs. The responses in patients were seen very soon after the onset of diarrhea and peaked around 1 week after onset. Vaccinees who had received two doses of the oral, killed whole-cell ETEC vaccine (CF-BS-ETEC) responded with plasma IgA antibodies to CFA/I, a component of the vaccine, but also to the CR CS14 antigen, which was not included in the vaccine, showing that antibody responses can be stimulated by a CFA/I-containing ETEC vaccine to a CR-reacting antigen in individuals in countries where ETEC is endemic.},
author = {Qadri, Firdausi and Ahmed, Firoz and Ahmed, Tanvir and Svennerholm, Ann Mari},
doi = {10.1128/IAI.00474-06},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Qadri et al. - Homologous and cross-reactive immune responses to enterotoxigenic Escherichia coli colonization factors in Bangladeshi ch.pdf:pdf},
isbn = {0019-9567 (Print)$\backslash$r0019-9567 (Linking)},
issn = {00199567},
journal = {Infection and Immunity},
number = {8},
pages = {4512--4518},
pmid = {16861637},
title = {{Homologous and cross-reactive immune responses to enterotoxigenic Escherichia coli colonization factors in Bangladeshi children}},
volume = {74},
year = {2006}
}
@article{Cevc1999,
abstract = {Membrane fusion is essential for cell survival and has attracted a great deal of both theoretical and experimental interest. Fluorescence (de)quenching measurements were designed to distinguish between bilayermerging and vesicle-mixing. Theoretical studies and various microscopic and diffraction methods have elucidated the mechanism of membrane fusion. These have revealed that membrane proximity and high defect density in the adjacent bilayers are the only prerequisites for fusion. Intermediates, such as stalk or inverse micellar structures can, but need not, be involved in vesicle fusion. Nonlamellar phase creation is accompanied by massive membrane fusion although it is not a requirement for bilayer merging. Propensity for membrane fusion is increased by increasing the local membrane disorder as well by performing manipulations that bring bilayers closer together. Membrane rigidification and enlarged bilayer separation opposes this trend. Membrane fusion is promoted by defects created in the bilayer due to the vicinity of lipid phase transition, lateral phase separation or domain generation, high local membrane curvature, osmotic or electric stress in or on the membrane; the addition of amphiphats or macromolecules which insert themselves into the membrane, freezing or other mechanical membrane perturbation have similar effects. Lowering the water activity by the addition of water soluble polymers or by partial system dehydration invokes membrane aggregation and hence facilitates fusion; as does the membrane charge neutralization after proton or other ion binding to the lipids and intermembrane scaffolding by proteins or other macromolecules. The alignment of defect rich domains and polypeptides or protein binding is pluripotent: not only does it increase the number of proximal defects in the bilayers, it triggers the vesicle aggregation and is fusogenic. Exceptions are the bound molecules that create steric or electrical barriers between the membranes which prevent fusion. Membrane fusion can be non-leaky but it is very common to lose material from the vesicle interior during the later stages of membrane unification, that is, after a few hundred microseconds following the induction of fusion.},
author = {Cevc, G and Richardsen, H},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Cevc, Richardsen - Lipid vesicles and membrane fusion - 1999.pdf:pdf},
issn = {1872-8294},
journal = {Advanced drug delivery reviews},
keywords = {drug delivery,lipid vesicles,liposomes,membrane fusion},
month = {aug},
number = {3},
pages = {207--232},
pmid = {10837758},
title = {{Lipid vesicles and membrane fusion}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10837758},
volume = {38},
year = {1999}
}
@article{Berg-Sørensen2004,
author = {Berg-S{\o}rensen, Kirstine and Flyvbjerg, Henrik},
doi = {10.1063/1.1645654},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Berg-S{\o}rensen, Flyvbjerg - Power spectrum analysis for optical tweezers - 2004.pdf:pdf},
issn = {00346748},
journal = {Review of Scientific Instruments},
number = {3},
pages = {594},
title = {{Power spectrum analysis for optical tweezers}},
url = {http://link.aip.org/link/RSINAK/v75/i3/p594/s1{\&}Agg=doi},
volume = {75},
year = {2004}
}
@article{Hermansson1999a,
author = {Hermansson, Malte},
doi = {10.1016/S0927-7765(99)00029-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hermansson - The DLVO theory in microbial adhesion - 1999.pdf:pdf},
issn = {09277765},
journal = {Colloids and Surfaces B: Biointerfaces},
keywords = {adhesion,bacteria,colloid stability,dlvo theory},
month = {aug},
number = {1-4},
pages = {105--119},
title = {{The DLVO theory in microbial adhesion}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0927776599000296},
volume = {14},
year = {1999}
}
@article{Evans1977,
abstract = {Enterotoxigenic Escherichia coli (ETEC) of several different serotypes isolated from adults with diarrhea and known to possess the colonization factor antigen (CFA) were found to cause mannose-resistant hemagglutination (HA) of human group A erythrocytes. CFA-negative E. coli isolated during the same study did not possess the mannose-resistant hemagglutinin, although some non-ETEC, CFA-negative isolates did exhibit mannose-sensitive HA activity. The mannoseresistant hemagglutinin of ETEC was found to possess many characteristics previously associated with CFA, which is a surface-associated fimbriate heatlabile antigen, and the functionally and morphologically similar K88 and K99 antigens of animal-specific ETEC. Mannose-resistant HA and CFA titers were maximal when ETEC cells were grown on an agar medium (CFA agar) composed primarily of 1{\%} Casamino Acids and 0.15{\%} yeast extract, pH 7.4. Neither CFA nor HA were produced at a growth temperature of 18 degrees C; HA was completely inhibited by pretreatment of CFA-positive cells with the anti-CFA serum. The mannose-resistant hemagglutinin was lost spontaneously and simultaneously with CFA when clinical ETEC isolates were passaged on artificial medium in the laboratory, indicating plasmid control of both entities. The mannose-resistant hemagglutinin of ETEC was shown to be thermolabile, i.e., sensitive to heating at 65 degrees C, as was the CFA. Also, there was correlation between possession of CFA, as detected serologically and by demonstration of biological activity (adherence in the infant rabbit small intestine), presence of CFA-type fimbriae, and the ability of various E. coli isolates to cause mannose-resistant HA of human group A erythrocytes. These results indicate that the mannose-resistant HA of ETEC is another manifestation of CFA.},
author = {Evans, D. G. and Evans, D. J. and Tjoa, W.},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Evans, Evans, Tjoa - Hemagglutination of human group A erythrocytes by enterotoxigenic Escherichia coli isolated from adults with diarrh.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Evans, Evans, Tjoa - Hemagglutination of human group A erythrocytes by enterotoxigenic Escherichia coli isolated from adults with diarrh.pdf:pdf},
issn = {00199567},
journal = {Infection and Immunity},
number = {2},
pages = {330--337},
pmid = {336541},
title = {{Hemagglutination of human group A erythrocytes by enterotoxigenic Escherichia coli isolated from adults with diarrhea: Correlation with colonization factor}},
volume = {18},
year = {1977}
}
@article{Zhou2012,
author = {Zhou, Yan and Torres, Ashley and Chen, Liangxian and Kong, Ying and Cirillo, Jeffrey D. and Liang, H.},
doi = {10.1063/1.4733685},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zhou et al. - Fluid-shear method to evaluate bacterial adhesion to glass surfaces - 2012.pdf:pdf},
issn = {00218979},
journal = {Journal of Applied Physics},
number = {1},
pages = {014703},
title = {{Fluid-shear method to evaluate bacterial adhesion to glass surfaces}},
url = {http://link.aip.org/link/JAPIAU/v112/i1/p014703/s1{\&}Agg=doi},
volume = {112},
year = {2012}
}
@article{Ashok2011b,
abstract = {We report the first implementation of the fiber based microfluidic Raman spectroscopic detection scheme, which can be scaled down to micrometre dimensions, allowing it to be combined with other microfluidic functional devices. This novel Raman spectroscopic detection scheme, which we termed as Waveguide Confined Raman Spectroscopy (WCRS), is achieved through embedding fibers on-chip in a geometry that confines the Raman excitation and collection region which ensures maximum Raman signal collection. This results in a microfluidic chip with completely alignment-free Raman spectroscopic detection scheme, which does not give any background from the substrate of the chip. These features allow a WCRS based microfluidic chip to be fabricated in polydimethylsiloxane (PDMS) which is a relatively cheap material but has inherent Raman signatures in fingerprint region. The effects of length, collection angle, and fiber core size on the collection efficiency and fluorescence background of WCRS were investigated. The ability of the device to predict the concentration was studied using urea as a model analyte. A major advantage of WCRS is its scalability that allows it to be combined with many existing microfluidic functional devices. The applicability of WCRS is demonstrated through two microfluidic applications: reaction monitoring in a microreactor and detection of analyte in a microdroplet based microfluidic system. The WCRS approach may lead to wider use of Raman spectroscopy based detection in microfluidics, and the development of portable, alignment-free microfluidic devices.},
author = {Ashok, Praveen C and Singh, Gajendra P and Rendall, Helen a and Krauss, Thomas F and Dholakia, Kishan},
doi = {10.1039/c0lc00462f},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ashok et al. - Waveguide confined Raman spectroscopy for microfluidic interrogation. - 2011.pdf:pdf},
issn = {1473-0197},
journal = {Lab on a chip},
month = {jan},
pages = {1262--1270},
pmid = {21225053},
title = {{Waveguide confined Raman spectroscopy for microfluidic interrogation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21225053},
year = {2011}
}
@article{Science2012,
author = {Science, Computer},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Science - y y - 2012.pdf:pdf},
isbn = {9781467314879},
keywords = {center detection,circle detection,concentric circle,parallel operator,partial circle,radius detection},
pages = {15--17},
title = {y y},
year = {2012}
}
@article{Roberts2004a,
abstract = {A critical early step in the establishment of Escherichia coli pyelonephritis is bacterial attachment via the tip protein of P fimbriae. This adhesin, PapG, binds to glycolipid receptors present on vaginal and kidney epithelial surfaces. In this study we investigated the efficacy of vaccination with purified PapDG protein complex in preventing pyelonephritis caused by E. coli.},
annote = {From Duplicate 1 ( Antibody responses and protection from pyelonephritis following vaccination with purified Escherichia coli PapDG protein. - Roberts, James a; Kaack, M Bernice; Baskin, Gary; Chapman, Matthew R; Hunstad, David a; Pinkner, Jerome S; Hultgren, Scott J )
},
author = {Roberts, James a and Kaack, M Bernice and Baskin, Gary and Chapman, Matthew R and Hunstad, David a and Pinkner, Jerome S and Hultgren, Scott J},
doi = {10.1097/01.ju.0000116123.05160.43},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Roberts et al. - Antibody responses and protection from pyelonephritis following vaccination with purified Escherichia coli PapDG protei.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Roberts et al. - Antibody responses and protection from pyelonephritis following vaccination with purified Escherichia coli PapDG pro(2).pdf:pdf},
issn = {0022-5347},
journal = {The Journal of urology},
keywords = {Adhesins,Animals,Antibodies,Bacterial,Bacterial: analysis,Bacterial: immunology,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli Infections: prevention {\&} control,Escherichia coli Vaccines,Escherichia coli Vaccines: immunology,Escherichia coli: immunology,Female,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: immunology,Macaca fascicularis,Pyelonephritis,Pyelonephritis: immunology,Pyelonephritis: microbiology,Pyelonephritis: prevention {\&} control},
month = {may},
number = {4},
pages = {1682--5},
pmid = {15017266},
title = {{Antibody responses and protection from pyelonephritis following vaccination with purified Escherichia coli PapDG protein.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2838480{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {171},
year = {2004}
}
@article{Tchesnokova2010a,
abstract = {In the intestine, enterotoxigenic Escherichia coli works against peristaltic forces, adhering to the epithelium via the colonization factor antigen I (CFA/I) fimbrial adhesin CfaE. The CfaE adhesin is similar in localization and tertiary (but not primary) structure to FimH, the type 1 fimbrial adhesin of uropathogenic E. coli, which shows shear-dependent binding to epithelial receptors by an allosteric catch-bond mechanism. Thus, we speculated that CfaE is also capable of shear-enhanced binding. Indeed, bovine erythrocytes coursing over immobilized CFA/I fimbriae in flow chambers exhibited low accumulation levels and fast rolling at low shear, but an 80-fold increase in accumulation and threefold decrease in rolling velocity at elevated shear. This effect was reversible and abolished by pre-incubation of fimbriae with anti-CfaE antibody. Erythrocytes bound to whole CfaE in the same shear-enhanced manner, but to CfaE adhesin domain in a shear-inhibitable fashion. Residue replacements designed to disrupt CfaE interdomain interaction decreased the shear dependency of adhesion and increased binding under static conditions to human intestinal epithelial cells. These findings indicate that close interaction between adhesive and anchoring pilin domains of CfaE keeps the former in a low-affinity state that toggles into a high-affinity state upon separation of two domains, all consistent with an allosteric catch-bond mechanism of CfaE binding.},
annote = {From Duplicate 2 ( Shear-enhanced binding of intestinal colonization factor antigen I of enterotoxigenic Escherichia coli. - Tchesnokova, Veronika; McVeigh, Annette L; Kidd, Brian; Yakovenko, Olga; Thomas, Wendy E; Sokurenko, Evgeni V; Savarino, Stephen J )
},
author = {Tchesnokova, Veronika and McVeigh, Annette L and Kidd, Brian and Yakovenko, Olga and Thomas, Wendy E and Sokurenko, Evgeni V and Savarino, Stephen J},
doi = {10.1111/j.1365-2958.2010.07116.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tchesnokova et al. - Shear-enhanced binding of intestinal colonization factor antigen I of enterotoxigenic Escherichia coli. - 2010.pdf:pdf},
issn = {1365-2958},
journal = {Molecular microbiology},
keywords = {Animals,Binding Sites,Cattle,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: pathogenicity,Erythrocytes,Erythrocytes: metabolism,Escherichia coli Proteins,Escherichia coli Proteins: metabolism,Fimbriae Proteins,Fimbriae Proteins: metabolism,Models,Molecular,Protein Binding,Protein Structure,Tertiary,Virulence Factors,Virulence Factors: metabolism},
month = {apr},
number = {2},
pages = {489--502},
pmid = {20345656},
title = {{Shear-enhanced binding of intestinal colonization factor antigen I of enterotoxigenic Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2929265{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {76},
year = {2010}
}
@article{Franze2010,
author = {Franze, Kristian and Guck, Jochen},
doi = {10.1088/0034-4885/73/9/094601},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Franze, Guck - The biophysics of neuronal growth - 2010.pdf:pdf},
issn = {0034-4885},
journal = {Reports on Progress in Physics},
number = {9},
pages = {094601},
title = {{The biophysics of neuronal growth}},
url = {http://stacks.iop.org/0034-4885/73/i=9/a=094601?key=crossref.1e6c2d7988b5dab945ccce0f5a6ef772},
volume = {73},
year = {2010}
}
@article{Fleckenstein2010,
abstract = {Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrheal illness in developing countries, and perennially the most common cause of traveller's diarrhea. ETEC constitute a diverse pathotype that elaborate heat-labile and/or heat-stable enterotoxins. Recent molecular pathogenesis studies reveal sophisticated pathogen-host interactions that might be exploited in efforts to prevent these important infections. While vaccine development for these important pathogens remains a formidable challenge, extensive efforts that attempt to exploit new genomic and proteomic technology platforms in discovery of novel targets are presently ongoing.},
author = {Fleckenstein, James M and Hardwidge, Philip R and Munson, George P and Rasko, David a and Sommerfelt, Halvor and Steinsland, Hans},
doi = {10.1016/j.micinf.2009.10.002},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Fleckenstein et al. - Molecular mechanisms of enterotoxigenic Escherichia coli infection. - 2010.pdf:pdf},
issn = {1769-714X},
journal = {Microbes and infection / Institut Pasteur},
keywords = {Adhesins, Escherichia coli,Adhesins, Escherichia coli: metabolism,Bacterial Vaccines,Dysentery,Dysentery: microbiology,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: genetics,Enterotoxigenic Escherichia coli: metabolism,Enterotoxigenic Escherichia coli: pathogenicity,Escherichia coli Infections,Escherichia coli Infections: microbiology,Fimbriae, Bacterial,Fimbriae, Bacterial: metabolism,Humans,Integration Host Factors,Intestine, Small,Intestine, Small: microbiology,Virulence,Virulence Factors,Virulence Factors: chemistry,Virulence Factors: metabolism,Virulence: genetics},
month = {feb},
number = {2},
pages = {89--98},
pmid = {19883790},
publisher = {Elsevier Masson SAS},
title = {{Molecular mechanisms of enterotoxigenic Escherichia coli infection.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19883790},
volume = {12},
year = {2010}
}
@article{Wong1999,
abstract = {The interaction between streptavidin and its ligand, biotin, were studied by direct force measurements. The complimentary approaches of surface force apparatus (SFA) and atomic force microscopy (AFM) were used to elucidate both long-range and short-range adhesive interactions of the streptavidin biotin interaction. The high spatial resolution of the SFA provided a detailed profile of the intersurface forces of apposing surfaces functionalized with streptavidin and biotin. Measurements obtained by the SFA corresponded to long and intermediate-range forces that are important in determining ligand receptor association. AFM was used to measure the unbinding force of individual streptavidin biotin complexes. These measurements revealed the short-range interactions (i.e. hydrophobic and hydrogen bonding forces) that stabilize the intermolecular bond.},
author = {Wong, J and Chilkoti, a and Moy, V T},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wong, Chilkoti, Moy - Direct force measurements of the streptavidin-biotin interaction. - 1999.pdf:pdf},
issn = {1389-0344},
journal = {Biomolecular engineering},
keywords = {Biophysics,Biophysics: instrumentation,Biotin,Biotin: chemistry,Biotin: metabolism,Hydrogen Bonding,Ligands,Microscopy, Atomic Force,Microscopy, Atomic Force: instrumentation,Protein Binding,Protein Engineering,Streptavidin,Streptavidin: chemistry,Streptavidin: metabolism,Surface Properties,Thermodynamics},
month = {dec},
number = {1-4},
pages = {45--55},
pmid = {10796984},
title = {{Direct force measurements of the streptavidin-biotin interaction.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10796984},
volume = {16},
year = {1999}
}
@article{Das2009,
author = {Das, Raibatak and Cairo, Christopher W. and Coombs, Daniel},
doi = {10.1371/journal.pcbi.1000556},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Das, Cairo, Coombs - A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytosk.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Das, Cairo, Coombs - A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cyt(2).PDF:PDF},
issn = {1553-7358},
journal = {PLoS Computational Biology},
number = {11},
pages = {e1000556},
title = {{A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1000556},
volume = {5},
year = {2009}
}
@article{Sjoberg1988,
abstract = {CS2 fimbriae of enterotoxigenic Escherichia coli were purified and characterized. The surface haemagglutinins (fimbriae) were detached by sonication from a strain producing only the CS2 fimbriae. Isolation was carried out by gel filtration on a Sepharose 4B column. After depolymerization, the fimbriae subunits were purified on a Sephacryl S-300 column in 8.0 M-guanidinium chloride. From 1 litre of medium, 4-6 mg of purified fimbriae was obtained. We found that CS2 fimbriae were completely dissociated by saturated guanidinium chloride into subunits with a molecular mass of 16.5 kDa. CS2 fimbriae was sialic acid-specific, since sialic acids were the most potent inhibitors, and neuraminidase treatment of erythrocytes abolished haemagglutination. Both fimbriae and fimbrial subunits were found to bind to bovine erythrocytes. The binding of subunits to erythrocytes could be inhibited with low concentrations of sialyl-lactose.},
author = {Sj{\"{o}}berg, P O and Lindahl, M and Porath, J and Wadstr{\"{o}}m, T},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sj{\"{o}}berg et al. - Purification and characterization of CS2, a sialic acid-specific haemagglutinin of enterotoxigenic Escherichia coli. -.pdf:pdf},
issn = {0264-6021},
journal = {The Biochemical journal},
pages = {105--111},
pmid = {2904260},
title = {{Purification and characterization of CS2, a sialic acid-specific haemagglutinin of enterotoxigenic Escherichia coli.}},
volume = {255},
year = {1988}
}
@misc{Fazal2011,
abstract = {Optical tweezers have become one of the primary weapons in the arsenal of biophysicists, and have revolutionized the new field of single-molecule biophysics. Today's techniques allow high-resolution experiments on biological macromolecules that were mere pipe dreams only a decade ago.},
author = {Fazal, Furqan M and Block, Steven M},
booktitle = {Nature Photonics},
number = {6},
pages = {318--321},
title = {{Optical tweezers study life under tension}},
volume = {5},
year = {2011}
}
@article{Svanborg-Eden1978,
abstract = {The adhesion of Escherichia coli to human urinary tract epithelial cells was inhibited by commercial gamma globulin, the total immunoglobulin fraction of human breast milk and urine, as well as the isolated immunoglobulin G and secretory immunoglobulin A fractions of urine from patients with acute pyelonephritis. Urinary anti-O6 antibodies reduced the adhesion of several O6 strains. Absorption of antibodies to the lipopolysaccharide of the adhering strain markedly decreased the antiadhesive capacity of all the immunoglobulin preparations, whereas elimination of antibodies to the capsular polysaccharide antigen consistently had a small but not significant effect. When urine was absorbed with whole, live bacteria of the patients' infecting strains, the antiadhesive effect completely disappeared. Absorption with bacteria lacking pili only partially reduced this effect.},
author = {Svanborg-Ed{\'{e}}n, C and Svennerholm, Ann-Mari},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Svanborg-Ed{\'{e}}n, Svennerholm - Secretory immunoglobulin A and G antibodies prevent adhesion of Escherichia coli to human urinary tract epi.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
keywords = {Antibodies,Antigens,Bacterial,Bacterial: immunology,Bacterial: urine,Epithelial Cells,Epithelium,Epithelium: microbiology,Escherichia coli,Escherichia coli: immunology,Escherichia coli: physiology,Human,Human: immunology,Humans,Immunoglobulin A,Immunoglobulin A: urine,Immunoglobulin G,Immunoglobulin G: urine,Milk,Polysaccharides,Secretory,Secretory: urine,Urinary Tract,Urinary Tract: cytology,Urinary Tract: microbiology,gamma-Globulins},
month = {dec},
number = {3},
pages = {790--7},
pmid = {83303},
title = {{Secretory immunoglobulin A and G antibodies prevent adhesion of Escherichia coli to human urinary tract epithelial cells.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=422230{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {22},
year = {1978}
}
@article{Steffen2005,
author = {Steffen, Robert},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Steffen - Epidemiology of Traveler ’ s Diarrhea - 2005.pdf:pdf},
journal = {Clinical Infectious Diseases},
number = {Suppl 8},
pages = {536--540},
title = {{Epidemiology of Traveler ’ s Diarrhea}},
volume = {41},
year = {2005}
}
@article{Moller2013,
abstract = {To clear pathogens from host tissues or biomaterial surfaces, phagocytes have to break the adhesive bacteria-substrate interactions. Here we analysed the mechanobiological process that enables macrophages to lift-off and phagocytose surface-bound Escherichia coli (E. coli). In this opsonin-independent process, macrophage filopodia hold on to the E. coli fimbriae long enough to induce a local protrusion of a lamellipodium. Specific contacts between the macrophage and E. coli are formed via the glycoprotein CD48 on filopodia and the adhesin FimH on type 1 fimbriae (hook). We show that bacterial detachment from surfaces occurrs after a lamellipodium has protruded underneath the bacterium (shovel), thereby breaking the multiple bacterium-surface interactions. After lift-off, the bacterium is engulfed by a phagocytic cup. Force activated catch bonds enable the long-term survival of the filopodium-fimbrium interactions while soluble mannose inhibitors and CD48 antibodies suppress the contact formation and thereby inhibit subsequent E. coli phagocytosis.},
author = {M{\"{o}}ller, Jens and L{\"{u}}hmann, Tessa and Chabria, Mamta and Hall, Heike and Vogel, Viola},
doi = {10.1038/srep02884},
file = {:E$\backslash$:/Mina Dokument/Mendeley/M{\"{o}}ller et al. - Macrophages lift off surface-bound bacteria using a filopodium-lamellipodium hook-and-shovel mechanism. - 2013.pdf:pdf},
issn = {2045-2322},
journal = {Scientific reports},
keywords = {paper3},
mendeley-tags = {paper3},
month = {jan},
pages = {2884},
pmid = {24097079},
title = {{Macrophages lift off surface-bound bacteria using a filopodium-lamellipodium hook-and-shovel mechanism.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3791455{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {3},
year = {2013}
}
@article{Block1989,
author = {Block, Steven M and Blair, David and Berg, Howard},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Block, Blair, Berg - © 1989 Nature Publishing Group - 1989.pdf:pdf},
journal = {Nature},
keywords = {flagella,optical tweezers,torque},
mendeley-tags = {flagella,optical tweezers,torque},
pages = {514--518},
title = {{© 1989 Nature Publishing Group}},
volume = {338},
year = {1989}
}
@article{Rad2003,
abstract = {The Circle Hough Transform (CHT) has become a common method for circle detection in numerous image processing applications. Because of its drawbacks, various modifications to the basic CHT method have been suggested. This paper presents an algorithm to find circles which are totally brighter or darker than their backgrounds. The method is size-invariant, and such circular shapes can be found very fast and accurately. Though Fast Circle Detection (FCD) method loses the generality of the CHT, we show that there are many applications that can use this method after a simple preprocessing and gain a considerable improvement in performance against the CHT or its modified versions. This method has been evaluated in some famous industrial and medical fields, and the results show a significant improvement of finding circular shape objects.},
author = {Rad, Ali Ajdari and Faez, Karim and Qaragozlou, Navid},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rad, Faez, Qaragozlou - Fast Circle Detection Using Gradient Pair Vectors - 2003.pdf:pdf},
journal = {VIIth Digital Image Computing: Techniques and Applications},
pages = {10--12},
title = {{Fast Circle Detection Using Gradient Pair Vectors}},
year = {2003}
}
@article{Evans1978,
abstract = {Enterotoxigenic Escherichia coli (ETEC) belonging to serogroups O6 and O8 do not possess the H-10407-type colonization factor antigen (CFA/I). However, these frequently isolated ETEC were found to possess a second and distinct heat-labile surface-associated colonization factor antigen, termed CFA/II. Whereas CFA/I mediates mannose-resistant hemagglutination of human group A erythrocytes, CFA/II does not. CFA/II mediates mannose-resistant hemagglutination of bovine erythrocytes, and mannose-resistant hemagglutination is rapid only at reduced temperature (4 degrees C). Because CFA/II, like CFA/I, is spontaneously lost by many ETEC isolates in the laboratory, it was possible to produce specific anti-CFA/II serum by preparing antiserum against living cells of a prototype strain (PB-176) and adsorbing this serum with living and heat-treated cells of its CFA/II-negative derivative strain PB-176-P. This serum, which neutralized the colonization factor activity of CFA/II-positive strains in infant rabbits, was employed to confirm the presence of CFA/II on ETEC which exhibited mannose-resistant hemagglutination of bovine but not human erythrocytes. CFA/II, like CFA/I, mediates adherence of the bacteria to the mucosal surface of the small intestine, as demonstrated by indirect immunofluorescence. CFA/II appears to be an important virulence factor for humans since CFA/II-positive ETEC are frequently isolated from diarrhea cases, particularly travelers' diarrhea, in Mexico; these ETEC were not uncommon in a collection of isolates from Bangladesh. The O6:H16 strain of ETEC responsible for an outbreak of diarrhea in the United States was also shown to be CFA/II positive. CFA/I and CFA/II were never found on the same serotypes of ETEC, but 98{\%} of the heat-stable and heat-labile enterotoxin-producing ETEC belonging to the frequently isolated serogroups O6, O8, O15, O25, O63, and O78 were positive for either CFA/I or CFA/II.},
author = {Evans, D. G. and Evans, D. J.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans, Evans - New surface-associated heat-labile colonization factor antigen (CFAII) produced by enterotoxigenic Escherichia coli of se.pdf:pdf},
isbn = {0019-9567 (Print)$\backslash$n0019-9567 (Linking)},
issn = {00199567},
journal = {Infection and Immunity},
number = {2},
pages = {638--647},
pmid = {80383},
title = {{New surface-associated heat-labile colonization factor antigen (CFA/II) produced by enterotoxigenic Escherichia coli of serogroups O6 and O8}},
volume = {21},
year = {1978}
}
@article{Jia2011,
author = {Jia, Li-Qin and Liu, Hong-Min and Wang, Zhi-Heng and Chen, Hong},
doi = {10.1109/ICMLC.2011.6016769},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jia et al. - An effective non-HT circle detection for centers and radii - 2011.pdf:pdf},
isbn = {978-1-4577-0305-8},
journal = {2011 International Conference on Machine Learning and Cybernetics},
keywords = {center detection,circle detection,concentric circle,partial circle,radius detection},
month = {jul},
pages = {814--818},
publisher = {Ieee},
title = {{An effective non-HT circle detection for centers and radii}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6016769},
year = {2011}
}
@article{Heng2013,
author = {Heng, Chin Tiong and Yeow, Siang Lin and Lee, Heow Pueh},
doi = {10.1080/21681163.2013.789676},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Heng, Yeow, Lee - A non-invasive, patient-specific method for estimating detrusor bladder pressure - 2013.pdf:pdf},
issn = {2168-1163},
journal = {Computer Methods in Biomechanics and Biomedical Engineering: Imaging {\&} Visualization},
keywords = {paper3},
mendeley-tags = {paper3},
month = {jun},
number = {October},
pages = {1--8},
title = {{A non-invasive, patient-specific method for estimating detrusor bladder pressure}},
url = {http://www.tandfonline.com/doi/abs/10.1080/21681163.2013.789676},
year = {2013}
}
@article{Li2013,
author = {Li, Tongcang and Raizen, Mark G.},
doi = {10.1002/andp.201200232},
issn = {00033804},
journal = {Annalen der Physik},
month = {apr},
number = {4},
pages = {281--295},
title = {{Brownian motion at short time scales}},
volume = {525},
year = {2013}
}
@article{Chattopadhyay2006,
abstract = {We use measurements of swimming bacteria in an optical trap to determine fundamental properties of bacterial propulsion. In particular, we directly measure the force required to hold the bacterium in the optical trap and determine the propulsion matrix, which relates the translational and angular velocity of the flagellum to the torques and forces propelling the bacterium. From the propulsion matrix, dynamical properties such as torques, swimming speed, and power can be obtained by measuring the angular velocity of the motor. We find significant heterogeneities among different individuals even though all bacteria started from a single colony. The propulsive efficiency, defined as the ratio of the propulsive power output to the rotary power input provided by the motors, is found to be approximately 2{\%}, which is consistent with the efficiency predicted theoretically for a rigid helical coil.},
author = {Chattopadhyay, Suddhashil and Moldovan, Radu and Yeung, Chuck and Wu, X L},
doi = {10.1073/pnas.0602043103},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chattopadhyay et al. - Swimming efficiency of bacterium Escherichia coli. - 2006.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Escherichia coli,Escherichia coli: physiology,Flagella,Flagella: physiology,Optics and Photonics,Rotation},
month = {sep},
number = {37},
pages = {13712--7},
pmid = {16954194},
title = {{Swimming efficiency of bacterium Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1564254{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {103},
year = {2006}
}
@article{Goldman1967,
author = {Goldman, A.J and Cox, R.G. and Brenner, H.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Goldman, Cox, Brenner - Slow viscous motion of a sphere parallel to a plane wall - I Motion through a quiescent fluid - 1967.pdf:pdf},
journal = {Chmeical Engineering Science},
keywords = {shear rate},
mendeley-tags = {shear rate},
pages = {637--651},
title = {{Slow viscous motion of a sphere parallel to a plane wall - I Motion through a quiescent fluid}},
volume = {22},
year = {1967}
}
@article{Gittes1998,
author = {Gittes, F and Schmidt, CF},
journal = {European Biophysics Journal},
keywords = {atomic,force microscopy,micromechanics,optical tweezers,single molecules,thermal noise},
pages = {75 -- 81},
title = {{Thermal noise limitations on micromechanical experiments}},
url = {http://www.springerlink.com/index/0KRW3PLUY7XRUUF9.pdf},
year = {1998}
}
@article{Sinclair2004,
abstract = {We report on the limitations of using a spatial light modulator (SLM) within optical tweezers to produce both lateral and axial displacements. We find that lateral displacements of optical traps are limited by the optical efficiency of the SLM, whereas the axial displacements are limited by the abberations of the objective lens. In addition, we show the SLM can be used for correcting abberations arising from trapping deep within the sample. The maximum possible lateral and axial displacements were 50pm and 40pm, respectively.},
author = {Sinclair, Gavin and Jordan, P and Leach, Jonathan and Padgett, Miles J and Cooper, J.},
doi = {10.1080/095003403},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sinclair et al. - Defining the trapping limits of holographical optical tweezers - 2004.pdf:pdf},
journal = {Journal of Modern Optics},
number = {October 2011},
pages = {409--414},
title = {{Defining the trapping limits of holographical optical tweezers}},
volume = {61},
year = {2004}
}
@article{Schnars2002,
abstract = {This article describes the principles and major applications of digital recording and numerical reconstruction of holograms (digital holography). Digital holography became feasible since charged coupled devices (CCDs) with suitable numbers and sizes of pixels and computers with sufficient speed became available. The Fresnel or Fourier holograms are recorded directly by the CCD and stored digitally. No film material involving wet-chemical or other processing is necessary. The reconstruction of the wavefield, which is done optically by illumination of a hologram, is performed by numerical methods. The numerical reconstruction process is based on the Fresnel–Kirchhoff integral, which describes the diffraction of the reconstructing wave at the micro-structure of the hologram. In the numerical reconstruction process not only the intensity, but also the phase distribution of the stored wavefield can be computed from the digital hologram. This offers new possibilities for a variety of applications. Digital holography is applied to measure shape and surface deformation of opaque bodies and refractive index fields within transparent media. Further applications are imaging and microscopy, where it is advantageous to refocusthe area under investigation by numerical methods.},
author = {Schnars, Ulf and Juptner, Werner},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schnars, Juptner - Digital recording and numerical - 2002.pdf:pdf},
issn = {0003-6935},
journal = {Institute of Physics Publishing},
keywords = {digital holography,holographic interferometry},
pages = {17},
pmid = {18323970},
title = {{Digital recording and numerical}},
volume = {13},
year = {2002}
}
@article{Li2009b,
abstract = {Adhesion pili (fimbriae) play a critical role in initiating the events that lead to intestinal colonization and diarrheal disease by enterotoxigenic Escherichia coli (ETEC), an E. coli pathotype that inflicts an enormous global disease burden. We elucidate atomic structures of an ETEC major pilin subunit, CfaB, from colonization factor antigen I (CFA/I) fimbriae. These data are used to construct models for 2 morphological forms of CFA/I fimbriae that are both observed in vivo: the helical filament into which it is typically assembled, and an extended, unwound conformation. Modeling and corroborative mutational data indicate that proline isomerization is involved in the conversion between these helical and extended forms. Our findings affirm the strong structural similarities seen between class 5 fimbriae (from bacteria primarily causing gastrointestinal disease) and class 1 pili (from bacteria that cause urinary, respiratory, and other infections) in the absence of significant primary sequence similarity. They also suggest that morphological and biochemical differences between fimbrial types, regardless of class, provide structural specialization that facilitates survival of each bacterial pathotype in its preferred host microenvironment. Last, we present structural evidence for bacterial use of antigenic variation to evade host immune responses, in that residues occupying the predicted surface-exposed face of CfaB and related class 5 pilins show much higher genetic sequence variability than the remainder of the pilin protein.},
author = {Li, Yong-Fu and Poole, Steven and Nishio, Kazuya and Jang, Ken and Rasulova, Fatima and McVeigh, Annette and Savarino, Stephen J and Xia, Di and Bullitt, Esther},
doi = {10.1073/pnas.0812843106},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Li et al. - Structure of CFAI fimbriae from enterotoxigenic Escherichia coli. - 2009.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Antigens,Bacterial,Bacterial: chemistry,Bacterial: genetics,Bacterial: immunology,Binding Sites,Crystallography,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: chemistry,Enterotoxigenic Escherichia coli: genetics,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli Infections: microbiology,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: genetics,Fimbriae Proteins: immunology,Models,Molecular,Mutation,Proline,Proline: chemistry,Proline: genetics,Protein Structure,Protein Subunits,Protein Subunits: chemistry,Protein Subunits: genetics,Secondary,Tertiary,X-Ray},
month = {jun},
number = {26},
pages = {10793--8},
pmid = {19515814},
title = {{Structure of CFA/I fimbriae from enterotoxigenic Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2705562{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {106},
year = {2009}
}
@article{Edmiston2001,
abstract = {Substantial costs are associated with the treatment of nosocomial infections, 2 million cases of which occur annually in the United States. Hospital-acquired, gram-negative infection has become an increasing problem, particularly in the intensive care unit where up to 40{\%} of the most frequently isolated strains of Enterobacteriaceae are resistant to standard beta-lactam antibiotics. Among several mechanisms of acquisition of resistance, beta-lactamase production accounts for a high percentage of treatment failures and relapses. By the end of the 1980s, some 10-30{\%} of all nosocomial infections were caused by type-1 beta-lactamase-producing gram-negative isolates, and Enterobacter species had emerged as a major resistant pathogen. The beta-lactam/beta-lactamase inhibitor combinations, such as ampicillin/sulbactam, represent an innovative approach to the problem of beta-lactamase-mediated resistance. Clinical use of these agents has been associated with low rates of resistance and new data suggest they may have a specific role in controlling the emergence and spread of nosocomial infections.},
author = {Edmiston, C E and Hennen, C and Seabrook, G R},
doi = {10.1089/10962960152742187},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Edmiston, Hennen, Seabrook - The importance of beta-lactamase resistance in surgical infections. - 2001.pdf:pdf},
issn = {1096-2964},
journal = {Surgical infections},
keywords = {Cross Infection,Cross Infection: drug therapy,Cross Infection: epidemiology,Cross Infection: prevention {\&} control,Female,Gram-Negative Bacteria,Gram-Negative Bacteria: drug effects,Gram-Positive Bacteria,Gram-Positive Bacteria: drug effects,Humans,Male,Microbial Sensitivity Tests,Postoperative Complications,Postoperative Complications: drug therapy,Postoperative Complications: microbiology,Risk Assessment,Sensitivity and Specificity,Surgical Procedures, Operative,Surgical Procedures, Operative: adverse effects,Surgical Procedures, Operative: methods,Surgical Wound Infection,Surgical Wound Infection: drug therapy,Surgical Wound Infection: microbiology,Treatment Outcome,United States,United States: epidemiology,beta-Lactam Resistance,beta-Lactamases,beta-Lactamases: pharmacology,beta-Lactamases: therapeutic use},
month = {jan},
pages = {S13--22},
pmid = {12594861},
title = {{The importance of beta-lactamase resistance in surgical infections.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15635887},
volume = {2 Suppl 1},
year = {2001}
}
@article{Bell1978b,
author = {Bell, George},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bell - Models for the Specific adhesion of cells to cells - 1978.pdf:pdf},
journal = {Science},
keywords = {Dynamic force spectroscopy,cell},
pages = {618--627},
title = {{Models for the Specific adhesion of cells to cells}},
volume = {200},
year = {1978}
}
@article{Castelain2009,
abstract = {S pili are members of the chaperone-usher-pathway-assembled pili family that are predominantly associated with neonatal meningitis (S(II)) and believed to play a role in ascending urinary tract infections (S(I)). We used force-measuring optical tweezers to characterize the intrinsic biomechanical properties and kinetics of S(II) and S(I) pili. Under steady-state conditions, a sequential unfolding of the layers in the helix-like rod occurred at somewhat different forces, 26 pN for S(II) pili and 21 pN for S(I) pili, and there was an apparent difference in the kinetics, 1.3 and 8.8 Hz. Tests with bacteria defective in a newly recognized sfa gene (sfaX (II)) indicated that absence of the sfaX (II) gene weakens the interactions of the fimbrium slightly and decreases the kinetics. Data of S(I) are compared with those of previously assessed pili primary associated with urinary tract infections, the P and type 1 pili. S pili have weaker layer-to-layer bonds than both P and type 1 pili, 21, 28 and 30 pN, respectively. In addition, the S pili kinetics are {\~{}}10 times faster than the kinetics of P pili and {\~{}}550 times faster than the kinetics of type 1 pili. Our results also show that the biomechanical properties of pili expressed ectopically from a plasmid in a laboratory strain (HB101) and pili expressed from the chromosome of a clinical isolate (IHE3034) are identical. Moreover, we demonstrate that it is possible to distinguish, by analyzing force-extension data, the different types of pili expressed by an individual cell of a clinical bacterial isolate.},
author = {Castelain, Micka{\"{e}}l and Sj{\"{o}}str{\"{o}}m, Annika E and F{\"{a}}llman, Erik and Uhlin, Bernt Eric and Andersson, Magnus},
doi = {10.1007/s00249-009-0552-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Castelain et al. - Unfolding and refolding properties of S pili on extraintestinal pathogenic Escherichia coli. - 2009.pdf:pdf},
issn = {1432-1017},
journal = {European biophysics journal},
keywords = {bond breaking {\'{a}} unfolding,coli {\'{a}},fimbriae {\'{a}} uropathogenic escherichia,{\'{a}} optical tweezers},
pages = {1105--1115},
pmid = {19885656},
title = {{Unfolding and refolding properties of S pili on extraintestinal pathogenic Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19885656},
volume = {39},
year = {2009}
}
@article{Su2009,
abstract = {We describe and solve a two-state kinetic model for the forced unfolding of proteins. The protein oligomer is modeled as a heterogeneous, freely jointed chain with two possible values of Kuhn length and contour length representing its folded and unfolded configurations. We obtain analytical solutions for the force-extension response of the protein oligomer for different types of loading conditions. We fit the analytical solutions for constant-velocity pulling to the force-extension data for ubiquitin and fibrinogen and obtain model parameters, such as Kuhn lengths and kinetic coefficients, for both proteins. We then predict their response under a linearly increasing force and find that our solutions for ubiquitin are consistent with a different set of experiments. Our calculations suggest that the refolding rate of proteins at low forces is several orders larger than the unfolding rate, and neglecting it can lead to lower predictions for the unfolding force, especially at high stretching velocities. By accounting for the refolding of proteins we obtain a critical force below which equilibrium is biased in favor of the folded state. Our calculations also suggest new methods to determine the distance of the transition state from the energy wells representing the folded and unfolded states of a protein.},
author = {Su, Tianxiang and Purohit, Prashant K},
doi = {10.1016/j.actbio.2009.01.038},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Su, Purohit - Mechanics of forced unfolding of proteins. - 2009.pdf:pdf},
issn = {1878-7568},
journal = {Acta biomaterialia},
keywords = {Computer Simulation,Mechanics,Models, Chemical,Models, Molecular,Protein Conformation,Protein Denaturation,Protein Folding,Proteins,Proteins: chemistry,Proteins: ultrastructure,Stress, Mechanical},
month = {jul},
number = {6},
pages = {1855--63},
pmid = {19251493},
publisher = {Acta Materialia Inc.},
title = {{Mechanics of forced unfolding of proteins.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19251493},
volume = {5},
year = {2009}
}
@article{Qadri2005,
abstract = {ETEC is an underrecognized but extremely important cause of diarrhea in the developing world where there is inadequate clean water and poor sanitation. It is the most frequent bacterial cause of diarrhea in children and adults living in these areas and also the most common cause of traveler's diarrhea. ETEC diarrhea is most frequently seen in children, suggesting that a protective immune response occurs with age. The pathogenesis of ETEC-induced diarrhea is similar to that of cholera and includes the production of enterotoxins and colonization factors. The clinical symptoms of ETEC infection can range from mild diarrhea to a severe cholera-like syndrome. The effective treatment of ETEC diarrhea by rehydration is similar to treatment for cholera, but antibiotics are not used routinely for treatment except in traveler's diarrhea. The frequency and characterization of ETEC on a worldwide scale are inadequate because of the difficulty in recognizing the organisms; no simple diagnostic tests are presently available. Protection strategies, as for other enteric infections, include improvements in hygiene and development of effective vaccines. Increases in antimicrobial resistance will dictate the drugs used for the treatment of traveler's diarrhea. Efforts need to be made to improve our understanding of the worldwide importance of ETEC.},
author = {Qadri, Firdausi and Svennerholm, Ann-Mari and Faruque, a S G and Sack, R Bradley},
doi = {10.1128/CMR.18.3.465-483.2005},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Qadri et al. - Enterotoxigenic Escherichia coli in developing countries epidemiology, microbiology, clinical features, treatment, and pr.pdf:pdf},
issn = {0893-8512},
journal = {Clinical microbiology reviews},
keywords = {Adolescent,Adult,Animals,Child,Child, Preschool,Developing Countries,Developing Countries: history,Diarrhea,Diarrhea: diagnosis,Diarrhea: drug therapy,Diarrhea: epidemiology,Diarrhea: history,Enterotoxins,Enterotoxins: metabolism,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: diagnosis,Escherichia coli Infections: drug therapy,Escherichia coli Infections: epidemiology,Escherichia coli Infections: history,Escherichia coli Proteins,Escherichia coli Proteins: metabolism,Escherichia coli: classification,Escherichia coli: metabolism,History, 20th Century,Humans,Infant,Infant, Newborn,Mice,Prevalence,Severity of Illness Index},
month = {jul},
number = {3},
pages = {465--83},
pmid = {16020685},
title = {{Enterotoxigenic Escherichia coli in developing countries: epidemiology, microbiology, clinical features, treatment, and prevention.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1195967{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {18},
year = {2005}
}
@article{Sheng2008,
abstract = {A digital holographic microscope is used to simultaneously measure the instantaneous 3D flow structure in the inner part of a turbulent boundary layer over a smooth wall, and the spatial distribution of wall shear stresses. The measurements are performed in a fully developed turbulent channel flow within square duct, at a moderately high Reynolds number. The sample volume size is 90 x 145 x 90 wall units, and the spatial resolution of the measurements is 3-8 wall units in streamwise and spanwise directions and one wall unit in the wall-normal direction. The paper describes the data acquisition and analysis procedures, including the particle tracking method and associated method for matching of particle pairs. The uncertainty in velocity is estimated to be better than 1 mm/s, less than 0.05{\%} of the free stream velocity, by comparing the statistics of the normalized velocity divergence to divergence obtained by randomly adding an error of 1 mm/s to the data. Spatial distributions of wall shear stresses are approximated with the least square fit of velocity measurements in the viscous sublayer. Mean flow profiles and statistics of velocity fluctuations agree very well with expectations. Joint probability density distributions of instantaneous spanwise and streamwise wall shear stresses demonstrate the significance of near-wall coherent structures. The near wall 3D flow structures are classified into three groups, the first containing a pair of counter-rotating, quasi streamwise vortices and high streak-like shear stresses; the second group is characterized by multiple streamwise vortices and little variations in wall stress; and the third group has no buffer layer structures},
author = {Sheng, J. and Malkiel, E. and Katz, J.},
doi = {10.1007/s00348-008-0524-2},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sheng, Malkiel, Katz - Using digital holographic microscopy for simultaneous measurements of 3D near wall velocity and wall shear stress.pdf:pdf},
isbn = {0723-4864},
issn = {07234864},
journal = {Experiments in Fluids},
number = {6},
pages = {1023--1035},
title = {{Using digital holographic microscopy for simultaneous measurements of 3D near wall velocity and wall shear stress in a turbulent boundary layer}},
volume = {45},
year = {2008}
}
@article{Hansen2006,
author = {Hansen, Poul Martin and Toli{\'{c}}-N{\o}rrelykke, Iva Marija and Flyvbjerg, Henrik and Berg-S{\o}rensen, Kirstine},
doi = {10.1016/j.cpc.2005.11.007},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Hansen et al. - tweezercalib 2.1 Faster version of MatLab package for precise calibration of optical tweezers☆ - 2006.pdf:pdf},
issn = {00104655},
journal = {Computer Physics Communications},
month = {mar},
number = {6},
pages = {518--520},
title = {{tweezercalib 2.0: Faster version of MatLab package for precise calibration of optical tweezers}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0010465505006247},
volume = {174},
year = {2006}
}
@article{Dombrowski2009,
abstract = {The mechanisms that determine bacterial shape are in many ways poorly understood. A prime example is the Lyme disease spirochete, Borrelia burgdorferi (B. burgdorferi), which mechanically couples its motility organelles, helical flagella, to its rod-shaped cell body, producing a striking flat-wave morphology. A mathematical model is developed here that accounts for the elastic coupling of the flagella to the cell cylinder and shows that the flat-wave morphology is in fact a natural consequence of the geometrical and material properties of the components. Observations of purified periplasmic flagella show two flagellar conformations. The mathematical model suggests that the larger waveform flagellum is the more relevant for determining the shape of B. burgdorferi. Optical trapping experiments were used to measure directly the mechanical properties of these spirochetes. These results imply relative stiffnesses of the two components, which confirm the predictions of the model and show that the morphology of B. burgdorferi is completely determined by the elastic properties of the flagella and cell body. This approach is applicable to a variety of other structures in which the shape of the composite system is markedly different from that of the individual components, such as coiled-coil domains in proteins and the eukaryotic axoneme.},
author = {Dombrowski, Christopher and Kan, Wanxi and Motaleb, Md Abdul and Charon, Nyles W and Goldstein, Raymond E and Wolgemuth, Charles},
doi = {10.1016/j.bpj.2009.02.066},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dombrowski et al. - The elastic basis for the shape of Borrelia burgdorferi. - 2009(2).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Dombrowski et al. - The elastic basis for the shape of Borrelia burgdorferi. - 2009.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {Algorithms,Biological,Borrelia burgdorferi,Borrelia burgdorferi: cytology,Borrelia burgdorferi: physiology,Elasticity,Flagella,Flagella: physiology,Models,Optical Tweezers},
month = {jun},
number = {11},
pages = {4409--17},
pmid = {19486665},
publisher = {Biophysical Society},
title = {{The elastic basis for the shape of Borrelia burgdorferi.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19486665},
volume = {96},
year = {2009}
}
@article{Mortezaei2015,
annote = {From Duplicate 1 ( 





























































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































},
author = {Mortezaei, Narges and Epler, Chelsea R. and P., Shao. Paul and Shirdel, Mariam and Singh, Bhupender and McVeigh, Annette and Uhlin, Bernt Eric and Savarino, Stephen J and Andersson, Magnus and Bullitt, Esther},
doi = {10.1111/mmi.12847},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mortezaei et al. - Structure and function of Enterotoxigenic Escherichia coli fimbriae from differing assembly pathways - 2015(2).pdf:pdf},
journal = {Molecular Microbiology},
keywords = {CS20},
number = {1},
pages = {116--126},
title = {{Structure and function of Enterotoxigenic Escherichia coli fimbriae from differing assembly pathways}},
volume = {95},
year = {2015}
}
@article{Paluch2009,
abstract = {Together with cell growth, division and death, changes in cell shape are of central importance for tissue morphogenesis during development. Cell shape is the product of a cell's material and active properties balanced by external forces. Control of cell shape, therefore, relies on both tight regulation of intracellular mechanics and the cell's physical interaction with its environment. In this review, we first discuss the biological and physical mechanisms of cell shape control. We next examine a number of developmental processes in which cell shape change - either individually or in a coordinated manner - drives embryonic morphogenesis and discuss how cell shape is controlled in these processes. Finally, we emphasize that cell shape control during tissue morphogenesis can only be fully understood by using a combination of cellular, molecular, developmental and biophysical approaches.},
author = {Paluch, Ewa and Heisenberg, Carl-Philipp},
doi = {10.1016/j.cub.2009.07.029},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Paluch, Heisenberg - Biology and physics of cell shape changes in development. - 2009.pdf:pdf},
isbn = {0960-9822},
issn = {1879-0445},
journal = {Current biology : CB},
number = {17},
pages = {R790--R799},
pmid = {19906581},
publisher = {Elsevier Ltd},
title = {{Biology and physics of cell shape changes in development.}},
url = {http://dx.doi.org/10.1016/j.cub.2009.07.029},
volume = {19},
year = {2009}
}
@article{Andreasson2010,
author = {Andreasson, Johan O L and Greenleaf, William J and Laporta, Arthur and Block, Steven M},
doi = {10.1016/S0076-6879(10)75015-1},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Andreasson et al. - An Optical Apparatus for Rotation and Trapping - 2010.pdf:pdf},
journal = {Methods},
number = {10},
title = {{An Optical Apparatus for Rotation and Trapping}},
volume = {475},
year = {2010}
}
@article{Fallman2004a,
abstract = {The ability of uropathogenic Escherichia coli (UPEC) to cause urinary tract infections is dependent on their ability to colonize the uroepithelium. Infecting bacteria ascend the urethra to the bladder and then kidneys by attaching to the uroepithelial cells via the differential expression of adhesins. P pili are associated with pyelonephritis, the more severe infection of the kidneys. In order to find means to treat pyelonephritis, it is therefore of interest to investigate the properties P pili. The mechanical behavior of individual P pili of uropathogenic Escherichia coli has recently been investigated using optical tweezers. P pili, whose main part constitutes the PapA rod, composed of similar to1000 PapA subunits in a helical arrangement, are distributed over the bacterial surface and mediate adhesion to host cells. We have earlier studied P pili regarding its stretclring/elongation properties where we have found and characterized three different elongation regions, of which one constitute an unfolding of the quaternary (helical) structure of the PapA rod. It was shown that this unfolding takes place at an elongation independent force of 27 +/- 2 pN. We have also recently performed studies on its folding properties and shown that the unfolding/folding of the PapA rod is completely reversible. Here we present a study of the dynamical properties of the PapA rod. We show, among other things, that the unfolding force increases and that the folding force decreases with the speed of unfolding and folding respectively. Moreover, the PapA rod can be folded-unfolded a significant number of times without loosing its characteristics, a phenomenon that is believed to be important for the bacterium to keep close contact to the host tissue and consequently helps the bacterium to colonize the host tissue.},
author = {F{\"{a}}llman, Erik and Andersson, Magnus and Schedin, Staffan and Jass, Jana and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1117/12.579893},
file = {:E$\backslash$:/Mina Dokument/Mendeley//F{\"{a}}llman et al. - Dynamic properties of bacterial pili measured by optical tweezers - 2004.pdf:pdf},
issn = {0277-786X},
journal = {Proceedings of SPIE},
keywords = {ADHESION PILI,DESIGN,ELECTRON-MICROSCOPY,EXTRAINTESTINAL INFECTIONS,P-PILI,TIP,UROPATHOGENIC ESCHERICHIA-COLI,adhesion of bacteria to,bacteria,bacteria express pili,bacteria-host contact during the,essential step in the,host tissue is an,infection by many gram-negative,initial stages of an,many gram-negative,mechanical properties,mediating adhesion and maintaining,optical tweezers,p pili,progression of an infection,unfolding,uropathogenic escherichia coli,which are implicated in,which are responsible for},
pages = {763},
publisher = {SPIE-INT SOC OPTICAL ENGINEERING},
title = {{Dynamic properties of bacterial pili measured by optical tweezers}},
url = {http://apps.isiknowledge.com/full{\_}record.do?product=WOS{\&}search{\_}mode=GeneralSearch{\&}qid=7{\&}SID=S1MHGALlH8ko5hHPpbg{\&}page=1{\&}doc=1 http://link.aip.org/link/?PSI/5514/763/1{\&}Agg=doi},
volume = {5514},
year = {2004}
}
@article{Ohlinger2012,
author = {Ohlinger, Alexander and Deak, Andras and Lutich, Andrey a. and Feldmann, Jochen},
doi = {10.1103/PhysRevLett.108.018101},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ohlinger et al. - Optically Trapped Gold Nanoparticle Enables Listening at the Microscale - 2012.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {jan},
number = {1},
pages = {018101},
title = {{Optically Trapped Gold Nanoparticle Enables Listening at the Microscale}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.108.018101},
volume = {108},
year = {2012}
}
@article{Lundmark2009a,
abstract = {The sorting nexin SNX9 has, in the past few years, been singled out as an important protein that participates in fundamental cellular activities. SNX9 binds strongly to dynamin and is partly responsible for the recruitment of this GTPase to sites of endocytosis. SNX9 also has a high capacity for modulation of the membrane and might therefore participate in the formation of the narrow neck of endocytic vesicles before scission occurs. Once assembled on the membrane, SNX9 stimulates the GTPase activity of dynamin to facilitate the scission reaction. It has also become clear that SNX9 has the ability to activate the actin regulator N-WASP in a membrane-dependent manner to coordinate actin polymerization with vesicle release. In this Commentary, we summarize several aspects of SNX9 structure and function in the context of membrane remodeling, discuss its interplay with various interaction partners and present a model of how SNX9 might work in endocytosis.},
author = {Lundmark, Richard and Carlsson, Sven R},
doi = {10.1242/jcs.037135},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Lundmark, Carlsson - SNX9 - a prelude to vesicle release - 2009.pdf:pdf},
issn = {0021-9533},
journal = {Journal of cell science},
keywords = {Actins,Actins: metabolism,Animals,Carrier Proteins,Carrier Proteins: genetics,Carrier Proteins: metabolism,Cell Membrane,Cell Membrane: metabolism,Dynamins,Dynamins: metabolism,Endocytosis: physiology,Humans,Models,Molecular,Molecular Sequence Data,Protein Structure,Tertiary,Transport Vesicles,Transport Vesicles: metabolism,Vesicular Transport Proteins,Vesicular Transport Proteins: genetics,Vesicular Transport Proteins: metabolism,clathrin,dynamin,endocytosis,n-wasp,snx9},
month = {jan},
number = {Pt 1},
pages = {5--11},
pmid = {19092055},
title = {{SNX9 - a prelude to vesicle release}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19092055},
volume = {122},
year = {2009}
}
@article{Khan1996a,
abstract = {Certain strains of enterotoxigenic Escherichia coli adhere to piglet intestinal epithelial cells by means of the 987P fimbriae. The 987P fimbrial structure consists of a helical arrangement of three fimbrial proteins, namely, the major subunit FasA and two minor subunits, FasF and FasG. FasG, which is located at the fimbrial tip and at various positions along the fimbriae, mediates 987P binding to glycoprotein receptors. In this study, we isolated and analyzed the structure of piglet glycolipid brush border receptors and characterized their cognate ligands on the 987P fimbriae. Two major glycolipid bands recognized by 987P fimbrial probes in thin-layer chromatography overlay assays were further purified by high-performance thin-layer chromatography and shown to comigrate with control galactosylceramide containing hydroxylated fatty acids and with sulfatide. Their structures were confirmed by fast atom bombardment mass spectrometry, which detected homologous series of ceramide monohexoside and sulfatide with hydroxylated fatty acyl chains ranging from h16:0 to h24:0. Assembled 987P fimbriae, pre- and postassembly dissociated fimbrial subunits, and Fab fragments of specific anti-FasG, -FasF, and -FasA were used to inhibit 987P-mediated bacterial binding to the two identified piglet glycolipids and corresponding isoreceptor controls. Only assembled fimbriae and anti-FasG Fab fragments were significantly able to inhibit bacterial binding to sulfatide, indicating that in addition to glycoproteins, FasG recognizes a specific glycolipid of piglet brush borders. In contrast, only anti-FasA Fab fragments were significantly able to inhibit bacterial binding to galactosylceramide with hydroxylated fatty acids and piglet hydroxylated ceramide monohexoside, indicating that FasA may determine a third type of ligand-receptor interaction in the piglet intestines. Since these bacterial adhesins recognize their respective glycolipid receptors only after being assembled in their final fimbrial quaternary structure, adhesin binding may involve cooperative interactions and the subunits by themselves may have very low binding affinities. Alternatively, conformation-sensitive domains of these subunits present in the assembled fimbriae may be required for glycolipid binding.},
author = {Khan, A. Salam and Johnston, Norah C. and Goldfine, Howard and Schifferli, Dieter M.},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Khan et al. - Porcine 987P glycolipid receptors on intestinal brush borders and their cognate bacterial ligands - 1996.pdf:pdf},
issn = {00199567},
journal = {Infection and Immunity},
number = {9},
pages = {3688--3693},
pmid = {8751918},
title = {{Porcine 987P glycolipid receptors on intestinal brush borders and their cognate bacterial ligands}},
volume = {64},
year = {1996}
}
@article{Waksman2009,
abstract = {The chaperone-usher (CU) pathway of pilus biogenesis is the most widespread of the five pathways that assemble adhesive pili at the surface of Gram-negative bacteria. Recent progress in the study of the structural biology of the CU pathway has unravelled the molecular basis of chaperone function and elucidated the mechanisms of fibre assembly at the outer membrane, leading to a comprehensive description of each step in the biogenesis pathway. Other studies have provided the molecular basis of host recognition by CU pili. The knowledge that has been gathered about both the assembly of and host recognition by CU pili has been harnessed to design promising antibiotic compounds.},
author = {Waksman, Gabriel and Hultgren, Scott J},
doi = {10.1038/nrmicro2220},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Waksman, Hultgren - Structural biology of the chaperone-usher pathway of pilus biogenesis. - 2009.pdf:pdf},
issn = {1740-1534},
journal = {Nature reviews. Microbiology},
keywords = {Amino Acid Sequence,Bacterial,Bacterial Proteins,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,Bacterial: chemistry,Bacterial: genetics,Bacterial: metabolism,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: genetics,Fimbriae Proteins: metabolism,Gene Expression Regulation,Gram-Negative Bacteria,Gram-Negative Bacteria: genetics,Gram-Negative Bacteria: metabolism,Gram-Negative Bacteria: pathogenicity,Gram-Negative Bacterial Infections,Gram-Negative Bacterial Infections: microbiology,Host-Pathogen Interactions,Humans,Models,Molecular,Molecular Chaperones,Molecular Chaperones: chemistry,Molecular Chaperones: genetics,Molecular Chaperones: metabolism,Molecular Sequence Data,Structure-Activity Relationship},
month = {nov},
number = {11},
pages = {765--74},
pmid = {19820722},
publisher = {Nature Publishing Group},
title = {{Structural biology of the chaperone-usher pathway of pilus biogenesis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19820722},
volume = {7},
year = {2009}
}
@article{Clemen2005,
abstract = {Myosin-V is a processive two-headed actin-based motor protein involved in many intracellular transport processes. A key question for understanding myosin-V function and the communication between its two heads is its behavior under load. Since in vivo myosin-V colocalizes with other much stronger motors like kinesins, its behavior under superstall forces is especially relevant. We used optical tweezers with a long-range force feedback to study myosin-V motion under controlled external forward and backward loads over its full run length. We find the mean step size remains constant at approximately 36 nm over a wide range of forces from 5 pN forward to 1.5 pN backward load. We also find two force-dependent transitions in the chemomechanical cycle. The slower ADP-release is rate limiting at low loads and depends only weakly on force. The faster rate depends more strongly on force. The stronger force dependence suggests this rate represents the diffusive search of the leading head for its binding site. In contrast to kinesin motors, myosin-V's run length is essentially independent of force between 5 pN of forward to 1.5 pN of backward load. At superstall forces of 5 pN, we observe continuous backward stepping of myosin-V, indicating that a force-driven reversal of the power stroke is possible.},
author = {Clemen, Anabel E-M and Vilfan, Mojca and Jaud, Johann and Zhang, Junshan and B{\"{a}}rmann, Michael and Rief, Matthias},
doi = {10.1529/biophysj.104.053504},
isbn = {0006-3495 (Print)},
issn = {00063495},
journal = {Biophysical journal},
number = {6},
pages = {4402--4410},
pmid = {15764664},
title = {{Force-dependent stepping kinetics of myosin-V.}},
volume = {88},
year = {2005}
}
@article{Sbalzarini2005,
abstract = {This paper presents a computationally efficient, two-dimensional, feature point tracking algorithm for the automated detection and quantitative analysis of particle trajectories as recorded by video imaging in cell biology. The tracking process requires no a priori mathematical modeling of the motion, it is self-initializing, it discriminates spurious detections, and it can handle temporary occlusion as well as particle appearance and disappearance from the image region. The efficiency of the algorithm is validated on synthetic video data where it is compared to existing methods and its accuracy and precision are assessed for a wide range of signal-to-noise ratios. The algorithm is well suited for video imaging in cell biology relying on low-intensity fluorescence microscopy. Its applicability is demonstrated in three case studies involving transport of low-density lipoproteins in endosomes, motion of fluorescently labeled Adenovirus-2 particles along microtubules, and tracking of quantum dots on the plasma membrane of live cells. The present automated tracking process enables the quantification of dispersive processes in cell biology using techniques such as moment scaling spectra.},
author = {Sbalzarini, I F and Koumoutsakos, P},
doi = {10.1016/j.jsb.2005.06.002},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sbalzarini, Koumoutsakos - Feature point tracking and trajectory analysis for video imaging in cell biology. - 2005.pdf:pdf},
issn = {1047-8477},
journal = {Journal of structural biology},
keywords = {Adenoviridae,Algorithms,Animals,Biology,Biology: methods,Cell Line,Cell Membrane,Computer Simulation,Endosomes,Endosomes: chemistry,Fluorescent Dyes,Humans,Image Processing, Computer-Assisted,Lipoproteins, LDL,Lipoproteins, LDL: metabolism,Microscopy, Fluorescence,Microscopy, Video,Microtubules,Microtubules: virology,Particle Size,Polyomavirus},
month = {aug},
number = {2},
pages = {182--95},
pmid = {16043363},
title = {{Feature point tracking and trajectory analysis for video imaging in cell biology.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16043363},
volume = {151},
year = {2005}
}
@article{Magnaudet2000,
author = {Magnaudet, J and Eames, I},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Magnaudet, Eames - The Motion of High-Reynolds-Number Bubbles in Inhomogeneous Flows - 2000.pdf:pdf},
journal = {Annual Review of Fluid Mechanics},
keywords = {added mass,bubbly flow,hydrodynamic force,shear-,surfactants},
pages = {659--708},
title = {{The Motion of High-Reynolds-Number Bubbles in Inhomogeneous Flows}},
volume = {32},
year = {2000}
}
@article{Grow2008,
author = {Grow, Ann E},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Grow - Label-Free Fingerprinting of Pathogens by Raman Spectroscopy Techniques - 2008.pdf:pdf},
journal = {Microscopy},
pages = {525--564},
title = {{Label-Free Fingerprinting of Pathogens by Raman Spectroscopy Techniques}},
year = {2008}
}
@techreport{Nordlander,
abstract = {Urinary tract infections are caused by Uropathogenic Escherichia coli. It is therefore of great interest to study how the adhesion of these bacteria to the walls of the urinary tract is affected by changes in pH and salt concentration in the urine. Using a multivariate experimental design, a mathematical model for how pH and different salinity affect E coli P pili refolding was calculated. The refolding of the P pili was measured at different levels of pH and salt concentration. The measurements were made using optical tweezers. By calculating the relative number of misfolding PapA units, the change in influence of pH and salinity was quantified. The biggest influence on the refolding process turned out to be pH. Though changes in both pH and salinity from the neutral region affect the refolding negatively. The final model for the refolding is , where MF is the quantification of the changes in the refolding process.},
author = {Nordlander, Jessica and Bj{\"{o}}rkqvist, Sara and Lundmark, Tobias and Staaf, Elina},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nordlander et al. - The influence of salinity and pH on the refolding of P pili expressed by UPEC - Unknown.pdf:pdf},
keywords = {pH,pili,salinity},
mendeley-tags = {pH,pili,salinity},
title = {{The influence of salinity and pH on the refolding of P pili expressed by UPEC}}
}
@incollection{Axner2011,
abstract = {Adhesion plays a major role in the bacterial lifestyle. Bacteria can adhere to organic and inorganic surfaces, to each other, and of course to host cells during pathogenesis. The focus of this book is: how are such adhesion phenomena best studied? Microbial genetics experiments have greatly enhanced our knowledge of what bacterial factors are involved in adhesion. For numerous reasons, though, biochemical and structural biology knowledge of the molecular interactions involved in adhesion are limited. One major problem has been a lack of interdisciplinary research and understanding in the field. On the one hand, the microbiologists lack detailed knowledge of the biophysical possibilities and have limited access to the frequently expensive instrumentation involved while on the other hand, the experts in these methods frequently do not have access to the biological materials, nor do they necessarily understand the biological questions to be answered. The purpose of this book is thus to overcome this gap in communication between researchers in biology, chemistry and physics and to display the many ways and means to investigate bacterial adhesion. We hope to stimulate new and ground-breaking research.},
author = {Axner, Ove and Andersson, Magnus and Bj{\"{o}}rnham, Oscar and Castelain, Micka{\"{e}}l and Klinth, Jeanna E and Koutris, Efstratios and Schedin, Staffan},
booktitle = {Bacterial Adhesion},
doi = {10.1007/978-94-007-0940-9{\_}19},
edition = {1st},
editor = {Linke, Dirk and Goldman, Adrian},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Axner et al. - Assessing Bacterial Adhesion on an Individual Adhesin and Single Pili Level Using Optical Tweezers - 2011.pdf:pdf},
keywords = {Bacterial Adhesion - Biophysics - Infectious Disea,P-pili,Type 1,pili},
mendeley-tags = {P-pili,Type 1,pili},
pages = {301--313},
publisher = {Springer Verlag},
title = {{Assessing Bacterial Adhesion on an Individual Adhesin and Single Pili Level Using Optical Tweezers}},
url = {http://www.springer.com/biomed/book/978-94-007-0939-3},
year = {2011}
}
@article{Dubois2014,
abstract = {For digital holographic microscopy applications, we modify the focus criterion based on the integration of the amplitude modulus to make possible its use regardless of the phase or amplitude nature of the objects under test. When applied on holographic data, the original criterion gives, at the focus plane, a minimum or a maximum, for amplitude or phase objects. The criterion we propose here operates on high-pass filtered complex amplitudes. It is shown that the proposed criterion gives a minimum for both types of objects when the focus plane is reached. Experimental results on real samples and simulations are provided, illustrating the efficiency and the potential of the method.},
author = {Dubois, Frank and {El Mallahi}, Ahmed and Dohet-Eraly, J{\'{e}}r{\^{o}}me and Yourassowsky, Catherine},
doi = {10.1364/OL.39.004286},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dubois et al. - Refocus criterion for both phase and amplitude objects in digital holographic microscopy. - 2014.pdf:pdf},
issn = {1539-4794},
journal = {Optics letters},
number = {15},
pages = {4286--9},
pmid = {25078158},
title = {{Refocus criterion for both phase and amplitude objects in digital holographic microscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25078158},
volume = {39},
year = {2014}
}
@article{Roux1999,
abstract = {Electron-microscopic (EM) analysis preceded crystallographic analysis [1,2] of Igs by over a decade and was for a time the only direct way of analyzing their 3-D molecular structure. Once the X-ray structures were deduced, the role of EM gradually shifted from gross structural analysis to the addressing of more sophisticated structural and functional questions. EM remains a vital adjunct to the many physicochemical, biochemical, and serological tools brought to bear on these remarkable molecules as we try to relate form to function. In this review I will highlight some of the many contributions that have been made possible by virtue of being able to 'see' Ig molecules and immune complexes.},
author = {Roux, K H},
doi = {24226},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Roux - Immunoglobulin structure and function as revealed by electron microscopy. - 1999.pdf:pdf},
issn = {1018-2438},
journal = {International archives of allergy and immunology},
keywords = {Animals,Crystallography,Electron,Humans,Immunoglobulin Fab Fragments,Immunoglobulin Fab Fragments: ultrastructure,Immunoglobulin G,Immunoglobulin G: ultrastructure,Immunoglobulin M,Immunoglobulin M: ultrastructure,Immunoglobulins,Immunoglobulins: chemistry,Immunoglobulins: physiology,Immunoglobulins: ultrastructure,Microscopy,X-Ray,antibodies},
mendeley-tags = {antibodies},
month = {oct},
number = {2},
pages = {85--99},
pmid = {10545762},
title = {{Immunoglobulin structure and function as revealed by electron microscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10545762},
volume = {120},
year = {1999}
}
@article{Ramser2005a,
abstract = {Using a lab-on-a-chip approach we demonstrate the possibility of selecting a single cell with certain properties and following its dynamics after an environmental stimulation in real time using Raman spectroscopy. This is accomplished by combining a micro Raman set-up with optical tweezers and a microfluidic system. The latter gives full control over the media surrounding the cell, and it consists of a pattern of channels and reservoirs defined by electron beam lithography that is moulded into rubber silicon (PDMS). Different buffers can be transported through the channels using electro-osmotic flow, while the resonance Raman response of an optically trapped red blood cell (RBC) is simultaneously registered. This makes it possible to monitor the oxygenation cycle of the cell in real time and to investigate effects like photo-induced chemistry caused by the illumination. The experimental set-up has high potential for in vivo monitoring of cellular drug response using a variety of spectroscopic probes.},
author = {Ramser, Kerstin and Enger, Jonas and Goks{\"{o}}r, Mattias and Hanstorp, Dag and Logg, Katarina and K{\"{a}}ll, Mikael},
doi = {10.1039/b416749j},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ramser et al. - A microfluidic system enabling Raman measurements of the oxygenation cycle in single optically trapped red blood cells..pdf:pdf},
issn = {1473-0197},
journal = {Lab on a chip},
keywords = {Adult,Erythrocytes,Erythrocytes: cytology,Erythrocytes: metabolism,Erythrocytes: radiation effects,Humans,Infrared Rays,Lasers,Light,Microfluidic Analytical Techniques,Microfluidic Analytical Techniques: instrumentatio,Microfluidic Analytical Techniques: methods,Microscopy, Confocal,Microscopy, Confocal: instrumentation,Optics and Photonics,Optics and Photonics: instrumentation,Oxygen,Oxygen: metabolism,Spectrum Analysis, Raman,Spectrum Analysis, Raman: instrumentation,Spectrum Analysis, Raman: methods,Time Factors},
month = {apr},
number = {4},
pages = {431--6},
pmid = {15791341},
title = {{A microfluidic system enabling Raman measurements of the oxygenation cycle in single optically trapped red blood cells.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15791341},
volume = {5},
year = {2005}
}
@article{Hill2007,
author = {Hill, Jane and Kalkanci, Ozge and McMurry, Jonathan L. and Koser, Hur},
doi = {10.1103/PhysRevLett.98.068101},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hill et al. - Hydrodynamic Surface Interactions Enable iEscherichia Colii to Seek Efficient Routes to Swim Upstream - 2007.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
number = {6},
pages = {068101},
title = {{Hydrodynamic Surface Interactions Enable <i>Escherichia Coli</i> to Seek Efficient Routes to Swim Upstream}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.98.068101},
volume = {98},
year = {2007}
}
@article{Wong2006,
author = {Wong, Wesley P. and Halvorsen, Ken},
doi = {10.1364/OE.14.012517},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wong, Halvorsen - The effect of integration time on fluctuation measurements calibrating an optical trap in the presence of motion blur.pdf:pdf},
issn = {1094-4087},
journal = {Optics Express},
number = {25},
pages = {12517},
title = {{The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=oe-14-25-12517},
volume = {14},
year = {2006}
}
@article{Hara2012,
author = {Hara, Christiane R O and Clark, Robert D and Hagobian, Todd and Mcgaughey, Karen},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hara et al. - Effects of Chainring Type ( Circular vs . Rotor Q-Ring ) on 1km Time Trial Performance Over Six Weeks in Competitive Cycli.pdf:pdf},
journal = {International Journal},
keywords = {cycling efficiency,cycling performance,non-circular chainrings,rotor q-ring},
number = {01},
pages = {025--040},
title = {{Effects of Chainring Type ( Circular vs . Rotor Q-Ring ) on 1km Time Trial Performance Over Six Weeks in Competitive Cyclists and Triathletes}},
volume = {06},
year = {2012}
}
@article{Ho1995,
author = {Ho, Chun-Ta and Chen, Ling-Hwei},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ho, Chen - A fast ellipsecircle detector using geometric symmetry - 1995.pdf:pdf},
number = {1},
pages = {117--124},
title = {{A fast ellipse/circle detector using geometric symmetry}},
volume = {28},
year = {1995}
}
@article{Watts2012,
abstract = {Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are a significant health concern, exacerbated by the rapid emergence of multidrug resistant strains refractory to antibiotic treatment. P fimbriae are strongly associated with upper urinary tract colonization due to specific binding to $\alpha$-D-galactopyranosyl-(1-4)-$\beta$-D-galactopyranoside receptors in the kidneys. Thus, inhibiting P-fimbrial adhesion may reduce the incidence of UPEC-mediated UTI. E. coli 83972 is an asymptomatic bacteriuria isolate successfully used as a prophylactic agent to prevent UTI in human studies. We constructed a recombinant E. coli 83972 strain displaying a surface-located oligosaccharide P fimbriae receptor mimic that bound to P-fimbriated E. coli producing any of the 3 PapG adhesin variants. The recombinant strain, E. coli 83972::lgtCE, impaired P fimbriae-mediated adhesion to human erythrocytes and kidney epithelial cells. Additionally, E. coli 83972::lgtCE impaired urine colonization by UPEC in a mouse UTI model, demonstrating its potential as a prophylactic agent to prevent UTI.},
author = {Watts, Rebecca E and Tan, Chee K and Ulett, Glen C and Carey, Alison J and Totsika, Makrina and Idris, Adi and Paton, Adrienne W and Morona, Renato and Paton, James C and Schembri, Mark a},
doi = {10.1093/infdis/jis493},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Watts et al. - Escherichia coli 83972 expressing a P fimbriae oligosaccharide receptor mimic impairs adhesion of uropathogenic E. coli..pdf:pdf},
issn = {1537-6613},
journal = {The Journal of infectious diseases},
keywords = {Animals,Bacterial Adhesion,Disease Models, Animal,Epithelial Cells,Epithelial Cells: microbiology,Erythrocytes,Erythrocytes: microbiology,Female,Fimbriae Proteins,Fimbriae Proteins: genetics,Fimbriae Proteins: metabolism,Humans,Mice,Mice, Inbred C57BL,Oligosaccharides,Oligosaccharides: genetics,Oligosaccharides: metabolism,Protein Binding,Urinary Tract Infections,Urinary Tract Infections: prevention {\&} control,Uropathogenic Escherichia coli,Uropathogenic Escherichia coli: genetics,Uropathogenic Escherichia coli: pathogenicity},
month = {oct},
number = {8},
pages = {1242--9},
pmid = {22872729},
title = {{Escherichia coli 83972 expressing a P fimbriae oligosaccharide receptor mimic impairs adhesion of uropathogenic E. coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22872729},
volume = {206},
year = {2012}
}
@article{Ericsson2000,
abstract = {We have developed a method, using laser, optical tweezers and direct microscopic analysis of reproductive potential and membrane integrity, to assess single-cell viability in a stationary-phase Escherichia coli population. It is demonstrated here that a reduction in cell integrity, determined by using the fluorescent nucleic acid stain propidium iodide, correlated well with a reduction in cell proliferating potential during the stationary-phase period studied. Moreover, the same cells that exhibited reduced integrity were found to be the ones that failed to divide upon nutrient addition. A small but significant number of the intact cells (496 of 7,466 [6.6{\%}]) failed to replicate. In other words, we did not find evidence for the existence of a large population of intact but nonculturable cells during the stationary-phase period studied but it is clear that reproductive ability can be lost prior to the loss of membrane integrity. In addition, about 1{\%} of the stationary-phase cells were able to divide only once upon nutrient addition, and in a few cases, only one of the two cells produced by division was able to divide a second time, indicating that localized cell deterioration, inherited by only one of the daughters, may occur. The usefulness of the optical trapping methodology in elucidating the mechanisms involved in stationary-phase-induced bacterial death and population heterogeneity is discussed.},
author = {Ericsson, M. and Hanstorp, D. and Hagberg, P. and Enger, J. and Nystrom, T.},
doi = {10.1128/JB.182.19.5551-5555.2000},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ericsson et al. - Sorting out bacterial viability with optical tweezers - 2000.pdf:pdf},
isbn = {0021-9193 (Print)},
issn = {00219193},
journal = {Journal of Bacteriology},
number = {19},
pages = {5551--5555},
pmid = {10986260},
title = {{Sorting out bacterial viability with optical tweezers}},
volume = {182},
year = {2000}
}
@article{Fedosov2010,
abstract = {Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary.},
author = {Fedosov, Dmitry a and Caswell, Bruce and Karniadakis, George Em},
doi = {10.1016/j.bpj.2010.02.002},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Fedosov, Caswell, Karniadakis - A multiscale red blood cell model with accurate mechanics, rheology, and dynamics. - 2010.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
month = {may},
number = {10},
pages = {2215--25},
pmid = {20483330},
publisher = {Biophysical Society},
title = {{A multiscale red blood cell model with accurate mechanics, rheology, and dynamics.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2872218{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {98},
year = {2010}
}
@article{Yang2011,
author = {Yang, Jing and Huber, Greg and Wolgemuth, Charles},
doi = {10.1103/PhysRevLett.107.268101},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yang, Huber, Wolgemuth - Forces and Torques on Rotating Spirochete Flagella - 2011.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {dec},
number = {26},
pages = {268101},
title = {{Forces and Torques on Rotating Spirochete Flagella}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.107.268101},
volume = {107},
year = {2011}
}
@article{Schmidt1999,
abstract = {A protocol is proposed to obtain the joint angles of wrist and elbow from tracked triads of surface markers on each limb segment. Cuffs placed on the limb support the rigidity of the triads. Additional markers are used to mark the approximate positions of joints. Corrections of surface marker data for skin motion are derived from a priori knowledge about plausible joint motions. In addition, ill-conditioned states are trapped when the elbow is nearly fully extended. The protocol is applied to sample motions which demonstrate the use and the effect of the corrections. The results show that the model assumptions are reasonable and that accurate joint rotations can be obtained. The correction steps prove to be an essential part of upper-extremity movement analysis.},
author = {Schmidt, R and Disselhorst-Klug, C and Silny, J and Rau, G},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schmidt et al. - A marker-based measurement procedure for unconstrained wrist and elbow motions. - 1999.pdf:pdf},
issn = {0021-9290},
journal = {Journal of biomechanics},
keywords = {Adult,Algorithms,Arm,Arm: physiology,Artifacts,Elbow Joint,Elbow Joint: physiology,Equipment Design,Female,Forearm,Forearm: physiology,Hand,Hand: physiology,Humans,Male,Models, Biological,Muscle Contraction,Muscle Contraction: physiology,Muscle, Skeletal,Muscle, Skeletal: physiology,Pronation,Pronation: physiology,Range of Motion, Articular,Range of Motion, Articular: physiology,Rotation,Shoulder Joint,Shoulder Joint: physiology,Skin,Supination,Supination: physiology,Wrist Joint,Wrist Joint: physiology},
month = {jun},
number = {6},
pages = {615--21},
pmid = {10332626},
title = {{A marker-based measurement procedure for unconstrained wrist and elbow motions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10332626},
volume = {32},
year = {1999}
}
@article{Andersson2012,
abstract = {Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrheal disease worldwide. Adhesion pili (or fimbriae), such as the CFA/I (colonization factor antigen I) organelles that enable ETEC to attach efficiently to the host intestinal tract epithelium, are critical virulence factors for initiation of infection. We characterized the intrinsic biomechanical properties and kinetics of individual CFA/I pili at the single-organelle level, demonstrating that weak external forces (7.5 pN) are sufficient to unwind the intact helical filament of this prototypical ETEC pilus and that it quickly regains its original structure when the force is removed. While the general relationship between exertion of force and an increase in the filament length for CFA/I pili associated with diarrheal disease is analogous to that of P pili and type 1 pili, associated with urinary tract and other infections, the biomechanical properties of these different pili differ in key quantitative details. Unique features of CFA/I pili, including the significantly lower force required for unwinding, the higher extension speed at which the pili enter a dynamic range of unwinding, and the appearance of sudden force drops during unwinding, can be attributed to morphological features of CFA/I pili including weak layer-to-layer interactions between subunits on adjacent turns of the helix and the approximately horizontal orientation of pilin subunits with respect to the filament axis. Our results indicate that ETEC CFA/I pili are flexible organelles optimized to withstand harsh motion without breaking, resulting in continued attachment to the intestinal epithelium by the pathogenic bacteria that express these pili.},
annote = {From Duplicate 1 ( 





























































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































},
author = {Andersson, Magnus and Bj{\"{o}}rnham, Oscar and Svantesson, Mats and Badahdah, Arwa and Uhlin, Bernt Eric and Bullitt, Esther},
doi = {10.1016/j.jmb.2011.12.006},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Andersson et al. - A structural basis for sustained bacterial adhesion biomechanical properties of CFAI pili. - 2012.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - A structural basis for sustained bacterial adhesion biomechanical properties of CFAI pili. - 2012(2).pdf:pdf},
issn = {1089-8638},
journal = {Journal of molecular biology},
keywords = {Adhesins,Bacterial,Bacterial Adhesion,Bacterial: physiology,Bacterial: ultrastructure,Biomechanics,Escherichia coli,Escherichia coli: physiology,Escherichia coli: ultrastructure,Fimbriae Proteins,Fimbriae Proteins: physiology,Fimbriae Proteins: ultrastructure,Protein Structure,Secondary,enterotoxigenic Escherichia coli,enterotoxigenic escherichia,fimbriae,force spectroscopy,optical tweezers,unwinding},
month = {feb},
number = {5},
pages = {918--28},
pmid = {22178477},
publisher = {Elsevier B.V.},
title = {{A structural basis for sustained bacterial adhesion: biomechanical properties of CFA/I pili.}},
url = {http://dx.doi.org/10.1016/j.jmb.2011.12.006 http://www.ncbi.nlm.nih.gov/pubmed/22178477},
volume = {415},
year = {2012}
}
@article{Nelson2006,
abstract = {The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bead tethered to a slide by a single DNA molecule. We describe an improved experimental protocol with which to form the tethers, an algorithm for analyzing bead motion visualized using differential interference contrast microscopy, and a physical model with which we have successfully simulated such DNA tethers. Both experiment and theory show that the statistics of the bead motion are quite different from those of a free semiflexible polymer. Our experimental data for chain extension versus tether length fit our model over a range of tether lengths from 109 to 3477 base pairs, using a value for the DNA persistence length that is consistent with those obtained under similar solution conditions by other methods. Moreover, we present the first experimental determination of the full probability distribution function of bead displacements and find excellent agreement with our theoretical prediction. Our results show that TPM is a useful tool for monitoring large conformational changes such as DNA looping.},
author = {Nelson, Philip C and Zurla, Chiara and Brogioli, Doriano and Beausang, John F and Finzi, Laura and Dunlap, David},
doi = {10.1021/jp0630673},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nelson et al. - Tethered particle motion as a diagnostic of DNA tether length. - 2006.pdf:pdf},
issn = {1520-6106},
journal = {The journal of physical chemistry. B},
keywords = {Biophysical Phenomena,Biophysics,Chemical,DNA,Elasticity,Microspheres,Models,Motion,Single-Stranded,Single-Stranded: chemistry,Surface Properties,TPM,Thermodynamics},
mendeley-tags = {TPM},
month = {aug},
number = {34},
pages = {17260--7},
pmid = {16928025},
title = {{Tethered particle motion as a diagnostic of DNA tether length.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16928025},
volume = {110},
year = {2006}
}
@article{Beaussart2016,
author = {Beaussart, Audrey and Abell{\'{a}}n-Flos, Marta and El-Kirat-Chatel, Sofiane and Vincent, St{\'{e}}phane P. and Dufr{\^{e}}ne, Yves F.},
doi = {10.1021/acs.nanolett.5b04689},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Beaussart et al. - Force Nanoscopy as a Versatile Platform for Quantifying the Activity of Antiadhesion Compounds Targeting Bacterial Pa.pdf:pdf},
issn = {1530-6984},
journal = {Nano Letters},
keywords = {AFM,fimbriae,fimh},
mendeley-tags = {AFM,fimbriae,fimh},
pages = {acs.nanolett.5b04689},
title = {{Force Nanoscopy as a Versatile Platform for Quantifying the Activity of Antiadhesion Compounds Targeting Bacterial Pathogens}},
url = {http://pubs.acs.org/doi/abs/10.1021/acs.nanolett.5b04689},
year = {2016}
}
@article{Kramers1940,
abstract = {A particle which is caught in a potential hole and which, through the shuttling action of Brownian motion, can escape over a potential barrier yields a suitable model for elucidating the applicability of the transition state method for calculating the rate of chemical reactions.},
author = {Kramers, H a},
doi = {10.1016/S0031-8914(40)90098-2},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kramers - Brownian motion in a field of force and the diffusion model of chemical reactions - 1940.pdf:pdf},
isbn = {0031-8914},
issn = {00318914},
journal = {Physica},
number = {4},
pages = {284--304},
pmid = {201402300032},
title = {{Brownian motion in a field of force and the diffusion model of chemical reactions}},
url = {http://www.sciencedirect.com/science/article/B6X42-4CB752H-3G/2/18dd09fed8a9142aed637597660731c5},
volume = {7},
year = {1940}
}
@article{Roberts1994,
author = {Roberts, James A and Marklundt, Britt-inger and Ilveri, D A G and Haslamt, Dave and Kaack, M Bernice and Baskin, Gary and Louis, Michel and Mllby, Roland and Winbergi, J A N and Ii, Staffan Normark},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Roberts et al. - The Gal ( al-4 ) Gal-specific tip adhesin of Escherichia coli P-fimbriae is needed for pyelonephritis to occur in the n.pdf:pdf},
number = {December},
pages = {11889--11893},
title = {{The Gal ( al-4 ) Gal-specific tip adhesin of Escherichia coli P-fimbriae is needed for pyelonephritis to occur in the normal urinary tract}},
volume = {91},
year = {1994}
}
@article{Segall2006,
author = {Segall, Darren and Nelson, Philip and Phillips, Rob},
doi = {10.1103/PhysRevLett.96.088306},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Segall, Nelson, Phillips - Volume-Exclusion Effects in Tethered-Particle Experiments Bead Size Matters - 2006.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {mar},
number = {8},
pages = {088306},
title = {{Volume-Exclusion Effects in Tethered-Particle Experiments: Bead Size Matters}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.96.088306},
volume = {96},
year = {2006}
}
@article{Neuman2004,
abstract = {Since their invention just over 20 years ago, optical traps have emerged as a powerful tool with broad-reaching applications in biology and physics. Capabilities have evolved from simple manipulation to the application of calibrated forces on-and the measurement of nanometer-level displacements of-optically trapped objects. We review progress in the development of optical trapping apparatus, including instrument design considerations, position detection schemes and calibration techniques, with an emphasis on recent advances. We conclude with a brief summary of innovative optical trapping configurations and applications.},
author = {Neuman, Keir C and Block, Steven M},
doi = {10.1063/1.1785844},
journal = {Rev Sci Instrum},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
number = {9},
pages = {2787--2809},
title = {{Optical trapping}},
volume = {75},
year = {2004}
}
@article{Rivetti1996,
abstract = {This paper reports a study of the deposition process of DNA molecules onto a mica surface for imaging under the scanning force microscope (SFM). Kinetic experiments indicate that the transport of DNA molecules from the solution drop onto the surface is governed solely by diffusion, and that the molecules are irreversibly adsorbed onto the substrate. A statistical polymer chain analysis has been applied to DNA molecules to determine the deposition conditions that lead to equilibrium and those that result in trapped configurations. Using the appropriate conditions, DNA molecules deposited onto freshly cleaved mica, are able to equilibrate on the surface as in an ideal two-dimensional solution. A persistence length of 53 nm was determined from those molecules. DNA fragments that were labeled on both ends with a horseradish peroxidase streptavidin fusion protein were still able to equilibrate on the surface, despite the additional protein-surface interaction. In contrast, DNA molecules deposited onto glow-discharged mica or H+-exchanged mica do not equilibrate on the surface. These molecules adopt conformations similar to those expected for a simple projection onto the surface plane, suggesting a process of kinetic trapping. These results validate recent SFM application to quantitatively analyze the conformation of complex macromolecular assemblies deposited on mica. Under equilibration conditions, the present study indicates that the SFM can be used to determine the persistence length of DNA molecules to a high degree of precision.},
author = {Rivetti, C and Guthold, M and Bustamante, C},
doi = {10.1006/jmbi.1996.0687},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rivetti, Guthold, Bustamante - Scanning force microscopy of DNA deposited onto mica equilibration versus kinetic trapping studied by sta.pdf:pdf},
isbn = {0022-2836 (Print)$\backslash$n0022-2836 (Linking)},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {dna,dna deposition,excluded volume effects,mica,persistence length,scanning force microscopy},
pages = {919--932},
pmid = {9000621},
title = {{Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis.}},
volume = {264},
year = {1996}
}
@article{Dubois2006,
author = {Dubois, Frank and Schockaert, C{\'{e}}dric and Callens, Natcaha and Yourassowsky, Catherine},
doi = {10.1364/OE.14.005895},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dubois et al. - Focus plane detection criteria in digital holography microscopy by amplitude analysis - 2006.pdf:pdf},
issn = {1094-4087},
journal = {Optics Express},
number = {13},
pages = {5895},
title = {{Focus plane detection criteria in digital holography microscopy by amplitude analysis}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=oe-14-13-5895},
volume = {14},
year = {2006}
}
@article{Sewald2006,
author = {Sewald, N. and Wilking, S.D. and Eckel, R. and Albu, S. and Wollschl$\backslash$$\backslash$"ager, K. and Gaus, Katharina and Becker, Anke and Bartels, F.W. and Ros, Robert and Anselmetti, Dario},
doi = {10.1002/psc},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sewald et al. - Probing DNA–peptide interaction forces at the single-molecule level - 2006.pdf:pdf},
issn = {1099-1387},
journal = {Journal of Peptide Science},
keywords = {atomic force,dna,microscopy,molecular recognition,optical tweezers,peptide,single-molecule force spectroscopy,transcription factor},
number = {12},
pages = {836--842},
publisher = {Wiley Online Library},
title = {{Probing DNA–peptide interaction forces at the single-molecule level}},
url = {http://onlinelibrary.wiley.com/doi/10.1002/psc.820/abstract},
volume = {12},
year = {2006}
}
@article{Honarvar2003,
author = {Honarvar, Shaya and Choi, Byung-Kwon and Schifferli, Dieter M.},
doi = {10.1046/j.1365-2958.2003.03419.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Honarvar, Choi, Schifferli - Phase variation of the 987P-like CS18 fimbriae of human enterotoxigenic Escherichia coli is regulated by si.pdf:pdf},
issn = {0950382X},
journal = {Molecular Microbiology},
month = {mar},
number = {1},
pages = {157--171},
title = {{Phase variation of the 987P-like CS18 fimbriae of human enterotoxigenic Escherichia coli is regulated by site-specific recombinases}},
url = {http://doi.wiley.com/10.1046/j.1365-2958.2003.03419.x},
volume = {48},
year = {2003}
}
@article{Hwang2008,
author = {Hwang, Sun-Uk and Lee, Yong-Gu},
doi = {10.1364/OE.16.021170},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Hwang, Lee - Simulation of an oil immersion objective lens a simplified ray-optics model considering Abbe’s sine condition - 2008.pdf:pdf},
issn = {1094-4087},
journal = {Optics Express},
month = {dec},
number = {26},
pages = {21170},
title = {{Simulation of an oil immersion objective lens: a simplified ray-optics model considering Abbe’s sine condition}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=oe-16-26-21170},
volume = {16},
year = {2008}
}
@article{Article2013,
author = {Article, Original},
doi = {10.1038/ismej.2012.80},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Article - Mechanisms determining the fate of dispersed bacterial communities in new environments - 2013.pdf:pdf},
keywords = {competition,dispersal,metacommunity,neutral model,salinity,species sorting},
pages = {61--71},
title = {{Mechanisms determining the fate of dispersed bacterial communities in new environments}},
year = {2013}
}
@article{An1997,
author = {An, Yuehuei H and Friedman, Richard J},
doi = {10.1016/S0167-7012(97)00058-4},
file = {:E$\backslash$:/Mina Dokument/Mendeley/An, Friedman - Laboratory methods for studies of bacterial adhesion - 1997.pdf:pdf},
issn = {01677012},
journal = {Journal of Microbiological Methods},
keywords = {bacterial adhesion,bacterial counting,biofilm,biofilm formation,biomaterials,microscopy,staphylococcus},
mendeley-tags = {biofilm},
month = {aug},
number = {2},
pages = {141--152},
title = {{Laboratory methods for studies of bacterial adhesion}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0167701297000584},
volume = {30},
year = {1997}
}
@article{Honda1989,
abstract = {A subtype (CS2) of the colonization factor antigen II (CFA/II) of human enterotoxigenic Escherichia coli (ETEC) was studied. Analysis revealed that CS2-possessing ETEC was predominant among isolates from traveller's diarrhea at Osaka, Japan. TH61 pili produced by a clinical strain (TH61) were purified as a native form to homogeneity by zone electrophoresis and successive column chromatographies on Sepharose 4B and Phenyl-Sepharose CL-4B. It was demonstrated by immunogold staining technique and bacterial agglutination test that antisera against the purified pili of strain TH61 recognized pili of both strain TH61 and strain {\#}C91f, a control strain possessing only CS2 pili. This suggests that TH61 pili purified in this study are CS2 pili. Subunit (pilin) of the purified pili has a molecular weight of about 16,000. Strains bearing CS2 could attach to human jejunal epithelial cells, and this attachment was inhibited by pretreating the enterocytes with purified pili. These indicate that CS2 pili are a factor responsible for attachment of ETEC bearing CS2 to human intestinal cells.},
author = {Honda, T and Cakir, N and Arita, M and Miwatani, T},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Honda et al. - Purification and characterization of the CS2 pili of colonization factor antigen II produced by human enterotoxigenic Esc.pdf:pdf},
issn = {03855600},
journal = {Microbiology and immunology},
number = {4},
pages = {265--275},
pmid = {2570344},
title = {{Purification and characterization of the CS2 pili of colonization factor antigen II produced by human enterotoxigenic Escherichia coli.}},
volume = {33},
year = {1989}
}
@misc{DERKSEN2011,
abstract = {Direct numerical simulations of the shear flow over assemblies of uniformly sized, solid spheres attached to a flat wall have been performed using the lattice-Boltzmann method. The random sphere assemblies comprised monolayers, double layers and triple layers. The Reynolds number based on the sphere radius and the overall shear rate was much smaller than 1. The results were interpreted in terms of the drag force (the force in the streamwise direction) and lift force (the force in the wall-normal direction) experienced by the spheres as a function of the denseness of the bed and the depth of the spheres in the bed. The average drag and lift forces decay monotonically as a function of the surface coverage of the spheres in the top layer of the bed. The sphere-to-sphere variation of the drag and lift forces is significant due to interactions between spheres via the interstitial fluid flow.},
author = {DERKSEN, J. J. and LARSEN, R. A.},
booktitle = {Journal of Fluid Mechanics},
pages = {548--573},
title = {{Drag and lift forces on random assemblies of wall-attached spheres in low-Reynolds-number shear flow}},
volume = {673},
year = {2011}
}
@article{Kimme1975,
author = {Kimme, Carolyn and Ballard, Dana},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kimme, Ballard - Finding Circles by an Array of Accumulators CT- - 1975.pdf:pdf},
number = {2},
pages = {2--4},
title = {{Finding Circles by an Array of Accumulators CT-}},
volume = {18},
year = {1975}
}
@article{Knutton1985,
abstract = {An improved enterocyte adhesion assay has been used to examine a collection of 44 strains of enterotoxigenic Escherichia coli (ETEC) for their ability to adhere to the brush border of isolated human duodenal enterocytes. Fourteen strains showed good adhesion; in each case the ability to adhere correlated with the production of colonization factor antigen I or II (CFA/I or CFA/II) fimbriae. CFA/II-positive producing coli surface antigens 1 and 3 (CS1 and CS3), coli surface antigens 2 and 3 (CS2 and CS3), and only coli surface antigen 3 (CS3) each showed good adhesion. CS3-mediated brush border attachment of CFA/II-positive ETEC was demonstrated by electron microscopy with monospecific antibody and an immunogold labeling technique. One CFA/I-positive ETEC strain was nonadherent in the assay, as were ETEC producing type 1 somatic fimbriae. Five animal ETEC strains producing K88, K99, F41, and 987P fimbriae were slightly more adhesive than control strains, but adhesion was significantly less than that of CFA-positive ETEC. Twenty five human ETEC strains that lacked CFA/I and CFA/II were nonadherent, suggesting either that the surface antigens responsible for adhesion to human intestinal mucosa in these strains were not being produced or that mucosal receptors for these strains are present in regions of the small intestine other than the duodenum.},
author = {Knutton, S and Lloyd, D R and Candy, D C and McNeish, a S},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Knutton et al. - Adhesion of enterotoxigenic Escherichia coli to human small intestinal enterocytes. - 1985.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
number = {3},
pages = {824--831},
pmid = {2860070},
title = {{Adhesion of enterotoxigenic Escherichia coli to human small intestinal enterocytes.}},
volume = {48},
year = {1985}
}
@article{McCord2005,
author = {McCord, Rachel Patton and Yukich, John N. and Bernd, Karen K.},
doi = {10.1002/cm.20071},
file = {:E$\backslash$:/Mina Dokument/Mendeley/McCord, Yukich, Bernd - Analysis of force generation during flagellar assembly through optical trapping of free-swimmingChlamydomonas re.pdf:pdf},
issn = {0886-1544},
journal = {Cell Motility and the Cytoskeleton},
keywords = {acid deflagellation,algae,dynein,microtubules,oda1,optical tweezers,propulsive force},
month = {jul},
number = {3},
pages = {137--144},
title = {{Analysis of force generation during flagellar assembly through optical trapping of free-swimmingChlamydomonas reinhardtii}},
url = {http://doi.wiley.com/10.1002/cm.20071},
volume = {61},
year = {2005}
}
@article{Fallman2005a,
abstract = {P pili are protein filaments expressed by uropathogenic Escherichia coli that mediate binding to glycolipids on epithelial cell surfaces, which is a prerequisite for bacterial infection. When a bacterium, attached to a cell surface, is exposed to external forces, the pili, which are composed of approximately 10(3) PapA protein subunits arranged in a helical conformation, can elongate by unfolding to a linear conformation. This property is considered important for the ability of a bacterium to withstand shear forces caused by urine flow. It has hitherto been assumed that this elongation is plastic, thus constituting a permanent conformational deformation. We demonstrate, using optical tweezers, that this is not the case; the unfolding of the helical structure to a linear conformation is fully reversible. It is surmised that this reversibility helps the bacteria regain close contact to the host cells after exposure to significant shear forces, which is believed to facilitate their colonization.},
author = {F{\"{a}}llman, Erik and Schedin, Staffan and Jass, Jana and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1038/sj.embor.7400310},
file = {:E$\backslash$:/Mina Dokument/Mendeley/F{\"{a}}llman et al. - The unfolding of the P pili quaternary structure by stretching is reversible, not plastic. - 2005.pdf:pdf},
issn = {1469-221X},
journal = {EMBO reports},
keywords = {Bacterial,Bacterial: chemistry,Bacterial: metabolism,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: metabolism,Escherichia coli: chemistry,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Protein Denaturation,Protein Folding,Protein Structure,Quaternary},
month = {jan},
number = {1},
pages = {52--6},
pmid = {15592451},
title = {{The unfolding of the P pili quaternary structure by stretching is reversible, not plastic.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1299220{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {6},
year = {2005}
}
@article{Hurley2011,
abstract = {Immunoglobulins form an important component of the immunological activity found in milk and colostrum. They are central to the immunological link that occurs when the mother transfers passive immunity to the offspring. The mechanism of transfer varies among mammalian species. Cattle provide a readily available immune rich colostrum and milk in large quantities, making those secretions important potential sources of immune products that may benefit humans. Immune milk is a term used to describe a range of products of the bovine mammary gland that have been tested against several human diseases. The use of colostrum or milk as a source of immunoglobulins, whether intended for the neonate of the species producing the secretion or for a different species, can be viewed in the context of the types of immunoglobulins in the secretion, the mechanisms by which the immunoglobulins are secreted, and the mechanisms by which the neonate or adult consuming the milk then gains immunological benefit. The stability of immunoglobulins as they undergo processing in the milk, or undergo digestion in the intestine, is an additional consideration for evaluating the value of milk immunoglobulins. This review summarizes the fundamental knowledge of immunoglobulins found in colostrum, milk, and immune milk.},
author = {Hurley, Walter L and Theil, Peter K},
doi = {10.3390/nu3040442},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hurley, Theil - Perspectives on immunoglobulins in colostrum and milk. - 2011.pdf:pdf},
issn = {2072-6643},
journal = {Nutrients},
keywords = {Animals,Cattle,Colostrum,Colostrum: immunology,Diarrhea,Diarrhea: immunology,Digestion,Drug Stability,Female,Humans,Immunity, Maternally-Acquired,Immunity, Maternally-Acquired: immunology,Immunization, Passive,Immunoglobulins,Immunoglobulins: analysis,Immunoglobulins: immunology,Infant, Newborn,Intestines,Intestines: immunology,Milk,Milk, Human,Milk, Human: immunology,Milk: immunology},
month = {apr},
number = {4},
pages = {442--74},
pmid = {22254105},
title = {{Perspectives on immunoglobulins in colostrum and milk.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3257684{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {3},
year = {2011}
}
@article{Heinrich1999a,
abstract = {A sufficiently large force acting on a single point of the fluid membrane of a flaccid phospholipid vesicle is known to cause the formation of a narrow bilayer tube (tether). We analyze this phenomenon by means of general mathematical methods allowing us to determine the shapes of strongly deformed vesicles including their stability. Starting from a free vesicle with an axisymmetric, prolate equilibrium shape, we consider an axial load that pulls (or pushes) the poles of the vesicle apart. Arranging the resulting shapes of strained vesicles in dependence of the axial deformation and of the area difference of monolayers, phase diagrams of stable shapes are presented comprising prolate shapes with or without equatorial mirror symmetry. For realistic values of membrane parameters, we study the force-extension relation of strained vesicles, and we demonstrate in detail how the initially elongated shape of an axially stretched vesicle transforms into a shape involving a membrane tether. This tethering transition may be continuous or discontinuous. If the free vesicle is mirror symmetric, the mirror symmetry is broken as the tether forms. The stability analysis of tethered shapes reveals that, for the considered vesicles, the stable shape is always asymmetric (polar), i.e., it involves only a single tether on one side of the main vesicle body. Although a bilayer tube formed from a closed vesicle is not an ideal cylinder, we show that, for most practical purposes, it is safe to assume a cylindrical geometry of tethers. This analysis is supplemented by the documentation of a prototype experiment supporting our theoretical predictions. It shows that the currently accepted model for the description of lipid-bilayer elasticity (generalized bilayer couple model) properly accounts for the tethering phenomenon.},
annote = {        From Duplicate 1 (                   Vesicle deformation by an axial load: from elongated shapes to tethered vesicles.                 - Heinrich, V; Bozic, B; Svetina, S; Zeks, B )
                
        
        
      },
author = {Heinrich, V and Bozic, B and Svetina, S and Zeks, B},
doi = {10.1016/S0006-3495(99)77362-5},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Heinrich et al. - Vesicle deformation by an axial load from elongated shapes to tethered vesicles - 1999.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Biophysical Phenomena,Biophysics,Chemical,Elasticity,Lipid Bilayers,Lipid Bilayers: chemistry,Liposomes,Liposomes: chemistry,Membrane Fluidity,Microscopy,Models,Phospholipids,Phospholipids: chemistry,Thermodynamics,Video},
month = {apr},
number = {4},
pages = {2056--71},
pmid = {10096901},
title = {{Vesicle deformation by an axial load: from elongated shapes to tethered vesicles}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300179{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {76},
year = {1999}
}
@article{Norregaard2013,
abstract = {Bacteriophage $\lambda$ stably maintains its dormant prophage state but efficiently enters lytic development in response to DNA damage. The mediator of these processes is the $\lambda$ repressor protein, CI, and its interactions with $\lambda$ operator DNA. This $\lambda$ switch is a model on the basis of which epigenetic switch regulation is understood. Using single molecule analysis, we directly examined the stability of the CI-operator structure in its natural, supercoiled state. We marked positions adjacent to the $\lambda$ operators with peptide nucleic acids and monitored their movement by tethered particle tracking. Compared with relaxed DNA, the presence of supercoils greatly enhances juxtaposition probability. Also, the efficiency and cooperativity of the $\lambda$ switch is significantly increased in the supercoiled system compared with a linear assay, increasing the Hill coefficient.},
author = {Norregaard, Kamilla and Andersson, Magnus and Sneppen, Kim and Nielsen, Peter Eigil and Brown, Stanley and Oddershede, Lene B.},
doi = {10.1073/pnas.1215907110},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Norregaard et al. - DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch - 2013.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Norregaard et al. - DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch - 2013.pdf:pdf},
isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = {oct},
number = {43},
pages = {17386--17391},
pmid = {24101469},
title = {{DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1215907110},
volume = {110},
year = {2013}
}
@article{Ashkin1987,
author = {Ashkin, A and Dziedzic, J M and Yamane, T},
doi = {10.1038/330769a0},
journal = {Nature},
number = {6150},
pages = {769--771},
title = {{OPTICAL TRAPPING AND MANIPULATION OF SINGLE CELLS USING INFRARED-LASER BEAMS}},
volume = {330},
year = {1987}
}
@article{Fletcher2004,
abstract = {Directed, purposeful movement is one of the qualities that we most closely associate with living organisms, and essentially all known forms of life on this planet exhibit some type of self-generated movement or motility. Even organisms that remain sessile most of the time, like flowering plants and trees, are quite busy at the cellular level, with large organelles, including chloroplasts, constantly racing around within cellular boundaries. Directed biological movement requires that the cell be able to convert its abundant stores of chemical energy into mechanical energy. Understanding how this mechanochemical energy transduction takes place and understanding how small biological forces generated at the molecular level are marshaled and organized for large-scale cellular or organismal movements are the focus of the field of cell motility. This tutorial, aimed at readers with a background in physical sciences, surveys the state of current knowledge and recent advances in modeling cell motility.},
author = {Fletcher, Daniel a and Theriot, Julie a},
doi = {10.1088/1478-3967/1/1/T01},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Fletcher, Theriot - An introduction to cell motility for the physical scientist. - 2004.pdf:pdf},
issn = {1478-3967},
journal = {Physical biology},
keywords = {Animals,Biophysical Phenomena,Biophysics,Cell Movement,Cell Movement: physiology,Models, Biological,Molecular Motor Proteins,Molecular Motor Proteins: metabolism},
month = {jun},
number = {1-2},
pages = {T1--10},
pmid = {16204816},
title = {{An introduction to cell motility for the physical scientist.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16204816},
volume = {1},
year = {2004}
}
@article{Holmgren2012,
author = {Holmgren, Jan and Svennerholm, Ann-Mari},
doi = {10.1016/j.coi.2012.03.014},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Holmgren, Svennerholm - Vaccines against mucosal infections - 2012.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Holmgren, Svennerholm - Vaccines against mucosal infections - 2012(2).pdf:pdf},
issn = {09527915},
journal = {Current Opinion in Immunology},
number = {3},
pages = {343--353},
publisher = {Elsevier Ltd},
title = {{Vaccines against mucosal infections}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0952791512000635},
volume = {24},
year = {2012}
}
@article{Zimmerberg2004,
abstract = {An important new structure suggests the BAR domain is a membrane-binding module that can both produce and sense membrane curvature. BAR resembles a banana that binds membranes electrostatically through its positively charged, concave surface.},
author = {Zimmerberg, Joshua and McLaughlin, Stuart},
doi = {10.1016/j.cub.2004.02.060},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zimmerberg, McLaughlin - Membrane curvature how BAR domains bend bilayers - 2004.pdf:pdf},
issn = {0960-9822},
journal = {Current biology : CB},
keywords = {ADP-Ribosylation Factors,ADP-Ribosylation Factors: metabolism,Animals,Biophysical Phenomena,Biophysics,Drosophila,GTPase-Activating Proteins,GTPase-Activating Proteins: metabolism,Lipid Bilayers,Lipid Bilayers: metabolism,Liposomes,Liposomes: metabolism,Nerve Tissue Proteins,Nerve Tissue Proteins: metabolism,Nerve Tissue Proteins: physiology,Protein Structure,Static Electricity,Tertiary,Tertiary: physiology},
month = {mar},
number = {6},
pages = {R250--2},
pmid = {15043839},
title = {{Membrane curvature: how BAR domains bend bilayers}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15043839},
volume = {14},
year = {2004}
}
@article{Bonds2001,
author = {Bonds, Selectin-carbohydrate and Tees, David F J and Waugh, Richard E and Hammer, Daniel A},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bonds et al. - A Microcantilever Device to Assess the Effect of Force on the Lifetime of - 2001.pdf:pdf},
journal = {Biophysical Journal},
number = {February},
pages = {668--682},
title = {{A Microcantilever Device to Assess the Effect of Force on the Lifetime of}},
volume = {80},
year = {2001}
}
@article{Kamada2015,
author = {Kamada, Nobuhiko and Sakamoto, Kei and Seo, Sang-Uk and Zeng, Melody Y. and Kim, Yun-Gi and Cascalho, Marilia and Vallance, Bruce A. and Puente, Jos{\'{e}} L. and N{\'{u}}{\~{n}}ez, Gabriel},
doi = {10.1016/j.chom.2015.04.001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kamada et al. - Humoral Immunity in the Gut Selectively Targets Phenotypically Virulent Attaching-and-Effacing Bacteria for Intraluminal.pdf:pdf},
issn = {19313128},
journal = {Cell Host {\&} Microbe},
keywords = {IgG,antibodies},
mendeley-tags = {IgG,antibodies},
pages = {617--627},
title = {{Humoral Immunity in the Gut Selectively Targets Phenotypically Virulent Attaching-and-Effacing Bacteria for Intraluminal Elimination}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1931312815001596},
year = {2015}
}
@article{Sauer2004,
abstract = {Bacterial pathogens utilize the chaperone-usher pathway to assemble extracellular multi-subunit fibers essential for virulence. The periplasmic chaperone facilitates the initial folding of fiber subunits but then traps them in activated folding transition states. Chaperone dissociation releases the folding energy that drives subunit incorporation into the fiber, which grows through a pore formed by the outer-membrane usher.},
author = {Sauer, Frederic G and Remaut, Han and Hultgren, Scott J and Waksman, Gabriel},
doi = {10.1016/j.bbamcr.2004.02.010},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sauer et al. - Fiber assembly by the chaperone-usher pathway. - 2004.pdf:pdf},
issn = {0006-3002},
journal = {Biochimica et biophysica acta},
keywords = {Bacterial Proteins,Bacterial Proteins: physiology,Fimbriae Proteins,Fimbriae Proteins: metabolism,Fimbriae Proteins: physiology,Fimbriae, Bacterial,Fimbriae, Bacterial: metabolism,Gram-Negative Bacteria,Gram-Negative Bacteria: physiology,Molecular Chaperones,Molecular Chaperones: genetics,Molecular Chaperones: physiology,Protein Conformation},
month = {nov},
number = {1-3},
pages = {259--67},
pmid = {15546670},
title = {{Fiber assembly by the chaperone-usher pathway.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15546670},
volume = {1694},
year = {2004}
}
@book{kim1991microhydrodynamics,
author = {Kim, S and Karrila, S J},
isbn = {9780750691734},
publisher = {Butterworth-Heinemann},
series = {Butterworth-Heinemann series in chemical engineering},
title = {{Microhydrodynamics: principles and selected applications}},
url = {http://books.google.se/books?id=P{\_}VQAAAAMAAJ},
year = {1991}
}
@article{Morrison2015,
author = {Morrison, Chris},
doi = {10.1038/nrd4770},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Morrison - Antibacterial antibodies gain traction - 2015.pdf:pdf},
issn = {1474-1776},
journal = {Nature Reviews Drug Discovery},
keywords = {IgG,antibodies},
mendeley-tags = {IgG,antibodies},
number = {11},
pages = {737--738},
publisher = {Nature Publishing Group},
title = {{Antibacterial antibodies gain traction}},
url = {http://www.nature.com/doifinder/10.1038/nrd4770},
volume = {14},
year = {2015}
}
@book{Peterman2010,
abstract = {The technically challenging field of single-molecule biophysics has established itself in the last decade by granting access to detailed information about the fate of individual biomolecules, unattainable in traditional biochemical assays. The appeal of single-molecule methods lies in the directness of the information obtained from individual biomolecules. Technological improvements in single-molecule methods have made it possible to combine optical tweezers, fluorescence microscopy, and microfluidic flow systems. Such a combination of techniques has opened new possibilities to study complex biochemical reactions on the single-molecule level. In this chapter, we provide general considerations for the development of a combined optical trapping, fluorescence microscopy, and microfluidics instrument, along with methods to solve technical issues that are critical for designing successful experiments. Finally, we present several experiments to illustrate the power of this combination of techniques.},
author = {Peterman, Erwin J G and Gross, Peter and Wuite, Gijs J L},
booktitle = {Single Molecule Tools Part BSuperResolution Particle Tracking Multiparameter and Force Based Methods},
doi = {10.1016/S0076-6879(10)75017-5},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Peterman, Gross, Wuite - Combining Optical Tweezers , Single-Molecule Fluorescence Microscopy , and Microfluidics for Studies of DNA – P.pdf:pdf},
issn = {00766879},
number = {10},
pages = {427--453},
pmid = {20627167},
publisher = {Elsevier Inc.},
title = {{Combining Optical Tweezers , Single-Molecule Fluorescence Microscopy , and Microfluidics for Studies of DNA – Protein Interactions}},
url = {http://dx.doi.org/10.1016/S0076-6879(10)75017-5},
volume = {475},
year = {2010}
}
@article{Mu2006a,
author = {Mu, X-Q and Savarino, Stephen J and Akay, Y and McVeigh, A and Cassels, F and Bullitt, Esther},
doi = {10.1017/S1431927606061411},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mu et al. - Structural Features of Colonization Factor Antigen I (CFAI) Pili (Fimbriae) of Enterotoxigenic Escherichia coli - 2006.pdf:pdf},
issn = {1431-9276},
journal = {Microscopy and Microanalysis},
month = {jul},
number = {S02},
pages = {356},
title = {{Structural Features of Colonization Factor Antigen I (CFA/I) Pili (Fimbriae) of Enterotoxigenic Escherichia coli}},
url = {http://www.journals.cambridge.org/abstract{\_}S1431927606061411},
volume = {12},
year = {2006}
}
@article{Kim1987a,
annote = {Kim, j moin, p moser, r},
author = {Kim, J and Moin, P and Moser, R},
doi = {10.1017/s0022112087000892},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kim, Moin, Moser - Turbulence statistics in fully-developed channel flow at low reynolds-number - 1987.pdf:pdf},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
pages = {133--166},
title = {{Turbulence statistics in fully-developed channel flow at low reynolds-number}},
url = {<Go to ISI>://WOS:A1987H239500008},
volume = {177},
year = {1987}
}
@article{Andersson2006d,
abstract = {Instrumentationand methodologies for single molecule force spectroscopy on bacterial adhesionorganelles by the use of force measuring optical tweezers havebeen developed. A thorough study of the biomechanical properties offimbrial adhesion organelles expressed by uropathogenic E. coli, so-called pili,is presented. Steady-state as well as dynamic force measurements onP pili, expressed by E. coli causing pyelonephritis, have revealed,among other things, various unfolding and refolding properties of thehelical structure of P pili, the PapA rod. Based onthese properties an energy landscape model has been constructed bywhich specific biophysical properties of the PapA rod have beenextracted, e.g. the number of subunits, the length of asingle pilus, bond lengths and activation energies for bond openingand closure. Moreover, long time repetitive measurements have shown thatthe rod can be unfolded and refolded repetitive times withoutlosing its intrinsic properties. These properties are believed to beof importance for the bacteria's ability to maintain close contactwith host cells during initial infections. The results presented areconsidered to be of importance for the field of biopolymersin general and the development of new pharmaceuticals towards urinarytract infections in particular. The results show furthermore that themethodology can be used to gain knowledge of the intrinsicbiomechanical function of adhesion organelles. The instrumentation is currently usedfor characterization of type 1 pili, expressed by E. colicausing cystitis, i.e. infections in the bladder. The first forcespectrometry investigations of these pili will be presented. ©2006 COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.},
address = {San Diego, CA, USA},
author = {Andersson, Magnus and Axner, Ove and Uhlin, Bernt Eric and F{\"{a}}llman, Erik},
editor = {Dholakia, Kishan and Spalding, Gabriel C.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - Optical tweezers for single molecule force spectroscopy on bacterial adhesion organelles - 2006.pdf:pdf},
journal = {Optical Trapping and Optical Micromanipulation III},
month = {aug},
number = {1},
pages = {632620--12},
publisher = {SPIE},
shorttitle = {Proc. SPIE},
title = {{Optical tweezers for single molecule force spectroscopy on bacterial adhesion organelles}},
url = {http://link.aip.org/link/?PSI/6326/632620/1},
volume = {6326},
year = {2006}
}
@article{Ruggeri2006,
abstract = {Platelet aggregation, which contributes to bleeding arrest and also to thrombovascular disorders, is thought to initiate after signaling-induced activation. We found that this paradigm does not apply under blood flow conditions comparable to those existing in stenotic coronary arteries. Platelets interacting with immobilized von Willebrand factor (VWF) aggregate independently of activation when soluble VWF is present and the shear rate exceeds 10 000 s(-1) (shear stress = 400 dyn/cm(2)). Above this threshold, active A1 domains become exposed in soluble VWF multimers and can bind to glycoprotein Ibalpha, promoting additional platelet recruitment. Aggregates thus formed are unstable until the shear rate approaches 20 000 s(-1) (shear stress = 800 dyn/cm.(2)). Above this threshold, adherent platelets at the interface of surface-immobilized and membrane-bound VWF are stretched into elongated structures and become the core of aggregates that can persist on the surface for minutes. When isolated dimeric A1 domain is present instead of native VWF multimers, activation-independent platelet aggregation occurs without requiring shear stress above a threshold level, but aggregates never become firmly attached to the surface and progressively disaggregate as shear rate exceeds 6000 s(-1). Platelet and VWF modulation by hydrodynamic force is a mechanism for activation-independent aggregation that may support thrombotic arterial occlusion.},
author = {Ruggeri, Zaverio M and Orje, Jennifer N and Habermann, Rolf and Federici, Augusto B and Reininger, Armin J},
doi = {10.1182/blood-2006-04-011551},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ruggeri et al. - Activation-independent platelet adhesion and aggregation under elevated shear stress. - 2006.pdf:pdf},
issn = {0006-4971},
journal = {Blood},
keywords = {Blood Platelets,Blood Platelets: physiology,Blood Platelets: ultrastructure,Electron,Hemorheology,Humans,Mechanical,Membrane Glycoproteins,Membrane Proteins,Membrane Proteins: metabolism,Microscopy,Multiprotein Complexes,Platelet Activation,Platelet Adhesiveness,Platelet Adhesiveness: physiology,Platelet Aggregation,Platelet Aggregation: physiology,Protein Binding,Protein Structure,Scanning,Solubility,Stress,Tertiary,paper3,von Willebrand Factor,von Willebrand Factor: chemistry,von Willebrand Factor: metabolism},
mendeley-tags = {paper3},
month = {sep},
number = {6},
pages = {1903--10},
pmid = {16772609},
title = {{Activation-independent platelet adhesion and aggregation under elevated shear stress.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1895550{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {108},
year = {2006}
}
@article{Liu2010a,
abstract = {Scope: Atomic force microscopy (AFM) was used to directly measure the nanoscale adhesion forces between P-fimbriated Escherichia coli (E. coli) and human uroepithelial cells exposed to cranberry juice, in order to reveal the molecular mechanisms by which cranberry juice cocktail (CJC) affects bacterial adhesion.Methods and results: Bacterial cell probes were created by attaching P-fimbriated E. coli HB101pDC1 or non-fimbriated E. coli HB101 to AFM tips, and the cellular probes were used to directly measure the adhesion forces between E. coli and uroepithelial cells in solutions containing: 0, 2.5, 5, 10, and 27 wt{\%} CJC. Macroscale attachment of E. coli to uroepithelial cells was measured and correlated to nanoscale adhesion force measurements. The adhesion forces between E. coli HB101pDC1 and uroepithelial cells were dose-dependent, and decreased from 9.32+/-2.37 nN in the absence of CJC to 0.75+/-0.19 nN in 27 wt{\%} CJC. Adhesion forces between E. coli HB101 and uroepithelial cells were low in buffer (0.74+/-0.18 nN), and did not change significantly in CJC (0.78+/-0.18 nN in 27 wt{\%} CJC; P=0.794).Conclusion: Our study shows that CJC significantly decreases nanoscale adhesion forces between P-fimbriated E. coli and uroepithelial cells.},
author = {Liu, Yatao and Pinz{\'{o}}n-Arango, Paola a and Gallardo-Moreno, Amparo M and Camesano, Terri a},
doi = {10.1002/mnfr.200900535},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Liu et al. - Direct adhesion force measurements between E. coli and human uroepithelial cells in cranberry juice cocktail. - 2010.pdf:pdf},
issn = {1613-4133},
journal = {Molecular nutrition {\&} food research},
keywords = {2009,2010,april 6,atomic force microscopy,bacterial adhesion,cranberry,november 6,received,revised,uroepithelial cell},
month = {jun},
pages = {1744--1752},
pmid = {20568234},
title = {{Direct adhesion force measurements between E. coli and human uroepithelial cells in cranberry juice cocktail.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20568234},
year = {2010}
}
@article{Huang2012,
author = {Huang, Yong-Huai and Chung, Kuo-Liang and Yang, Wei-Ning and Chiu, Shih-Hsuan},
doi = {10.1016/j.patrec.2012.06.016},
issn = {01678655},
journal = {Pattern Recognition Letters},
month = {dec},
number = {16},
pages = {2071--2076},
publisher = {Elsevier B.V.},
title = {{Efficient symmetry-based screening strategy to speed up randomized circle-detection}},
volume = {33},
year = {2012}
}
@article{Mullard2011,
author = {Mullard, Asher},
doi = {10.1038/nrd3545},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mullard - Reliability of 'new drug target' claims called into question. - 2011.pdf:pdf},
issn = {1474-1784},
journal = {Nature reviews. Drug discovery},
month = {jan},
number = {9},
pages = {643--4},
pmid = {21878966},
title = {{Reliability of 'new drug target' claims called into question.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21878966},
volume = {10},
year = {2011}
}
@article{Evans1978a,
author = {Evans, D G and Jr, D J Evans and Tjoa, W S and Dupont, H L},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans et al. - Detection and characterization of colonization factor of enterotoxigenic Escherichia coli isolated from adults with Detec.pdf:pdf},
journal = {Infect. Immun.},
number = {2},
pages = {727--736},
title = {{Detection and characterization of colonization factor of enterotoxigenic Escherichia coli isolated from adults with Detection and Characterization of Colonization Factor of Enterotoxigenic Escherichia coli Isolated from Adults with Diarrhea}},
volume = {19},
year = {1978}
}
@article{Touhami2006,
author = {Touhami, Ahmed and Jericho, M.H. and Boyd, J.M. and Beveridge, T.J.},
doi = {10.1128/JB.188.2.370},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Touhami et al. - Nanoscale characterization and determination of adhesion forces of Pseudomonas aeruginosa pili by using atomic force mi.pdf:pdf},
issn = {0021-9193},
journal = {Journal of bacteriology},
number = {2},
pages = {370},
publisher = {Am Soc Microbiol},
title = {{Nanoscale characterization and determination of adhesion forces of Pseudomonas aeruginosa pili by using atomic force microscopy}},
url = {http://jb.asm.org/cgi/content/abstract/188/2/370},
volume = {188},
year = {2006}
}
@article{Brandner2006,
author = {Brandner, Birgit and Norrefeldt, Martin},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Brandner, Norrefeldt - Explosives Detection by LI-MS and Explosives Detection by LI-MS and Resonance Raman spectroscopy Resonance Raman.pdf:pdf},
journal = {Time},
number = {December},
title = {{Explosives Detection by LI-MS and Explosives Detection by LI-MS and Resonance Raman spectroscopy Resonance Raman spectroscopy Explosives Detection by LI-MS and Resonance Raman spectroscopy}},
year = {2006}
}
@article{Puorger2011,
abstract = {Filamentous type 1 pili are responsible for attachment of uropathogenic Escherichia coli strains to host cells. They consist of a linear tip fibrillum and a helical rod formed by up to 3000 copies of the main structural pilus subunit FimA. The subunits in the pilus interact via donor strand complementation, where the incomplete, immunoglobulin-like fold of each subunit is complemented by an N-terminal donor strand of the subsequent subunit. Here, we show that folding of FimA occurs at an extremely slow rate (half-life: 1.6 h) and is catalyzed more than 400-fold by the pilus chaperone FimC. Moreover, FimA is capable of intramolecular self-complementation via its own donor strand, as evidenced by the loss of folding competence upon donor strand deletion. Folded FimA is an assembly-incompetent monomer of low thermodynamic stability (-10.1 kJ mol(-1)) that can be rescued for pilus assembly at 37 °C because FimC selectively pulls the fraction of unfolded FimA molecules from the FimA folding equilibrium and allows FimA refolding on its surface. Elongation of FimA at the C-terminus by its own donor strand generated a self-complemented variant (FimAa) with alternative folding possibilities that spontaneously adopts the more stable conformation (-85.0 kJ mol(-1)) in which the C-terminal donor strand is inserted in the opposite orientation relative to that in FimA. The solved NMR structure of FimAa revealed extensive $\beta$-sheet hydrogen bonding between the FimA pilin domain and the C-terminal donor strand and provides the basis for reconstruction of an atomic model of the pilus rod.},
author = {Puorger, Chasper and Vetsch, Michael and Wider, Gerhard and Glockshuber, Rudi},
doi = {10.1016/j.jmb.2011.07.044},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Puorger et al. - Structure, Folding and Stability of FimA, the Main Structural Subunit of Type 1 Pili from Uropathogenic Escherichia col.pdf:pdf},
issn = {1089-8638},
journal = {Journal of molecular biology},
keywords = {FimA,alternative folding possibilities,donor strand complementation,protein folding,type 1 pilus assembly},
month = {sep},
number = {3},
pages = {520--35},
pmid = {21816158},
publisher = {Elsevier B.V.},
title = {{Structure, Folding and Stability of FimA, the Main Structural Subunit of Type 1 Pili from Uropathogenic Escherichia coli Strains.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21816158},
volume = {412},
year = {2011}
}
@article{Busscher2006,
author = {Busscher, Henk J and Mei, Henny C Van Der},
doi = {10.1128/CMR.19.1.127},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Busscher, Mei - Microbial Adhesion in Flow Displacement Systems - 2006.pdf:pdf},
journal = {Society},
number = {1},
pages = {127--141},
title = {{Microbial Adhesion in Flow Displacement Systems}},
volume = {19},
year = {2006}
}
@article{Monteiro2013,
author = {Monteiro, Diana C F and Kamdoum, Wilfride V Petnga and Paci, Emanuele},
doi = {10.1371/journal.pone.0063065},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Monteiro, Kamdoum, Paci - Growth Kinetics of Bacterial Pili from Pairwise Pilin Association Rates - 2013.pdf:pdf},
journal = {PLoS ONE},
number = {5},
pages = {8--12},
title = {{Growth Kinetics of Bacterial Pili from Pairwise Pilin Association Rates}},
volume = {8},
year = {2013}
}
@article{Li2007b,
abstract = {CfaE is the minor, tip-localized adhesive subunit of colonization factor antigen I fimbriae (CFA/I) of enterotoxigenic Escherichia coli and is thought to be essential for the attachment of enterotoxigenic E. coli to the human small intestine early in diarrhea pathogenesis. The crystal structure of an in cis donor strand complemented CfaE was determined, providing the first atomic view of a fimbrial subunit assembled by the alternate chaperone pathway. The in cis donor strand complemented variant of CfaE structure consists of an N-terminal adhesin domain and a C-terminal pilin domain of similar size, each featuring a variable immunoglobulin-like fold. Extensive interactions exist between the two domains and appear to rigidify the molecule. The upper surface of the adhesin domain distal to the pilin domain reveals a depression consisting of conserved residues including Arg(181), previously shown to be necessary for erythrocyte adhesion. Mutational analysis revealed a cluster of conserved, positively charged residues that are required for CFA/I-mediated hemagglutination, implicating this as the receptor-binding pocket. Mutations in a few subclass-specific residues that surround the cluster displayed differential effects on the two red cell species used in hemagglutination, suggesting that these residues play a role in host or cell specificity. The C-terminal donor strand derived from the major subunit CfaB is folded as a beta-strand and fits into a hydrophobic groove in the pilin domain to complete the immunoglobulin fold. The location of this well ordered donor strand suggests the positioning and orientation of the subjacent major fimbrial subunit CfaB in the native assembly of CFA/I fimbriae.},
author = {Li, Yong Fu and Poole, Steven and Rasulova, Fatima and McVeigh, Annette L. and Savarino, Stephen J. and Xia, Di},
doi = {10.1074/jbc.M700921200},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Li et al. - A receptor-binding site as revealed by the crystal structure of CfaE, the colonization factor antigen I fimbrial adhesin (3).pdf:pdf},
isbn = {0021-9258 (Print)},
issn = {00219258},
journal = {Journal of Biological Chemistry},
number = {33},
pages = {23970--23980},
pmid = {17569668},
title = {{A receptor-binding site as revealed by the crystal structure of CfaE, the colonization factor antigen I fimbrial adhesin of enterotoxigenic Escherichia coli}},
volume = {282},
year = {2007}
}
@article{Wullt2002,
author = {Wullt, Bj{\"{o}}rn and Bergsten, G{\"{o}}ran and Samuelsson, Martin and Svanborg, Catharina},
doi = {dx.doi.org/10.1016/S0924-8579(02)00103-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wullt et al. - The role of P fimbriae for Escherichia coli establishment and mucosal inflammation in the human urinary tract - 2002.pdf:pdf},
journal = {International Journal of Antimicrobial Agents},
keywords = {electron microscopy,hemagglutination,urinary tract infections},
pages = {522--538},
title = {{The role of P fimbriae for Escherichia coli establishment and mucosal inflammation in the human urinary tract}},
volume = {19},
year = {2002}
}
@article{Karmous2011,
author = {Karmous, Mohamed Salah},
doi = {10.4236/wjnse.2011.12009},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Karmous - Theoretical Study of Kaolinite Structure Energy Minimization and Crystal Properties - 2011.pdf:pdf},
issn = {2161-4954},
journal = {World Journal of Nano Science and Engineering},
keywords = {calculation,crystal properties,elasticity,energy,gulp,kaolinite},
number = {02},
pages = {62--66},
title = {{Theoretical Study of Kaolinite Structure; Energy Minimization and Crystal Properties}},
url = {http://www.scirp.org/journal/PaperDownload.aspx?DOI=10.4236/wjnse.2011.12009},
volume = {01},
year = {2011}
}
@article{Castelain2009a,
abstract = {Bacterial adhesion organelles, known as fimbria or pili, are expressed by gram-positive as well as gram-negative bacteria families. These appendages play a key role in the first steps of the invasion and infection processes, and they therefore provide bacteria with pathogenic abilities. To improve the knowledge of pili-mediated bacterial adhesion to host cells and how these pili behave under the presence of an external force, we first characterize, using force measuring optical tweezers, open coil-like T4 pili expressed by gram-positive Streptococcus pneumoniae with respect to their biomechanical properties. It is shown that their elongation behavior can be well described by the worm-like chain model and that they possess a large degree of flexibility. Their properties are then compared with those of helix-like pili expressed by gram-negative uropathogenic Escherichia coli (UPEC), which have different pili architecture. The differences suggest that these two types of pili have distinctly dissimilar mechanisms to adhere and sustain external forces. Helix-like pili expressed by UPEC bacteria adhere to host cells by single adhesins located at the distal end of the pili while their helix-like structures act as shock absorbers to dampen the irregularly shear forces induced by urine flow and to increase the cooperativity of the pili ensemble, whereas open coil-like pili expressed by S. pneumoniae adhere to cells by a multitude of adhesins distributed along the pili. It is hypothesized that these two types of pili represent different strategies of adhering to host cells in the presence of external forces. When exposed to significant forces, bacteria expressing helix-like pili remain attached by distributing the external force among a multitude of pili, whereas bacteria expressing open coil-like pili sustain large forces primarily by their multitude of binding adhesins which presumably detach sequentially.},
author = {Castelain, Micka{\"{e}}l and Koutris, Efstratios and Andersson, Magnus and Wiklund, Krister and Bj{\"{o}}rnham, Oscar and Schedin, Staffan and Axner, Ove},
doi = {10.1002/cphc.200900195},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Castelain et al. - Characterization of the biomechanical properties of T4 pili expressed by Streptococcus pneumoniae--a comparison betwe.pdf:pdf},
issn = {1439-7641},
journal = {ChemPhysChem},
keywords = {Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: chemistry,Bacterial: physiology,Biomechanics,Fimbriae,Optical Tweezers,Streptococcus pneumoniae,Streptococcus pneumoniae: chemistry,Streptococcus pneumoniae: physiology},
month = {jul},
number = {9-10},
pages = {1533--1540},
pmid = {19565578},
publisher = {WILEY-V C H VERLAG GMBH},
title = {{Characterization of the biomechanical properties of T4 pili expressed by Streptococcus pneumoniae--a comparison between helix-like and open coil-like pili.}},
url = {http://apps.isiknowledge.com/full{\_}record.do?product=WOS{\&}search{\_}mode=GeneralSearch{\&}qid=1{\&}SID=S1MHGALlH8ko5hHPpbg{\&}page=1{\&}doc=1},
volume = {10},
year = {2009}
}
@article{Ptashne1966,
author = {Ptashne, Mark},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ptashne - SoniCate Supernatant - 1966.pdf:pdf},
pages = {306--313},
title = {{SoniCate Supernatant}},
year = {1966}
}
@article{Ghunaim2014,
abstract = {Avian pathogenic Escherichia coli (APEC) is one of the most economically devastating pathogens affecting the poultry industry. This group of extra-intestinal E. coli causes a variety of clinical conditions including airsacculitis and cellulitis. The economic impact of APEC is mainly due to mortality, slower growth rates, and carcass downgrading. In commercial broiler operations, APEC infections are controlled indirectly by vaccination against other respiratory diseases and minimizing stress conditions, and directly by administration of antimicrobial agents to suppress the infection in already infected flocks. The fact that most APEC strains possess some common virulence factors suggests that an effective vaccine against APEC is a viable option. The most important virulence factors that have been investigated over the years include type I and P fimbriae, aerobactin iron-acquisition system, and serum resistance traits. Despite the potential for developing an efficacious vaccine to combat this economically important poultry disease, several obstacles hinder such efforts. Those obstacles include the cost, vaccine delivery method and timing of vaccination as the birds should be immune to APEC by 21 days of age. Herein, we review the various attempts to develop an effective vaccine against the respiratory form of APEC diseases in poultry. We also discuss in-depth the potentials and limitations of such vaccines.},
author = {Ghunaim, Haitham and Abu-Madi, Marwan Abdelhamid and Kariyawasam, Subhashinie},
doi = {10.1016/j.vetmic.2014.04.019},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ghunaim, Abu-Madi, Kariyawasam - Advances in vaccination against avian pathogenic Escherichia coli respiratory disease Potentials and li.pdf:pdf},
issn = {1873-2542},
journal = {Veterinary microbiology},
month = {may},
pmid = {24878325},
publisher = {Elsevier B.V.},
title = {{Advances in vaccination against avian pathogenic Escherichia coli respiratory disease: Potentials and limitations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24878325},
year = {2014}
}
@article{Ashkin1987b,
abstract = {Optical trapping and manipulation of viruses and bacteria by laser radiation pressure were demonstrated with single-beam gradient traps. Individual tobacco mosaic viruses and dense oriented arrays of viruses were trapped in aqueous solution with no apparent damage using approximately 120 milliwatts of argon laser power. Trapping and manipulation of single live motile bacteria and Escherichia coli bacteria were also demonstrated in a high-resolution microscope at powers of a few milliwatts.},
author = {Ashkin, A and Dziedzic, J M},
doi = {10.1126/science.3547653},
isbn = {0036-8075},
issn = {0036-8075},
journal = {Science (New York, N.Y.)},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
number = {4795},
pages = {1517--1520},
pmid = {3547653},
title = {{Optical trapping and manipulation of viruses and bacteria.}},
volume = {235},
year = {1987}
}
@article{Jia2011a,
author = {Jia, Li-qin and Peng, Cheng-zhang and Liu, Hong-min and Wang, Zhi-heng},
doi = {10.1109/CISP.2011.6100372},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jia et al. - A fast randomized circle detection algorithm - 2011.pdf:pdf},
isbn = {978-1-4244-9306-7},
journal = {2011 4th International Congress on Image and Signal Processing},
month = {oct},
pages = {820--823},
publisher = {Ieee},
title = {{A fast randomized circle detection algorithm}},
year = {2011}
}
@article{Sheng2006,
abstract = {Better understanding of particle-particle and particle-fluid interactions requires accurate 3D measurements of particle distributions and motions. We introduce the application of in-line digital holographic microscopy as a viable tool for measuring distributions of dense micrometer (3.2 microm) and submicrometer (0.75 microm) particles in a liquid solution with large depths of 1-10 mm. By recording a magnified hologram, we obtain a depth of field of approximately 1000 times the object diameter and a reduced depth of focus of approximately 10 particle diameters, both representing substantial improvements compared to a conventional microscope and in-line holography. Quantitative information on depth of field, depth of focus, and axial resolution is provided. We demonstrate that digital holographic microscopy can resolve the locations of several thousand particles and can measure their motions and trajectories using cinematographic holography. A sample trajectory and detailed morphological information of a free-swimming copepod nauplius are presented.},
author = {Sheng, Jian and Malkiel, Edwin and Katz, Joseph},
doi = {10.1364/AO.45.003893},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sheng, Malkiel, Katz - Digital holographic microscope for measuring three-dimensional particle distributions and motions. - 2006.pdf:pdf},
isbn = {0003-6935},
issn = {0003-6935},
journal = {Applied optics},
number = {16},
pages = {3893--3901},
pmid = {16724155},
title = {{Digital holographic microscope for measuring three-dimensional particle distributions and motions.}},
volume = {45},
year = {2006}
}
@article{Roux2004,
abstract = {2G12 is one of only a few cloned antibodies with broadly neutralizing specificity to HIV-1 envelope proteins. Crystallographic and electron microscopic (EM) data showed that the Fab arms are locked together via a novel VH domain exchange. Both the conventional and the unprecedented additional VH-VH antigen binding sites show specificity for high mannose oligosaccharides on the silent face of gp120. We have now extended the EM and biochemical analysis of 2G12. Unligated 2G12 IgG1 molecules clearly show paired (parallel attached) Fab arms in the "doughnut" configuration attached to the Fc both in individual and computationally averaged images. A minority of the IgG molecules in the 2G12 prep showed the open "Y" configuration of conventional IgG. The averaged EM image compares well to the atomic structure model of 2G12. Papain digests of 2G12 yielded paired Fab arms (Fab dimer), as observed by EM, which dissociated into Fab-sized fragments in non-reducing SDS-PAGE. Purified 2G12 reduced and alkylated H and L chains can reassociate to form IgG molecules with the Fab dimer configuration and can combine with L and H chains from conventional human IgG to form hybrid molecules. 2G12 is heavily aggregated following brief acid exposure possibly as a result of its unique structure. A model of the aggregation process is proposed. An anti-Id MAb was shown by EM to react with neither the conventional nor additional antigen binding sites, but bound to the lateral faces of the Fab arms of intact, reduced and alkylated, and reconstructed 2G12 molecules. Efforts to identify IgG molecules with a similar intertwined Fab dimer structure in a large IgG pool were unsuccessful.},
author = {Roux, K H and Zhu, Ping and Seavy, Margaret and Katinger, Hermann and Kunert, Renate and Seamon, Vanessa},
doi = {10.1016/j.molimm.2004.05.008},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Roux et al. - Electron microscopic and immunochemical analysis of the broadly neutralizing HIV-1-specific, anti-carbohydrate antibody, 2.pdf:pdf},
issn = {0161-5890},
journal = {Molecular immunology},
keywords = {Antibodies, Monoclonal,Antibodies, Monoclonal: immunology,Antibodies, Monoclonal: ultrastructure,Carbohydrates,Carbohydrates: immunology,HIV-1,HIV-1: immunology,Humans,Immunoglobulin Fab Fragments,Immunoglobulin Fab Fragments: immunology,Immunoglobulin Fc Fragments,Immunoglobulin Fc Fragments: immunology,Immunoglobulin Fc Fragments: ultrastructure,Immunohistochemistry,Microscopy, Electron},
month = {aug},
number = {10},
pages = {1001--11},
pmid = {15302162},
title = {{Electron microscopic and immunochemical analysis of the broadly neutralizing HIV-1-specific, anti-carbohydrate antibody, 2G12.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15302162},
volume = {41},
year = {2004}
}
@article{Azegami2014,
abstract = {The mucosal surface is the largest route through which pathogens enter the human body. To control the outbreak of mucosal infectious diseases, we must use our knowledge of the mucosal immune system to create vaccines that elicit protective mucosal and systemic immunity. Mucosal vaccines have advantages over traditional injectable vaccines in that they not only induce effective mucosal immune responses, but they also do not cause physical or psychological discomfort. Mucosal vaccines currently licensed for human use include oral vaccines against Vibrio cholerae, Salmonella typhi, poliovirus and rotavirus, and nasal vaccines against influenza virus. To further improve the existing vaccines, it will be necessary to develop novel vaccine production, storage and delivery systems through innovative strategies derived from interdisciplinary scientific research. Our accumulated knowledge of the innate and acquired arms of the mucosal immune system and the recent scientific and technical advancements in the fields of molecular biology, plant biology, bio-engineering and chemical engineering, genome biology and systems biology have created a unique research and development platform for the development of the next generation of mucosal vaccines. This review summarizes the current perspectives and future directions of mucosal vaccine development with emphasis on oral and nasal vaccines for the control of infectious diseases.},
author = {Azegami, Tatsuhiko and Yuki, Yoshikazu and Kiyono, Hiroshi},
doi = {10.1093/intimm/dxu063},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Azegami, Yuki, Kiyono - Challenges in mucosal vaccines for the control of infectious diseases. - 2014.pdf:pdf},
issn = {1460-2377},
journal = {International immunology},
keywords = {mucorice,nasal vaccine,oral vaccine,rice-based vaccine},
month = {sep},
number = {9},
pages = {517--528},
pmid = {24914172},
title = {{Challenges in mucosal vaccines for the control of infectious diseases.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24914172},
volume = {26},
year = {2014}
}
@article{Rusciano2008,
abstract = {This review presents the development of a Raman Tweezers system for detecting hemoglobin-related blood disorders at a single cell level. The study demonstrates that the molecular fingerprint insight provided by Raman analysis holds great promise for distinguishing between healthy and diseased cells in the field of biomedicine. Herein a Raman Tweezers system has been applied to investigate the effects of thalassemia, a blood disease quite diffuse in the Mediterranean Sea region. By resonant excitation of hemoglobin Raman bands, we examined the oxygenation capability of normal, alpha- and beta-thalassemic erythrocytes. A reduction of this fundamental red blood cell function, particularly severe for beta-thalassemia, has been found. Raman spectroscopy was also used to draw hemoglobin distribution inside single erythrocytes; the results confirmed the characteristic anomaly (target shape), occurring in thalassemia and some other blood disorders. The success of resonance Raman spectroscopy for thalassemia detection reported in this review provide an interesting starting point to explore the application of a Raman Tweezers system in the analysis of several blood disorders.},
author = {Rusciano, Giulia and {De Luca}, Anna C. and Pesce, Giuseppe and Sasso, Antonio},
doi = {10.3390/s8127818},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rusciano et al. - Raman Tweezers as a Diagnostic Tool of Hemoglobin-Related Blood Disorders - 2008.pdf:pdf},
issn = {1424-8220},
journal = {Sensors},
keywords = {Hb-related disorders.,Tweezers,biosensor,thalassemia},
month = {dec},
number = {12},
pages = {7818--7832},
title = {{Raman Tweezers as a Diagnostic Tool of Hemoglobin-Related Blood Disorders}},
url = {http://www.mdpi.com/1424-8220/8/12/7818/},
volume = {8},
year = {2008}
}
@article{Rusconi2014,
abstract = {... Journal name: Nature Physics Year published: (2014) DOI: doi:10.1038/nphys2883 Received 22 May 2013 Accepted 08 January 2014 Published online 23 February 2014 ... {\&} Stocker , R. Fluid mechanics of planktonic microorganisms. Annu. Rev. Fluid Mech. 44, 373–400 (2012). ... $\backslash$n},
author = {Rusconi, Roberto and Guasto, Jeffrey S and Stocker, Roman},
doi = {10.1038/NPHYS2883},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rusconi, Guasto, Stocker - Bacterial transport suppressed by fluid shear - 2014.pdf:pdf},
issn = {1745-2473},
journal = {Nature Physics},
number = {3},
pages = {212--217},
title = {{Bacterial transport suppressed by fluid shear}},
url = {http://www.nature.com/doifinder/10.1038/nphys2883$\backslash$npapers2://publication/doi/10.1038/nphys2883},
volume = {10},
year = {2014}
}
@article{Langermann1997,
author = {Langermann, S.},
doi = {10.1126/science.276.5312.607},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Langermann - Prevention of Mucosal Escherichia coli Infection by FimH-Adhesin-Based Systemic Vaccination - 1997.pdf:pdf},
issn = {00368075},
journal = {Science},
month = {apr},
number = {5312},
pages = {607--611},
title = {{Prevention of Mucosal Escherichia coli Infection by FimH-Adhesin-Based Systemic Vaccination}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.276.5312.607},
volume = {276},
year = {1997}
}
@article{Casaburi2005,
author = {Casaburi, a and Pesce, G and Zemanek, P and Sasso, a},
doi = {10.1016/j.optcom.2005.03.029},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Casaburi et al. - Two- and three-beam interferometric optical tweezers - 2005.pdf:pdf},
isbn = {3908167612},
issn = {00304018},
journal = {Optics Communications},
keywords = {interferometric optical tweezers,mie particle,optical force,optical trapping},
month = {jul},
number = {4-6},
pages = {393--404},
title = {{Two- and three-beam interferometric optical tweezers}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0030401805002294},
volume = {251},
year = {2005}
}
@article{Hacker1993,
abstract = {S fimbrial adhesins (Sfa), which are able to recognize sialic acid-containing receptors on eukaryotic cells, are produced by Escherichia coli strains causing urinary tract infections or newborn meningitis. We recently described the cloning and molecular characterization of a determinant, termed sfaI, from the chromosome of an E. coli urinary tract infection strain. Here we present data concerning a S fimbria-specific gene cluster, designated sfaII, of an E. coli newborn meningitis strain. Like the SfaI complex, SfaII consists of the major subunit protein SfaA (16 kDa) and the minor subunit proteins SfaG (17 kDa), SfaS (15 kDa), and SfaH (29 kDa). The genes encoding the subunit proteins of SfaII were identified and sequenced. Their protein sequences were calculated from the DNA sequences and compared with those of the SfaI complex subunits. Although the sequences of the two major SfaA subunits differed markedly, the sequences of the minor subunits showed only a few amino acid exchanges (SfaG, SfaH) or were completely identical (SfaS). The introduction of a site-specific mutation into the gene sfaSII and subsequent analysis of an SfaS-negative clone indicated that sfaSII codes for the sialic acid-specific adhesin of the meninigitis isolate. These data were confirmed by the isolation and characterization of the SfaSII protein and the determination of its N-terminal amino acid sequence. The identity between the sialic acid-specific adhesins of SfaI and SfaII revealed that differences between the two Sfa complexes with respect to their capacities to agglutinate erythrocytes must result from sequence alterations of subunit proteins other than SfaS.},
author = {Hacker, J. and Kestler, H. and Hoschutzky, H. and Jann, K. and Lottspeich, F. and Korhonen, T. K.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hacker et al. - Cloning and characterization of the S fimbrial adhesin II complex of an Escherichia coli O18K1 meningitis isolate - 1993.pdf:pdf},
isbn = {0019-9567 (Print)$\backslash$r0019-9567 (Linking)},
issn = {00199567},
journal = {Infection and Immunity},
number = {2},
pages = {544--550},
pmid = {8093693},
title = {{Cloning and characterization of the S fimbrial adhesin II complex of an Escherichia coli O18:K1 meningitis isolate}},
volume = {61},
year = {1993}
}
@article{Rusconi2011,
abstract = {In most environments, such as natural aquatic systems, bacteria are found predominantly in self-organized sessile communities known as biofilms. In the presence of a significant flow, mature multispecies biofilms often develop into long filamentous structures called streamers, which can greatly influence ecosystem processes by increasing transient storage and cycling of nutrients. However, the interplay between hydrodynamic stresses and streamer formation is still unclear. Here, we show that suspended thread-like biofilms steadily develop in zigzag microchannels with different radii of curvature. Numerical simulations of a low-Reynolds-number flow around these corners indicate the presence of a secondary vortical motion whose intensity is related to the bending angle of the turn. We demonstrate that the formation of streamers is directly proportional to the intensity of the secondary flow around the corners. In addition, we show that a model of an elastic filament in a two-dimensional corner flow is able to explain how the streamers can cross fluid streamlines and connect corners located at the opposite sides of the channel.},
author = {Rusconi, Roberto and Lecuyer, Sigolene and Autrusson, Nicolas and Guglielmini, Laura and Stone, Howard a},
doi = {10.1016/j.bpj.2011.01.065},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rusconi et al. - Secondary flow as a mechanism for the formation of biofilm streamers. - 2011.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {Biofilms,Hydrodynamics,Microfluidic Analytical Techniques,Models, Biological,Pseudomonas aeruginosa,Pseudomonas aeruginosa: physiology,Time Factors,Viscosity},
month = {mar},
number = {6},
pages = {1392--9},
pmid = {21402020},
publisher = {Biophysical Society},
title = {{Secondary flow as a mechanism for the formation of biofilm streamers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3059581{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {100},
year = {2011}
}
@article{Neuman1999,
abstract = {Optical tweezers (infrared laser-based optical traps) have emerged as a powerful tool in molecular and cell biology. However, their usefulness has been limited, particularly in vivo, by the potential for damage to specimens resulting from the trapping laser. Relatively little is known about the origin of this phenomenon. Here we employed a wavelength-tunable optical trap in which the microscope objective transmission was fully characterized throughout the near infrared, in conjunction with a sensitive, rotating bacterial cell assay. Single cells of Escherichia coli were tethered to a glass coverslip by means of a single flagellum: such cells rotate at rates proportional to their transmembrane proton potential (Manson et al.,1980. J. Mol. Biol. 138:541-561). Monitoring the rotation rates of cells subjected to laser illumination permits a rapid and quantitative measure of their metabolic state. Employing this assay, we characterized photodamage throughout the near-infrared region favored for optical trapping (790-1064 nm). The action spectrum for photodamage exhibits minima at 830 and 970 nm, and maxima at 870 and 930 nm. Damage was reduced to background levels under anaerobic conditions, implicating oxygen in the photodamage pathway. The intensity dependence for photodamage was linear, supporting a single-photon process. These findings may help guide the selection of lasers and experimental protocols best suited for optical trapping work.},
author = {Neuman, K C and Chadd, E H and Liou, G F and Bergman, K and Block, S M},
doi = {10.1016/S0006-3495(99)77117-1},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Neuman et al. - Characterization of photodamage to Escherichia coli in optical traps. - 1999.pdf:pdf},
isbn = {0006-3495},
issn = {00063495},
journal = {Biophysical journal},
number = {5},
pages = {2856--2863},
pmid = {10545383},
publisher = {Elsevier},
title = {{Characterization of photodamage to Escherichia coli in optical traps.}},
url = {http://dx.doi.org/10.1016/S0006-3495(99)77117-1},
volume = {77},
year = {1999}
}
@article{Towles,
archivePrefix = {arXiv},
arxivId = {arXiv:0806.1551v2},
author = {Towles, Kevin B and Beausang, John F and Garcia, Hernan G and Phillips, Rob and Nelson, Philip C and Monte, S},
eprint = {arXiv:0806.1551v2},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Towles et al. - Supplementary Information First-principles calculation of DNA looping in tethered particle experiments - Unknown.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Towles et al. - Supplementary Information First-principles calculation of DNA looping in tethered particle experiments - Unknown.pdf:pdf},
title = {{Supplementary Information : First-principles calculation of DNA looping in tethered particle experiments}}
}
@article{Yuen1989,
author = {Yuen, H. K. and Princen, J. and Dlingworth, J. and Kittler, J.},
doi = {10.5244/C.3.29},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yuen et al. - A Comparative Study of Hough Transform Methods for Circle Finding - 1989.pdf:pdf},
journal = {Procedings of the Alvey Vision Conference 1989},
pages = {29.1--29.6},
publisher = {Alvey Vision Club},
title = {{A Comparative Study of Hough Transform Methods for Circle Finding}},
url = {http://www.bmva.org/bmvc/1989/avc-89-029.html},
year = {1989}
}
@article{Swidsinski2007,
abstract = {BACKGROUND: Migration is an important virulence factor for intestinal bacteria. However, the role of bacterial mobility in the penetration of viscous mucus and their spatial organization within the colon is relatively unknown. METHODS: Movements of fecal bacteria were assessed in gels of varying agarose concentrations and were compared with patterns of bacterial distribution observed in colons from conventional and Enterobacter cloacae-monoassociated mice. Bacteria were visualized using fluorescence in situ hybridization. RESULTS: Long curly bacteria moved best in moderate viscosity gels, short rods and cocci preferred a low viscous environment, whereas high viscosity immobilized all bacterial groups. The spatial distribution of bacteria in the murine colon was also shape- and not taxonomy-dependent, indicating the existence of vertical (surface to lumen) and longitudinal (proximal to distal colon) viscosity gradients within the mucus layer. Our results suggest that mucus viscosity is low in goblet cells, at the crypt basis and close to the intestinal lumen, whereas sites adjacent to the columnar epithelium have a high mucus viscosity. The mucus viscosity increased progressively toward the distal colon, separating bacteria selectively in the proximal colon and completely in the distal colon. CONCLUSIONS: The site-specific regulation of mucus secretion and dehydration make the mucus layer firm and impenetrable for bacteria in regions close to the intestinal mucosa but loose and lubricating in regions adjacent to the luminal contents. Selective control of mucus secretion and dehydration may prove to be a key factor in the management of chronic diseases in which intestinal pathogens are involved.},
author = {Swidsinski, Alexander and Sydora, Beate C and Doerffel, Yvonne and Loening-Baucke, Vera and Vaneechoutte, Mario and Lupicki, Maryla and Scholze, Juergen and Lochs, Herbert and Dieleman, Levinus a},
doi = {10.1002/ibd.20163},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Swidsinski et al. - Viscosity gradient within the mucus layer determines the mucosal barrier function and the spatial organization of th.pdf:pdf},
issn = {1078-0998},
journal = {Inflammatory bowel diseases},
keywords = {Animals,Colon,Colon: microbiology,Enterobacter cloacae,Enterobacter cloacae: physiology,Gels,In Situ Hybridization, Fluorescence,Intestinal Mucosa,Intestinal Mucosa: physiology,Mice,Viscosity},
month = {aug},
number = {8},
pages = {963--70},
pmid = {17455202},
title = {{Viscosity gradient within the mucus layer determines the mucosal barrier function and the spatial organization of the intestinal microbiota.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17455202},
volume = {13},
year = {2007}
}
@article{Sackmann2004,
author = {Sackmann, Erich and Seifert, Udo and Smith, Ana-Sun{\v{c}}ana},
doi = {10.1103/PhysRevLett.92.208101},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Sackmann, Seifert, Smith - Pulling Tethers from Adhered Vesicles - 2004.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {may},
number = {20},
pages = {1--4},
title = {{Pulling Tethers from Adhered Vesicles}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.92.208101},
volume = {92},
year = {2004}
}
@article{Higuchi2011a,
abstract = {We firstly demonstrate the three-dimensional (3D) measurement of a nanometer-sized sphere held in optical tweezers in water using an in-line digital holographic microscope with a green light emitting diode. Suppressing the movement with optical tweezers enabled us to detect the three-dimensional position of a polystyrene sphere with a diameter of 200 nm. The positioning resolutions of the microscope were 3.2 nm in the transverse direction and 3.4 nm in the axial direction, from the standard deviation of measurements of the 200 nm sphere fixed on glass. Changes in the Brownian motion in response to a change in the trapping laser power were measured. We also demonstrated that this holographic measurement is an effective method for determining the threshold power of the optical trapping.},
author = {Higuchi, Takayuki and Pham, Quang Duc and Hasegawa, Satoshi and Hayasaki, Yoshio},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Higuchi et al. - Three-dimensional positioning of optically trapped nanoparticles. - 2011(2).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Higuchi et al. - Three-dimensional positioning of optically trapped nanoparticles. - 2011.pdf:pdf},
issn = {1539-4522},
journal = {Applied optics},
month = {dec},
number = {34},
pages = {H183--8},
pmid = {22193006},
title = {{Three-dimensional positioning of optically trapped nanoparticles.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22193006},
volume = {50},
year = {2011}
}
@article{Roichman2006,
abstract = {We assess the influence of geometric aberrations on the in-plane performance of optical traps by studying the dynamics of trapped colloidal spheres in deliberately distorted holographic optical tweezers. The lateral stiffness of the traps turns out to be insensitive to moderate amounts of coma, astigmatism, and spherical aberration. Moreover holographic aberration correction enables us to compensate inherent shortcomings in the optical train, thereby adaptively improving its performance. We also demonstrate the effects of geometric aberrations on the intensity profiles of optical vortices, whose readily measured deformations suggest a method for rapidly estimating and correcting geometric aberrations in holographic trapping systems.},
author = {Roichman, Yael and Waldron, Alex and Gardel, Emily and Grier, David G},
doi = {10.1364/AO.45.003425},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Roichman et al. - Optical traps with geometric aberrations. - 2006.pdf:pdf},
isbn = {0003-6935},
issn = {0003-6935},
journal = {Applied Optics},
number = {15},
pages = {3425--3429},
pmid = {16708086},
title = {{Optical traps with geometric aberrations.}},
volume = {45},
year = {2006}
}
@article{Hayasaki2012,
author = {Hayasaki, Yoshio and Sato, Akira},
doi = {10.1109/ISOT.2012.6403247},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hayasaki, Sato - Holographic position measurement of nanoparticles trapped with optical tweezers - 2012.pdf:pdf},
isbn = {978-1-4673-2877-7},
journal = {2012 International Symposium on Optomechatronic Technologies (ISOT 2012)},
keywords = {digital holography,low coherence,optical tweezers},
month = {oct},
pages = {1--2},
publisher = {Ieee},
title = {{Holographic position measurement of nanoparticles trapped with optical tweezers}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6403247},
year = {2012}
}
@article{Harada1996,
abstract = {Electronic Article Available from Elsevier Science.},
author = {Harada, Yasuhiro and Asakura, Toshimitsu},
doi = {10.1016/0030-4018(95)00753-9},
isbn = {0030-4018},
issn = {00304018},
journal = {Optics Communications},
number = {5-6},
pages = {529--541},
title = {{Radiation forces on a dielectric sphere in the Rayleigh scattering regime}},
volume = {124},
year = {1996}
}
@article{Bjornham2009,
abstract = {Detailed analyses of the mechanisms that mediate binding of the uropathogenic Escherichia coli to host cells are essential, as attachment is a prerequisite for the subsequent infection process. We explore, by means of force measuring optical tweezers, the interaction between the galabiose receptor and the adhesin PapG expressed by P pili on single bacterial cells. Two variants of dynamic force spectroscopy were applied based on constant and non-linear loading force. The specific PapG-galabiose binding showed typical slip-bond behaviour in the force interval (30-100 pN) set by the pilus intrinsic biomechanical properties. Moreover, it was found that the bond has a thermodynamic off-rate and a bond length of 2.6 x 10(-3) s(-1) and 5.0 A, respectively. Consequently, the PapG-galabiose complex is significantly stronger than the internal bonds in the P pilus structure that stabilizes the helical chain-like macromolecule. This finding suggests that the specific binding is strong enough to enable the P pili rod to unfold when subjected to strong shear forces in the urinary tract. The unfolding process of the P pili rod promotes the formation of strong multipili interaction, which is important for the bacterium to maintain attachment to the host cells.},
author = {Bj{\"{o}}rnham, Oscar and Nilsson, H{\aa}kan and Andersson, Magnus and Schedin, Staffan},
doi = {10.1007/s00249-008-0376-y},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bj{\"{o}}rnham et al. - Physical properties of the specific PapG-galabiose binding in E. coli P pili-mediated adhesion. - 2009.pdf:pdf},
issn = {1432-1017},
journal = {European biophysics journal},
keywords = {Adhesins,Atomic Force,Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: chemistry,Bacterial: physiology,Biological,Disaccharides,Disaccharides: chemistry,Disaccharides: metabolism,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: cytology,Escherichia coli: metabolism,Escherichia coli: physiology,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Microscopy,Models,Optical Tweezers,Protein Binding,Protein Binding: physiology,Tensile Strength,Tensile Strength: physiology},
number = {2},
pages = {245--54},
pmid = {18923826},
title = {{Physical properties of the specific PapG-galabiose binding in E. coli P pili-mediated adhesion.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18923826},
volume = {38},
year = {2009}
}
@article{Lozano2012,
abstract = {BACKGROUND: Reliable and timely information on the leading causes of death in populations, and how these are changing, is a crucial input into health policy debates. In the Global Burden of Diseases, Injuries, and Risk Factors Study 2010 (GBD 2010), we aimed to estimate annual deaths for the world and 21 regions between 1980 and 2010 for 235 causes, with uncertainty intervals (UIs), separately by age and sex.

METHODS: We attempted to identify all available data on causes of death for 187 countries from 1980 to 2010 from vital registration, verbal autopsy, mortality surveillance, censuses, surveys, hospitals, police records, and mortuaries. We assessed data quality for completeness, diagnostic accuracy, missing data, stochastic variations, and probable causes of death. We applied six different modelling strategies to estimate cause-specific mortality trends depending on the strength of the data. For 133 causes and three special aggregates we used the Cause of Death Ensemble model (CODEm) approach, which uses four families of statistical models testing a large set of different models using different permutations of covariates. Model ensembles were developed from these component models. We assessed model performance with rigorous out-of-sample testing of prediction error and the validity of 95{\%} UIs. For 13 causes with low observed numbers of deaths, we developed negative binomial models with plausible covariates. For 27 causes for which death is rare, we modelled the higher level cause in the cause hierarchy of the GBD 2010 and then allocated deaths across component causes proportionately, estimated from all available data in the database. For selected causes (African trypanosomiasis, congenital syphilis, whooping cough, measles, typhoid and parathyroid, leishmaniasis, acute hepatitis E, and HIV/AIDS), we used natural history models based on information on incidence, prevalence, and case-fatality. We separately estimated cause fractions by aetiology for diarrhoea, lower respiratory infections, and meningitis, as well as disaggregations by subcause for chronic kidney disease, maternal disorders, cirrhosis, and liver cancer. For deaths due to collective violence and natural disasters, we used mortality shock regressions. For every cause, we estimated 95{\%} UIs that captured both parameter estimation uncertainty and uncertainty due to model specification where CODEm was used. We constrained cause-specific fractions within every age-sex group to sum to total mortality based on draws from the uncertainty distributions.

FINDINGS: In 2010, there were 52·8 million deaths globally. At the most aggregate level, communicable, maternal, neonatal, and nutritional causes were 24·9{\%} of deaths worldwide in 2010, down from 15·9 million (34·1{\%}) of 46·5 million in 1990. This decrease was largely due to decreases in mortality from diarrhoeal disease (from 2·5 to 1·4 million), lower respiratory infections (from 3·4 to 2·8 million), neonatal disorders (from 3·1 to 2·2 million), measles (from 0·63 to 0·13 million), and tetanus (from 0·27 to 0·06 million). Deaths from HIV/AIDS increased from 0·30 million in 1990 to 1·5 million in 2010, reaching a peak of 1·7 million in 2006. Malaria mortality also rose by an estimated 19·9{\%} since 1990 to 1·17 million deaths in 2010. Tuberculosis killed 1·2 million people in 2010. Deaths from non-communicable diseases rose by just under 8 million between 1990 and 2010, accounting for two of every three deaths (34·5 million) worldwide by 2010. 8 million people died from cancer in 2010, 38{\%} more than two decades ago; of these, 1·5 million (19{\%}) were from trachea, bronchus, and lung cancer. Ischaemic heart disease and stroke collectively killed 12·9 million people in 2010, or one in four deaths worldwide, compared with one in five in 1990; 1·3 million deaths were due to diabetes, twice as many as in 1990. The fraction of global deaths due to injuries (5·1 million deaths) was marginally higher in 2010 (9·6{\%}) compared with two decades earlier (8·8{\%}). This was driven by a 46{\%} rise in deaths worldwide due to road traffic accidents (1·3 million in 2010) and a rise in deaths from falls. Ischaemic heart disease, stroke, chronic obstructive pulmonary disease (COPD), lower respiratory infections, lung cancer, and HIV/AIDS were the leading causes of death in 2010. Ischaemic heart disease, lower respiratory infections, stroke, diarrhoeal disease, malaria, and HIV/AIDS were the leading causes of years of life lost due to premature mortality (YLLs) in 2010, similar to what was estimated for 1990, except for HIV/AIDS and preterm birth complications. YLLs from lower respiratory infections and diarrhoea decreased by 45-54{\%} since 1990; ischaemic heart disease and stroke YLLs increased by 17-28{\%}. Regional variations in leading causes of death were substantial. Communicable, maternal, neonatal, and nutritional causes still accounted for 76{\%} of premature mortality in sub-Saharan Africa in 2010. Age standardised death rates from some key disorders rose (HIV/AIDS, Alzheimer's disease, diabetes mellitus, and chronic kidney disease in particular), but for most diseases, death rates fell in the past two decades; including major vascular diseases, COPD, most forms of cancer, liver cirrhosis, and maternal disorders. For other conditions, notably malaria, prostate cancer, and injuries, little change was noted.

INTERPRETATION: Population growth, increased average age of the world's population, and largely decreasing age-specific, sex-specific, and cause-specific death rates combine to drive a broad shift from communicable, maternal, neonatal, and nutritional causes towards non-communicable diseases. Nevertheless, communicable, maternal, neonatal, and nutritional causes remain the dominant causes of YLLs in sub-Saharan Africa. Overlaid on this general pattern of the epidemiological transition, marked regional variation exists in many causes, such as interpersonal violence, suicide, liver cancer, diabetes, cirrhosis, Chagas disease, African trypanosomiasis, melanoma, and others. Regional heterogeneity highlights the importance of sound epidemiological assessments of the causes of death on a regular basis.

FUNDING: Bill {\&} Melinda Gates Foundation.},
author = {Lozano, Rafael and Naghavi, Mohsen and Foreman, Kyle and Lim, Stephen and Shibuya, Kenji and Aboyans, Victor and Abraham, Jerry and Adair, Timothy and Aggarwal, Rakesh and Ahn, Stephanie Y and Alvarado, Miriam and Anderson, H Ross and Anderson, Laurie M and Andrews, Kathryn G and Atkinson, Charles and Baddour, Larry M and Barker-Collo, Suzanne and Bartels, David H and Bell, Michelle L and Benjamin, Emelia J and Bennett, Derrick and Bhalla, Kavi and Bikbov, Boris and {Bin Abdulhak}, Aref and Birbeck, Gretchen and Blyth, Fiona and Bolliger, Ian and Boufous, Soufiane and Bucello, Chiara and Burch, Michael and Burney, Peter and Carapetis, Jonathan and Chen, Honglei and Chou, David and Chugh, Sumeet S and Coffeng, Luc E and Colan, Steven D and Colquhoun, Samantha and Colson, K Ellicott and Condon, John and Connor, Myles D and Cooper, Leslie T and Corriere, Matthew and Cortinovis, Monica and de Vaccaro, Karen Courville and Couser, William and Cowie, Benjamin C and Criqui, Michael H and Cross, Marita and Dabhadkar, Kaustubh C and Dahodwala, Nabila and {De Leo}, Diego and Degenhardt, Louisa and Delossantos, Allyne and Denenberg, Julie and {Des Jarlais}, Don C and Dharmaratne, Samath D and Dorsey, E Ray and Driscoll, Tim and Duber, Herbert and Ebel, Beth and Erwin, Patricia J and Espindola, Patricia and Ezzati, Majid and Feigin, Valery and Flaxman, Abraham D and Forouzanfar, Mohammad H and Fowkes, Francis Gerry R and Franklin, Richard and Fransen, Marlene and Freeman, Michael K and Gabriel, Sherine E and Gakidou, Emmanuela and Gaspari, Flavio and Gillum, Richard F and Gonzalez-Medina, Diego and Halasa, Yara a and Haring, Diana and Harrison, James E and Havmoeller, Rasmus and Hay, Roderick J and Hoen, Bruno and Hotez, Peter J and Hoy, Damian and Jacobsen, Kathryn H and James, Spencer L and Jasrasaria, Rashmi and Jayaraman, Sudha and Johns, Nicole and Karthikeyan, Ganesan and Kassebaum, Nicholas and Keren, Andre and Khoo, Jon-Paul and Knowlton, Lisa Marie and Kobusingye, Olive and Koranteng, Adofo and Krishnamurthi, Rita and Lipnick, Michael and Lipshultz, Steven E and Ohno, Summer Lockett and Mabweijano, Jacqueline and MacIntyre, Michael F and Mallinger, Leslie and March, Lyn and Marks, Guy B and Marks, Robin and Matsumori, Akira and Matzopoulos, Richard and Mayosi, Bongani M and McAnulty, John H and McDermott, Mary M and McGrath, John and Mensah, George a and Merriman, Tony R and Michaud, Catherine and Miller, Matthew and Miller, Ted R and Mock, Charles and Mocumbi, Ana Olga and Mokdad, Ali a and Moran, Andrew and Mulholland, Kim and Nair, M Nathan and Naldi, Luigi and Narayan, K M Venkat and Nasseri, Kiumarss and Norman, Paul and O'Donnell, Martin and Omer, Saad B and Ortblad, Katrina and Osborne, Richard and Ozgediz, Doruk and Pahari, Bishnu and Pandian, Jeyaraj Durai and Rivero, Andrea Panozo and Padilla, Rogelio Perez and Perez-Ruiz, Fernando and Perico, Norberto and Phillips, David and Pierce, Kelsey and Pope, C Arden and Porrini, Esteban and Pourmalek, Farshad and Raju, Murugesan and Ranganathan, Dharani and Rehm, J{\"{u}}rgen T and Rein, David B and Remuzzi, Guiseppe and Rivara, Frederick P and Roberts, Thomas and {De Le{\'{o}}n}, Felipe Rodriguez and Rosenfeld, Lisa C and Rushton, Lesley and Sacco, Ralph L and Salomon, Joshua a and Sampson, Uchechukwu and Sanman, Ella and Schwebel, David C and Segui-Gomez, Maria and Shepard, Donald S and Singh, David and Singleton, Jessica and Sliwa, Karen and Smith, Emma and Steer, Andrew and Taylor, Jennifer a and Thomas, Bernadette and Tleyjeh, Imad M and Towbin, Jeffrey a and Truelsen, Thomas and Undurraga, Eduardo a and Venketasubramanian, N and Vijayakumar, Lakshmi and Vos, Theo and Wagner, Gregory R and Wang, Mengru and Wang, Wenzhi and Watt, Kerrianne and Weinstock, Martin a and Weintraub, Robert and Wilkinson, James D and Woolf, Anthony D and Wulf, Sarah and Yeh, Pon-Hsiu and Yip, Paul and Zabetian, Azadeh and Zheng, Zhi-Jie and Lopez, Alan D and Murray, Christopher J L and AlMazroa, Mohammad a and Memish, Ziad a},
doi = {10.1016/S0140-6736(12)61728-0},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lozano et al. - Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010 a systematic analysis for the.pdf:pdf},
issn = {1474-547X},
journal = {Lancet},
keywords = {Adolescent,Adult,Age Factors,Aged,Aged, 80 and over,Cause of Death,Cause of Death: trends,Child,Child, Preschool,Female,Humans,Infant,Infant, Newborn,Male,Middle Aged,Mortality,Mortality: trends,Sex Factors,World Health,World Health: statistics {\&} numerical data,Young Adult},
month = {dec},
number = {9859},
pages = {2095--128},
pmid = {23245604},
title = {{Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23245604},
volume = {380},
year = {2012}
}
@article{Pierres2013,
archivePrefix = {arXiv},
arxivId = {arXiv:0809.1961v1},
author = {Pierres, Anne and Vitte, Joana and Benoliel, Anne-marie and Bongrand, Pierre},
eprint = {arXiv:0809.1961v1},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Pierres et al. - DISSECTING INDIVIDUAL LIGAND-RECEPTOR - 2013.pdf:pdf},
keywords = {bond strength,intermediate state,off-rate,on-rate},
pages = {1--24},
title = {{DISSECTING INDIVIDUAL LIGAND-RECEPTOR}},
year = {2013}
}
@article{Liu2009a,
abstract = {Rapid and accurate diagnosis for pathogens and their antibiotic susceptibility is critical for controlling bacterial infections. Conventional methods for determining bacterium's sensitivity to antibiotic depend mostly on measuring the change of microbial proliferation in response to the drug. Such "biological assay" inevitably takes time, ranging from days for fast-growing bacteria to weeks for slow-growers. Here, a novel tool has been developed to detect the "chemical features" of bacterial cell wall that enables rapid identification of drug resistant bacteria within hours. The surface-enhanced Raman scattering (SERS) technique based on our newly developed SERS-active substrate was applied to assess the fine structures of the bacterial cell wall. The SERS profiles recorded by such a platform are sensitive and stable, that could readily reflect different bacterial cell walls found in Gram-positive, Gram-negative, or mycobacteria groups. Moreover, characteristic changes in SERS profile were noticed in the drug-sensitive bacteria at the early period (i.e., approximately 1 hr) of antibiotic exposure, which could be used to differentiate them from the drug-resistant ones. The SERS-based diagnosis could be applied to a single bacterium. The high-speed SERS detection represents a novel approach for microbial diagnostics. The single-bacterium detection capability of SERS makes possible analyses directly on clinical specimen instead of pure cultured bacteria.},
author = {Liu, Ting-Ting and Lin, You-Hsuan and Hung, Chia-Sui and Liu, Tian-Jiun and Chen, Yu and Huang, Yung-Ching and Tsai, Tsung-Heng and Wang, Huai-Hsien and Wang, Da-Wei and Wang, Juen-Kai and Wang, Yuh-Lin and Lin, Chi-Hung},
doi = {10.1371/journal.pone.0005470},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Liu et al. - A high speed detection platform based on surface-enhanced Raman scattering for monitoring antibiotic-induced chemical chang.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Anti-Bacterial Agents,Anti-Bacterial Agents: pharmacology,Cell Wall,Cell Wall: chemistry,Gram-Negative Bacteria,Gram-Negative Bacteria: drug effects,Gram-Negative Bacteria: growth {\&} development,Gram-Negative Bacteria: isolation {\&} purification,Gram-Positive Bacteria,Gram-Positive Bacteria: drug effects,Gram-Positive Bacteria: growth {\&} development,Gram-Positive Bacteria: isolation {\&} purification,Spectrum Analysis, Raman,Spectrum Analysis, Raman: instrumentation,Spectrum Analysis, Raman: methods},
month = {jan},
number = {5},
pages = {e5470},
pmid = {19421405},
title = {{A high speed detection platform based on surface-enhanced Raman scattering for monitoring antibiotic-induced chemical changes in bacteria cell wall.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19421405},
volume = {4},
year = {2009}
}
@article{Bon2012,
author = {Bon, Pierre and Rolly, Brice and Bonod, Nicolas and Wenger, Jerome and Stout, Brian and Monneret, Serge and Rigneault, Herve},
journal = {Optics letters},
number = {17},
pages = {3531--3533},
title = {{Imaging the Gouy phase shift in photonic jets with a wavefront sensor}},
volume = {37},
year = {2012}
}
@article{Tolic-Nørrelykke2004,
author = {Toli{\'{c}}-N{\o}rrelykke, Iva Marija and Berg-S{\o}rensen, Kirstine and Flyvbjerg, Henrik},
doi = {10.1016/j.cpc.2004.02.012},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Toli{\'{c}}-N{\o}rrelykke, Berg-S{\o}rensen, Flyvbjerg - MatLab program for precision calibration of optical tweezers - 2004.pdf:pdf},
issn = {00104655},
journal = {Computer Physics Communications},
month = {jun},
number = {3},
pages = {225--240},
title = {{MatLab program for precision calibration of optical tweezers}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0010465504001043},
volume = {159},
year = {2004}
}
@article{Capitanio2013,
author = {Capitanio, Marco and Pavone, Francesco S.},
doi = {10.1016/j.bpj.2013.08.007},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Capitanio, Pavone - Interrogating Biology with Force Single Molecule High-Resolution Measurements with Optical Tweezers - 2013.pdf:pdf},
issn = {00063495},
journal = {Biophysical Journal},
month = {sep},
number = {6},
pages = {1293--1303},
publisher = {Biophysical Society},
title = {{Interrogating Biology with Force: Single Molecule High-Resolution Measurements with Optical Tweezers}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349513009144},
volume = {105},
year = {2013}
}
@article{Missirlis2007a,
author = {Missirlis, Y.F. and Katsikogianni, M. G},
doi = {10.1002/mawe.200700240},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Missirlis, Katsikogianni - Theoretical and experimental approaches of bacteria-biomaterial interactions - 2007.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Missirlis, Katsikogianni - Theoretical and experimental approaches of bacteria-biomaterial interactions - 2007(2).pdf:pdf},
issn = {09335137},
journal = {Materialwissenschaft und Werkstofftechnik},
month = {dec},
number = {12},
pages = {983--994},
title = {{Theoretical and experimental approaches of bacteria-biomaterial interactions}},
url = {http://doi.wiley.com/10.1002/mawe.200700240},
volume = {38},
year = {2007}
}
@article{Fry2011a,
annote = {From Duplicate 1 ( Modeling the Urinary Tract — Computational , Physical , and Biological Methods - Fry, C H; Sadananda, P; Wood, D N; Thiruchelvam, N; Jabr, R I; Clayton, R )
},
author = {Fry, C H and Sadananda, P and Wood, D N and Thiruchelvam, N and Jabr, R I and Clayton, R},
doi = {10.1002/nau},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Fry et al. - Modeling the Urinary Tract — Computational , Physical , and Biological Methods - 2011.pdf:pdf},
journal = {Neurourology and Urodynamics},
keywords = {encrustation,lower urinary tract,mathematical modeling,neurological models,paper3,tissue engineering},
mendeley-tags = {paper3},
number = {January},
pages = {692--699},
title = {{Modeling the Urinary Tract — Computational , Physical , and Biological Methods}},
volume = {699},
year = {2011}
}
@article{Capitani2006,
abstract = {Type 1 pili are filamentous protein complexes that are anchored to the outer membrane of uropathogenic Escherichia coli and mediate bacterial adhesion to the surface of urinary epithelium cells. We review here the current status of structural and functional studies on the assembly of type 1 pili.},
author = {Capitani, Guido and Eidam, Oliv and Glockshuber, Rudi and Gr{\"{u}}tter, Markus G},
doi = {10.1016/j.micinf.2006.03.013},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Capitani et al. - Structural and functional insights into the assembly of type 1 pili from Escherichia coli. - 2006.pdf:pdf},
issn = {1286-4579},
journal = {Microbes and infection / Institut Pasteur},
keywords = {Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: metabolism,Escherichia coli: physiology,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Models, Biological,Models, Molecular},
month = {jul},
number = {8},
pages = {2284--90},
pmid = {16793308},
title = {{Structural and functional insights into the assembly of type 1 pili from Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16793308},
volume = {8},
year = {2006}
}
@article{VonMentzer2014,
abstract = {Enterotoxigenic Escherichia coli (ETEC), a major cause of infectious diarrhea, produce heat-stable and/or heat-labile enterotoxins and at least 25 different colonization factors that target the intestinal mucosa. The genes encoding the enterotoxins and most of the colonization factors are located on plasmids found across diverse E. coli serogroups. Whole-genome sequencing of a representative collection of ETEC isolated between 1980 and 2011 identified globally distributed lineages characterized by distinct colonization factor and enterotoxin profiles. Contrary to current notions, these relatively recently emerged lineages might harbor chromosome and plasmid combinations that optimize fitness and transmissibility. These data have implications for understanding, tracking and possibly preventing ETEC disease.},
author = {von Mentzer, Astrid and Connor, Thomas R and Wieler, Lothar H and Semmler, Torsten and Iguchi, Atsushi and Thomson, Nicholas R and Rasko, David a and Joffre, Enrique and Corander, Jukka and Pickard, Derek and Wiklund, Gudrun and Svennerholm, Ann-Mari and Sj{\"{o}}ling, Asa and Dougan, Gordon},
doi = {10.1038/ng.3145},
file = {:E$\backslash$:/Mina Dokument/Mendeley/von Mentzer et al. - Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. - 2014.pdf:pdf},
issn = {1546-1718},
journal = {Nature genetics},
number = {12},
pages = {1321--1326},
pmid = {25383970},
publisher = {Nature Publishing Group},
title = {{Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25383970},
volume = {46},
year = {2014}
}
@article{Kemper2008,
author = {Kemper, Bj{\"{o}}rn and von Bally, Gert},
journal = {Applied optics},
pages = {A52--A61},
title = {{Digital holographic microscopy for live cell applications and technical inspection}},
volume = {47},
year = {2008}
}
@article{Harman2012,
abstract = {The Lyme disease spirochete Borrelia burgdorferi exists in nature in an enzootic cycle that involves the arthropod vector Ixodes scapularis and mammalian reservoirs. To disseminate within and between these hosts, spirochetes must migrate through complex, polymeric environments such as the basement membrane of the tick midgut and the dermis of the mammal. To date, most research on the motility of B. burgdorferi has been done in media that do not resemble the tissue milieus that B. burgdorferi encounter in vivo. Here we show that the motility of Borrelia in gelatin matrices in vitro resembles the pathogen's movements in the chronically infected mouse dermis imaged by intravital microscopy. More specifically, B. burgdorferi motility in mouse dermis and gelatin is heterogeneous, with the bacteria transitioning between at least three different motility states that depend on transient adhesions to the matrix. We also show that B. burgdorferi is able to penetrate matrices with pore sizes much smaller than the diameter of the bacterium. We find a complex relationship between the swimming behavior of B. burgdorferi and the rheological properties of the gelatin, which cannot be accounted for by recent theoretical predictions for microorganism swimming in gels. Our results also emphasize the importance of considering borrelial adhesion as a dynamic rather than a static process.},
author = {Harman, Michael W and Dunham-Ems, Star M and Caimano, Melissa J and Belperron, Alexia a and Bockenstedt, Linda K and Fu, Henry C and Radolf, Justin D and Wolgemuth, Charles},
doi = {10.1073/pnas.1114362109},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Harman et al. - The heterogeneous motility of the Lyme disease spirochete in gelatin mimics dissemination through tissue. - 2012.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Animals,Bacterial Adhesion,Bacterial Adhesion: drug effects,Biological,Borrelia burgdorferi,Borrelia burgdorferi: drug effects,Borrelia burgdorferi: physiology,Dermis,Dermis: drug effects,Dermis: microbiology,Gelatin,Gelatin: pharmacology,Inbred C57BL,Kinetics,Lyme Disease,Lyme Disease: microbiology,Methylcellulose,Methylcellulose: pharmacology,Mice,Models,Movement,Movement: drug effects,Rheology,Rheology: drug effects,Solutions,Time-Lapse Imaging},
month = {feb},
number = {8},
pages = {3059--64},
pmid = {22315410},
title = {{The heterogeneous motility of the Lyme disease spirochete in gelatin mimics dissemination through tissue.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3286914{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {109},
year = {2012}
}
@article{Dai1999a,
abstract = {Membrane tension has been proposed to be important in regulating cell functions such as endocytosis and cell motility. The apparent membrane tension has been calculated from tether forces measured with laser tweezers. Both membrane-cytoskeleton adhesion and membrane tension contribute to the tether force. Separation of the plasma membrane from the cytoskeleton occurs in membrane blebs, which could remove the membrane-cytoskeleton adhesion term. In renal epithelial cells, tether forces are significantly lower on blebs than on membranes that are supported by cytoskeleton. Furthermore, the tether forces are equal on apical and basolateral blebs. In contrast, tether forces from membranes supported by the cytoskeleton are greater in apical than in basolateral regions, which is consistent with the greater apparent cytoskeletal density in the apical region. We suggest that the tether force on blebs primarily contains only the membrane tension term and that the membrane tension may be uniform over the cell surface. Additional support for this hypothesis comes from observations of melanoma cells that spontaneously bleb. In melanoma cells, tether forces on blebs are proportional to the radius of the bleb, and as large blebs form, there are spikes in the tether force in other cell regions. We suggest that an internal osmotic pressure inflates the blebs, and the pressure calculated from the Law of Laplace is similar to independent measurements of intracellular pressures. When the membrane tension term is subtracted from the apparent membrane tension over the cytoskeleton, the membrane-cytoskeleton adhesion term can be estimated. In both cell systems, membrane-cytoskeleton adhesion was the major factor in generating the tether force.},
annote = {From Duplicate 1 ( Membrane tether formation from blebbing cells. - Dai, J; Sheetz, M P )
},
author = {Dai, J and Sheetz, M P},
doi = {10.1016/S0006-3495(99)77168-7},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Dai, Sheetz - Membrane tether formation from blebbing cells - 1999.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Adhesiveness,Animals,Biophysical Phenomena,Biophysics,Cell Membrane,Cell Membrane: physiology,Cell Membrane: ultrastructure,Cell Polarity,Cultured,Cytoskeleton,Cytoskeleton: physiology,Cytoskeleton: ultrastructure,Humans,Kidney Tubules,Lasers,Melanoma,Melanoma: physiopathology,Melanoma: ultrastructure,Osmotic Pressure,Pressure,Proximal,Proximal: physiology,Proximal: ultrastructure,Rabbits,Surface Tension,Tumor Cells},
month = {dec},
number = {6},
pages = {3363--70},
pmid = {10585959},
title = {{Membrane tether formation from blebbing cells}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300608{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {77},
year = {1999}
}
@article{Manninen2008,
abstract = {An experimental instrument for measuring a laser-induced fluorescence spectrum from a single aerosol particle is described. As a demonstration of instrument capabilities, the results of monodisperse 4.7 microm sodium chloride particles doped with fluorescent riboflavin, produced with an inkjet aerosol generator, are presented. The fluorescence of the aerosol particles is excited in the wide range from 210 to 419 nm using a pulsed, tunable optical parametric oscillator laser. The maximum of the fluorescence emission of separately measured particles is detected at 560 nm. The dependence of the fluorescence on the excitation wavelength is studied and fluorescence cross sections are estimated. Agreement between the measured fluorescence data and the literature data for riboflavin is observed.},
author = {Manninen, a and Putkiranta, M and Rostedt, a and Saarela, J and Laurila, T and Marjam{\"{a}}ki, M and Keskinen, J and Hernberg, R},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Manninen et al. - Instrumentation for measuring fluorescence cross sections from airborne microsized particles. - 2008.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
keywords = {Aerosols,Aerosols: analysis,Air Pollutants,Air Pollutants: analysis,Environmental Monitoring,Environmental Monitoring: instrumentation,Equipment Design,Equipment Failure Analysis,Flow Injection Analysis,Flow Injection Analysis: instrumentation,Lasers,Microspheres,Particle Size,Reproducibility of Results,Sensitivity and Specificity,Spectrometry, Fluorescence,Spectrometry, Fluorescence: instrumentation},
month = {jan},
number = {2},
pages = {110--5},
pmid = {18188190},
title = {{Instrumentation for measuring fluorescence cross sections from airborne microsized particles.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18188190},
volume = {47},
year = {2008}
}
@article{Kim2015,
author = {Kim, Kwanoh and Guo, Jianhe and Xu, Xiaobin and Fan, D. L.},
doi = {10.1002/smll.201500407},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kim et al. - Recent Progress on Man-Made Inorganic Nanomachines - 2015.pdf:pdf},
issn = {16136810},
journal = {Small},
number = {33},
pages = {4037--4057},
title = {{Recent Progress on Man-Made Inorganic Nanomachines}},
url = {http://doi.wiley.com/10.1002/smll.201500407},
volume = {11},
year = {2015}
}
@article{Soto1999a,
author = {Soto, Gabriel E and Hultgren, Scott J},
number = {4},
pages = {1059--1071},
title = {{Bacterial Adhesins : Common Themes and Variations in Architecture and Assembly MINIREVIEW Bacterial Adhesins : Common Themes and Variations in Architecture and Assembly}},
volume = {181},
year = {1999}
}
@article{Rose2008,
abstract = {P pili are multisubunit fibers essential for the attachment of uropathogenic Escherichia coli to the kidney. These fibers are formed by the noncovalent assembly of six different homologous subunit types in an array that is strictly defined in terms of both the number and order of each subunit type. Assembly occurs through a mechanism termed "donor-strand exchange (DSE)" in which an N-terminal extension (Nte) of one subunit donates a beta-strand to an adjacent subunit, completing its Ig fold. Despite structural determination of the different subunits, the mechanism determining specificity of subunit ordering in pilus assembly remained unclear. Here, we have used noncovalent mass spectrometry to monitor DSE between all 30 possible pairs of P pilus subunits and their Ntes. We demonstrate a striking correlation between the natural order of subunits in pili and their ability to undergo DSE in vitro. The results reveal insights into the molecular mechanism by which subunit ordering during the assembly of this complex is achieved.},
author = {Rose, Rebecca J and Verger, Denis and Daviter, Tina and Remaut, Han and Paci, Emanuele and Waksman, Gabriel and Ashcroft, Alison E and Radford, Sheena E},
doi = {10.1073/pnas.0802177105},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rose et al. - Unraveling the molecular basis of subunit specificity in P pilus assembly by mass spectrometry. - 2008.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Amino Acid Sequence,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Models, Molecular,Molecular Chaperones,Molecular Sequence Data,Peptides,Peptides: chemistry,Protein Subunits,Protein Subunits: chemistry,Spectrometry, Mass, Electrospray Ionization},
month = {sep},
number = {35},
pages = {12873--8},
pmid = {18728178},
title = {{Unraveling the molecular basis of subunit specificity in P pilus assembly by mass spectrometry.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2525559{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {105},
year = {2008}
}
@article{Wang1997,
author = {Wang, MD and Yin, H and Landick, R},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wang, Yin, Landick - Stretching DNA with optical tweezers. - 1997.pdf:pdf},
journal = {Biophysical journal},
pages = {1335--1346},
title = {{Stretching DNA with optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/pmc1184516/},
volume = {72},
year = {1997}
}
@article{Gyrya2010a,
abstract = {Recently, there has been a number of experimental studies convincingly demonstrating that a suspension of self-propelled bacteria (microswimmers in general) may have an effective viscosity significantly smaller than the viscosity of the ambient fluid. This is in sharp contrast with suspensions of hard passive inclusions, whose presence always increases the viscosity. Here we present a 2D model for a suspension of microswimmers in a fluid and analyze it analytically in the dilute regime (no swimmer-swimmer interactions) and numerically using a Mimetic Finite Difference discretization. Our analysis shows that in the dilute regime (in the absence of rotational diffusion) the effective shear viscosity is not affected by self-propulsion. But at the moderate concentrations (due to swimmer-swimmer interactions) the effective viscosity decreases linearly as a function of the propulsion strength of the swimmers. These findings prove that (i) a physically observable decrease of viscosity for a suspension of self-propelled microswimmers can be explained purely by hydrodynamic interactions and (ii) self-propulsion and interaction of swimmers are both essential to the reduction of the effective shear viscosity. We also performed a number of numerical experiments analyzing the dynamics of swimmers resulting from pairwise interactions. The numerical results agree with the physically observed phenomena (e.g., attraction of swimmer to swimmer and swimmer to the wall). This is viewed as an additional validation of the model and the numerical scheme.},
author = {Gyrya, V and Lipnikov, K and Aranson, I S and Berlyand, L},
doi = {10.1007/s00285-010-0351-y},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gyrya et al. - Effective shear viscosity and dynamics of suspensions of micro-swimmers from small to moderate concentrations. - 2010.pdf:pdf},
issn = {1432-1416},
journal = {Journal of mathematical biology},
month = {jun},
pmid = {20563812},
title = {{Effective shear viscosity and dynamics of suspensions of micro-swimmers from small to moderate concentrations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20563812},
year = {2010}
}
@article{Mahamdeh2009,
abstract = {In optical tweezers, thermal drift is detrimental for highr-esolution measurements. In particular, absorption of the trapping laser light by the microscope objective that focuses the beam leads to heating of the objective and subsequent drift. This entails long equilibration times which may limit sensitive biophysical assays. Here, we introduce an objective temperature feedback system for minimizing thermal drift. We measured that the infrared laser heated the objective by 0.7K per watt of laser power and that the laser focus moved relative to the sample by approximately 1 nm/mK due to thermal expansion of the objective. The feedback stabilized the temperature of the trapping objective with millikelvin precision. This enhanced the long-term temperature stability and significantly reduced the settling time of the instrument to about 100 s after a temperature disturbance while preserving single DNA base-pair resolution of surface-coupled assays. Minimizing systematic temperature changes of the objective and concurrent drift is of interest for other high-resolution microscopy techniques. Furthermore, temperature control is often a desirable parameter in biophysical experiments.},
author = {Mahamdeh, Mohammed and Sch{\"{a}}ffer, Erik},
journal = {Opt Express},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
number = {19},
pages = {17190--17199},
title = {{Optical tweezers with millikelvin precision of temperature-controlled objectives and base-pair resolution}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=19770938},
volume = {17},
year = {2009}
}
@article{Liang2000,
abstract = {Mechanisms of bacterial pathogenesis have become an increasingly important subject as pathogens have become increasingly resistant to current antibiotics. The adhesion of microorganisms to the surface of host tissue is often a first step in pathogenesis and is a plausible target for new antiinfective agents. Examination of bacterial adhesion has been difficult both because it is polyvalent and because bacterial adhesins often recognize more than one type of cell-surface molecule. This paper describes an experimental procedure that measures the forces of adhesion resulting from the interaction of uropathogenic Escherichia coli to molecularly well defined models of cellular surfaces. This procedure uses self-assembled monolayers (SAMs) to model the surface of epithelial cells and optical tweezers to manipulate the bacteria. Optical tweezers orient the bacteria relative to the surface and, thus, limit the number of points of attachment (that is, the valency of attachment). Using this combination, it was possible to quantify the force required to break a single interaction between pilus and mannose groups linked to the SAM. These results demonstrate the deconvolution and characterization of complicated events in microbial adhesion in terms of specific molecular interactions. They also suggest that the combination of optical tweezers and appropriately functionalized SAMs is a uniquely synergistic system with which to study polyvalent adhesion of bacteria to biologically relevant surfaces and with which to screen for inhibitors of this adhesion.},
author = {Liang, M N and Smith, S P and Metallo, S J and Choi, I S and Prentiss, M and Whitesides, G M},
doi = {10.1073/pnas.230451697},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Liang et al. - Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces. -.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Bacterial Adhesion,Bacterial Adhesion: physiology,Epithelial Cells,Epithelial Cells: microbiology,Escherichia coli,Escherichia coli: pathogenicity,Escherichia coli: physiology,Escherichia coli: ultrastructure,Humans,Mannose,Microscopy, Electron,Models, Biological,Pyelonephritis,Pyelonephritis: microbiology},
month = {nov},
number = {24},
pages = {13092--6},
pmid = {11078520},
title = {{Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=27183{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {97},
year = {2000}
}
@article{Xie2007,
author = {Xie, X and Li, Y and Chwang, A.T.Y and Ho, P.L. and Seto, W.H},
doi = {10.1111/j.1600-0668.2006.00469.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Xie et al. - How far droplets can move in indoor environments – revisiting the Wells evaporation – falling curve - 2007.pdf:pdf},
journal = {Indoor air},
keywords = {droplet evaporation,droplet movement,infection transmission,large droplet,respiratory jet},
pages = {211--225},
title = {{How far droplets can move in indoor environments – revisiting the Wells evaporation – falling curve}},
volume = {17},
year = {2007}
}
@article{He2009,
author = {He, Guang S. and Qin, Hai-Yan and Zheng, Qingdong},
doi = {10.1063/1.3068473},
file = {:E$\backslash$:/Mina Dokument/Mendeley/He, Qin, Zheng - Rayleigh, Mie, and Tyndall scatterings of polystyrene microspheres in water Wavelength, size, and angle dependences - 2.pdf:pdf},
issn = {00218979},
journal = {Journal of Applied Physics},
number = {2},
pages = {023110},
title = {{Rayleigh, Mie, and Tyndall scatterings of polystyrene microspheres in water: Wavelength, size, and angle dependences}},
url = {http://scitation.aip.org/content/aip/journal/jap/105/2/10.1063/1.3068473},
volume = {105},
year = {2009}
}
@article{Lumma2003,
author = {Lumma, D. and Keller, S. and Vilgis, T. and R{\"{a}}dler, J.},
doi = {10.1103/PhysRevLett.90.218301},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lumma et al. - Dynamics of Large Semiflexible Chains Probed by Fluorescence Correlation Spectroscopy - 2003.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {may},
number = {21},
pages = {1--4},
title = {{Dynamics of Large Semiflexible Chains Probed by Fluorescence Correlation Spectroscopy}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.90.218301},
volume = {90},
year = {2003}
}
@book{Giuliani2007,
author = {Giuliani, Andrea and Pirri, Giovanna and Nicoletto, Silvia Fabiole},
booktitle = {Central European Journal of Biology},
doi = {10.2478/s11535-007-0010-5},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Giuliani, Pirri, Nicoletto - Antimicrobial peptides an overview of a promising class of therapeutics - 2007.pdf:pdf},
isbn = {1153500700105},
issn = {1895-104X},
keywords = {amps,antimicrobial peptides,dendrimeric peptides,mode of action,proteases stability,therapeutic use},
month = {mar},
number = {1},
pages = {1--33},
title = {{Antimicrobial peptides: an overview of a promising class of therapeutics}},
url = {http://www.springerlink.com/index/10.2478/s11535-007-0010-5},
volume = {2},
year = {2007}
}
@article{Thomas2009a,
abstract = {When cell receptors bind to immobilized ligands, the resulting bond can be subjected to tensile mechanical force. This might be expected to shorten bond lifetimes. However, cells from bacteria to blood cells express receptors that are activated by tensile force to form longer-lived bonds, referred to as catch bonds. The process of catch bond activation involves non-equilibrium processes that are poorly probed by experimental and computational structural methods alike. However, I argue here that the preponderance of data indicates that force acts on an interdomain region which regulates the conformation of a distal ligand-binding site, in a process closely related to mechanochemistry and allosteric regulation.},
author = {Thomas, Wendy E},
doi = {10.1016/j.sbi.2008.12.006},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Thomas - Mechanochemistry of receptor-ligand bonds. - 2009.pdf:pdf},
issn = {1879-033X},
journal = {Current opinion in structural biology},
keywords = {Allosteric Regulation,Animals,Binding Sites,Cell Surface,Cell Surface: chemistry,Cell Surface: metabolism,Humans,Ligands,Models,Molecular,Protein Conformation,Proteins,Proteins: chemistry,Proteins: metabolism,Receptors,von Willebrand Factor,von Willebrand Factor: chemistry,von Willebrand Factor: metabolism},
month = {feb},
number = {1},
pages = {50--5},
pmid = {19157853},
title = {{Mechanochemistry of receptor-ligand bonds.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19157853},
volume = {19},
year = {2009}
}
@article{Wu2009,
author = {Wu, Zhigang and Willing, Ben and Bjerketorp, Joakim and Jansson, Janet K. and Hjort, Klas},
doi = {10.1039/b817611f},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wu et al. - Soft inertial microfluidics for high throughput separation of bacteria from human blood cells - 2009.pdf:pdf},
issn = {1473-0197},
journal = {Lab on a Chip},
keywords = {Drag,flow,microfluidics},
mendeley-tags = {Drag,flow,microfluidics},
number = {9},
pages = {1193},
title = {{Soft inertial microfluidics for high throughput separation of bacteria from human blood cells}},
url = {http://xlink.rsc.org/?DOI=b817611f},
volume = {9},
year = {2009}
}
@article{Wuite2000,
abstract = {We have developed an integrated laser trap/flow control video microscope for mechanical manipulation of single biopolymers. The instrument is automated to maximize experimental throughput. A single-beam optical trap capable of trapping micron-scale polystyrene beads in the middle of a 200-microm-deep microchamber is used, making it possible to insert a micropipette inside this chamber to hold a second bead by suction. Together, these beads function as easily exchangeable surfaces between which macromolecules of interest can be attached. A computer-controlled flow system is used to exchange the liquid in the chamber and to establish a flow rate with high precision. The flow and the optical trap can be used to exert forces on the beads, the displacements of which can be measured either by video microscopy or by laser deflection. To test the performance of this instrument, individual biotinylated DNA molecules were assembled between two streptavidin beads, and the DNA elasticity was characterized using both laser trap and flow forces. DNA extension under varying forces was measured by video microscopy. The combination of the flow system and video microscopy is a versatile design that is particularly useful for the study of systems susceptible to laser-induced damage. This capability was demonstrated by following the translocation of transcribing RNA polymerase up to 650 s.},
author = {Wuite, G J and Davenport, R J and Rappaport, a and Bustamante, C},
doi = {10.1016/S0006-3495(00)76369-7},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wuite et al. - An integrated laser trapflow control video microscope for the study of single biomolecules. - 2000.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Calibration,DNA,DNA-Directed RNA Polymerases,DNA-Directed RNA Polymerases: chemistry,DNA-Directed RNA Polymerases: ultrastructure,DNA: chemistry,DNA: ultrastructure,Elasticity,Equipment Design,Lasers,Microscopy, Video,Microscopy, Video: instrumentation,Microscopy, Video: methods,Nucleic Acid Conformation,Optics and Photonics},
month = {aug},
number = {2},
pages = {1155--67},
pmid = {10920045},
publisher = {Elsevier},
title = {{An integrated laser trap/flow control video microscope for the study of single biomolecules.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1301011{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {79},
year = {2000}
}
@article{Castelain2011,
abstract = {Uropathogenic Escherichia coli (UPEC) express various kinds of organelles, so-called pili or fimbriae, that mediate adhesion to host tissue in the urinary tract through specific receptor-adhesin interactions. The biomechanical properties of these pili have been considered important for the ability of bacteria to withstand shear forces from rinsing urine flows. Force-measuring optical tweezers have been used to characterize individual organelles of F1C type expressed by UPEC bacteria with respect to such properties. Qualitatively, the force-versus-elongation response was found to be similar to that of other types of helix-like pili expressed by UPEC, i.e., type 1, P, and S, with force-induced elongation in three regions, one of which represents the important uncoiling mechanism of the helix-like quaternary structure. Quantitatively, the steady-state uncoiling force was assessed as 26.4 ±1.4 pN, which is similar to those of other pili (which range from 21 pN for S(I) to 30 pN for type 1). The corner velocity for dynamic response (1,400 nm/s) was found to be larger than those of the other pili (400-700 nm/s for S and P pili, and 6 nm/s for type 1). The kinetics were found to be faster, with a thermal opening rate of 17 Hz, a few times higher than S and P pili, and three orders of magnitude higher than type 1. These data suggest that F1C pili are, like P and S pili, evolutionarily selected to primarily withstand the conditions expressed in the upper urinary tract.},
author = {Castelain, Micka{\"{e}}l and Ehlers, Sarah and Klinth, Jeanna E and Lindberg, Stina and Andersson, Magnus and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1007/s00249-010-0648-1},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Castelain et al. - Fast uncoiling kinetics of F1C pili expressed by uropathogenic Escherichia coli are revealed on a single pilus level.pdf:pdf},
issn = {1432-1017},
journal = {European biophysics journal},
keywords = {andersson {\'{a}},bacterial adhesion {\'{a}} dynamic,castelain {\'{a}} s,ehlers {\'{a}} j,force,kinetics,klinth {\'{a}} m,m,spectroscopy {\'{a}} pili relaxation,{\'{a}} uncoiling {\'{a}} bond},
month = {mar},
number = {3},
pages = {305--316},
pmid = {21161524},
title = {{Fast uncoiling kinetics of F1C pili expressed by uropathogenic Escherichia coli are revealed on a single pilus level using force-measuring optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21161524},
volume = {40},
year = {2011}
}
@article{Jertborn2001,
abstract = {The immunogenicity of different preparations of an oral inactivated enterotoxigenic Escherichia coli (ETEC) vaccine was evaluated in Swedish volunteers previously unexposed to ETEC infection. The vaccine preparations consisted of recombinant cholera toxin B subunit (CTB) and various amounts of formalin-killed whole bacteria expressing the most prevalent colonization factor antigens (CFAs). Significant immunoglobulin A (IgA) antibody-secreting cell (ASC) responses against CTB and the various CFA components were seen in a majority of volunteers after two doses of ETEC vaccine independent of the vaccine lot given. The IgA ASC responses against CTB were significantly higher after the second than after the first immunization, whereas the CFA-specific IgA ASC responses were almost comparable after the first and second doses of ETEC vaccine. Two immunizations with one-third of a full dose of CFA-ETEC bacteria induced lower frequencies of IgA ASC responses against all the different CFAs than two full vaccine doses, i.e., 63 versus 80{\%} for CFA/I, 56 versus 70{\%} for CS1, 31 versus 65{\%} for CS2, and 56 versus 75{\%} for CS4. The proportion of vaccinees responding with rises in the titer of serum IgA antibody against the various CFA antigens was also lower after immunization with the reduced dose of CFA-ETEC bacteria. These findings suggest that measurements of circulating IgA ASCs can be used not only for qualitative but also for quantitative assessments of the immunogenicity of individual fimbrial antigens in various preparations of ETEC vaccine.},
author = {Jertborn, M and Ahr{\'{e}}n, C and Svennerholm, Ann-Mari},
doi = {10.1128/CDLI.8.2.424-428.2001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jertborn, Ahr{\'{e}}n, Svennerholm - Dose-dependent circulating immunoglobulin A antibody-secreting cell and serum antibody responses in Swedi.pdf:pdf},
isbn = {1071412X (ISSN)},
issn = {1556-6811},
journal = {Clinical and diagnostic laboratory immunology},
pages = {424--428},
pmid = {11238232},
title = {{Dose-dependent circulating immunoglobulin A antibody-secreting cell and serum antibody responses in Swedish volunteers to an oral inactivated enterotoxigenic Escherichia coli vaccine.}},
volume = {8},
year = {2001}
}
@article{Griffiths1983,
annote = {From Duplicate 1 ( The mechanics of urine transport in the upper urinary tract: 2. The discharge of the bolus into the bladder and dynamics at high rates of flow - Griffiths, Derek J. )



From Duplicate 2 ( The mechanics of urine transport in the upper urinary tract: 2. The discharge of the bolus into the bladder and dynamics at high rates of flow - Griffiths, Derek J. )
},
author = {Griffiths, Derek J.},
doi = {10.1002/nau.1930020210},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Griffiths - The mechanics of urine transport in the upper urinary tract 2. The discharge of the bolus into the bladder and dynamics at h.pdf:pdf},
issn = {07332467},
journal = {Neurourology and Urodynamics},
keywords = {bolus discharge,diuresis,pelvic pressure,peristaltic transport,ureterovesical junction},
number = {2},
pages = {167--173},
title = {{The mechanics of urine transport in the upper urinary tract: 2. The discharge of the bolus into the bladder and dynamics at high rates of flow}},
url = {http://doi.wiley.com/10.1002/nau.1930020210},
volume = {2},
year = {1983}
}
@article{Svennerholm1990,
abstract = {The roles of the subcomponents of colonization factor antigen II, the coli surface antigens CS1, CS2, and CS3, as colonization factors and protective antigens was studied in a nonligated rabbit intestine model (RITARD). Infection with enterotoxigenic Escherichia coli (ETEC) carrying CS3 alone or CS1 plus CS3 induced diarrhea in most (80{\%}) of the rabbits, whereas nonenterotoxigenic strains expressing CS1 or CS2 rarely induced diarrhea. Strains carrying CS1, CS2, or CS3 alone were all shed in stools for a significantly longer period than normal fecal flora-type E. coli. Initial infection with ETEC positive for CS1 plus CS3 induced significant protection against disease caused by reinfection with a highly diarrheagenic dose of the homologous strain; rabbits previously infected with serotype-heterologous, nontoxigenic bacteria carrying CS1 only were also protected against this challenge, whereas no such protection was induced by serogroup-homologous E. coli carrying CS2 only. Animals previously infected with CS1-, CS3-, or CS1-plus-CS3-positive bacteria excreted the CS1-plus-CS3 challenge strain for a significantly shorter period than did "nonimmunized" rabbits, whereas initial infection with bacteria carrying CS2 only did not result in such reduced shedding. Monoclonal antibodies against CS1, CS2, or CS3 all protected against experimental infection with ETEC carrying the corresponding CS factor. These results suggest that all the subcomponents of colonization factor antigen II are colonization factors and may induce anticolonization immunity.},
author = {Svennerholm, Ann-Mari and Wenneras, C. and Holmgren, J. and McConnell, M. M. and Rowe, B.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Svennerholm et al. - Roles of different coli surface antigens of colonization factor antigen II in colonization by and protective immuno.pdf:pdf},
isbn = {0019-9567},
issn = {00199567},
journal = {Infection and Immunity},
number = {24},
pages = {341--346},
pmid = {1967593},
title = {{Roles of different coli surface antigens of colonization factor antigen II in colonization by and protective immunogenicity of enterotoxigenic Escherichia coli in rabbits}},
volume = {58},
year = {1990}
}
@article{Jauffred2007a,
abstract = {Tethers were created between a living Escherichia coli bacterium and a bead by unspecifically attaching the bead to the outer membrane and pulling it away using optical tweezers. Upon release, the bead returned to the bacterium, thus showing the existence of an elastic tether between the bead and the bacterium. These tethers can be tens of microns long, several times the bacterial length. Using mutants expressing different parts of the outer membrane structure, we have shown that an intact core lipopolysaccharide is a necessary condition for tether formation, regardless of whether the beads were uncoated polystyrene or beads coated with lectin. A physical characterization of the tethers has been performed yielding visco-elastic tether force-extension relationships: for first pull tethers, a spring constant of 10-12 pN/mum describes the tether visco-elasticity, for subsequent pulls the spring constant decreases to 6-7 pN/mum, and typical relaxation timescales of hundreds of seconds are observed. Studies of tether stability in the presence of proteases, lipases, and amylases lead us to propose that the extracted tether is primarily composed of the asymmetric lipopolysaccharide containing bilayer of the outer membrane. This unspecific tethered attachment mechanism could be important in the initiation of bacterial adhesion.},
author = {Jauffred, Liselotte and Callisen, Thomas H{\o}nger and Oddershede, Lene B.},
doi = {10.1529/biophysj.107.103861},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Jauffred, Callisen, Oddershede - Visco-elastic membrane tethers extracted from Escherichia coli by optical tweezers. - 2007.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {Bacterial Adhesion,Bacterial Adhesion: physiology,Cell Surface Extensions,Cell Surface Extensions: chemistry,Cell Surface Extensions: physiology,Elasticity,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: physiology,Optical Tweezers,Viscosity},
month = {dec},
number = {11},
pages = {4068--75},
pmid = {17704145},
publisher = {Elsevier},
title = {{Visco-elastic membrane tethers extracted from Escherichia coli by optical tweezers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2084229{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {93},
year = {2007}
}
@article{Qin2010,
abstract = {The animal cell cytoskeleton consists of three interconnected filament systems: actin microfilaments, microtubules and the lesser known intermediate filaments (IFs). All mature IF proteins share a common tripartite domain structure and the ability to assemble into 8-12nm wide filaments. At the time of their discovery in the 1980s, IFs were only considered as passive elements of the cytoskeleton mainly involved in maintaining the mechanical integrity of tissues. Since then, our knowledge of IFs structure, assembly plan and functions has improved dramatically. Especially, single IFs show a unique combination of extensibility, flexibility and toughness that is a direct consequence of their unique assembly plan. In this review we will first discuss the mechanical design of IFs by combining the experimental data with recent multi-scale modeling results. Then we will discuss how mechanical forces may interact with IFs in vivo both directly and through the activation of other proteins such as kinases.},
author = {Qin, Zhao and Buehler, Markus J and Kreplak, Laurent},
doi = {10.1016/j.jbiomech.2009.09.004},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Qin, Buehler, Kreplak - A multi-scale approach to understand the mechanobiology of intermediate filaments. - 2010.pdf:pdf},
issn = {1873-2380},
journal = {Journal of biomechanics},
keywords = {Actin Cytoskeleton,Actin Cytoskeleton: physiology,Animals,Biomechanics,Cell Movement,Cytoskeleton,Cytoskeleton: physiology,Humans,Intermediate Filaments,Intermediate Filaments: chemistry,Intermediate Filaments: physiology,Intermediate Filaments: ultrastructure,Microtubules,Microtubules: physiology,Models, Biological,Tensile Strength},
month = {jan},
number = {1},
pages = {15--22},
pmid = {19811783},
publisher = {Elsevier},
title = {{A multi-scale approach to understand the mechanobiology of intermediate filaments.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19811783},
volume = {43},
year = {2010}
}
@article{Schrodinger1944,
author = {Schrodinger, Erwin},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schrodinger - What is Life - 1944.pdf:pdf},
title = {{What is Life}},
year = {1944}
}
@article{Echelman2016,
author = {Echelman, Daniel J. and Alegre-Cebollada, Jorge and Badilla, Carmen L. and Chang, Chungyu and Ton-That, Hung and Fern{\'{a}}ndez, Julio M.},
doi = {10.1073/pnas.1522946113},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Echelman et al. - CnaA domains in bacterial pili are efficient dissipaters of large mechanical shocks - 2016.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
pages = {201522946},
title = {{CnaA domains in bacterial pili are efficient dissipaters of large mechanical shocks}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1522946113},
year = {2016}
}
@article{Evans1998,
abstract = {Beyond covalent connections within protein and lipid molecules, weak noncovalent interactions between large molecules govern properties of cellular structure and interfacial adhesion in biology. These bonds and structures have limited lifetimes and so will fail under any level of force if pulled on for the right length of time. As such, the strength of interaction is the level of force most likely to disrupt a bond on a particular time scale. For instance, strength is zero on time scales longer than the natural lifetime for spontaneous dissociation. On the other hand, if driven to unbind or change structure on time scales shorter than needed for diffusive relaxation, strength will reach an adiabatic limit set by the maximum gradient in a potential of mean force. Over the enormous span of time scales between spontaneous dissociation and adiabatic detachment, theory predicts that bond breakage under steadily rising force occurs most frequently at a force determined by the rate of loading. Moreover, the continuous plot (spectrum) of strength expressed on a scale of loge(loading rate) provides a map of the prominent barriers traversed in the energy landscape along the force-driven pathway and reveals the differences in energy between barriers. Illustrated with results from recent laboratory measurements, dynamic strength spectra provide a new view into the inner complexity of receptor-ligand interactions and receptor lipid anchoring.},
author = {Evans, E},
doi = {10.1039/a809884k},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans - Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy. - 1998.pdf:pdf},
isbn = {0301-7249},
issn = {13596640},
journal = {Faraday discussions},
number = {111},
pages = {1--16},
pmid = {10822596},
title = {{Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy.}},
year = {1998}
}
@article{Bergsten2005,
abstract = {Urinary tract infections (UTI) are among the most common bacterial infections in humans. Symptomatic UTIs may be acute, recurrent or chronic but the most frequent form of UTI is asymptomatic bacteruria (ABU). In ABU, the mucosa remains inert, despite the presence of large bacterial numbers in urine. The difference in disease severity reflects the virulence of the infecting strain and the propensity of the host to respond to infection. It is essential to understand the molecular basis of disease diversity and the molecular interactions between bacteria and host that determine asymptomatic carriage and the transition to disease. We discuss the initial interactions between bacteria and the mucosal surfaces in the human urinary tract, and the bacterial factors involved in the breach of mucosal inertia. Specifically, the contribution of P and type 1 fimbriae to bacterial establishment and host response induction are investigated. The results show that P fimbriae serve as independent virulence factors when expressed by an ABU strain, by promoting the establishment of bacteriuria and the innate host response, which is the cause of symptoms and tissue damage. P fimbriae thus fulfil the molecular Koch postulates as independent virulence factors in the human urinary tract. Type 1 fimbriae, in contrast, did not act as virulence factors in this model, and thus appear to serve a different function in man than in the murine model.},
author = {Bergsten, G{\"{o}}ran and Wullt, Bj{\"{o}}rn and Svanborg, Catharina},
doi = {10.1016/j.ijmm.2005.07.008},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bergsten, Wullt, Svanborg - Escherichia coli, fimbriae, bacterial persistence and host response induction in the human urinary tract. -.pdf:pdf},
issn = {1438-4221},
journal = {International journal of medical microbiology : IJMM},
keywords = {Adhesins, Bacterial,Adhesins, Bacterial: metabolism,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: metabolism,Escherichia coli Infections: microbiology,Escherichia coli Infections: pathology,Escherichia coli: pathogenicity,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Humans,Inflammation,Inflammation: etiology,Urinary Tract Infections,Urinary Tract Infections: metabolism,Urinary Tract Infections: microbiology,Urinary Tract Infections: pathology,Virulence},
month = {oct},
number = {6-7},
pages = {487--502},
pmid = {16238023},
title = {{Escherichia coli, fimbriae, bacterial persistence and host response induction in the human urinary tract.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16238023},
volume = {295},
year = {2005}
}
@article{Reihani2007a,
abstract = {The efficiency of an optical trap is limited by its axial strength. Light focused by oil-immersion objectives provides stronger traps but suffers from spherical aberrations, thus restricting the axial stability and working distance. By changing the refractive index of the immersion media we compensate spherical aberrations and measure axial trapping strengths at least twice as large as previously reported. Moreover, the spherical aberrations can be compensated at any desired depth. The improved trapping efficiency implies significantly less heating of the particles, thus diminishing previously published concerns about using gold nanoparticles as handles for optical manipulation.},
author = {Reihani, S Nader S and Oddershede, Lene B.},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Reihani, Oddershede - Optimizing immersion media refractive index improves optical trapping by compensating spherical aberrations. - 200.pdf:pdf},
issn = {0146-9592},
journal = {Optics letters},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
month = {jul},
number = {14},
pages = {1998--2000},
pmid = {17632622},
title = {{Optimizing immersion media refractive index improves optical trapping by compensating spherical aberrations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17632622},
volume = {32},
year = {2007}
}
@article{Park2002,
abstract = {A cell-scaled microbead system was used to analyze the force-dependent kinetics of P-selectin adhesive bonds independent of micromechanical properties of the neutrophil's surface microvilli, an elastic structure on which P-selectin ligand glycoprotein-1 (PSGL-1) is localized. Microvillus extension has been hypothesized in contributing to the dynamic range of leukocyte rolling observed in vivo during inflammatory processes. To evaluate PSGL-1/P-selectin bond kinetics of microbeads and neutrophils, rolling and tethering on P-selectin-coated substrates were compared in a parallel-plate flow chamber. The dissociation rates for PSGL-1 microbeads on P-selectin were briefer than those of neutrophils for any wall shear stress, and increased more rapidly with increasing flow. The microvillus length necessary to reconcile dissociation constants of PSGL-1 microbeads and neutrophils on P-selectin was 0.21 microm at 0.4 dyn/cm2, and increased to 1.58 microm at 2 dyn/cm2. The apparent elastic spring constant of the microvillus ranged from 1340 to 152 pN/microm at 0.4 and 2.0 dyn/cm2 wall shear stress. Scanning electron micrographs of neutrophils rolling on P-selectin confirmed the existence of micrometer-scaled tethers. Fixation of neutrophils to abrogate microvillus elasticity resulted in rolling behavior similar to PSGL-1 microbeads. Our results suggest that microvillus extension during transient PSGL-1/P-selectin bonding may enhance the robustness of neutrophil rolling interactions.},
author = {Park, Eric Y H and Smith, McRae J and Stropp, Emily S and Snapp, Karen R and DiVietro, Jeffrey a and Walker, William F and Schmidtke, David W and Diamond, Scott L and Lawrence, Michael B},
doi = {10.1016/S0006-3495(02)75534-3},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Park et al. - Comparison of PSGL-1 microbead and neutrophil rolling microvillus elongation stabilizes P-selectin bond clusters. - 2002.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Antibodies, Monoclonal,Antibodies, Monoclonal: metabolism,Biophysical Phenomena,Biophysics,Elasticity,Flow Cytometry,Humans,Kinetics,Membrane Glycoproteins,Membrane Glycoproteins: chemistry,Microscopy, Electron, Scanning,Microscopy, Video,Microspheres,Microvilli,Microvilli: metabolism,Models, Statistical,Neutrophils,Neutrophils: metabolism,P-Selectin,P-Selectin: chemistry,Polystyrenes,Polystyrenes: chemistry,Protein Binding,Stress, Mechanical,Time Factors},
month = {apr},
number = {4},
pages = {1835--47},
pmid = {11916843},
publisher = {Elsevier},
title = {{Comparison of PSGL-1 microbead and neutrophil rolling: microvillus elongation stabilizes P-selectin bond clusters.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1301981{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {82},
year = {2002}
}
@article{Reboux2008,
author = {Reboux, S. and Richardson, G. and Jensen, O.E.},
doi = {10.1098/rspa.2007.0210},
issn = {1364-5021},
journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
keywords = {adhesion,bistability,cell rolling,molecular friction},
number = {2090},
pages = {447--467},
title = {{Bond tilting and sliding friction in a model of cell adhesion}},
url = {http://rspa.royalsocietypublishing.org/cgi/doi/10.1098/rspa.2007.0210},
volume = {464},
year = {2008}
}
@article{Pesce2014,
abstract = {In this work we report on the simultaneous measurement of the hydrodynamic coefficient and the electric charge of single Bacillus subtilis spores. The latter has great importance in protein binding to spores and in the adhesion of spores onto surfaces. The charge and the hydrodynamic coefficient were measured by an accurate procedure based on the analysis of the motion of single spores confined by an optical trap. The technique has been validated using charged spherical polystyrene beads. The excellent agreement of our results with the expected values demonstrates the quality of our procedure. We measured the charge of spores of B. subtilis purified from a wild type strain and from two isogenic mutants characterized by an altered spore surface. Our technique is able to discriminate the three spore types used, by their charge and by their hydrodynamic coefficient which is related to the hydrophobic properties of the spore surface.},
author = {Pesce, Giuseppe and Rusciano, Giulia and Sasso, Antonio and Isticato, Rachele and Sirec, Teja and Ricca, Ezio},
doi = {10.1016/j.colsurfb.2014.01.039},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Pesce et al. - Surface charge and hydrodynamic coefficient measurements of Bacillus subtilis spore by optical tweezers. - 2014.pdf:pdf},
issn = {1873-4367},
journal = {Colloids and surfaces. B, Biointerfaces},
month = {apr},
pages = {568--75},
pmid = {24583259},
publisher = {Elsevier B.V.},
title = {{Surface charge and hydrodynamic coefficient measurements of Bacillus subtilis spore by optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24583259},
volume = {116},
year = {2014}
}
@article{Kim2001,
abstract = {This paper proposes a two-step circle detection algorithm using pairs of chords. It is shown how a pair of two intersecting chords locates the center of the circle. Based on this idea, in the first step, a 2D Hough transform (HT) method is employed to find the centers of the circles in the image. In the second step, a 1D radius histogram is used to compute the radii. The experimental results demonstrate that the proposed method can detect the circles effectively. ?? 2001 Elsevier Science B.V. All rights reserved.},
author = {Kim, Heung Soo and Kim, Jong Hwan},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kim, Kim - A two-step circle detection algorithm from the intersecting chords - 2001.pdf:pdf},
journal = {Pattern Recognition Letters},
number = {6-7},
pages = {787--798},
title = {{A two-step circle detection algorithm from the intersecting chords}},
volume = {22},
year = {2001}
}
@article{Mu2008,
abstract = {To survive the harsh environment of a churning intestinal tract, bacteria attach to the host epithelium via thin fibers called pili (or fimbriae). Enterotoxigenic Escherichia coli bacteria expressing colonization factor antigen I (CFA/I) pili and related pili are the most common known bacterial cause of diarrheal disease, including traveler's diarrhea. CFA/I pili, assembled via the alternate chaperone pathway, are essential for binding and colonization of the small bowel by these pathogenic bacteria. Herein, we elucidate unique structural features of CFA/I pili that appear to optimize their function as bacterial tethers in the intestinal tract. Using transmission electron microscopy of negatively stained samples in combination with iterative three-dimensional helical reconstruction methods for image processing, we determined the structure of the CFA/I pilus filament. Our results indicate that strong end-to-end protein interactions and weak interactions between the coils of a sturdy spring-like helix provide the combination of strength, stability, and flexibility required to sustain bacterial adhesion and incite intestinal disease. We propose that CFA/I pili behave like a spring to maintain attachment to the gut lining during vortex mixing and downward flow of the intestinal contents, thereby persisting long enough for these bacteria to colonize the host epithelium and cause enteric disease.},
author = {Mu, Xiang-Qi and Savarino, Stephen J and Bullitt, Esther},
doi = {10.1016/j.jmb.2007.10.067},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mu, Savarino, Bullitt - The three-dimensional structure of CFAI adhesion pili traveler's diarrhea bacteria hang on by a spring. - 2008.pdf:pdf},
issn = {1089-8638},
journal = {Journal of molecular biology},
keywords = {Bacterial,Bacterial: ultrastructure,Electron,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: chemistry,Enterotoxigenic Escherichia coli: metabolism,Enterotoxigenic Escherichia coli: ultrastructure,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: metabolism,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Microscopy,Models,Molecular,Transmission},
month = {feb},
number = {3},
pages = {614--20},
pmid = {18166195},
title = {{The three-dimensional structure of CFA/I adhesion pili: traveler's diarrhea bacteria hang on by a spring.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2265596{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {376},
year = {2008}
}
@article{Guasto2012,
author = {Guasto, Jeffrey S. and Rusconi, Roberto and Stocker, Roman},
doi = {10.1146/annurev-fluid-120710-101156},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Guasto, Rusconi, Stocker - Fluid Mechanics of Planktonic Microorganisms - 2012.pdf:pdf},
issn = {0066-4189},
journal = {Annual Review of Fluid Mechanics},
keywords = {low,nutrient uptake,reynolds number flow,shear,swimming,transport},
number = {1},
pages = {373--400},
title = {{Fluid Mechanics of Planktonic Microorganisms}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-fluid-120710-101156},
volume = {44},
year = {2012}
}
@article{Merz2000,
abstract = {Twitching and social gliding motility allow many gram negative bacteria to crawl along surfaces, and are implicated in a wide range of biological functions. Type IV pili (Tfp) are required for twitching and social gliding, but the mechanism by which these filaments promote motility has remained enigmatic. Here we use laser tweezers to show that Tfp forcefully retract. Neisseria gonorrhoeae cells that produce Tfp actively crawl on a glass surface and form adherent microcolonies. When laser tweezers are used to place and hold cells near a microcolony, retractile forces pull the cells toward the microcolony. In quantitative experiments, the Tfp of immobilized bacteria bind to latex beads and retract, pulling beads from the tweezers at forces that can exceed 80 pN. Episodes of retraction terminate with release or breakage of the Tfp tether. Both motility and retraction mediated by Tfp occur at about 1 microm s(-1) and require protein synthesis and function of the PilT protein. Our experiments establish that Tfp filaments retract, generate substantial force and directly mediate cell movement.},
author = {Merz, a J and So, M and Sheetz, M P},
doi = {10.1038/35024105},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Merz, So, Sheetz - Pilus retraction powers bacterial twitching motility. - 2000.pdf:pdf},
isbn = {0028-0836 (Print)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
number = {6800},
pages = {98--102},
pmid = {10993081},
title = {{Pilus retraction powers bacterial twitching motility.}},
volume = {407},
year = {2000}
}
@article{Liaqat2012,
author = {Liaqat, Iram and Sakellaris, Harry},
doi = {10.1590/S1517-83822012000300018},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Liaqat, Sakellaris - Biofilm formation and binding specificities of CFAI, CFAII and CS2 adhesions of enterotoxigenic Escherichia coli an.pdf:pdf},
issn = {15178382},
journal = {Brazilian Journal of Microbiology},
keywords = {Asialo-GM1,Biofilm formation,CFA/I,CFA/II,CS2,ELISA assays,ETEC,R181-cotD,dsc19CotD(His)6},
pages = {969--980},
title = {{Biofilm formation and binding specificities of CFA/I, CFA/II and CS2 adhesions of enterotoxigenic Escherichia coli and CFAE-R181A mutant}},
volume = {43},
year = {2012}
}
@incollection{Axner2010,
abstract = {Many types of bacterium express micrometer-long attachment organelles (so-called pili) whose role is to mediate adhesion to host tissue. Until recently, little was known about their function in the adhesion process. Force-measuring optical tweezers (FMOT) have since then been used to unravel the biomechanical properties of various types of pili, primarily those from uropathogenic E. coli, in particular their force-vs.-elongation response, but lately also some properties of the adhesin are situated at the distal end of the pilus. This knowledge provides an understanding of how piliated bacteria can sustain external shear forces caused by rinsing processes, e.g., urine flow. It has been found that many types of pilus exhibit unique and complex force-vs.-elongation responses. It has been conjectured that their dissimilar properties impose significant differences in their ability to sustain external forces and that different types of pilus therefore have dissimilar predisposition to withstand different types of rinsing conditions. An understanding of these properties is of high importance since it can serve as a basis for finding new means to combat bacterial adhesion, including that caused by antibiotic-resistance bacteria. This work presents a review of the current status of the assessment of biophysical properties of individual pili on single bacteria exposed to strain/stress, primarily by the FMOT technique. It also addresses, for the first time, how the elongation and retraction properties of the rod couple to the adhesive properties of the tip adhesin.},
address = {Berlin, Heidelberg},
annote = {From Duplicate 1 ( 











































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































The shaft of the type 1 fimbriae regulates an externalforce to match the FimH catch bond











































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































- Zakrisson, Johan; Wiklund, Krister; Axner, Ove; Andersson, Magnus )































































































































































































































































},
author = {Axner, Ove and Bj{\"{o}}rnham, Oscar and Castelain, Micka{\"{e}}l and Koutris, Efstratios and Schedin, Staffan and F{\"{a}}llman, Erik and Andersson, Magnus},
booktitle = {Springer series in chemical physics: single molecule spectroscopy in chemistry, physics and biology},
chapter = {18},
doi = {10.1007/978-3-642-02597-6},
editor = {Gr{\"{a}}slund, Astrid and Rigler, Rudolf and Widengren, Jerker},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Axner et al. - Unraveling the Secrets of Bacterial Adhesion Organelles using Single Molecule Force Spectroscopy - 2010.pdf:pdf},
isbn = {978-3-642-02596-9},
keywords = {Physics},
pages = {337--362},
publisher = {Springer Berlin Heidelberg},
series = {Springer Series in Chemical Physics},
title = {{Unraveling the Secrets of Bacterial Adhesion Organelles using Single Molecule Force Spectroscopy}},
url = {http://www.springerlink.com/content/u27n41330181040j/},
volume = {96},
year = {2010}
}
@article{Hyuk2010,
author = {Hyuk, Kyu Pak},
doi = {10.3938/jkps.56.977},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hyuk - Observation of a colloidal particle dynamics nearby flat wall using oscillating optical tweezers - 2010.pdf:pdf},
issn = {0374-4884},
journal = {Journal of the Korean Physical Society},
keywords = {10,3938,56,977,doi,drag,hydrodynamics,jkps,optical tweezers,stokes},
month = {mar},
number = {31},
pages = {977},
title = {{Observation of a colloidal particle dynamics nearby flat wall using oscillating optical tweezers}},
url = {http://www.kps.or.kr/jkps/abstract{\_}view.asp?articleuid=4736768D-408A-49DB-8D0B-8FA305BC9C55},
volume = {56},
year = {2010}
}
@article{Dewenter,
author = {Dewenter, Lena and Alpmann, Christina and Woerdemann, Mike and Denz, Cornelia},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dewenter et al. - Video-based analysis of the rotational behaviour of rod-shaped , self- propelled bacteria in holographic optical tweez.pdf:pdf},
keywords = {bacillus subtilis,bacterial dynamics,biophysical properties,high speed video analysis,holographic optical tweezers,hydrodynamic,interactions,position detection},
title = {{Video-based analysis of the rotational behaviour of rod-shaped , self- propelled bacteria in holographic optical tweezers}}
}
@article{Tomotika1953,
author = {Tomotika, By S},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tomotika - The steady flow of a viscous fluid past an elliptic cylinder and a flat plate at small Reynolds numbers - 1953.pdf:pdf},
number = {April 1952},
title = {{The steady flow of a viscous fluid past an elliptic cylinder and a flat plate at small Reynolds numbers}},
volume = {VI},
year = {1953}
}
@article{Chen2001,
abstract = {Detecting circles from a digital image is very important in shape recognition. In this paper, an efficient randomized algorithm (RCD) for detecting circles is presented, which is not based on the Hough transform (HT). Instead of using an accumulator for saving the information of the related parameters in the HT-based methods, the proposed RCD does not need an accumulator. The main concept used in the proposed RCD is that we first randomly select four edge pixels in the image and define a distance criterion to determine whether there is a possible circle in the image; after finding a possible circle, we apply an evidence-collecting process to further determine whether the possible circle is a true circle or not. Some synthetic images with different levels of noises and some realistic images containing circular objects with some occluded circles and missing edges have been taken to test the performance. Experimental results demonstrate that the proposed RCD is faster than other HT-based methods for the noise level between the light level and the modest level. For a heavy noise level, the randomized HT could be faster than the proposed RCD, but at the expense of massive memory requirements.},
author = {Chen, Teh-Chuan and Chung, Kuo-Liang},
doi = {10.1006/cviu.2001.0923},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chen, Chung - An Efficient Randomized Algorithm for Detecting Circles - 2001.pdf:pdf},
issn = {10773142},
journal = {Computer Vision and Image Understanding},
month = {aug},
number = {2},
pages = {172--191},
title = {{An Efficient Randomized Algorithm for Detecting Circles}},
volume = {83},
year = {2001}
}
@article{Chan2010,
abstract = {The development of therapeutic antibodies has evolved over the past decade into a mainstay of therapeutic options for patients with autoimmune and inflammatory diseases. Substantial advances in understanding the biology of human diseases have been made and tremendous benefit to patients has been gained with the first generation of therapeutic antibodies. The lessons learnt from these antibodies have provided the foundation for the discovery and development of future therapeutic antibodies. Here we review how key insights obtained from the development of therapeutic antibodies complemented by newer antibody engineering technologies are delivering a second generation of therapeutic antibodies with promise for greater clinical efficacy and safety.},
author = {Chan, Andrew C and Carter, Paul J},
doi = {10.1038/nri2761},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chan, Carter - Therapeutic antibodies for autoimmunity and inflammation. - 2010.pdf:pdf},
issn = {1474-1741},
journal = {Nature reviews. Immunology},
keywords = {Animals,Antibodies, Bispecific,Antibodies, Bispecific: therapeutic use,Antibodies, Monoclonal,Antibodies, Monoclonal: pharmacokinetics,Antibodies, Monoclonal: therapeutic use,Antibody-Dependent Cell Cytotoxicity,Autoimmune Diseases,Autoimmune Diseases: drug therapy,Cytokines,Cytokines: antagonists {\&} inhibitors,Half-Life,Humans,Inflammation,Inflammation: drug therapy,Intercellular Signaling Peptides and Proteins,Intercellular Signaling Peptides and Proteins: imm},
month = {may},
number = {5},
pages = {301--16},
pmid = {20414204},
publisher = {Nature Publishing Group},
title = {{Therapeutic antibodies for autoimmunity and inflammation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20414204},
volume = {10},
year = {2010}
}
@article{Jonsson2006,
author = {Jonsson, Per and Kullander, Fredrik and Vahlberg, Claes and Jelger, Par and Tiihonen, Mikael and Wasterby, Par and Tjarnhage, Torbj{\"{o}}rn and Lindgren, Mikael},
doi = {10.1117/12.689666},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jonsson et al. - Spectral detection of ultraviolet laser induced fluorescence from individual bio-aerosol particles - 2006.pdf:pdf},
issn = {0277786X},
journal = {Proceedings of SPIE},
keywords = {bioaerosol detection,biological warfare agent,fluorescence spectroscopy,point,ultraviolet laser excitation},
pages = {63980F--63980F--12},
publisher = {Spie},
title = {{Spectral detection of ultraviolet laser induced fluorescence from individual bio-aerosol particles}},
url = {http://link.aip.org/link/PSISDG/v6398/i1/p63980F/s1{\&}Agg=doi},
volume = {6398},
year = {2006}
}
@article{Stahlhut2013,
abstract = {Type 3 fimbriae are adhesive organelles found in enterobacterial pathogens. The fimbriae promote biofilm formation on biotic and abiotic surfaces; however, the exact identity of the receptor for the type 3 fimbriae adhesin, MrkD, remains elusive. We analyzed naturally occurring structural and functional variabilities of the MrkD adhesin from Klebsiella pneumoniae and Escherichia coli isolates of diverse origins. We identified a total of 33 allelic variants of mrkD among 90 K. pneumoniae isolates and 10 allelic variants among 608 E. coli isolates, encoding 11 and 9 protein variants, respectively. Based on the level of accumulated silent variability between the alleles, mrkD was acquired a relatively long time ago in K. pneumoniae but recently in E. coli. However, unlike K. pneumoniae, mrkD in E. coli is actively evolving under a strong positive selection by accumulation of mutations, often targeting the same positions in the protein. Several naturally occurring MrkD protein variants from E. coli were found to be significantly less adherent when tested in a mannan-binding assay and showed reduced biofilm-forming capacity. Functional examination of the MrkD adhesin in flow chamber experiments determined that it interacts with Saccharomyces cerevisiae cells in a shear-dependent manner, i.e., the binding is catch-bond-like and enhanced under increasing shear conditions. Homology modeling strongly suggested that MrkD has a two-domain structure, comprising a pilin domain anchoring the adhesin to the fimbrial shaft and a lectin domain containing the binding pocket; this is similar to structures found in other catch-bond-forming fimbrial adhesins in enterobacteria.},
author = {Stahlhut, Steen G and Chattopadhyay, Sujay and Kisiela, Dagmara I and Hvidtfeldt, Kristian and Clegg, Steven and Struve, Carsten and Sokurenko, Evgeni V and Krogfelt, Karen a},
doi = {10.1128/JB.00753-13},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Stahlhut et al. - Structural and population characterization of MrkD, the adhesive subunit of type 3 fimbriae. - 2013.pdf:pdf},
issn = {1098-5530},
journal = {Journal of bacteriology},
month = {dec},
number = {24},
pages = {5602--13},
pmid = {24123820},
title = {{Structural and population characterization of MrkD, the adhesive subunit of type 3 fimbriae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24123820},
volume = {195},
year = {2013}
}
@article{Koster2005,
author = {Koster, Gerbrand and Cacciuto, Angelo and Der{\'{e}}nyi, Imre and Frenkel, Daan and Dogterom, Marileen},
doi = {10.1103/PhysRevLett.94.068101},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Koster et al. - Force Barriers for Membrane Tube Formation - 2005.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {feb},
number = {6},
pages = {16--19},
title = {{Force Barriers for Membrane Tube Formation}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.94.068101},
volume = {94},
year = {2005}
}
@article{Ren2010,
author = {Ren, Yu-xuan and Wu, Jian-guang and Li, Yin-mei},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ren, Wu, Li - Application of Monte Carlo Simulation in Optical Tweezers - 2010.pdf:pdf},
journal = {Science And Technology},
title = {{Application of Monte Carlo Simulation in Optical Tweezers}},
year = {2010}
}
@article{Roy2005,
abstract = {The internalization of various cargo proteins and lipids from the mammalian cell surface occurs through the clathrin and lipid-raft endocytic pathways. Protein-lipid and protein-protein interactions control the targeting of signalling molecules and their partners to various specialized membrane compartments in these pathways. This functions to control the activity of signalling cascades and the termination of signalling events, and therefore has a key role in defining how a cell responds to its environment.},
author = {Roy, Christine Le and Wrana, Jeffrey L and {Le Roy}, Christine},
doi = {10.1038/nrm1571},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Roy, Wrana, Le Roy - Clathrin- and non-clathrin-mediated endocytic regulation of cell signalling - 2005.pdf:pdf},
issn = {1471-0072},
journal = {Nature reviews. Molecular cell biology},
keywords = {Biological,Chemical,Clathrin,Clathrin: chemistry,Clathrin: physiology,Endocytosis,Epidermal Growth Factor,Epidermal Growth Factor: metabolism,Fluorescence,Glycosphingolipids,Glycosphingolipids: chemistry,Lipids,Lipids: chemistry,Membrane Microdomains,Microscopy,Models,Receptor,Receptors,Signal Transduction,Transforming Growth Factor beta,Transforming Growth Factor beta: metabo},
month = {feb},
number = {2},
pages = {112--26},
pmid = {15687999},
title = {{Clathrin- and non-clathrin-mediated endocytic regulation of cell signalling}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15687999},
volume = {6},
year = {2005}
}
@article{Gittes1998a,
author = {Gittes, F and Schmidt, C F},
journal = {Method Cell Biol},
keywords = {Actin,Atomic-Force Microscopy,Laser,Movements,Optical Tweezers,Resolution,Single Kinesin Molecules,Tracking,Trap,calibration},
mendeley-tags = {calibration},
pages = {129--156},
title = {{Signals and noise in micromechanical measurements}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=000073062000008},
volume = {55},
year = {1998}
}
@article{Vahidi2011,
abstract = {Ureteral peristaltic mechanism facilitates urine transport from the kidney to the bladder. Numerical analysis of the peristaltic flow in the ureter aims to further our understanding of the reflux phenomenon and other ureteral abnormalities. Fluid-structure interaction (FSI) plays an important role in accuracy of this approach and the arbitrary Lagrangian-Eulerian (ALE) formulation is a strong method to analyze the coupled fluid-structure interaction between the compliant wall and the surrounding fluid. This formulation, however, was not used in previous studies of peristalsis in living organisms. In the present investigation, a numerical simulation is introduced and solved through ALE formulation to perform the ureteral flow and stress analysis. The incompressible Navier-Stokes equations are used as the governing equations for the fluid, and a linear elastic model is utilized for the compliant wall. The wall stimulation is modeled by nonlinear contact analysis using a rigid contact surface since an appropriate model for simulation of ureteral peristalsis needs to contain cell-to-cell wall stimulation. In contrast to previous studies, the wall displacements are not predetermined in the presented model of this finite-length compliant tube, neither the peristalsis needs to be periodic. Moreover, the temporal changes of ureteral wall intraluminal shear stress during peristalsis are included in our study. Iterative computing of two-way coupling is used to solve the governing equations. Two phases of nonperistaltic and peristaltic transport of urine in the ureter are discussed. Results are obtained following an analysis of the effects of the ureteral wall compliance, the pressure difference between the ureteral inlet and outlet, the maximum height of the contraction wave, the contraction wave velocity, and the number of contraction waves on the ureteral outlet flow. The results indicate that the proximal part of the ureter is prone to a higher shear stress during peristalsis compared with its middle and distal parts. It is also shown that the peristalsis is more efficient as the maximum height of the contraction wave increases. Finally, it is concluded that improper function of ureteropelvic junction results in the passage of part of urine back flow even in the case of slow start-up of the peristaltic contraction wave.},
annote = {        From Duplicate 1 (                   A mathematical simulation of the ureter: effects of the model parameters on ureteral pressure/flow relations.                 - Vahidi, Bahman; Fatouraee, Nasser; Imanparast, Ali; Moghadam, Abbas Nasiraei )
                
        
        
      },
author = {Vahidi, Bahman and Fatouraee, Nasser and Imanparast, Ali and Moghadam, Abbas Nasiraei},
doi = {10.1115/1.4003316},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Vahidi et al. - A mathematical simulation of the ureter effects of the model parameters on ureteral pressureflow relations. - 2011.pdf:pdf},
issn = {1528-8951},
journal = {Journal of biomechanical engineering},
keywords = {Biological,Computer Simulation,Humans,Hydrodynamics,Linear Models,Mechanical,Models,Peristalsis,Peristalsis: physiology,Pressure,Shear Strength,Shear Strength: physiology,Stress,Ureter,Ureter: physiology,Urination,Urination: physiology,Urine,Urine: physiology},
month = {mar},
number = {3},
pages = {031004},
pmid = {21303180},
title = {{A mathematical simulation of the ureter: effects of the model parameters on ureteral pressure/flow relations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21303180},
volume = {133},
year = {2011}
}
@article{Ashkin1970,
author = {Ashkin, A},
journal = {Physical review letters},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
number = {4},
pages = {24--27},
title = {{Acceleration and Trapping of Particlesby Radiation Pressure}},
year = {1970}
}
@article{Walker2007,
abstract = {Enterotoxigenic Escherichia coli (ETEC) is the most common bacterial cause of diarrhoea in the world, annually affecting up to 400,000,000 children under 5 years of age living in developing countries (DCs). Although ETEC possesses numerous antigens, the relatively conserved colonization factor (CF) antigens and the heat labile enterotoxin (LT) have been associated with protection and most vaccine candidates have exploited these antigens. A safe and effective vaccine against ETEC is a feasible goal as supported by the acquisition of protective immunity. The success of an ETEC vaccine targeting infants and children in DCs will depend on a combination of maximally antigenic vaccine preparations and regimens for their delivery which will produce optimal immune responses to these antigens. Vaccine candidates having a high priority for accelerated development and clinical testing for eventual use in infants would include inactivated ETEC or Shigella hybrids expressing ETEC antigens as well as attenuated ETEC strains which express the major CF antigens and LT toxin B-subunit, as well as attenuated Shigella, Vibrio cholerae and Salmonella typhi hybrids engineered to deliver antigens of ETEC. Candidates for an ETEC vaccine would have to meet the minimal requirement of providing at least 50{\%} protection against severe disease in DCs during the first 2 years of life. The critical roadblock to achieving this goal has not been the science as much as the lack of a sufficiently funded and focused effort to bring it to realization. However, a Product Development Partnership to overcome this hurdle could accelerate the time lines towards when control of ETEC disease in DCs is substantially closer.},
author = {Walker, Richard I and Steele, Duncan and Aguado, Teresa},
doi = {10.1016/j.vaccine.2006.12.028},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Walker, Steele, Aguado - Analysis of strategies to successfully vaccinate infants in developing countries against enterotoxigenic E. col.pdf:pdf},
issn = {0264-410X},
journal = {Vaccine},
keywords = {Adhesins, Escherichia coli,Adhesins, Escherichia coli: immunology,Bacterial Toxins,Bacterial Toxins: immunology,Developing Countries,Enterotoxins,Enterotoxins: immunology,Escherichia coli Infections,Escherichia coli Infections: prevention {\&} control,Escherichia coli Proteins,Escherichia coli Proteins: immunology,Escherichia coli Vaccines,Escherichia coli Vaccines: administration {\&} dosage,Escherichia coli Vaccines: adverse effects,Escherichia coli Vaccines: immunology,Humans,Infant,Infant, Newborn,Vaccination,Vaccines, DNA,Vaccines, DNA: immunology,Vaccines, Inactivated,Vaccines, Inactivated: immunology,Vaccines, Synthetic,Vaccines, Synthetic: immunology},
month = {mar},
number = {14},
pages = {2545--66},
pmid = {17224212},
title = {{Analysis of strategies to successfully vaccinate infants in developing countries against enterotoxigenic E. coli (ETEC) disease.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17224212},
volume = {25},
year = {2007}
}
@book{Goodman2005,
author = {Goodman, Joseph W.},
publisher = {Roberts {\&} Company},
title = {{Introduction to Fourier Optics 3rd Ed.}},
year = {2005}
}
@article{Young2006,
abstract = {Why do bacteria have shape? Is morphology valuable or just a trivial secondary characteristic? Why should bacteria have one shape instead of another? Three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. All of these imply that shape is a selectable feature that aids survival. The aim of this review is to spell out the physical, environmental, and biological forces that favor different bacterial morphologies and which, therefore, contribute to natural selection. Specifically, cell shape is driven by eight general considerations: nutrient access, cell division and segregation, attachment to surfaces, passive dispersal, active motility, polar differentiation, the need to escape predators, and the advantages of cellular differentiation. Bacteria respond to these forces by performing a type of calculus, integrating over a number of environmental and behavioral factors to produce a size and shape that are optimal for the circumstances in which they live. Just as we are beginning to answer how bacteria create their shapes, it seems reasonable and essential that we expand our efforts to understand why they do so.},
author = {Young, Kevin D},
doi = {10.1128/MMBR.00001-06},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Young - The selective value of bacterial shape. - 2006.pdf:pdf},
isbn = {1092-2172 (Print)},
issn = {1092-2172},
journal = {Microbiology and molecular biology reviews : MMBR},
number = {3},
pages = {660--703},
pmid = {16959965},
title = {{The selective value of bacterial shape.}},
volume = {70},
year = {2006}
}
@article{Katsikogianni2006,
abstract = {Staphylococcus epidermidis has emerged as a pathogen associated with infections of implanted medical devices. Bacterial adhesion is a crucial step in infection on biomaterial surfaces. To quantitatively determine the relationship between poly (vinyl chloride) (PVC) surface properties and bacterial adhesion, we have compared attachment of slime-producing S. epidermidis strains on PVC and various coatings under flow conditions. Bacterial adhesion and colonization was quantified by counting the viable organisms on the adherent surface as well as by scanning electron microscopy, epifluorescence microscopy and atomic force microscopy. Fluorination of the PVC surface encourages S. epidermidis adhesion whereas; diamond-like carbon (DLC) and especially silver (Ag) coatings seem to inhibit its adhesion. In most materials, the number of adherent bacteria decreased with the increase of shear rate. These results indicate that bacterial adhesion is influenced by the chemical properties of the polymeric surfaces, the surface roughness and the associated flow conditions.},
author = {Katsikogianni, M G and Spiliopoulou, I and Dowling, D P and Missirlis, Y F},
doi = {10.1007/s10856-006-9678-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Katsikogianni et al. - Adhesion of slime producing Staphylococcus epidermidis strains to PVC and diamond-like carbonsilverfluorinated co.pdf:pdf},
issn = {0957-4530},
journal = {Journal of materials science. Materials in medicine},
keywords = {Atomic Force,Bacterial Adhesion,Biocompatible,Biocompatible: chemistry,Carbon,Carbon: chemistry,Coated Materials,Diamond,Materials Testing,Microscopy,Polyvinyl Chloride,Polyvinyl Chloride: chemistry,Resin Cements,Resin Cements: chemistry,Silver,Silver: chemistry,Staphylococcus epidermidis,Staphylococcus epidermidis: physiology,Surface Properties},
month = {aug},
number = {8},
pages = {679--89},
pmid = {16897160},
title = {{Adhesion of slime producing Staphylococcus epidermidis strains to PVC and diamond-like carbon/silver/fluorinated coatings.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16897160},
volume = {17},
year = {2006}
}
@article{Jahns2015,
author = {Jahns, S. and Gutekunst, S. B. and Selhuber-Unkel, C. and Nazirizadeh, Y. and Gerken, M.},
doi = {10.1007/s00542-015-2746-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jahns et al. - Human blood microfluidic test chip for imaging, label-free biosensor - 2015.pdf:pdf},
isbn = {0054201527},
issn = {0946-7076},
journal = {Microsystem Technologies},
pages = {1--6},
publisher = {Springer Berlin Heidelberg},
title = {{Human blood microfluidic test chip for imaging, label-free biosensor}},
url = {http://link.springer.com/10.1007/s00542-015-2746-6},
year = {2015}
}
@article{Marquet2005,
abstract = {We have developed a digital holographic microscope (DHM), in a transmissionmode, especially dedicated to the quantitative visualization of phase objectssuch as living cells. The method is based on an original numerical algorithmpresented in detail elsewhere [Cuche et al.,Appl.Opt.38, 6994 (1999)]. DHM images of living cells in culture areshown for what is to our knowledge the first time. They represent the distributionof the optical path length over the cell, which has been measured with subwavelengthaccuracy. These DHM images are compared with those obtained by use of thewidely used phase contrast and Nomarski differential interference contrasttechniques.},
author = {Marquet, Pierre and Rappaz, Benjamin and Magistretti, Pierre J and Cuche, Etienne and Emery, Yves and Colomb, Tristan and Depeursinge, Christian},
doi = {10.1364/OL.30.000468},
journal = {Optics Letters},
keywords = {Aberration compensation,Coherence imaging,Digital image processing,Holography},
number = {5},
pages = {468--470},
publisher = {OSA},
title = {{Digital holographic microscopy:?a noninvasive contrastimaging technique allowing quantitative visualization ofliving cells with subwavelength axial accuracy}},
url = {http://ol.osa.org/abstract.cfm?URI=ol-30-5-468},
volume = {30},
year = {2005}
}
@article{Bullitt1998,
abstract = {P-pili on uropathogenic bacteria are 68-A-diameter rods typically 1 microm in length. These structures project from the outer membrane of Escherichia coli, and contain on their distal tip a thin fibrillum, 25 A in diameter and 150 A long, displaying an adhesin protein responsible for the binding of the bacterium to the surface of epithelial cells lining the urinary tract. Operationally, it is possible to identify three morphologically distinct states of the 68-A-diameter P-pili rods, based on the degree of curvature each can adopt. These states are designated "straight," "curved," and "highly curved." The rods can also be unwound to form thin "threads" that are very similar to the tip fibrillae. Electron microscope data are used to distinguish among these four morphological states and to define limits on the shapes of the pilus proteins. The mechanical properties of the PapA polymers are assessed, and implications of rod polymorphism for pilus function are discussed. A wide variety of data are considered in light of the possibility that all pilins are similar in molecular architecture, with specific differences designed to optimize their specialized functions in the pilus assembly.},
author = {Bullitt, Esther and Makowski, L},
doi = {10.1016/S0006-3495(98)77821-X},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bullitt, Makowski - Bacterial adhesion pili are heterologous assemblies of similar subunits. - 1998.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Amino Acid,Amino Acid Sequence,Bacterial,Bacterial Outer Membrane Proteins,Bacterial Outer Membrane Proteins: biosynthesis,Bacterial Outer Membrane Proteins: chemistry,Bacterial Outer Membrane Proteins: ultrastructure,Codon,Conserved Sequence,Electron,Escherichia coli,Escherichia coli: metabolism,Escherichia coli: pathogenicity,Escherichia coli: ultrastructure,Fimbriae Proteins,Gene Expression Regulation,Macromolecular Substances,Microscopy,Models,Molecular,Molecular Sequence Data,Pili,Sequence Alignment,Sequence Homology,Sex,Sex: chemistry,Sex: ultrastructure},
month = {jan},
number = {1},
pages = {623--32},
pmid = {9449363},
title = {{Bacterial adhesion pili are heterologous assemblies of similar subunits.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1299415{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {74},
year = {1998}
}
@article{Hart2009,
author = {Hart, Peter E},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Hart - How the Hough Transform Was Invented EDITOR ’ S INTRODUCTION - 2009.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Hart - How the Hough Transform Was Invented EDITOR ’ S INTRODUCTION - 2009.pdf:pdf},
number = {November},
pages = {18--22},
title = {{How the Hough Transform Was Invented EDITOR ’ S INTRODUCTION}},
year = {2009}
}
@article{Capitanio2002,
abstract = {A comparison of different calibration methods for optical tweezers with the differential interference contrast (DIC) technique was performed to establish the uses and the advantages of each method. A detailed experimental and theoretical analysis of each method was performed with emphasis on the anisotropy involved in the DIC technique and the noise components in the detection. Finally, a time of flight method that permits the reconstruction of the optical potential well was demonstrated. (C) 2002 American Institute of Physics.},
author = {Capitanio, M. and Romano, G. and Ballerini, R. and Giuntini, M. and Pavone, F. S. and Dunlap, D. and Finzi, L.},
doi = {10.1063/1.1460929},
isbn = {0034-6748},
issn = {00346748},
journal = {Review of Scientific Instruments},
number = {4},
pages = {1687},
title = {{Calibration of optical tweezers with differential interference contrast signals}},
volume = {73},
year = {2002}
}
@article{Yehoshua2015,
abstract = {ABSTRACT Optical tweezers have revolutionized our understanding of the microscopic world. Axial optical tweezers, which apply force to a surface-tethered molecule by directly moving either the trap or the stage along the laser beam axis, offer several potential benefits when studying a range of novel biophysical phenomena. This geometry, although it is conceptually straight- forward, suffers from aberrations that result in variation of the trap stiffness when the distance between the microscope coverslip and the trap focus is being changed. Many standard techniques, such as back-focal-plane interferometry, are difficult to employ in this geometry due to back-scattered light between the bead and the coverslip, whereas the noise inherent in a surface- tethered assay can severely limit the resolution of an experiment. Because of these complications, precision force spectroscopy measurements have adapted alternative geometries such as the highly successful dumbbell traps. In recent years, however, most of the difficulties inherent in constructing a precision axial optical tweezers have been solved. This review article aims to inform the reader about recent progress in axial optical trapping, as well as the potential for these devices to perform inno- vative biophysical measurements.},
author = {Yehoshua, Samuel and Pollari, Russell and Milstein, Joshua N},
doi = {10.1016/j.bpj.2015.05.014},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yehoshua, Pollari, Milstein - Axial Optical Traps A New Direction for Optical Tweezers - 2015.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical Journal},
number = {12},
pages = {2759--2766},
publisher = {Biophysical Society},
title = {{Axial Optical Traps : A New Direction for Optical Tweezers}},
url = {http://dx.doi.org/10.1016/j.bpj.2015.05.014},
volume = {108},
year = {2015}
}
@article{Mico2010,
author = {Mic{\'{o}}, V and Ferreira, C and Zalevsky, Z and Garc{\'{\i}}a, J},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mic{\'{o}} et al. - Basic principles and applications of digital holographic microscopy - 2010.pdf:pdf},
keywords = {and digital holographic microscopy,coherent imaging,digital and classical holography,interferometry},
pages = {1411--1418},
title = {{Basic principles and applications of digital holographic microscopy}},
year = {2010}
}
@article{Egelman2000,
abstract = {Some of the earliest methods for three-dimensional reconstruction from electron microscopic images were developed for helical objects. Single-particle methods have been used with great success for the three-dimensional reconstruction of macromolecular assemblies that have no internal symmetry or closed point group symmetries. An approach is presented for the application of single-particle methods to helical filaments that surmounts many of the difficulties of helical image analysis, including indexing, unbending and the need to find long helically symmetric filament segments. It is shown using both human Rad51 and E. coli RecA nucleoprotein filaments that this approach converges without user intervention to a stable solution, and that it has the potential to overcome many of the problems associated with image analysis of disordered helical polymers. The method can be applied transparently to structures where Bessel overlap would greatly complicate helical analysis. In addition, the procedure allows for the ab initio determination of helical symmetry, when no prior knowledge exists.},
author = {Egelman, E H},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Egelman - A robust algorithm for the reconstruction of helical filaments using single-particle methods. - 2000.pdf:pdf},
issn = {0304-3991},
journal = {Ultramicroscopy},
keywords = {Algorithms,DNA, Single-Stranded,DNA, Single-Stranded: metabolism,DNA-Binding Proteins,DNA-Binding Proteins: chemistry,DNA-Binding Proteins: metabolism,DNA-Binding Proteins: ultrastructure,Escherichia coli,Escherichia coli: metabolism,Humans,Image Processing, Computer-Assisted,Microscopy, Electron,Microscopy, Electron: methods,Protein Conformation,Rad51 Recombinase,Rec A Recombinases,Rec A Recombinases: chemistry,Rec A Recombinases: metabolism,Rec A Recombinases: ultrastructure},
month = {dec},
number = {4},
pages = {225--34},
pmid = {11125866},
title = {{A robust algorithm for the reconstruction of helical filaments using single-particle methods.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11125866},
volume = {85},
year = {2000}
}
@article{Kastanos2010a,
author = {Kastanos, Evdokia K. and Kyriakides, Alexandros and Hadjigeorgiou, Katerina and Pitris, Costas},
doi = {10.1002/jrs.2540},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kastanos et al. - A novel method for urinary tract infection diagnosis and antibiogram using Raman spectroscopy - 2010.pdf:pdf},
issn = {03770486},
journal = {Journal of Raman Spectroscopy},
keywords = {antibiogram,bacteria,classification,raman spectroscopy},
month = {sep},
number = {9},
pages = {958--963},
title = {{A novel method for urinary tract infection diagnosis and antibiogram using Raman spectroscopy}},
url = {http://doi.wiley.com/10.1002/jrs.2540},
volume = {41},
year = {2010}
}
@article{Ponniah1991,
abstract = {Cells of the gram-negative bacterium Escherichia coli are able to attach to various host cells by means of a mannose-specific adhesin associated with type 1 fimbriae. Here we show that fragmentation of type 1 fimbriae by freezing and thawing results in increased mannose-binding activity as demonstrated by increased hemagglutination, increased stimulation of human lymphocyte proliferation, and increased binding of the mannose-containing enzyme horseradish peroxidase. Increased activity in all three assays was mannose sensitive and was not exhibited by FimH- mutant type 1 fimbriae lacking the adhesin. Scatchard analysis of the data from peroxidase binding assays showed that unfrozen and frozen fimbriae contain binding sites displaying two classes of affinity. Frozen and thawed fimbriae expressed an increase in the number of high-affinity binding sites. These results show that fragmentation of the fimbrial structure exposes cryptic mannose-binding activity associated with type 1 fimbriae, presumably that of internally located adhesin molecules. Our data support earlier observations that adhesin moieties of type 1 fimbriae are located both at the tips and at intervals along the length of the fimbriae. In addition, our data suggest that only the adhesin moieties that are located at the fimbrial tips are functional in binding mannose. Adhesins located along the length of the fimbriae have their mannose-binding activity buried within the fimbrial structure and hence are not functional. We propose an updated model for the structure of type 1 fimbriae that is in agreement with the above observations.},
author = {Ponniah, S and Endres, R O and Hasty, D L and Abraham, S N},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ponniah et al. - Fragmentation of Escherichia coli type 1 fimbriae exposes cryptic D-mannose-binding sites. - 1991.pdf:pdf},
issn = {0021-9193},
journal = {Journal of bacteriology},
keywords = {Bacterial Adhesion,Escherichia coli,Escherichia coli: physiology,Escherichia coli: ultrastructure,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Fimbriae, Bacterial: ultrastructure,Freezing,Hemagglutination,Horseradish Peroxidase,Horseradish Peroxidase: metabolism,Humans,Lymphocyte Activation,Mannose,Mannose: metabolism},
month = {jul},
number = {13},
pages = {4195--202},
pmid = {1676398},
title = {{Fragmentation of Escherichia coli type 1 fimbriae exposes cryptic D-mannose-binding sites.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=208070{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {173},
year = {1991}
}
@article{Sirigu1995,
abstract = {The mucosal surface of the human urothelium represents a very large exposure area to exogenous agents, including potentially harmful microorganisms. Male human urothelium was treated for the immunohistochemical demonstration of secretory IgA (sIgA) in order to verify its own possible antimicrobial properties. An intense immunoreactivity for sIgA was observed in the apical cells of the urethral and vesical epithelia. The ureteric epithelium, at the luminal surface, showed discontinuous areas of less dense or completely absent reaction product. A less intense immunoreactivity was observed in the pelvic apical epithelial cells. The results suggest that sIgA play a prominent role in the local defence mechanisms of the lower urinary tract against ascending infections, whereas in the upper urinary tract the immuno-specific local defences seem reduced.},
author = {Sirigu, P and Perra, M T and Turno, F and Usai, E},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sirigu et al. - Immunohistochemical demonstration of secretory IgA in human urothelium. - 1995.pdf:pdf},
issn = {0213-3911},
journal = {Histology and histopathology},
keywords = {Adult,Aged,Epithelium,Epithelium: metabolism,Epithelium: pathology,Humans,Immunoglobulin A, Secretory,Immunoglobulin A, Secretory: metabolism,Immunohistochemistry,Male,Middle Aged,Mucous Membrane,Mucous Membrane: metabolism,Paraffin Embedding,Ureter,Ureter: metabolism,Ureter: pathology,Urethra,Urethra: metabolism,Urethra: pathology,Urinary Bladder,Urinary Bladder Neoplasms,Urinary Bladder Neoplasms: pathology,Urinary Bladder: metabolism,Urinary Bladder: pathology,Urinary Tract,Urinary Tract: metabolism,Urinary Tract: pathology},
month = {jul},
number = {3},
pages = {645--50},
pmid = {7579813},
title = {{Immunohistochemical demonstration of secretory IgA in human urothelium.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/7579813},
volume = {10},
year = {1995}
}
@inproceedings{Diaz2004a,
abstract = {Abstract – Urinary system concerns with the excretion of urine, and the waste products of metabolism. The kidneys separate urea, mineral salts, toxins, and other waste products from the blood, and to conserve water, salts, and electrolytes. At least one kidney must function properly for life to be maintained. Each kidney contains 1.2 million filtering units called nephrons. After filtration, blood leaving the glomerulus flows through the network of capillaries that surrounds each tubule; water and certain salts, are restored to the blood. The purified blood returns to the renal vein. Urine from the kidney pelvis passes into the ureters. Muscles in the walls of the ureters send the urine in small spurts into the bladder, for temporary storage of urine. A full bladder stimulates sensory nerves in the bladder wall that relax the sphincter and allow release of the urine. The released urine enters the urethra, a tube lined with mucus membrane that conveys the urine to the outside. The male urethra terminates at the tip of the penis. The female urethra is less than 5 cm long and opens just in front of the entrance to the vagina. The urinary system disorders are: Congenital malformation, injury, infection, presence of kidney stones, or calculi, other types of obstruction, and tumors, cystitis, nephritis, nephrosis.},
annote = {        From Duplicate 1 (                   Biofluid dynamics of the human urinary system 1                 - Diaz, Luis De Jesus; Rosado, Yarimar Padua; Gonz{\'{a}}lez, Melissa P{\'{e}}rez )
                
        
        
        From Duplicate 2 (                   Biofluid dynamics of the human urinary system 1                 - Diaz, Luis De Jesus; Rosado, Yarimar Padua; Gonz{\'{a}}lez, Melissa P{\'{e}}rez )
                
        
        
      },
author = {Diaz, Luis De Jesus and Rosado, Yarimar Padua and Gonz{\'{a}}lez, Melissa P{\'{e}}rez},
booktitle = {Engineering},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Diaz, Rosado, Gonz{\'{a}}lez - Biofluid dynamics of the human urinary system 1 - 2004.pdf:pdf},
keywords = {biofluids of human body,body,human,kidneys,newtonian fluids,systems of human,urine},
pages = {1--36},
title = {{Biofluid dynamics of the human urinary system 1}},
year = {2004}
}
@article{McKenzie2006,
abstract = {A vaccine against enterotoxigenic Escherichia coli (ETEC) is needed to prevent diarrheal illness among children in developing countries and at-risk travelers. Two live attenuated ETEC strains, PTL002 and PTL003, which express the ETEC colonization factor CFA/II, were evaluated for safety and immunogenicity. In a randomized, double-blind, placebo-controlled trial, 19 subjects ingested one dose, and 21 subjects ingested two doses (days 0 and 10) of PTL-002 or PTL-003 at 2 x 10(9) CFU/dose. Anti-CFA/II mucosal immune responses were determined from the number of antibody-secreting cells (ASC) in blood measured by enzyme-linked immunospot assay, the antibody in lymphocyte supernatants (ALS) measured by enzyme-linked immunosorbent assay (ELISA), and fecal immunoglobulin A (IgA) levels determined by ELISA. Time-resolved fluorescence (TRF) ELISA was more sensitive than standard colorimetric ELISA for measuring serum antibody responses to CFA/II and its components, CS1 and CS3. Both constructs were well tolerated. Mild diarrhea occurred after 2 of 31 doses (6{\%}) of PTL-003. PTL-003 produced more sustained intestinal colonization than PTL-002 and better IgA response rates: 90{\%} versus 55{\%} (P = 0.01) for anti-CFA/II IgA-ASCs, 55{\%} versus 30{\%} (P = 0.11) for serum anti-CS1 IgA by TRF, and 65{\%} versus 25{\%} (P = 0.03) for serum anti-CS3 IgA by TRF. Serum IgG response rates to CS1 or CS3 were 55{\%} in PTL-003 recipients and 15{\%} in PTL-002 recipients (P = 0.02). Two doses of either strain were not significantly more immunogenic than one. Based on its superior immunogenicity, which was comparable to that of a virulent ETEC strain and other ETEC vaccine candidates, PTL-003 will be developed further as a component of a live, oral attenuated ETEC vaccine.},
author = {McKenzie, Robin and Bourgeois, a. Louis and Engstrom, Fayette and Hall, Eric and Chang, H. Sunny and Gomes, Joseph G. and Kyle, Jennifer L. and Cassels, Fred and Turner, Arthur K. and Randall, Roger and Darsley, Michael and Lee, Cynthia and Bedford, Philip and Shimko, Janet and Sack, David a.},
doi = {10.1128/IAI.74.2.994-1000.2006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/McKenzie et al. - Comparative safety and immunogenicity of two attenuated enterotoxigenic Escherichia coli vaccine strains in healthy ad.pdf:pdf},
isbn = {0019-9567},
issn = {00199567},
journal = {Infection and Immunity},
pages = {994--1000},
pmid = {16428745},
title = {{Comparative safety and immunogenicity of two attenuated enterotoxigenic Escherichia coli vaccine strains in healthy adults}},
volume = {74},
year = {2006}
}
@article{Kweon2007,
author = {Kweon, Gyeong-Il and Kim, Cheol-Ho},
doi = {10.3938/jkps.51.93},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kweon, Kim - Aspherical Lens Design by Using a Numerical Analysis - 2007.pdf:pdf},
issn = {0374-4884},
journal = {Journal of the Korean Physical Society},
keywords = {geometrical optics,lens design,numerical analysis,optical aberration,spherical aberration},
number = {1},
pages = {93},
title = {{Aspherical Lens Design by Using a Numerical Analysis}},
volume = {51},
year = {2007}
}
@article{Reihani2011,
author = {Reihani, S Nader S and Mir, Shahid a and Richardson, Andrew C and Oddershede, Lene B.},
doi = {10.1088/2040-8978/13/10/105301},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Reihani et al. - Significant improvement of optical traps by tuning standard water immersion objectives - 2011.pdf:pdf},
issn = {2040-8978},
journal = {Journal of Optics},
keywords = {aberration,infrared,optical trapping,trap efficiency,water immersion objective},
month = {oct},
number = {10},
pages = {105301},
title = {{Significant improvement of optical traps by tuning standard water immersion objectives}},
url = {http://stacks.iop.org/2040-8986/13/i=10/a=105301?key=crossref.0eda0b6af4fe6828da11f5852bb088e1},
volume = {13},
year = {2011}
}
@article{Ramser2007a,
abstract = {We describe the possibility of using a microresonance Raman spectrometer combined with a microfluidic system and optical tweezers to study Escherichia coli (E. coli) overexpressing wild type (wt) neuroglobin (NGB) and its E7Leu mutant, respectively. NGB is a recently discovered heme protein and its function still is a matter of debate. So far, the protein has been studied in its purified form, and in vivo measurements on the single cell level could give more information. To study the feasibility of the combined techniques, the possibilities of the setup are investigated by taking spectra from single cells and clusters of cells. We find that the microresonance Raman technique enables studies of the wt NGB protein in a living cell under fluctuating aerobic and anaerobic conditions. E. coli cells overexpressing wt NGB are stable, and the reversible oxygenation-deoxygenation can be studied over a long period of time. Further, the experiment indicates the presence of an enzymatic system in the bacteria reducing the ferric form NGB. The study of E. coli cells overexpressing E7Leu NGB, on the other hand, gives insight into limiting factors of the setup, such as cell lysis, photoinduced chemistry, and protein concentrations.},
author = {Ramser, Kerstin and Wenseleers, Wim and Dewilde, Sylvia and {Van Doorslaer}, Sabine and Moens, Luc and Hanstorp, Dag},
doi = {10.1117/1.2753478},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ramser et al. - Micro-resonance Raman study of optically trapped Escherichia coli cells overexpressing human neuroglobin. - 2007.pdf:pdf},
issn = {1083-3668},
journal = {Journal of biomedical optics},
keywords = {Escherichia coli,Escherichia coli: physiology,Globins,Globins: genetics,Globins: metabolism,Humans,Microfluidic Analytical Techniques,Microfluidic Analytical Techniques: methods,Nerve Tissue Proteins,Nerve Tissue Proteins: genetics,Nerve Tissue Proteins: metabolism,Optical Tweezers,Protein Engineering,Protein Engineering: methods,Spectrum Analysis, Raman,Spectrum Analysis, Raman: methods},
number = {4},
pages = {044009},
pmid = {17867813},
title = {{Micro-resonance Raman study of optically trapped Escherichia coli cells overexpressing human neuroglobin.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17867813},
volume = {12},
year = {2007}
}
@book{Born1998,
author = {Born, M and Wolf, E},
edition = {6th},
isbn = {978-0-08-026482-0},
publisher = {Cambridge University Press},
title = {{Principles of Optics}},
year = {1998}
}
@article{Langermann2000,
abstract = {Escherichia coli FimH adhesin mediates binding to the bladder mucosa. In mice, a FimH vaccine protects against bacterial challenge. In this study, 4 monkeys were inoculated with 100 microgram of FimCH adhesin-chaperone complex mixed with MF59 adjuvant, and 4 monkeys were given adjuvant only intramuscularly. After 2 doses (day 0 and week 4), a booster at 48 weeks elicited a strong IgG antibody response to FimH in the vaccinated monkeys. All 8 monkeys were challenged with 1 mL of 108 E. coli cystitis isolate NU14. Three of the 4 vaccinated monkeys were protected from bacteruria and pyuria; all control monkeys were infected. These findings suggest that a vaccine based on the FimH adhesin of E. coli type 1 pili may have utility in preventing cystitis in humans.},
author = {Langermann, S and M{\"{o}}llby, R and Burlein, J E and Palaszynski, S R and Auguste, C G and DeFusco, A and Strouse, R and Schenerman, M a and Hultgren, Scott J and Pinkner, J S and Winberg, J and Guldevall, L and S{\"{o}}derh{\"{a}}ll, M and Ishikawa, K and Normark, S and Koenig, S},
doi = {10.1086/315258},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Langermann et al. - Vaccination with FimH adhesin protects cynomolgus monkeys from colonization and infection by uropathogenic Escherich.pdf:pdf},
issn = {0022-1899},
journal = {The Journal of infectious diseases},
keywords = {Adhesins,Animals,Antibodies,Bacterial,Bacterial Vaccines,Bacterial Vaccines: administration {\&} dosage,Bacterial Vaccines: immunology,Bacterial: administration {\&} dosage,Bacterial: blood,Bacterial: immunology,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli Infections: prevention {\&} control,Escherichia coli: growth {\&} development,Escherichia coli: immunology,Escherichia coli: pathogenicity,Feces,Feces: microbiology,Fimbriae Proteins,Humans,Macaca fascicularis,Stomach,Stomach: microbiology,Urinary Bladder,Urinary Bladder: microbiology,Urinary Tract Infections,Urinary Tract Infections: microbiology,Urinary Tract Infections: prevention {\&} control,Vaccination},
month = {feb},
number = {2},
pages = {774--8},
pmid = {10669375},
title = {{Vaccination with FimH adhesin protects cynomolgus monkeys from colonization and infection by uropathogenic Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10669375},
volume = {181},
year = {2000}
}
@article{Zavyalov2009,
abstract = {Abstract This review summarizes current knowledge on the structure, function, assembly and biomedical applications of the superfamily of adhesive fimbrial organelles exposed on the surface of Gram-negative pathogens with the classical chaperone/usher machinery. High-resolution three-dimensional (3D) structure studies of the minifibers assembling with the FGL (having a long F1-G1 loop) and FGS (having a short F1-G1 loop) chaperones show that they exploit the same principle of donor-strand complementation for polymerization of subunits. The 3D structure of adhesive subunits bound to host-cell receptors and the final architecture of adhesive fimbrial organelles reveal two functional families of the organelles, respectively, possessing polyadhesive and monoadhesive binding. The FGL and FGS chaperone-assembled polyadhesins are encoded exclusively by the gene clusters of the gamma3- and kappa-monophyletic groups, respectively, while gene clusters belonging to the gamma1-, gamma2-, gamma4-, and pi-fimbrial clades exclusively encode FGS chaperone-assembled monoadhesins. Novel approaches are suggested for a rational design of antimicrobials inhibiting the organelle assembly or inhibiting their binding to host-cell receptors. Vaccines are currently under development based on the recombinant subunits of adhesins.},
author = {Zav'yalov, Vladimir and Zavialov, Anton and Zav'yalova, Galina and Korpela, Timo},
doi = {10.1111/j.1574-6976.2009.00201.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zav'yalov et al. - Adhesive organelles of Gram-negative pathogens assembled with the classical chaperoneusher machinery structure and fu.pdf:pdf},
issn = {1574-6976},
journal = {FEMS microbiology reviews},
keywords = {chaperone,fimbrial adhesions,gram-negative pathogens,immunomodulatory,mono- and,polyadhesive binding,usher machinery},
month = {dec},
pmid = {20070375},
title = {{Adhesive organelles of Gram-negative pathogens assembled with the classical chaperone/usher machinery: structure and function from a clinical standpoint.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20070375},
year = {2009}
}
@article{Andersson2006c,
abstract = {The rapid development of the optical tweezers technique has broadened the applicability of the technique from physics to biology. Although the construction of an optical tweezers system only requires basic skills in optics, the realization of an optical tweezers set LIP is not always as easy as it seems. A number of designs for moveable traps have been presented in the literature. It is not clear to the readers, however, how the movability of the trap affects its quality. We have therefore scrutinized and compared the most commonly used techniques for steering of an optical trap in terms of the aberrations they introduce. The study shows that a moveable trap based on the movement of a lens introduces significantly more aberration than the systems based on fiber optics or the tilting of a mirror.},
annote = {From Duplicate 1 ( Techniques for moveable traps: the influence of aberration in optical tweezers - F{\"{a}}llman, Erik, Andersson, Magnus; Axner, Ove; )
},
author = {Andersson, Magnus and F{\"{a}}llman, Erik and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1117/12.642206},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - Force measuring optical tweezers system for long time measurements of P pili stability - 2006.pdf:pdf},
issn = {0277786X},
journal = {Proceedings of SPIE},
keywords = {BIOLOGICAL APPLICATIONS,CONSTRUCTION,DESIGN,FORCE,LASER,MANIPULATION,MICROMANIPULATION,MICROSCOPE,beam steering,dual trap,force measurement,optical tweezers},
pages = {286--295},
publisher = {SPIE},
title = {{Force measuring optical tweezers system for long time measurements of P pili stability}},
url = {http://apps.isiknowledge.com/full{\_}record.do?product=WOS{\&}search{\_}mode=GeneralSearch{\&}qid=6{\&}SID=S1MHGALlH8ko5hHPpbg{\&}page=1{\&}doc=1},
volume = {6088},
year = {2006}
}
@article{Appleyard2007,
author = {Appleyard, D. C. and Vandermeulen, K. Y. and Lee, H. and Lang, M. J.},
doi = {10.1119/1.2366734},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Appleyard et al. - Optical trapping for undergraduates - 2007.pdf:pdf},
issn = {00029505},
journal = {American Journal of Physics},
number = {1},
pages = {5},
title = {{Optical trapping for undergraduates}},
url = {http://link.aip.org/link/AJPIAS/v75/i1/p5/s1{\&}Agg=doi},
volume = {75},
year = {2007}
}
@article{Kalafut2008,
author = {Kalafut, Bennett and Visscher, Koen},
doi = {10.1016/j.cpc.2008.06.008},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kalafut, Visscher - An objective, model-independent method for detection of non-uniform steps in noisy signals - 2008.pdf:pdf},
issn = {00104655},
journal = {Computer Physics Communications},
month = {nov},
number = {10},
pages = {716--723},
publisher = {Elsevier B.V.},
title = {{An objective, model-independent method for detection of non-uniform steps in noisy signals}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0010465508002282},
volume = {179},
year = {2008}
}
@article{Dong2000,
abstract = {The mechanics of leukocyte (white blood cell; WBC) deformation and adhesion to endothelial cells (EC) has been investigated using a novel in vitro side-view flow assay. HL-60 cell rolling adhesion to surface-immobilized P-selectin was used to model the WBC-EC adhesion process. Changes in flow shear stress, cell deformability, or substrate ligand strength resulted in significant changes in the characteristic adhesion binding time, cell-surface contact and cell rolling velocity. A 2-D model indicated that cell-substrate contact area under a high wall shear stress (20 dyn/cm2) could be nearly twice of that under a low stress (0.5 dyn/cm2) due to shear flow-induced cell deformation. An increase in contact area resulted in more energy dissipation to both adhesion bonds and viscous cytoplasm, whereas the fluid energy that inputs to a cell decreased due to a flattened cell shape. The model also predicted a plateau of WBC rolling velocity as flow shear stresses further increased. Both experimental and computational studies have described how WBC deformation influences the WBC-EC adhesion process in shear flow.},
author = {Dong, C and Lei, X X},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dong, Lei - Biomechanics of cell rolling shear flow, cell-surface adhesion, and cell deformability. - 2000.pdf:pdf},
issn = {0021-9290},
journal = {Journal of biomechanics},
keywords = {Biomechanics,Cell Adhesion,Cell Adhesion: physiology,Cell Membrane,Cell Membrane: physiology,Cell Movement,Cell Movement: physiology,Cell Size,Cell Size: physiology,Endothelium,Endothelium: cytology,Endothelium: physiology,HL-60 Cells,Humans,Leukocytes,Leukocytes: physiology,Models, Biological},
month = {jan},
number = {1},
pages = {35--43},
pmid = {10609516},
title = {{Biomechanics of cell rolling: shear flow, cell-surface adhesion, and cell deformability.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10609516},
volume = {33},
year = {2000}
}
@article{Novikova2013,
author = {Novikova, Elizaveta A. and Storm, Cornelis},
doi = {10.1016/j.bpj.2013.07.039},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Novikova, Storm - Contractile Fibers and Catch-Bond Clusters a Biological Force Sensor - 2013.pdf:pdf},
issn = {00063495},
journal = {Biophysical Journal},
month = {sep},
number = {6},
pages = {1336--1345},
publisher = {Biophysical Society},
title = {{Contractile Fibers and Catch-Bond Clusters: a Biological Force Sensor?}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349513008618},
volume = {105},
year = {2013}
}
@article{Mauritz2010,
abstract = {Investigation of the homeostasis of red blood cells upon infection by Plasmodium falciparum poses complex experimental challenges. Changes in red cell shape, volume, protein, and ion balance are difficult to quantify. In this article, we review a wide range of optical techniques for quantitative measurements of critical homeostatic parameters in malaria-infected red blood cells. Fluorescence lifetime imaging and tomographic phase microscopy, quantitative deconvolution microscopy, and X-ray microanalysis, are used to measure haemoglobin concentration, cell volume, and ion contents. Atomic force microscopy is briefly reviewed in the context of these optical methodologies. We also describe how optical tweezers and optical stretchers can be usefully applied to empower basic malaria research to yield diagnostic information on cell compliance changes upon malaria infection. The combined application of these techniques sheds new light on the detailed mechanisms of malaria infection providing potential for new diagnostic or therapeutic approaches.},
author = {Mauritz, Jakob M a and Esposito, Alessandro and Tiffert, Teresa and Skepper, Jeremy N and Warley, Alice and Yoon, Young-Zoon and Cicuta, Pietro and Lew, Virgilio L and Guck, Jochen R and Kaminski, Clemens F},
doi = {10.1007/s11517-010-0668-0},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Mauritz et al. - Biophotonic techniques for the study of malaria-infected red blood cells. - 2010.pdf:pdf},
issn = {1741-0444},
journal = {Medical {\&} biological engineering {\&} computing},
keywords = {epxma {\'{a}} red cell,flim {\'{a}} fret {\'{a}},haemoglobin concentration {\'{a}} x-ray,malaria {\'{a}} plasmodium falciparum,microanalysis {\'{a}},micropositioning {\'{a}} eds {\'{a}},model {\'{a}},optical tweezers {\'{a}} optical,stretcher {\'{a}},{\'{a}}},
month = {oct},
number = {10},
pages = {1055--63},
pmid = {20661776},
title = {{Biophotonic techniques for the study of malaria-infected red blood cells.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20661776},
volume = {48},
year = {2010}
}
@article{Johnson1991,
abstract = {Uropathogenic strains of Escherichia coli are characterized by the expression of distinctive bacterial properties, products, or structures referred to as virulence factors because they help the organism overcome host defenses and colonize or invade the urinary tract. Virulence factors of recognized importance in the pathogenesis of urinary tract infection (UTI) include adhesins (P fimbriae, certain other mannose-resistant adhesins, and type 1 fimbriae), the aerobactin system, hemolysin, K capsule, and resistance to serum killing. This review summarizes the virtual explosion of information regarding the epidemiology, biochemistry, mechanisms of action, and genetic basis of these urovirulence factors that has occurred in the past decade and identifies areas in need of further study. Virulence factor expression is more common among certain genetically related groups of E. coli which constitute virulent clones within the larger E. coli population. In general, the more virulence factors a strain expresses, the more severe an infection it is able to cause. Certain virulence factors specifically favor the development of pyelonephritis, others favor cystitis, and others favor asymptomatic bacteriuria. The currently defined virulence factors clearly contribute to the virulence of wild-type strains but are usually insufficient in themselves to transform an avirulent organism into a pathogen, demonstrating that other as-yet-undefined virulence properties await discovery. Virulence factor testing is a useful epidemiological and research tool but as yet has no defined clinical role. Immunological and biochemical anti-virulence factor interventions are effective in animal models of UTI and hold promise for the prevention of UTI in humans.},
author = {Johnson, J R},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Johnson - Virulence factors in Escherichia coli urinary tract infection. - 1991.pdf:pdf},
issn = {0893-8512},
journal = {Clinical microbiology reviews},
keywords = {Adhesins,Animals,Antigens,Bacterial,Bacterial Adhesion,Bacterial Outer Membrane Proteins,Blood Bactericidal Activity,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli: immunology,Escherichia coli: pathogenicity,Fimbriae,Hemolysin Proteins,Humans,Hydroxamic Acids,Surface,Virulence},
month = {jan},
number = {1},
pages = {80--128},
pmid = {1672263},
title = {{Virulence factors in Escherichia coli urinary tract infection.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=358180{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {4},
year = {1991}
}
@article{Sauer2002,
abstract = {Periplasmic chaperones direct the assembly of adhesive, multi-subunit pilus fibers that play critical roles in bacterial pathogenesis. Pilus assembly occurs via a donor strand exchange mechanism in which the N-terminal extension of one subunit replaces the chaperone G(1) strand that transiently occupies a groove in the neighboring subunit. Here, we show that the chaperone primes the subunit for assembly by holding the groove in an open, activated conformation. During donor strand exchange, the subunit undergoes a topological transition that triggers the closure of the groove and seals the N-terminal extension in place. It is this topological transition, made possible only by the priming action of the chaperone that drives subunit assembly into the fiber.},
author = {Sauer, Frederic G and Pinkner, Jerome S and Waksman, Gabriel and Hultgren, Scott J},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sauer et al. - Chaperone priming of pilus subunits facilitates a topological transition that drives fiber formation. - 2002.pdf:pdf},
issn = {0092-8674},
journal = {Cell},
keywords = {Bacterial Proteins,Bacterial Proteins: chemistry,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Escherichia coli Proteins: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: metabolism,Membrane Proteins,Models, Molecular,Molecular Chaperones,Molecular Chaperones: chemistry,Molecular Chaperones: genetics,Molecular Chaperones: metabolism,Periplasmic Proteins,Periplasmic Proteins: chemistry,Periplasmic Proteins: genetics,Periplasmic Proteins: metabolism,Protein Structure, Tertiary,Proton-Translocating ATPases,Recombinant Fusion Proteins,Recombinant Fusion Proteins: chemistry,Recombinant Fusion Proteins: genetics,Recombinant Fusion Proteins: metabolism},
month = {nov},
number = {4},
pages = {543--51},
pmid = {12437927},
title = {{Chaperone priming of pilus subunits facilitates a topological transition that drives fiber formation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12437927},
volume = {111},
year = {2002}
}
@article{Lundmark2003,
abstract = {Sorting nexin 9 (SNX9) belongs to a family of proteins, the sorting nexins, that are characterized by the presence of a subclass of the phosphoinositide-binding phox domain. SNX9 has in its amino terminus a Src homology 3 domain and a region with predicted low complexity followed by a carboxyl-terminal part containing the phox domain. We previously found that SNX9 is one of the major proteins in hematopoietic cells that binds to the alpha and beta2-appendages of adaptor protein complex 2 (AP-2), a protein with a critical role in the formation of clathrin-coated vesicles at the plasma membrane. In the present study we show that clathrin and dynamin-2, two other essential molecules in the endocytic process, also interact with SNX9. We found that both AP-2 and clathrin bind to the low complexity region in SNX9 in a cooperative manner, whereas dynamin-2 binds to the Src homology 3 domain. In the cytosol, SNX9 is present in a 14.5 S complex containing dynamin-2 and an unidentified 41-kDa protein. In HeLa cells, SNX9 co-localized with both AP-2 and dynamin-2 at the plasma membrane or on vesicular structures derived from it but not with the early endosomal marker EEA1 or with AP-1. The results suggest that SNX9 may be recruited together with dynamin-2 and become co-assembled with AP-2 and clathrin at the plasma membrane. Overexpression in both K562 and HeLa cells of truncated forms of SNX9 interfered with the uptake of transferrin, consistent with a role of SNX9 in endocytosis.},
annote = {        From Duplicate 1 (                   Sorting nexin 9 participates in clathrin-mediated endocytosis through interactions with the core components.                 - Lundmark, Richard; Carlsson, Sven R )
                
        
        
      },
author = {Lundmark, Richard and Carlsson, Sven R},
doi = {10.1074/jbc.M307334200},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Lundmark, Carlsson - Sorting nexin 9 participates in clathrin-mediated endocytosis through interactions with the core components - 2003.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Adaptor Protein Complex 2,Adaptor Protein Complex 2: metabolism,Binding Sites,Carrier Proteins,Carrier Proteins: genetics,Carrier Proteins: metabolism,Carrier Proteins: physiology,Clathrin,Clathrin-Coated Vesicles,Clathrin-Coated Vesicles: metabolism,Clathrin: metabolism,Dynamin II,Dynamin II: metabolism,Endocytosis,Hela Cells,Humans,K562 Cells,Protein Binding,Sequence Deletion,Transfection,Vesicular Transport Proteins,src Homology Domains},
month = {nov},
number = {47},
pages = {46772--81},
pmid = {12952949},
title = {{Sorting nexin 9 participates in clathrin-mediated endocytosis through interactions with the core components}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12952949},
volume = {278},
year = {2003}
}
@article{Sekirov2010,
author = {Sekirov, Inna and Russell, Shannon L and Antunes, L Caetano M and Finlay, B Brett},
doi = {10.1152/physrev.00045.2009.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sekirov et al. - Gut Microbiota in Health and Disease - 2010.pdf:pdf},
journal = {Physiological Reviews},
number = {3},
pages = {859--904},
title = {{Gut Microbiota in Health and Disease}},
volume = {90},
year = {2010}
}
@article{DeMarco2014,
author = {{De Marco}, Tommaso and Cazzato, Dario and Leo, Marco and Distante, Cosimo},
doi = {10.1016/j.patcog.2014.08.007},
file = {:E$\backslash$:/Mina Dokument/Mendeley/De Marco et al. - Randomized circle detection with isophotes curvature analysis - 2014.pdf:pdf},
issn = {00313203},
journal = {Pattern Recognition},
keywords = {Circle detection,Density estimation,Isophotes,Sampling strategy},
month = {aug},
pages = {1--11},
publisher = {Elsevier},
title = {{Randomized circle detection with isophotes curvature analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0031320314002982},
year = {2014}
}
@article{Keller2003,
abstract = {Measurements made on large ensembles of molecules are routinely interpreted using thermodynamics, but the normal rules of thermodynamics may not apply to measurements made on single molecules. Using a polymer stretching experiment as an example, it is shown that in the limit of a single, short molecule the outcome of experimental measurements may depend on which variables are held fixed and which are allowed to fluctuate. Thus an experiment in which the end-to-end distance of the polymer molecule is fixed and the tension fluctuates yields a different result than an experiment where the force is fixed and the end-to-end distance fluctuates. It is further shown that this difference is due to asymmetry in the distribution of end-to-end distances for a single molecule, and that the difference vanishes in the appropriate thermodynamic limit; that is, as the polymer molecule becomes long compared to its persistence length. Despite these differences, much of the thermodynamic formalism still applies on the single-molecule level if the thermodynamic free energies are replaced with appropriate potentials of mean force. The primary remaining differences are consequences of the fact that unlike the free energies, the potentials of mean force are not in general homogeneous functions of their variables. The basic thermodynamic concepts of an intensive or extensive quantity, and the thermodynamic relationships that follow from them, are therefore less useful for interpreting single-molecule experiments.},
author = {Keller, David and Swigon, David and Bustamante, Carlos},
doi = {10.1016/S0006-3495(03)74892-9},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Keller, Swigon, Bustamante - Relating single-molecule measurements to thermodynamics. - 2003.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Anisotropy,Biopolymers,Biopolymers: chemistry,Computer Simulation,DNA,DNA: chemistry,Elasticity,Energy Transfer,Kinetics,Micromanipulation,Micromanipulation: methods,Models, Molecular,Models, Statistical,Molecular Conformation,Motion,Nucleic Acid Conformation,Polymers,Polymers: chemistry,Protein Conformation,Research Design,Sensitivity and Specificity,Stress, Mechanical,Thermodynamics},
month = {feb},
number = {2 Pt 1},
pages = {733--8},
pmid = {12547757},
publisher = {Elsevier},
title = {{Relating single-molecule measurements to thermodynamics.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302653{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {84},
year = {2003}
}
@article{Evans1999a,
abstract = {Weak non-covalent interactions between large molecules govern interfacial structure and adhesion in biology. Because of thermal activation, these bonds have modest lifetimes and bond lifetimes are progressively shortened under application of external force. Theory predicts that bond survival time depends on how fast the force is applied and the expected survival time specifies the most likely breakage force (strength) at a given loading rate (force/time). Plotted as a function of log(e) (loading rate), the dynamic spectrum of bond strength provides an image of the prominent barriers traversed in the energy landscape along the unbinding pathway, which establishes a direct link between measurements of bond force and molecular-scale chemistry. Experimentally, the challenge is to measure bond strength over several orders of magnitude in loading rate. With a recently designed probe technique, we have measured strengths of single receptor-ligand bonds and receptor-membrane anchoring over an enormous range of loading rates from 10-1 pN/s to 105 pN/s, which reveals an inner view of the complexity of these interactions. Copyright (C) 1999 Elsevier Science B.V.},
author = {Evans, Evan},
doi = {10.1016/S0301-4622(99)00108-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans - Looking inside molecular bonds at biological interfaces with dynamic force spectroscopy - 1999.pdf:pdf},
isbn = {0301-4622},
issn = {03014622},
journal = {Biophysical Chemistry},
keywords = {Dynamic force spectroscopy,Energy landscapes of biomolecular bonds,Receptor-ligand interactions,Receptor-membrane anchoring},
number = {2-3},
pages = {83--97},
pmid = {10631793},
title = {{Looking inside molecular bonds at biological interfaces with dynamic force spectroscopy}},
volume = {82},
year = {1999}
}
@article{Stirnemann2013,
abstract = {Force spectroscopies have emerged as a powerful and unprecedented tool to study and manipulate biomolecules directly at a molecular level. Usually, protein and DNA behavior under force is described within the framework of the worm-like chain (WLC) model for polymer elasticity. Although it has been surprisingly successful for the interpretation of experimental data, especially at high forces, the WLC model lacks structural and dynamical molecular details associated with protein relaxation under force that are key to the understanding of how force affects protein flexibility and reactivity. We use molecular dynamics simulations of ubiquitin to provide a deeper understanding of protein relaxation under force. We find that the WLC model successfully describes the simulations of ubiquitin, especially at higher forces, and we show how protein flexibility and persistence length, probed in the force regime of the experiments, are related to how specific classes of backbone dihedral angles respond to applied force. Although the WLC model is an average, backbone model, we show how the protein side chains affect the persistence length. Finally, we find that the diffusion coefficient of the protein's end-to-end distance is on the order of 10(8) nm(2)/s, is position and side-chain dependent, but is independent of the length and independent of the applied force, in contrast with other descriptions.},
author = {Stirnemann, Guillaume and Giganti, David and Fernandez, Julio M and Berne, B J},
doi = {10.1073/pnas.1300596110},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Stirnemann et al. - Elasticity, structure, and relaxation of extended proteins under force. - 2013.pdf:pdf},
isbn = {1091-6490 (Electronic)$\backslash$n0027-8424 (Linking)},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Biophysical Phenomena,Computer Simulation,Elasticity,Microscopy, Atomic Force,Models, Molecular,Molecular Dynamics Simulation,Proteins,Proteins: chemistry,Stress, Mechanical,Ubiquitin,Ubiquitin: chemistry},
number = {10},
pages = {3847--52},
pmid = {23407163},
title = {{Elasticity, structure, and relaxation of extended proteins under force.}},
url = {http://www.pnas.org/content/early/2013/02/13/1300596110.abstract},
volume = {110},
year = {2013}
}
@article{Zhang2010,
annote = {From Duplicate 1 ( Computational Fluid Dynamics Model of Bladder-Urethra System for SUI - Zhang, X J; Li, X Y; Wang, J L )
},
author = {Zhang, X J and Li, X Y and Wang, J L},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zhang, Li, Wang - Computational Fluid Dynamics Model of Bladder-Urethra System for SUI - 2010.pdf:pdf},
journal = {Fluid Dynamics},
keywords = {bladder-urethra system,cfd,paper3,sui,urodynam-},
mendeley-tags = {paper3},
pages = {1495--1498},
title = {{Computational Fluid Dynamics Model of Bladder-Urethra System for SUI}},
year = {2010}
}
@article{Jauffred2008a,
abstract = {We show that individual colloidal CdSe-core quantum dots can be optically trapped and manipulated in three dimensions by an infrared continuous wave laser operated at low laser powers. This makes possible utilizing quantum dots not only for visualization but also for manipulation, an important advantage for single molecule experiments. Moreover, we provide quantitative information about the magnitude of forces applicable to a single quantum dot and of the polarizability of an individual quantum dot.},
author = {Jauffred, Liselotte and Richardson, Andrew C and Oddershede, Lene B.},
doi = {10.1021/nl801962f},
journal = {Nano Lett},
keywords = {Blinking,Fluorescence,In-Vivo,Nanoparticles,Semiconductor Nanocrystals,Tweezers,quantum dots},
mendeley-tags = {quantum dots},
number = {10},
pages = {3376--3380},
title = {{Three-Dimensional Optical Control of Individual Quantum Dots}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=000259906800055},
volume = {8},
year = {2008}
}
@article{Nilsson2006,
abstract = {The FimH protein is the adhesive subunit of Escherichia coli type 1 fimbriae. It mediates shear-dependent bacterial binding to monomannose (1M)-coated surfaces manifested by the existence of a shear threshold for binding, below which bacteria do not adhere. The 1M-specific shear-dependent binding of FimH is consistent with so-called catch bond interactions, whose lifetime is increased by tensile force. We show here that the oligosaccharide-specific interaction of FimH with another of its ligands, trimannose (3M), lacks a shear threshold for binding, since the number of bacteria binding under static conditions is higher than under any flow. However, similar to 1M, the binding strength of surface-interacting bacteria is enhanced by shear. Bacteria transition from rolling into firm stationary surface adhesion as the shear increases. The shear-enhanced bacterial binding on 3M is mediated by catch bond properties of the 1M-binding subsite within the extended oligosaccharide-binding pocket of FimH, since structural mutations in the putative force-responsive region and in the binding site affect 1M- and 3M-specific binding in an identical manner. A shear-dependent conversion of the adhesion mode is also exhibited by P-fimbriated E. coli adhering to digalactose surfaces.},
author = {Nilsson, Lina M and Thomas, Wendy E and Trintchina, Elena and Vogel, Viola and Sokurenko, Evgeni V},
doi = {10.1074/jbc.M511496200},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nilsson et al. - Catch bond-mediated adhesion without a shear threshold trimannose versus monomannose interactions with the FimH adhesin.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Adhesins, Bacterial,Adhesins, Bacterial: chemistry,Adhesins, Escherichia coli,Adhesins, Escherichia coli: chemistry,Adhesins, Escherichia coli: metabolism,Cell Adhesion,Escherichia coli,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Galactose,Galactose: chemistry,Lectins,Lectins: chemistry,Ligands,Mannose,Mannose: chemistry,Models, Molecular,Oligosaccharides,Oligosaccharides: chemistry,Protein Structure, Tertiary,Stress, Mechanical},
month = {jun},
number = {24},
pages = {16656--63},
pmid = {16624825},
title = {{Catch bond-mediated adhesion without a shear threshold: trimannose versus monomannose interactions with the FimH adhesin of Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16624825},
volume = {281},
year = {2006}
}
@article{Bullitt1995,
abstract = {Bacterial adhesion pili are designed to bind specifically and maintain attachment of bacteria to target cells. Uropathogenic P-pili are sufficiently mechanically resilient to resist the cleansing action of urine flow that removes most other bacteria. P-pili are 68 A in diameter and approximately 1 micron long, and are composed of approximately 1,000 copies of the principal structural protein, PapA. They are attached to the outer membrane by a minor structural protein, PapH and are terminated by an approximately 20 A diameter fibrillus composed of PapK, PapE and PapF, which presents the host-binding adhesin PapG. The amino-acid sequences of PapA, PapE, and PapF are similar, with highly conserved C-termini being responsible for binding to PapD, the periplasmic chaperone. Our three-dimensional reconstruction indicates that pili are formed by the tight winding of a much thinner structure. A structural transition allows the pilus to unravel without depolymerizing, producing a thin, extended structure five times the length of the original pilus.},
author = {Bullitt, Esther and Makowski, Lee},
journal = {Nature},
number = {6510},
pages = {164--167},
title = {{Structural polymorphism of bacterial adhesion pili.}},
volume = {373},
year = {1995}
}
@phdthesis{Tanskanen2002,
author = {Tanskanen, Jarna},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tanskanen - Expression of bacterial adhesins in E . coli From mapping of adhesive epitopes to structure - 2002.pdf:pdf},
title = {{Expression of bacterial adhesins in E . coli : From mapping of adhesive epitopes to structure}},
year = {2002}
}
@article{Lanata2013,
abstract = {Estimation of pathogen-specific causes of child diarrhea deaths is needed to guide vaccine development and other prevention strategies. We did a systematic review of articles published between 1990 and 2011 reporting at least one of 13 pathogens in children <5 years of age hospitalized with diarrhea. We included 2011 rotavirus data from the Rotavirus Surveillance Network coordinated by WHO. We excluded studies conducted during diarrhea outbreaks that did not discriminate between inpatient and outpatient cases, reporting nosocomial infections, those conducted in special populations, not done with adequate methods, and rotavirus studies in countries where the rotavirus vaccine was used. Age-adjusted median proportions for each pathogen were calculated and applied to 712 000 deaths due to diarrhea in children under 5 years for 2011, assuming that those observed among children hospitalized for diarrhea represent those causing child diarrhea deaths. 163 articles and WHO studies done in 31 countries were selected representing 286 inpatient studies. Studies seeking only one pathogen found higher proportions for some pathogens than studies seeking multiple pathogens (e.g. 39{\%} rotavirus in 180 single-pathogen studies vs. 20{\%} in 24 studies with 5-13 pathogens, p<0.0001). The percentage of episodes for which no pathogen could be identified was estimated to be 34{\%}; the total of all age-adjusted percentages for pathogens and no-pathogen cases was 138{\%}. Adjusting all proportions, including unknowns, to add to 100{\%}, we estimated that rotavirus caused 197 000 [Uncertainty range (UR) 110 000-295 000], enteropathogenic E. coli 79 000 (UR 31 000-146 000), calicivirus 71 000 (UR 39 000-113 000), and enterotoxigenic E. coli 42 000 (UR 20 000-76 000) deaths. Rotavirus, calicivirus, enteropathogenic and enterotoxigenic E. coli cause more than half of all diarrheal deaths in children <5 years in the world.},
author = {Lanata, Claudio F and Fischer-Walker, Christa L and Olascoaga, Ana C and Torres, Carla X and Aryee, Martin J and Black, Robert E},
doi = {10.1371/journal.pone.0072788},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lanata et al. - Global causes of diarrheal disease mortality in children 5 years of age a systematic review. - 2013.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Caliciviridae Infections,Caliciviridae Infections: epidemiology,Caliciviridae Infections: etiology,Caliciviridae Infections: mortality,Child, Preschool,Diarrhea,Diarrhea: epidemiology,Diarrhea: etiology,Diarrhea: mortality,Escherichia coli Infections,Escherichia coli Infections: epidemiology,Escherichia coli Infections: etiology,Escherichia coli Infections: mortality,Humans,Infant,Infant, Newborn,Rotavirus Infections,Rotavirus Infections: epidemiology,Rotavirus Infections: etiology,Rotavirus Infections: mortality},
month = {jan},
number = {9},
pages = {e72788},
pmid = {24023773},
title = {{Global causes of diarrheal disease mortality in children <5 years of age: a systematic review.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3762858{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {8},
year = {2013}
}
@article{Reihani2006,
author = {Reihani, S and Khalesifard, H and Golestanian, R},
doi = {10.1016/j.optcom.2005.08.018},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Reihani, Khalesifard, Golestanian - Measuring lateral efficiency of optical traps The effect of tube length - 2006.pdf:pdf},
issn = {00304018},
journal = {Optics Communications},
keywords = {optical trap,spherical aberration,trap efficiency,tube length},
month = {mar},
number = {1},
pages = {204--211},
title = {{Measuring lateral efficiency of optical traps: The effect of tube length}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0030401805008321},
volume = {259},
year = {2006}
}
@article{Costa2015,
author = {Costa, Tiago R. D. and Felisberto-Rodrigues, Catarina and Meir, Amit and Prevost, Marie S. and Redzej, Adam and Trokter, Martina and Waksman, Gabriel},
doi = {10.1038/nrmicro3456},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Costa et al. - Secretion systems in Gram-negative bacteria structural and mechanistic insights - 2015.pdf:pdf},
issn = {1740-1526},
journal = {Nature Reviews Microbiology},
number = {6},
pages = {343--359},
publisher = {Nature Publishing Group},
title = {{Secretion systems in Gram-negative bacteria: structural and mechanistic insights}},
url = {http://www.nature.com/doifinder/10.1038/nrmicro3456},
volume = {13},
year = {2015}
}
@article{Akinlar2013,
abstract = {We propose a real-time, parameter-free circle detection algorithm that has high detection rates, produces accurate results and controls the number of false circle detections. The algorithm makes use of the contiguous (connected) set of edge segments produced by our parameter-free edge segment detector, the Edge Drawing Parameter Free (EDPF) algorithm; hence the name EDCircles. The proposed algorithm first computes the edge segments in a given image using EDPF, which are then converted into line segments. The detected line segments are converted into circular arcs, which are joined together using two heuristic algorithms to detect candidate circles and near-circular ellipses. The candidates are finally validated by an a contrario validation step due to the Helmholtz principle, which eliminates false detections leaving only valid circles and near-circular ellipses. We show through experimentation that EDCircles works real-time (10-20 ms for 640??480 images), has high detection rates, produces accurate results, and is very suitable for the next generation real-time vision applications including automatic inspection of manufactured products, eye pupil detection, circular traffic sign detection, etc. ?? 2012 Elsevier Ltd.},
author = {Akinlar, Cuneyt and Topal, Cihan},
doi = {10.1016/j.patcog.2012.09.020},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Akinlar, Topal - EDCircles A real-time circle detector with a false detection control - 2013.pdf:pdf},
issn = {00313203},
journal = {Pattern Recognition},
month = {mar},
number = {3},
pages = {725--740},
publisher = {Elsevier},
title = {{EDCircles: A real-time circle detector with a false detection control}},
volume = {46},
year = {2013}
}
@article{Vogel2004b,
author = {Vogel, Alexandre and Elmabsout, Badaoui and Gintz, Daniel},
doi = {10.1016/j.crme.2004.03.017},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Vogel, Elmabsout, Gintz - Mod{\'{e}}lisation du champ des vitesses de l'urine dans un bolus ur{\'{e}}t{\'{e}}ral - 2004.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Vogel, Elmabsout, Gintz - Mod{\'{e}}lisation du champ des vitesses de l'urine dans un bolus ur{\'{e}}t{\'{e}}ral - 2004.doc:doc},
issn = {16310721},
journal = {Comptes Rendus M{\'{e}}canique},
keywords = {0,03 m s,1,2,abridged english version,and gintz et al,between the bladder and,biomechanics,bolus,by isolated pockets,called bolus,gintz,it,modelling,on the work of,speed v 0,the kidney,this study is based,through the,ureter,ureter at a constant,urine flow,urine transport is made},
month = {sep},
number = {9},
pages = {737--742},
title = {{Mod{\'{e}}lisation du champ des vitesses de l'urine dans un bolus ur{\'{e}}t{\'{e}}ral}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1631072104001184},
volume = {332},
year = {2004}
}
@article{Li2007a,
abstract = {CfaE is the minor, tip-localized adhesive subunit of colonization factor antigen I fimbriae (CFA/I) of enterotoxigenic Escherichia coli and is thought to be essential for the attachment of enterotoxigenic E. coli to the human small intestine early in diarrhea pathogenesis. The crystal structure of an in cis donor strand complemented CfaE was determined, providing the first atomic view of a fimbrial subunit assembled by the alternate chaperone pathway. The in cis donor strand complemented variant of CfaE structure consists of an N-terminal adhesin domain and a C-terminal pilin domain of similar size, each featuring a variable immunoglobulin-like fold. Extensive interactions exist between the two domains and appear to rigidify the molecule. The upper surface of the adhesin domain distal to the pilin domain reveals a depression consisting of conserved residues including Arg(181), previously shown to be necessary for erythrocyte adhesion. Mutational analysis revealed a cluster of conserved, positively charged residues that are required for CFA/I-mediated hemagglutination, implicating this as the receptor-binding pocket. Mutations in a few subclass-specific residues that surround the cluster displayed differential effects on the two red cell species used in hemagglutination, suggesting that these residues play a role in host or cell specificity. The C-terminal donor strand derived from the major subunit CfaB is folded as a beta-strand and fits into a hydrophobic groove in the pilin domain to complete the immunoglobulin fold. The location of this well ordered donor strand suggests the positioning and orientation of the subjacent major fimbrial subunit CfaB in the native assembly of CFA/I fimbriae.},
author = {Li, Yong-Fu and Poole, Steven and Rasulova, Fatima and McVeigh, Annette L and Savarino, Stephen J and Xia, Di},
doi = {10.1074/jbc.M700921200},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Li et al. - A receptor-binding site as revealed by the crystal structure of CfaE, the colonization factor antigen I fimbrial adhesin of.pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Adhesins, Bacterial,Adhesins, Bacterial: chemistry,Binding Sites,Colicins,Colicins: chemistry,Crystallography, X-Ray,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Protein Structure, Tertiary,Protein Subunits,Protein Subunits: chemistry},
month = {aug},
number = {33},
pages = {23970--80},
pmid = {17569668},
title = {{A receptor-binding site as revealed by the crystal structure of CfaE, the colonization factor antigen I fimbrial adhesin of enterotoxigenic Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17569668},
volume = {282},
year = {2007}
}
@article{Ayano2006,
abstract = {We quantitatively examined the possible damage to the growth and cell division ability of Escherichia coli caused by 1064-nm optical trapping. Using the synchronous behavior of two sister E. coli cells, the growth and interdivision times between those two cells, one of which was trapped by optical tweezers, the other was not irradiated, were compared using an on-chip single cell cultivation system. Cell growth stopped during the optical trapping period, even with the smallest irradiated power on the trapped cells. Moreover, the damage to the cell's growth and interdivision period was proportional to the total irradiated energy (work) on the cell, i.e., irradiation time multiplied by irradiation power. The division ability was more easily affected by a smaller energy, 0.36 J, which was 30{\%} smaller than the energy that adversely affected growth, 0.54 J. The results indicate that the damage caused by optical trapping can be estimated from the total energy applied to cells, and furthermore, that the use of optical trapping for manipulating cells might cause damage to cell division and growth mechanisms, even at wavelengths under 1064 nm, if the total irradiation energy is excessive. ?? 2006 Elsevier Inc. All rights reserved.},
author = {Ayano, Satoru and Wakamoto, Yuichi and Yamashita, Shinobu and Yasuda, Kenji},
doi = {10.1016/j.bbrc.2006.09.115},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ayano et al. - Quantitative measurement of damage caused by 1064-nm wavelength optical trapping of Escherichia coli cells using on-chip.pdf:pdf},
isbn = {0006-291X},
issn = {0006291X},
journal = {Biochemical and Biophysical Research Communications},
keywords = {1064-nm wavelength laser,Cell division,Cell growth,Damage,Escherichia coli,Hyperbolic curve of damage,Isolated cultivation,On-chip single-cell cultivation,Optical tweezers},
number = {3},
pages = {678--684},
pmid = {17027921},
title = {{Quantitative measurement of damage caused by 1064-nm wavelength optical trapping of Escherichia coli cells using on-chip single cell cultivation system}},
volume = {350},
year = {2006}
}
@article{Sjostrom1987,
author = {Sjostrom, Michael and Wold, Svante and Wieslander, Ake and Rilfors, Leif},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sjostrom et al. - Signal peptide amino acid sequences in Escherichia coli contain information related to fmal protein localization . A m.pdf:pdf},
keywords = {amino acid sequencelescherichia colil,multivariate data analysis,signal peptide,targeting information},
number = {3},
pages = {823--831},
title = {{Signal peptide amino acid sequences in Escherichia coli contain information related to fmal protein localization . A multivariate data analysis SRQFRALI PFFAAFC LPVFAHE EE-I-}},
volume = {6},
year = {1987}
}
@article{Rappaz2005,
abstract = {We have developed a digital holographic microscope (DHM), in a transmission mode, adapted to the quantitative study of cellular dynamics. Living cells in culture are optically probed by measuring the phase shift they produce on the transmitted wave front. The high temporal stability of the phase signal, equivalent to ?/1800, and the low acquisition time ({\~{}}20�s) enable to monitor cellular dynamics processes. An experimental procedure allowing to calculate both the integral refractive index and the cellular thickness (morphometry) from the measured phase shift is presented. Specifically, the method has been applied to study the dynamics of neurons in culture during a hypotonic stress. Such stress produces a paradoxical decrease of the phase which can be entirely resolved by applying the methodological approach described in this article; indeed the method allows to determine independently the thickness and the integral refractive index of cells.},
author = {Rappaz, Benjamin and Marquet, Pierre and Cuche, Etienne and Emery, Yves and Depeursinge, Christian and Magistretti, Pierre},
doi = {10.1364/OPEX.13.009361},
journal = {Optics Express},
keywords = {Cell analysis,Computer holography,Metrology,Phase measurement},
number = {23},
pages = {9361--9373},
publisher = {OSA},
title = {{Measurement of the integral refractive index and dynamic cell morphometry of living cells with digital holographic microscopy}},
url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-13-23-9361},
volume = {13},
year = {2005}
}
@article{Jonsson2004,
author = {Jonsson, Per},
doi = {10.1117/12.578231},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jonsson - Development of a fluorescence-based point detector for biological sensing - 2004.pdf:pdf},
issn = {0277786X},
journal = {Proceedings of SPIE},
keywords = {biological agent detection,photomultiplier tube array,time-resolved fluorescence,uv induced fluorescence},
pages = {60--74},
publisher = {Spie},
title = {{Development of a fluorescence-based point detector for biological sensing}},
url = {http://link.aip.org/link/?PSI/5617/60/1{\&}Agg=doi},
volume = {5617},
year = {2004}
}
@article{Rudin1994,
author = {Rudin, Anna and Mcconnell, Moyra M},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rudin, Mcconnell - Monoclonal antibodies against enterotoxigenic Escherichia coli colonization factor antigen I ( CFA I ) that cross-re.pdf:pdf},
title = {{Monoclonal antibodies against enterotoxigenic Escherichia coli colonization factor antigen I ( CFA / I ) that cross-react immunologically with Monoclonal Antibodies against Enterotoxigenic Escherichia coli Colonization Factor Antigen I ( CFA / I ) That Cr}},
year = {1994}
}
@article{Selvaggi2010,
abstract = {Cell mechanical properties play an important role in determining many cellular activities. Passive microrheology techniques, such as Multiple-Particle-Tracking (MPT) give an insight into the structural rearrangements and viscoelastic response of a wide range of materials, in particular soft materials and complex fluids like cell cytoplasm in living cells. The technique finds an important field of application in large cells such as oocytes where, during their growth, several organelles and molecules are displaced in specific territories of the cell instrumental for later embryonic development. To measure cell mechanics, cells are usually deformed by many techniques that are slow and often invasive. To overcome these limits, the MPT technique is applied. Probe particles are embedded in the viscoelastic sample and their properties are extracted from the thermal fluctuation spectra measured using digital video-microscopy. The Brownian motion of a probe particle immersed in a network is directly related to the network's mechanical properties. Particles exhibit larger motions when their local environments are less rigid or less viscous. The mean-square-displacement (MSD) of the particle's trajectory is used to quantify its amplitude of motions over different time scales.},
author = {Selvaggi, Lara and Salemme, Marinella and Vaccaro, Carmen and Pesce, Giuseppe and Rusciano, Giulia and Sasso, Antonio and Campanella, Chiara and Carotenuto, Rosa},
doi = {10.1016/j.ymeth.2009.12.008},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Selvaggi et al. - Multiple-Particle-Tracking to investigate viscoelastic properties in living cells. - 2010.pdf:pdf},
issn = {1095-9130},
journal = {Methods (San Diego, Calif.)},
keywords = {Animals,Biophysics,Biophysics: methods,COS Cells,Cercopithecus aethiops,Cytological Techniques,Cytoplasm,Cytoplasm: metabolism,Elasticity,Microscopy, Video,Microscopy, Video: methods,Models, Biological,Oligonucleotide Probes,Oligonucleotide Probes: metabolism,Oocytes,Oocytes: metabolism,Particle Size,Rheology,Viscosity,Xenopus laevis,Xenopus laevis: metabolism},
month = {may},
number = {1},
pages = {20--6},
pmid = {20035872},
publisher = {Elsevier Inc.},
title = {{Multiple-Particle-Tracking to investigate viscoelastic properties in living cells.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20035872},
volume = {51},
year = {2010}
}
@article{Baga1988,
abstract = {E. coil expressing the papA-I genes produce pili that mediate specific adhesion to mammalian cells. We show that the major pilus subunit gene, papA, is part of a polycistronic transcriptional unit subject to specific posttranscriptional processing. A primary transcript also encoding the papB regulatory gene product is endon cleolytically cleaved, resulting in the rapid decay of the papB-encoding 5′ half of the mRNA, whereas the papA-encoding 3′ half remains as a quite stable transcript. Processing and differential mRNA stability thereby result in accumulation of mRNAs encoding only the major pilus subunit. A sequence immediately downstream of the papA coding region may serve as a stability determinant for the papA transcript and concomitantly attenuate read-through transcription into the minor pilus subunit gene papH. This suggests that differential expression of genes within an operon may include endo- and exonucleolytic processing of the mRNA.},
author = {B{\aa}ga, M and G{\"{o}}ransson, Mikael and Normark, S and Uhlin, Bernt Eric},
doi = {dx.doi.org/10.1016/0092-8674(88)90508-9},
journal = {Cell},
number = {2},
pages = {197--206},
title = {{Processed mRNA with differential stability in the regulation of E. coli pilin gene expression}},
volume = {52},
year = {1988}
}
@article{Bianco2007,
abstract = {Titin is a giant protein that determines the elasticity of striated muscle and is thought to play important roles in numerous regulatory processes. Previous studies have shown that titin's PEVK domain interacts with F-actin, thereby creating viscous forces of unknown magnitude that may modulate muscle contraction. Here we measured, with optical tweezers, the forces necessary to dissociate F-actin from individual molecules of recombinant PEVK fragments rich either in polyE or PPAK motifs. Rupture forces at a stretch rate of 250 nm/s displayed a wide, nonnormal distribution with a peak at approximately 8 pN in the case of both fragments. Dynamic force spectroscopy experiments revealed low spontaneous off-rates that were increased even by low forces. The loading-rate dependence of rupture force was biphasic for polyE in contrast with the monophasic response observed for PPAK. Analysis of the molecular lengths at which rupture occurred indicated that there are numerous actin-binding regions along the PEVK fragments' contour, suggesting that the PEVK domain is a promiscuous actin-binding partner. The complexity of PEVK-actin interaction points to an adaptable viscoelastic mechanism that safeguards sarcomeric structural integrity in the relaxed state and modulates thixotropic behavior during contraction.},
author = {Bianco, Pasquale and Nagy, Attila and Kengyel, Andr{\'{a}}s and Szatm{\'{a}}ri, D{\'{a}}vid and M{\'{a}}rtonfalvi, Zsolt and Huber, Tam{\'{a}}s and Kellermayer, Mikl{\'{o}}s S Z},
doi = {10.1529/biophysj.107.106153},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bianco et al. - Interaction forces between F-actin and titin PEVK domain measured with optical tweezers. - 2007.pdf:pdf},
isbn = {3672536261},
issn = {00063495},
journal = {Biophysical journal},
number = {6},
pages = {2102--2109},
pmid = {17513381},
title = {{Interaction forces between F-actin and titin PEVK domain measured with optical tweezers.}},
volume = {93},
year = {2007}
}
@article{Anantha2004b,
abstract = {Colonization factor antigen I (CFA/I) is the archetype of eight genetically related fimbriae of enterotoxigenic Escherichia coli (ETEC) designated class 5 fimbriae. Assembled by the alternate chaperone pathway, these organelles comprise a rigid stalk of polymerized major subunits and an apparently tip-localized minor adhesive subunit. We examined the evolutionary relationships of class 5-specific structural proteins and correlated these with functional properties. We sequenced the gene clusters encoding coli surface antigen 4 (CS4), CS14, CS17, CS19, and putative colonization factor antigen O71 (PCFO71) and analyzed the deduced proteins and the published homologs of CFA/I, CS1, and CS2. Multiple alignment and phylogenetic analysis of the proteins encoded by each operon define three subclasses, 5a (CFA/I, CS4, and CS14), 5b (CS1, CS17, CS19, and PCFO71), and 5c (CS2). These share distant evolutionary relatedness to fimbrial systems of three other genera. Subclass divisions generally correlate with distinguishing in vitro adherence phenotypes of strains bearing the ETEC fimbriae. Phylogenetic comparisons of the individual structural proteins demonstrated greater intrasubclass conservation among the minor subunits than the major subunits. To correlate this with functional attributes, we made antibodies against CFA/I and CS17 whole fimbriae and maltose-binding protein fusions with the amino-terminal half of the corresponding minor subunits. Anti-minor subunit Fab preparations showed hemagglutination inhibition (HAI) of ETEC expressing homologous and intrasubclass heterologous colonization factors while anti-fimbrial Fab fractions showed HAI activity limited to colonization factor-homologous ETEC. These results were corroborated with similar results from the Caco-2 cell adherence assay. Our findings suggest that the minor subunits of class 5 fimbriae may be superior to whole fimbriae in inducing antiadhesive immunity.},
author = {Anantha, Ravi P. R.P. and McVeigh, A.L. Annette L. and Lee, L.H. Lanfong H. and Agnew, M.K. Mary K. and Cassels, Frederick J. F.J. and Scott, Daniel a. D.A. and Whittam, T.S. Thomas S. and Savarino, Stephen J},
doi = {10.1128/IAI.72.12.7190},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Anantha et al. - Evolutionary and functional relationships of colonization factor antigen I and other class 5 adhesive fimbriae of enter.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Anantha et al. - Evolutionary and functional relationships of colonization factor antigen I and other class 5 adhesive fimbriae of en(2).pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
number = {12},
pages = {7190},
pmid = {15557644},
publisher = {Am Soc Microbiol},
title = {{Evolutionary and functional relationships of colonization factor antigen I and other class 5 adhesive fimbriae of enterotoxigenic Escherichia coli}},
url = {http://iai.asm.org/cgi/content/abstract/72/12/7190},
volume = {72},
year = {2004}
}
@article{Phan2011,
abstract = {Type 1 pili are the archetypal representative of a widespread class of adhesive multisubunit fibres in Gram-negative bacteria. During pilus assembly, subunits dock as chaperone-bound complexes to an usher, which catalyses their polymerization and mediates pilus translocation across the outer membrane. Here we report the crystal structure of the full-length FimD usher bound to the FimC-FimH chaperone-adhesin complex and that of the unbound form of the FimD translocation domain. The FimD-FimC-FimH structure shows FimH inserted inside the FimD 24-stranded $\beta$-barrel translocation channel. FimC-FimH is held in place through interactions with the two carboxy-terminal periplasmic domains of FimD, a binding mode confirmed in solution by electron paramagnetic resonance spectroscopy. To accommodate FimH, the usher plug domain is displaced from the barrel lumen to the periplasm, concomitant with a marked conformational change in the $\beta$-barrel. The amino-terminal domain of FimD is observed in an ideal position to catalyse incorporation of a newly recruited chaperone-subunit complex. The FimD-FimC-FimH structure provides unique insights into the pilus subunit incorporation cycle, and captures the first view of a protein transporter in the act of secreting its cognate substrate.},
author = {Phan, Gilles and Remaut, Han and Wang, Tao and Allen, William J and Pirker, Katharina F and Lebedev, Andrey and Henderson, Nadine S and Geibel, Sebastian and Volkan, Ender and Yan, Jun and Kunze, Micha B a and Pinkner, Jerome S and Ford, Bradley and Kay, Christopher W M and Li, Huilin and Hultgren, Scott J and Thanassi, David G and Waksman, Gabriel},
doi = {10.1038/nature10109},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Phan et al. - Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate. - 2011.pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Adhesins, Escherichia coli,Adhesins, Escherichia coli: chemistry,Adhesins, Escherichia coli: metabolism,Crystallization,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Models, Molecular,Protein Binding,Protein Structure, Quaternary},
month = {jun},
number = {7349},
pages = {49--53},
pmid = {21637253},
title = {{Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21637253},
volume = {474},
year = {2011}
}
@article{Gintz1999,
author = {Gintz, D and Elmabsout, B and Renaudeaux, J},
doi = {10.1016/S1287-4620(00)88651-2},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gintz, Elmabsout, Renaudeaux - Mod{\'{e}}lisation du flot urinaire dans l'uret{\`{e}}re chez l'Homme - 1999.pdf:pdf},
issn = {12874620},
journal = {Comptes Rendus de l'Acad{\'{e}}mie des Sciences - Series IIB - Mechanics-Physics-Astronomy},
month = {nov},
number = {12},
pages = {1265--1268},
title = {{Mod{\'{e}}lisation du flot urinaire dans l'uret{\`{e}}re chez l'Homme}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1287462000886512},
volume = {327},
year = {1999}
}
@article{Gottesman2004,
author = {Gottesman, Max E and Weisberg, Robert A},
doi = {10.1128/MMBR.68.4.796},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gottesman, Weisberg - Little Lambda , Who Made Thee † - 2004.pdf:pdf},
journal = {Society},
number = {4},
pages = {796--813},
title = {{Little Lambda , Who Made Thee ?†}},
volume = {68},
year = {2004}
}
@article{Frank1996,
abstract = {The SPIDER system has evolved into a comprehensive tool set for image processing, making use of modern graphics interfacing in the VMS and UNIX environment. SPIDER and WEB handle the complementary tasks of batch processing and visualization of the results. The emphasis of the SPIDER system remains in the area of single particle averaging and reconstruction, although a variety of other application areas have been added. Novel features are a suite of operations relating to the determination, modeling, and correction of the contrast transfer function and the availability of the entire documentation in hypertext format.},
author = {Frank, J and Radermacher, M and Penczek, P and Zhu, J and Li, Y and Ladjadj, M and Leith, a},
doi = {10.1006/jsbi.1996.0030},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Frank et al. - SPIDER and WEB processing and visualization of images in 3D electron microscopy and related fields. - 1996.pdf:pdf},
issn = {1047-8477},
journal = {Journal of structural biology},
keywords = {Animals,Antigen-Antibody Complex,Antigen-Antibody Complex: ultrastructure,Calcium Channels,Calcium Channels: ultrastructure,Computer Graphics,Computer Simulation,Hemocyanin,Hemocyanin: ultrastructure,Immunoglobulin Fab Fragments,Immunoglobulin Fab Fragments: ultrastructure,Microscopy, Electron,Models, Structural,Protein Conformation,Software},
number = {1},
pages = {190--9},
pmid = {8742743},
title = {{SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8742743},
volume = {116},
year = {1996}
}
@article{Norregaard2014a,
abstract = {This protocol describes how to monitor individual naturally supercoiled circular DNA plasmids bound via peptide nucleic acid (PNA) handles between a bead and a surface. The protocol was developed for single-molecule investigation of the dynamics of supercoiled DNA, and it allows the investigation of both the dynamics of the molecule itself and of its interactions with a regulatory protein. Two bis-PNA clamps designed to bind with extremely high affinity to predetermined homopurine sequence sites in supercoiled DNA are prepared: one conjugated with digoxigenin for attachment to an anti-digoxigenin-coated glass cover slide, and one conjugated with biotin for attachment to a submicron-sized streptavidin-coated polystyrene bead. Plasmids are constructed, purified and incubated with the PNA handles. The dynamics of the construct is analyzed by tracking the tethered bead using video microscopy: less supercoiling results in more movement, and more supercoiling results in less movement. In contrast to other single-molecule methodologies, the current methodology allows for studying DNA in its naturally supercoiled state with constant linking number and constant writhe. The protocol has potential for use in studying the influence of supercoils on the dynamics of DNA and its associated proteins, e.g., topoisomerase. The procedure takes ∼4 weeks.},
author = {Norregaard, Kamilla and Andersson, Magnus and Nielsen, Peter Eigil and Brown, Stanley and Oddershede, Lene B.},
doi = {10.1038/nprot.2014.152},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Norregaard et al. - Tethered particle analysis of supercoiled circular DNA using peptide nucleic acid handles. - 2014.pdf:pdf},
issn = {1750-2799},
journal = {Nature protocols},
month = {sep},
number = {9},
pages = {2206--23},
pmid = {25144271},
title = {{Tethered particle analysis of supercoiled circular DNA using peptide nucleic acid handles.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25144271},
volume = {9},
year = {2014}
}
@techreport{Weitz2008,
author = {Weitz, David a},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Weitz - Weitzlab Guide to Writing a Good Paper - 2008 - 2008.pdf:pdf},
pages = {4},
title = {{Weitzlab Guide to Writing a Good Paper - 2008}},
url = {papers2://publication/uuid/932FFB09-38D2-4750-A154-3DAF8A793C29},
year = {2008}
}
@article{Republic2010,
author = {Republic, Slovak and Science, Faculty O F},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Republic, Science - Development and application of Surface - Enhanced Raman Scattering probes for the study of drug action in cancer cel.pdf:pdf},
journal = {Philosophy},
title = {{Development and application of Surface - Enhanced Raman Scattering probes for the study of drug action in cancer cells}},
year = {2010}
}
@article{Langermann2001,
author = {Langermann, S and Ballou, W R},
doi = {10.1086/318857},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Langermann, Ballou - Vaccination utilizing the FimCH complex as a strategy to prevent Escherichia coli urinary tract infections. - 2001.pdf:pdf},
issn = {0022-1899},
journal = {The Journal of infectious diseases},
keywords = {Adhesins, Bacterial,Adhesins, Escherichia coli,Bacterial Outer Membrane Proteins,Bacterial Proteins,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: prevention {\&} control,Escherichia coli Proteins,Escherichia coli Vaccines,Escherichia coli Vaccines: administration {\&} dosage,Escherichia coli: chemistry,Escherichia coli: immunology,Fimbriae Proteins,Humans,Urinary Tract Infections,Urinary Tract Infections: microbiology,Urinary Tract Infections: prevention {\&} control,Vaccination},
month = {mar},
number = {Suppl 1},
pages = {S84--6},
pmid = {11171023},
title = {{Vaccination utilizing the FimCH complex as a strategy to prevent Escherichia coli urinary tract infections.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11171023},
volume = {183 Suppl },
year = {2001}
}
@article{Wriedt2006,
author = {Wriedt, Thomas and Hellmers, Jens and Eremina, Elena and Schuh, Roman},
doi = {10.1016/j.jqsrt.2005.11.057},
issn = {00224073},
journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
month = {jul},
number = {1-3},
pages = {444--456},
title = {{Light scattering by single erythrocyte: Comparison of different methods}},
volume = {100},
year = {2006}
}
@article{Cravioto1982,
abstract = {We examined 205 enterotoxigenic strains of Escherichia coli for colonization factor antigens (CFA) I and II, using an immunodiffusion technique with specific antisera. A total of 36 strains of serogroups O63, O78, O114, O128, and O153 and 1 rough strain possessed CFA/I and gave a single precipitin line; 47 strains of serogroups O6, O8, O80, and O115 possessed CFA/II. The latter strains gave a major precipitin line (component 3) when tested with specific antisera prepared against strain E1392 or PB-176 (both E. coli O6.H16; biotype A). However, all 16 strains of E. coli O6.H16 belonging to biotype A gave a second precipitin line (component 1) when tested with both antisera. When CFA/II-positive strains were tested with a specific antiserum prepared against E. coli O6.H16 strains of biotype B or C, all strains gave component 3, but 16 of 17 strains of E. coli O6.H16 belonging to biotype B, C, or F gave a second precipitin line (component 2) not given by strains of biotype A. CFA/II-positive strains of serogroups other than O6 gave only component 3 in tests with all specific antisera. Nine enterotoxigenic strains of serotypes O7, O15, O25, O115, and O128 gave mannose-resistant hemagglutination of human or calf erythrocytes but lacked CFA/I or CFA/II. Although mannose-resistant hemagglutination was common in non-enterotoxigenic strains of E. coli, none of the non-enterotoxigenic strains possessed CFA/I or CFA/II; these strains included fecal strains of serogroups O6, O8, O63, and O78, fecal strains of enteropathogenic serogroups, and strains from extraintestinal sources.},
author = {Cravioto, A. and Scotland, S. M. and Rowe, B.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Cravioto, Scotland, Rowe - Hemagglutination activity and colonization factor antigens I and II in enterotoxigenic and non-enterotoxigeni.pdf:pdf},
isbn = {0019-9567 (Print)$\backslash$n0019-9567 (Linking)},
issn = {00199567},
journal = {Infection and Immunity},
number = {1},
pages = {189--197},
pmid = {7042570},
title = {{Hemagglutination activity and colonization factor antigens I and II in enterotoxigenic and non-enterotoxigenic strains of Escherichia coli isolated from humans}},
volume = {36},
year = {1982}
}
@article{Boks2008,
abstract = {Using a parallel-plate flow chamber, the hydrodynamic shear forces to prevent bacterial adhesion (F(prev)) and to detach adhering bacteria (F(det)) were evaluated for hydrophilic glass, hydrophobic, dimethyldichlorosilane (DDS)-coated glass and six different bacterial strains, in order to test the following three hypotheses. 1. A strong hydrodynamic shear force to prevent adhesion relates to a strong hydrodynamic shear force to detach an adhering organism. 2. A weak hydrodynamic shear force to detach adhering bacteria implies that more bacteria will be stimulated to detach by passing an air-liquid interface (an air bubble) through the flow chamber. 3. DLVO (Derjaguin, Landau, Verwey, Overbeek) interactions determine the characteristic hydrodynamic shear forces to prevent adhesion and to detach adhering micro-organisms as well as the detachment induced by a passing air-liquid interface. F(prev) varied from 0.03 to 0.70 pN, while F(det) varied from 0.31 to over 19.64 pN, suggesting that after initial contact, strengthening of the bond occurs. Generally, it was more difficult to detach bacteria from DDS-coated glass than from hydrophilic glass, which was confirmed by air bubble detachment studies. Calculated attractive forces based on the DLVO theory (F(DLVO)) towards the secondary interaction minimum were higher on glass than on DDS-coated glass. In general, all three hypotheses had to be rejected, showing that it is important to distinguish between forces acting parallel (hydrodynamic shear) and perpendicular (DLVO, air-liquid interface passages) to the substratum surface.},
author = {Boks, Niels P and Norde, Willem and van der Mei, Henny C and Busscher, Henk J},
doi = {10.1099/mic.0.2008/018622-0},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Boks et al. - Forces involved in bacterial adhesion to hydrophilic and hydrophobic surfaces. - 2008.pdf:pdf},
issn = {1350-0872},
journal = {Microbiology (Reading, England)},
keywords = {Air,Bacteria,Bacteria: growth {\&} development,Bacterial Adhesion,Glass,Glass: chemistry,Hydrophobic and Hydrophilic Interactions,Shear Strength,Silanes,Silanes: chemistry,Surface Properties,paper3},
mendeley-tags = {paper3},
month = {oct},
number = {Pt 10},
pages = {3122--33},
pmid = {18832318},
title = {{Forces involved in bacterial adhesion to hydrophilic and hydrophobic surfaces.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18832318},
volume = {154},
year = {2008}
}
@article{Martinez-Borges2006,
abstract = {Benign prostatic hyperplasia (BPH) is the most common form of prostate disease in middle-aged and elderly men, and leads to severe impairment later in life. Despite its significant impact on public health, the underlying cause of BPH is yet to be determined. This hypothesis proposes a new causal factor for BPH. Applying concepts of dynamics of fluids to the process of urination it could be stated that a turbulent urinary flow through the passage of the urethra. The turbulent urinary flow in the urethra applies pressure and stretch forces to the surrounding tissue. This stimulus repeated over time and coupled with age-related changes of the urethral tissue could contribute to the development of BPH. In support of this hypothesis, several mechanotransduction studies have shown that vibration and pressure forces applied to different cell tissues can provoke cellular and molecular changes. Another supportive data is the presence of the hyperplasic reaction surrounding the urethra specifically located in the transition zone, the only zone where BPH develops. It is crucial to identify causal factors to understanding the disease and to determine effective primary prevention strategies. Future studies of the dynamics of fluids in the urethra are warranted. The finding of significant forces transmitted to the periurethral tissue from a turbulent urinary flow could give us the clue to the underlying cause of BPH. If this hypothesis proves to be valid there are several primary prevention measures that could be implemented to impede the development of BPH. Educational intervention measures in younger populations to avoid frequent urinary retention and active urination (process of forcing the urine through the urethra at a high velocity) could be considered. Studies of the impact of turbulence in the standing vs. sitting position during urination in men should also be considered.},
author = {Martinez-Borges, Anibal R},
doi = {10.1016/j.mehy.2006.02.055},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Martinez-Borges - Turbulent urinary flow in the urethra could be a causal factor for benign prostatic hyperplasia. - 2006.pdf:pdf},
issn = {0306-9877},
journal = {Medical hypotheses},
keywords = {Aged,Humans,Male,Middle Aged,Models, Biological,Prostatic Hyperplasia,Prostatic Hyperplasia: etiology,Prostatic Hyperplasia: pathology,Urethra,Urethra: physiology,Urodynamics},
month = {jan},
number = {4},
pages = {871--5},
pmid = {16764996},
title = {{Turbulent urinary flow in the urethra could be a causal factor for benign prostatic hyperplasia.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16764996},
volume = {67},
year = {2006}
}
@article{Ioannou1999,
abstract = {We present a two-step algorithm for the recognition of circles. The first step uses a 2D Hough Transform for the detection of the centres of the circles and the second step validates their existence by radius histogramming. The 2D Hough Transform technique makes use of the property that every chord of a circle passes through its centre. We present results of experiments with synthetic data demonstrating that our method is more robust to noise than standard gradient based methods. The promise of the method is demonstrated with its application on a natural image and on a digitized mammogram.},
author = {Ioannou, Dimitrios and Huda, Walter and Laine, Andrew F.},
doi = {10.1016/S0262-8856(98)00090-0},
issn = {02628856},
journal = {Image and Vision Computing},
pages = {15--26},
title = {{Circle recognition through a 2D Hough Transform and radius histogramming}},
volume = {17},
year = {1999}
}
@article{Wu2010a,
abstract = {We present an optical tweezer sensor for shear stress mapping in microfluidic systems of different internal geometries. The sensor is able to measure the shear stress acting on microspheres of different sizes that model cell based biological operations. Without the need for a spatial modulator or a holographic disk, the sensor allows for direct shear stress detection at arbitrary positions in straight and curved microfluidic devices. Analytical calculations are carried out and compared with the experimental results. It is observed that a decrease in the microsphere size results in an increase in the shear stress the particle experiences.},
annote = {        From Duplicate 1 (                   Shear stress mapping in microfluidic devices by optical tweezers.                 - Wu, Jing; Day, Daniel; Gu, Min )
                
        
        
      },
author = {Wu, Jing and Day, Daniel and Gu, Min},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wu, Day, Gu - Shear stress mapping in microfluidic devices by optical tweezers. - 2010.pdf:pdf},
issn = {1094-4087},
journal = {Optics express},
month = {apr},
number = {8},
pages = {7611--6},
pmid = {20588600},
title = {{Shear stress mapping in microfluidic devices by optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20588600},
volume = {18},
year = {2010}
}
@article{Otto2014,
abstract = {Bacterial surface colonizers are subject to a variety of physical stresses. During the colonization of human epithelia such as on the skin or the intestinal mucosa, bacteria mainly have to withstand the mechanical stress of being removed by fluid flow, scraping, or epithelial turnover. To that end, they express a series of molecules to establish firm attachment to the epithelial surface, such as fibrillar protrusions (pili) and surface-anchored proteins that bind to human matrix proteins. In addition, some bacteria - in particular gut and urinary tract pathogens - use internalization by epithelial cells and other methods such as directed inhibition of epithelial turnover to ascertain continued association with the epithelial layer. Furthermore, many bacteria produce multi-layered agglomerations called biofilms with a sticky extracellular matrix, providing additional protection from removal. This review will give an overview over the mechanisms human bacterial colonizers have to withstand physical stresses with a focus on bacterial adhesion. This article is protected by copyright. All rights reserved.},
author = {Otto, Michael},
doi = {10.1111/1574-6976.12088},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Otto - Physical stress and bacterial colonization. - 2014.pdf:pdf},
issn = {1574-6976},
journal = {FEMS microbiology reviews},
month = {sep},
pmid = {25212723},
title = {{Physical stress and bacterial colonization.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25212723},
year = {2014}
}
@article{Lugmaier2008,
abstract = {P-pili of uropathogenic Escherichia coli mediate the attachment to epithelial cells in the human urinary tract and kidney and therefore play an important role in infection. A better understanding of this mechanism could help to prevent bacteria from spreading but also provides interesting insights into molecular mechanics for future nanotech applications. The helical rod design of P-pili provides an efficient design to withstand hydrodynamic shear forces. The adhesive PapG unit at the distal end of the P-pilus forms a specific bond with the glycolipid Galabiose. This bond has a potential width Deltax = 0.7 +/- 0.15 nm and a dissociation rate K (Off) = 8.0.10(-4) +/- 5.0.10(-4) s(-1). It withstands a force of approximately 49 pN under physiological conditions. Additionally, we analyzed the behavior of unstacking and restacking of the P-pilus with dynamic force spectroscopy at velocities between 200 and 7,000 nm/s. Up to a critical extension of 66{\%} of the totally stretched P-pilus, un/re-stacking was found to be fully reversible at velocities up to 200 nm/s. If the P-pilus is stretched beyond this critical extension a characteristic hysteresis appears upon restacking. This hysteresis originates from a nucleation process comparable to a first-order phase transition in an undercooled liquid. Analysis of the measurement data suggests that 20 PapA monomers are involved in the formation of a nucleation kernel.},
author = {Lugmaier, Robert A and Schedin, Staffan and K{\"{u}}hner, Ferdinand and Benoit, Martin},
doi = {10.1007/s00249-007-0183-x},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Lugmaier et al. - Dynamic restacking of Escherichia coli P-pili. - 2008.pdf:pdf},
issn = {0175-7571},
journal = {European biophysics journal : EBJ},
keywords = {Adhesins,Atomic Force,Bacterial,Bacterial: chemistry,Bacterial: metabolism,Biological,Disaccharides,Disaccharides: metabolism,Escherichia coli,Escherichia coli: cytology,Escherichia coli: metabolism,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: metabolism,Kinetics,Microscopy,Models,Monte Carlo Method,Substrate Specificity},
month = {feb},
number = {2},
pages = {111--20},
pmid = {17554533},
title = {{Dynamic restacking of Escherichia coli P-pili.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17554533},
volume = {37},
year = {2008}
}
@article{Wilks2012,
abstract = {Most pathogens gain access to the host through surfaces of the body that are exposed to the surrounding environment and rife with resident microorganisms, termed microbiota. Microbiota play an integral role in modulating host health. One significant benefit of the microbiota is that they provide protection against incoming bacterial pathogens 1. Commensals make their immediate environment inhospitable to many pathogens by producing biosurfactants, by competing for sites of attachment and nutrients, and by excreting metabolites with antimicrobial effects 1. Furthermore, the presence of commensals promotes maturation of secondary lymphoid organs in the intestine, which are the first line of defense in the intestinal mucosa 2. Therefore, when a pathogen infiltrates the host, it is not entering a sterile environment, but one that has been shaped by a dynamic commensal community. Although many interactions between bacterial pathogens and the microbiota have been characterized 1, little is known about the interplay between viral pathogens and the natural flora of the host. Are viral pathogens blind to the commensal microbes surrounding them? Judging from recent publications, this appears not to be the case. There is strong evidence that the microbiota can either protect the host from virally induced disease or promote viral propagation/transmission, through direct or indirect mechanisms.},
author = {Wilks, Jessica and Golovkina, Tatyana},
doi = {10.1371/journal.ppat.1002681},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wilks, Golovkina - Influence of microbiota on viral infections - 2012.pdf:pdf},
isbn = {1553-7374 (Electronic)$\backslash$r1553-7366 (Linking)},
issn = {15537366},
journal = {PLoS Pathogens},
number = {5},
pages = {5--7},
pmid = {22615558},
title = {{Influence of microbiota on viral infections}},
volume = {8},
year = {2012}
}
@article{Underdown1986,
annote = {From Duplicate 1 ( 

Immunoglobulin A: strategic defense initiative at the mucosal surface.

- Underdown, B J; Schiff, J M )

},
author = {Underdown, Brian J and Ln, Canada and Sch, J Michael and Schiff, J M},
doi = {10.1146/annurev.iy.04.040186.002133},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Underdown et al. - Immunoglobulin A strategic defense initiative at the mucosal surface. - 1986.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Underdown et al. - Immunoglobulin A strategic defense initiative at the mucosal surface. - 1986.pdf:pdf},
issn = {0732-0582},
journal = {Annual review of immunology},
keywords = {Active,Animals,Antigens,Antigens: immunology,B-Lymphocytes,B-Lymphocytes: immunology,Biliary Tract,Biliary Tract: immunology,Biological,Biological Transport,Endocytosis,Humans,Immunity,Immunoglobulin A,Immunoglobulin A: immunology,Immunoglobulin A: metabolism,Liver,Liver: immunology,Models,Mucous Membrane,Mucous Membrane: immunology,Protein Conformation,Secretory Component,T-Lymphocytes,T-Lymphocytes: immunology},
month = {jan},
pages = {389--417},
pmid = {3518747},
title = {{Immunoglobulin A: strategic defense initiative at the mucosal surface.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/3518747},
volume = {4},
year = {1986}
}
@article{Roos2006,
author = {Roos, Viktoria and Ulett, Gc},
doi = {10.1128/IAI.74.1.615},
journal = {Infection and immunity},
number = {1},
pages = {615--24},
title = {{The asymptomatic bacteriuria Escherichia coli strain 83972 outcompetes uropathogenic E. coli strains in human urine}},
volume = {74},
year = {2006}
}
@article{Svoboda1994,
abstract = {Metallic objects reflect light and have generally been considered poor candidates for optical traps, particularly with optical tweezers, which rely on a gradient force to provide trapping. We demonstrate that stable trapping can occur with optical tweezers when they are used with small metallic Rayleigh particles. In this size regime, the scattering pictures for metals and dielectrics are similar, and the larger polarizability of metals implies that trapping forces are greater. The latter fact makes the use of metal particles attractive for certain biological applications. Comparison of trapping forces for latex and gold spheres demonstrates that the gradient force is the major determinant of trapping strength and that competing effects, such as scattering or radiometric forces, are relatively minor.},
author = {Svoboda, K and Block, S M},
doi = {10.1364/OL.19.000930},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Svoboda, Block - Optical trapping of metallic Rayleigh particles. - 1994.pdf:pdf},
isbn = {0146-9592},
issn = {0146-9592},
journal = {Optics letters},
number = {13},
pages = {930--932},
pmid = {19844491},
title = {{Optical trapping of metallic Rayleigh particles.}},
volume = {19},
year = {1994}
}
@article{Lecuyer2011a,
abstract = {Although ubiquitous, the processes by which bacteria colonize surfaces remain poorly understood. Here we report results for the influence of the wall shear stress on the early-stage adhesion of Pseudomonas aeruginosa PA14 on glass and polydimethylsiloxane surfaces. We use image analysis to measure the residence time of each adhering bacterium under flow. Our main finding is that, on either surface, the characteristic residence time of bacteria increases approximately linearly as the shear stress increases (0-3.5 Pa). To investigate this phenomenon, we used mutant strains defective in surface organelles (type I pili, type IV pili, or the flagellum) or extracellular matrix production. Our results show that, although these bacterial surface features influence the frequency of adhesion events and the early-stage detachment probability, none of them is responsible for the trend in the shear-enhanced adhesion time. These observations bring what we believe are new insights into the mechanism of bacterial attachment in shear flows, and suggest a role for other intrinsic features of the cell surface, or a dynamic cell response to shear stress.},
author = {Lecuyer, Sigolene and Rusconi, Roberto and Shen, Yi and Forsyth, Alison and Vlamakis, Hera and Kolter, Roberto and Stone, Howard A},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lecuyer et al. - Shear stress increases the residence time of adhesion of Pseudomonas aeruginosa. - 2011.pdf:pdf},
institution = {Harvard University, Cambridge, Massachusetts, USA.},
journal = {Biophysical Journal},
number = {2},
pages = {341--350},
pmid = {21244830},
publisher = {Biophysical Society},
title = {{Shear stress increases the residence time of adhesion of Pseudomonas aeruginosa.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21244830},
volume = {100},
year = {2011}
}
@article{Visser2010,
abstract = {One of the most poorly understood subjects in physical optics is the origin of the Gouy phase (sometimes called "the phase anomaly near focus"). This is evident from the large number of publications on the subject, many of which attribute it to quite different causes. In this paper we show that the Gouy phase anomaly can be clearly understood from elementary properties of normal congruences of light rays and from the relationship between geometrical optics and physical optics. We also show that the Gouy phase anomaly may be regarded as a degenerate case of a rapid ??/2 phase change that is found to occur at each focal line of an astigmatic pencil of rays. The intensity distribution in the region of the phase changes is also presented. Furthermore, symmetry relations for both the phase anomaly and the intensity distribution are derived. ?? 2010 Elsevier B.V. All rights reserved.},
author = {Visser, T. D. and Wolf, E.},
doi = {10.1016/j.optcom.2010.04.099},
issn = {00304018},
journal = {Optics Communications},
number = {18},
pages = {3371--3375},
publisher = {Elsevier B.V.},
title = {{The origin of the Gouy phase anomaly and its generalization to astigmatic wavefields}},
volume = {283},
year = {2010}
}
@article{Ganz2003,
abstract = {The production of natural antibiotic peptides has emerged as an important mechanism of innate immunity in plants and animals. Defensins are diverse members of a large family of antimicrobial peptides, contributing to the antimicrobial action of granulocytes, mucosal host defence in the small intestine and epithelial host defence in the skin and elsewhere. This review, inspired by a spate of recent studies of defensins in human diseases and animal models, focuses on the biological function of defensins.},
author = {Ganz, Tomas},
doi = {10.1038/nri1180},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ganz - Defensins antimicrobial peptides of innate immunity. - 2003.pdf:pdf},
issn = {1474-1733},
journal = {Nature reviews. Immunology},
keywords = {Amino Acid Sequence,Animals,Defensins,Defensins: chemistry,Defensins: genetics,Defensins: immunology,Humans,Immunity, Innate,Immunity, Innate: immunology,Models, Molecular,Molecular Sequence Data,Salmonella,Salmonella Infections,Salmonella Infections: immunology,Salmonella: immunology,Sequence Alignment},
month = {oct},
number = {9},
pages = {710--20},
pmid = {12949495},
title = {{Defensins: antimicrobial peptides of innate immunity.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12949495},
volume = {3},
year = {2003}
}
@article{Huang2001,
abstract = {Juxtaposition kinetics between specific sites in supercoiled DNA is investigated at close to physiological ionic conditions by Brownian dynamics simulations. At such conditions, supercoiled DNA is interwound, and the probability of spatial site juxtaposition is much higher than in relaxed DNA. We find, however, that supercoiling does not correspondingly increase the rate of juxtaposition at these physiological conditions. An explanation to this unexpected finding emerges on analysis of the juxtaposition dynamics. We note that although a particular site i(1) in supercoiled DNA is often in close proximity (juxtaposed) to another site i(2), the change of i(2) occurs very slowly and depends largely on internal slithering of opposite segments of the DNA superhelix. Such slithering results in long correlations between successive values of i(2); these correlations increase the average time of juxtaposition between two DNA sites. Random collisions between sites located on different superhelix branches-although increasing in importance with DNA size-contribute less substantially to site juxtaposition at high salt than slithering for DNA up to 6 kb in length.},
author = {Huang, J and Schlick, T and Vologodskii, a},
doi = {10.1073/pnas.98.3.968},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Huang, Schlick, Vologodskii - Dynamics of site juxtaposition in supercoiled DNA. - 2001.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Algorithms,Computer Simulation,DNA, Superhelical,DNA, Superhelical: chemistry,Kinetics,Models, Molecular,Monte Carlo Method,Nucleic Acid Conformation},
month = {jan},
number = {3},
pages = {968--73},
pmid = {11158579},
title = {{Dynamics of site juxtaposition in supercoiled DNA.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=14693{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {98},
year = {2001}
}
@book{Janeway2001,
address = {New York},
author = {Janeway, A Charles and Travers, Paul and Walport, Mark and Shlomchik, J Mark},
isbn = {081533642X},
keywords = {antibodies},
mendeley-tags = {antibodies},
publisher = {Garland publishing},
title = {{Immunobiology, 5th edition - The Immune System in Health and Disease}},
year = {2001}
}
@article{Zakrisson2015a,
author = {Zakrisson, Johan and Schedin, Staffan and Andersson, Magnus},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zakrisson, Schedin, Andersson - Cell shape identification using digital holographic microscopy - 2015.pdf:pdf},
journal = {Applied optics},
number = {24},
pages = {7442--7448},
title = {{Cell shape identification using digital holographic microscopy}},
volume = {54},
year = {2015}
}
@article{Li2009d,
abstract = {Enterotoxigenic Escherichia coli (ETEC), a major global cause of diarrhea, initiates the pathogenic process via fimbriae-mediated attachment to the small intestinal epithelium. A common prototypic ETEC fimbria, colonization factor antigen I (CFA/I), consists of a tip-localized minor adhesive subunit CfaE and the stalk-forming major subunit CfaB, both of which are necessary for fimbrial assembly. To elucidate the structure of CFA/I at atomic resolution, three recombinant proteins were generated consisting of fusions of the minor and major subunits (CfaEB) and of two (CfaBB) and three (CfaBBB) repeats of the major subunit. Crystals of CfaEB diffracted X-rays to 2.1 A resolution and displayed the symmetry of space group P2(1). CfaBB exhibited a crystal diffraction limit of 2.3 A resolution and had the symmetry of space group P2(1)2(1)2. CfaBBB crystallized in the monoclinic space group C2 and diffracted X-rays to 2.3 A resolution. These structures were determined using the molecular-replacement method.},
author = {Li, Yong Fu and Poole, Steven and Rasulova, Fatima and McVeigh, Annette L and Savarino, Stephen J and Xia, Di},
doi = {10.1107/S1744309109001584},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Li et al. - Crystallization and preliminary X-ray diffraction analyses of several forms of the CfaB major subunit of enterotoxigenic Esc.pdf:pdf},
issn = {1744-3091},
journal = {Acta crystallographica. Section F, Structural biology and crystallization communications},
keywords = {Crystallization,Crystallography, X-Ray,Cytoprotection,Electrophoresis, Polyacrylamide Gel,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: chemistry,Enterotoxigenic Escherichia coli: cytology,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: isolation {\&} purificatio,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: isolation {\&} purification,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Protein Subunits,Protein Subunits: chemistry,Protein Subunits: isolation {\&} purification,Recombinant Fusion Proteins,Recombinant Fusion Proteins: chemistry,Recombinant Fusion Proteins: isolation {\&} purificat},
number = {Pt 3},
pages = {242--7},
pmid = {19255474},
title = {{Crystallization and preliminary X-ray diffraction analyses of several forms of the CfaB major subunit of enterotoxigenic Escherichia coli CFA/I fimbriae.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2650451{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {65},
year = {2009}
}
@article{Langstraat2001,
author = {Langstraat, Jennifer and Bohse, Megan and Clegg, Steven},
doi = {10.1128/IAI.69.9.5805},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Langstraat, Bohse, Clegg - Type 3 Fimbrial Shaft ( MrkA ) of Klebsiella pneumoniae , but Not the Fimbrial Adhesin ( MrkD ), Facilitates.pdf:pdf},
journal = {Society},
number = {9},
pages = {5805--5812},
title = {{Type 3 Fimbrial Shaft ( MrkA ) of Klebsiella pneumoniae , but Not the Fimbrial Adhesin ( MrkD ), Facilitates Biofilm Formation}},
volume = {69},
year = {2001}
}
@article{Jun2014,
author = {Jun, Yonggun and Tripathy, Suvranta K and Narayanareddy, Babu R J and Mattson-hoss, Michelle K and Gross, Steven P},
doi = {10.1016/j.bpj.2014.07.033},
issn = {0006-3495},
journal = {Biophysj},
number = {September},
pages = {1474--1484},
pmid = {25229154},
publisher = {Biophysical Society},
title = {{Calibration of Optical Tweezers for In Vivo Force Measurements : How do Different Approaches Compare ?}},
volume = {107},
year = {2014}
}
@article{Berg1993,
abstract = {Cells of the bacterium Escherichia coli were tethered and spun in a high-frequency rotating electric field at a series of discrete field strengths. This was done first at low field strengths, then at field strengths generating speeds high enough to disrupt motor function, and finally at low field strengths. Comparison of the initial and final speed versus applied-torque plots yielded relative motor torque. For backward rotation, motor torque rose steeply at speeds close to zero, peaking, on average, at about 2.2 times the stall torque. For forward rotation, motor torque remained approximately constant up to speeds of about 60{\%} of the zero-torque speed. Then the torque dropped linearly with speed, crossed zero, and reached a minimum, on average, at about -1.7 times the stall torque. The zero-torque speed increased with temperature (about 90 Hz at 11 degrees C, 140 Hz at 16 degrees C, and 290 Hz at 23 degrees C), while other parameters remained approximately constant. Sometimes the motor slipped at either extreme (delivered constant torque over a range of speeds), but eventually it broke. Similar results were obtained whether motors broke catastrophically (suddenly and completely) or progressively or were de-energized by brief treatment with an uncoupler. These results are consistent with a tightly coupled ratchet mechanism, provided that elastic deformation of force-generating elements is limited by a stop and that mechanical components yield at high applied torques.},
author = {Berg, H C and Turner, L},
doi = {10.1016/S0006-3495(93)81278-5},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Berg, Turner - Torque generated by the flagellar motor of Escherichia coli. - 1993.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Biomechanics,Biophysical Phenomena,Biophysics,Buffers,Electromagnetic Fields,Escherichia coli,Escherichia coli: physiology,Flagella,Flagella: physiology,Models, Biological,Movement,Movement: physiology,Rotation,Temperature},
month = {nov},
number = {5},
pages = {2201--16},
pmid = {8298044},
publisher = {Elsevier},
title = {{Torque generated by the flagellar motor of Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1225952{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {65},
year = {1993}
}
@article{Jannasch2008,
author = {Jannasch, Anita and Bormuth, Volker and Kats, Carlos M Van and Blaaderen, Alfons Van and Howard, Jonathon and Sch{\"{a}}ffer, Erik},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jannasch et al. - Coated microspheres as enhanced probes for optical trapping - 2008.pdf:pdf},
keywords = {anti-reflective coating,back,calibration,core-shell particles,focal plane detection,generalized lorenz-mie theory,optical tweezers},
pages = {1--8},
title = {{Coated microspheres as enhanced probes for optical trapping}},
year = {2008}
}
@article{Stærk2015,
author = {St{\ae}rk, Kristian and Khandige, Surabhi and Kolmos, Hans J{\o}rn and M{\o}ller-Jensen, Jakob and Andersen, Thomas Emil},
doi = {10.1093/infdis/jiv422},
file = {:E$\backslash$:/Mina Dokument/Mendeley/St{\ae}rk et al. - Uropathogenic iEscherichia colii Express Type 1 Fimbriae Only in Surface Adherent Populations Under Physiological Growth.pdf:pdf},
issn = {0022-1899},
journal = {Journal of Infectious Diseases},
keywords = {bio fi lm,catheter associated infection,coli,coli uti89,e,type 1 fi mbriae,urinary tract infection,uropathogenic e},
pages = {jiv422},
title = {{Uropathogenic <i>Escherichia coli</i> Express Type 1 Fimbriae Only in Surface Adherent Populations Under Physiological Growth Conditions}},
url = {http://jid.oxfordjournals.org/lookup/doi/10.1093/infdis/jiv422},
volume = {213},
year = {2015}
}
@article{Weisel2003,
author = {Weisel, John W and Shuman, Henry and Litvinov, Rustem},
doi = {10.1016/S0959-440X(03)00039-3},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Weisel, Shuman, Litvinov - Protein–protein unbinding induced by force single-molecule studies - 2003.pdf:pdf},
issn = {0959440X},
journal = {Current Opinion in Structural Biology},
month = {apr},
number = {2},
pages = {227--235},
title = {{Protein–protein unbinding induced by force: single-molecule studies}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0959440X03000393},
volume = {13},
year = {2003}
}
@article{Boylan1988,
abstract = {The plasmid pCS001, isolated from an enterotoxigenic strain of Escherichia coli, mediates expression of the CS1 or CS2 and CS3 fimbrial adhesins in appropriate E. coli hosts. To characterize this further, HindIII-generated DNA fragments of this plasmid were cloned into the vector plasmid pBR322. A chimaera, called pCS200, which mediated expression of the CS1 or CS2 fimbrial antigen but not of CS3 fimbrial antigen in appropriate host strains, was obtained. The DNA inserted into the vector sequences of plasmid pCS200 comprised HindIII fragments of 4.7 kbp and 0.8 kbp. Plasmid pCS200-carrying wild-type E. coli hosts of serotype O6:K15:H16 that expressed the CS1 or CS2 antigen also caused mannose-resistant agglutination of bovine red blood cells, suggesting that functional fimbriae were present on the bacterial surface. As previously observed with strain K12 recipients of CS-fimbriae-associated plasmids mobilized from wild-type enterotoxigenic E. coli, K12 recipients of the chimaeric plasmid pCS200 did not express the CS1 or CS2 fimbrial antigen. An oligonucleotide probe, synthesized on the basis of the published N-terminal amino acid sequence of the CS2 fimbrial subunit, hybridized to plasmid pCS200, indicating that the gene for the structural subunit of this fimbria resided on the plasmid.},
author = {Boylan, M and Coleman, D C and Scott, J R and Smyth, C J},
doi = {10.1099/00221287-134-8-2189},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Boylan et al. - Molecular cloning of the plasmid-located determinants for CS1 and CS2 fimbriae of enterotoxigenic Escherichia coli of se.pdf:pdf},
issn = {1350-0872},
journal = {Journal of general microbiology},
pages = {2189--2199},
pmid = {2473163},
title = {{Molecular cloning of the plasmid-located determinants for CS1 and CS2 fimbriae of enterotoxigenic Escherichia coli of serotype O6:K15:H16 of human origin.}},
volume = {134},
year = {1988}
}
@article{Klinth2012,
abstract = {Gram-negative bacteria often initiate their colonization by use of extended attachment organelles, so called pili. When exposed to force, the rod of helix-like pili has been found to be highly extendable, mainly attributed to uncoiling and recoiling of its quaternary structure. This provides the bacteria with the ability to redistribute an external force among a multitude of pili, which enables them to withstand strong rinsing flows, which, in turn, facilitates adherence and colonization processes critical to virulence. Thus, pili fibers are possible targets for novel antibacterial agents. By use of a substance that compromises compliance of the pili, the ability of bacteria to redistribute external forces can be impaired, so they will no longer be able to resist strong urine flow and thus be removed from the host. It is possible such a substance can serve as an alternative to existing antibiotics in the future or be a part of a multi-drug. In this work we investigated whether it is possible to achieve this by targeting the recoiling process. The test substance was purified PapD. The effect of PapD on the compliance of P pili was assessed at the single organelle level by use of force-measuring optical tweezers. We showed that the recoiling process, and thus the biomechanical compliance, in particular the recoiling process, can be impaired by the presence of PapD. This leads to a new concept in the search for novel drug candidates combating uropathogenic bacterial infections--"coilicides", targeting the subunits of which the pilus rod is composed.},
author = {Klinth, Jeanna E and Pinkner, Jerome S and Hultgren, Scott J and Almqvist, Fredrik and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1007/s00249-011-0784-2},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Klinth et al. - Impairment of the biomechanical compliance of P pili a novel means of inhibiting uropathogenic bacterial infections - 20.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Klinth et al. - Impairment of the biomechanical compliance of P pili a novel means of inhibiting uropathogenic bacterial infections - 20.pdf:pdf},
isbn = {0024901107842},
issn = {1432-1017},
journal = {European biophysics journal : EBJ},
keywords = {Anti-Bacterial Agents,Anti-Bacterial Agents: pharmacology,Anti-Bacterial Agents: therapeutic use,Bacterial,Bacterial: drug effects,Bacterial: metabolism,Biomechanics,Escherichia coli Infections,Escherichia coli Infections: drug therapy,Escherichia coli Infections: microbiology,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: metabolism,Fimbriae,Mechanical Processes,Models,Molecular,Optical Tweezers,Protein Conformation,Urinary Tract Infections,Urinary Tract Infections: drug therapy,Urinary Tract Infections: microbiology,Uropathogenic Escherichia coli,Uropathogenic Escherichia coli: cytology,Uropathogenic Escherichia coli: drug effects,Uropathogenic Escherichia coli: metabolism},
month = {mar},
number = {3},
pages = {285--95},
pmid = {22237603},
title = {{Impairment of the biomechanical compliance of P pili: a novel means of inhibiting uropathogenic bacterial infections?}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3281203{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {41},
year = {2012}
}
@article{Xie2005,
abstract = {We report on a novel technique for sorting and identification of single biological cells and food-borne bacteria based on laser tweezers and Raman spectroscopy (LTRS). With this technique, biological cells of different physiological states in a sample chamber were identified by their Raman spectral signatures and then they were selectively manipulated into a clean collection chamber with optical tweezers through a microchannel. As an example, we sorted the live and dead yeast cells into the collection chamber and validated this with a standard staining technique. We also demonstrated that bacteria existing in spoiled foods could be discriminated from a variety of food particles based on their characteristic Raman spectra and then isolated with laser manipulation. This label-free LTRS sorting technique may find broad applications in microbiology and rapid examination of food-borne diseases.},
author = {Xie, Changan and Chen, De and Li, Yong-Qing},
doi = {10.1364/OL.30.001800},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Xie, Chen, Li - Raman sorting and identification of single living micro-organisms with optical tweezers. - 2005.pdf:pdf},
isbn = {0146-9592},
issn = {0146-9592},
journal = {Optics letters},
number = {14},
pages = {1800--1802},
pmid = {16092350},
title = {{Raman sorting and identification of single living micro-organisms with optical tweezers.}},
volume = {30},
year = {2005}
}
@article{Berquand2005,
abstract = {We used atomic force microscopy (AFM) to explore the antigen binding forces of individual Fv fragments of antilysozyme antibodies (Fv). To detect single molecular recognition events, genetically engineered histidine-tagged Fv fragments were coupled onto AFM tips modified with mixed self-assembled monolayers (SAMs) of nitrilotriacetic acid- and tri(ethylene glycol)-terminated alkanethiols while lysozyme (Lyso) was covalently immobilized onto mixed SAMs of carboxyl- and hydroxyl-terminated alkanethiols. The quality of the functionalization procedure was validated using X-ray photoelectron spectroscopy (surface chemical composition), AFM imaging (surface morphology in aqueous solution), and surface plasmon resonance (SPR, specific binding in aqueous solution). AFM force-distance curves recorded at a loading rate of 5000 pN/s between Fv- and Lyso-modified surfaces yielded a distribution of unbinding forces composed of integer multiples of an elementary force quantum of approximately 50 pN that we attribute to the rupture of a single antibody-antigen pair. Injection of a solution containing free Lyso caused a dramatic reduction of adhesion probability, indicating that the measured 50 pN unbinding forces are due to the specific antibody-antigen interaction. To investigate the dynamics of the interaction, force-distance curves were recorded at various loading rates. Plots of unbinding force vs log(loading rate) revealed two distinct linear regimes with ascending slopes, indicating multiple barriers were present in the energy landscape. The kinetic off-rate constant of dissociation (k(off) approximately = 1 x 10(-3) s(-1)) obtained by extrapolating the data of the low-strength regime to zero force was in the range of the k(off) estimated by SPR.},
author = {Berquand, Alexandre and Xia, Nan and Castner, David G and Clare, Brian H and Abbott, Nicholas L and Dupres, Vincent and Adriaensen, Yasmine and Dufr{\^{e}}ne, Yves F},
doi = {10.1021/la050162e},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Berquand et al. - Antigen binding forces of single antilysozyme Fv fragments explored by atomic force microscopy. - 2005.pdf:pdf},
issn = {0743-7463},
journal = {Langmuir : the ACS journal of surfaces and colloids},
keywords = {Antigen-Antibody Complex,Antigen-Antibody Complex: chemistry,Antigen-Antibody Reactions,Immunoglobulin Fragments,Immunoglobulin Fragments: chemistry,Microscopy, Atomic Force,Microscopy, Atomic Force: methods,Muramidase,Muramidase: chemistry,Muramidase: immunology,Surface Properties},
month = {jun},
number = {12},
pages = {5517--23},
pmid = {15924483},
title = {{Antigen binding forces of single antilysozyme Fv fragments explored by atomic force microscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15924483},
volume = {21},
year = {2005}
}
@article{Bormuth2009,
abstract = {Friction limits the operation of macroscopic engines and is critical to the performance of micromechanical devices. We report measurements of friction in a biological nanomachine. Using optical tweezers, we characterized the frictional drag force of individual kinesin-8 motor proteins interacting with their microtubule tracks. At low speeds and with no energy source, the frictional drag was related to the diffusion coefficient by the Einstein relation. At higher speeds, the frictional drag force increased nonlinearly, consistent with the motor jumping 8 nanometers between adjacent tubulin dimers along the microtubule, and was asymmetric, reflecting the structural polarity of the microtubule. We argue that these frictional forces arise from breaking bonds between the motor domains and the microtubule, and they limit the speed and efficiency of kinesin.},
author = {Bormuth, Volker and Varga, Vladimir and Howard, Jonathon and Sch{\"{a}}ffer, Erik},
doi = {10.1126/science.1174923},
journal = {Science},
keywords = {Adenosine Diphosphate,Adenosine Triphosphate,Diffusion,Friction,Microspheres,Microtubule-Associated Proteins,Microtubules,Molecular Motor Proteins,Optical Tweezers,Physicochemical Processes,Recombinant Fusion Proteins,Saccharomyces cerevisiae Proteins,Thermodynamics},
number = {5942},
pages = {870--873},
title = {{Protein friction limits diffusive and directed movements of kinesin motors on microtubules}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=19679813 http://www.sciencemag.org/cgi/content/full/325/5942/870},
volume = {325},
year = {2009}
}
@article{Kinn1996,
abstract = {The development of new surgical techniques for bladder substitution and continent urinary diversion has extended interest in urodynamics of the upper urinary tract. From a subdiscipline attracting mainly scientists and bioengineers, renal pelvic kinetics and ureteral peristalsis have evolved as important factors in routine clinical urology. The observed changes in peristaltic pattern during high diuresis, obstruction and urinary reflux have influenced management of stone disease and neurogenic bladder. The demonstration that high intravesical pressure is reflected to the kidney not only when the ureteric orifice is incompetent, but also during high diuresis, established the necessity for low pressures in neobladders. Much further clarification of urinary transport from the renal tubules to the bladder should be achievable by refined techniques of fluoroscopy, isotopic renography and manometry.},
author = {Kinn, a C},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kinn - Progress in urodynamic research on the upper urinary tract implications for practical urology. - 1996.pdf:pdf},
issn = {0300-5623},
journal = {Urological research},
keywords = {Humans,Hydronephrosis,Hydronephrosis: physiopathology,Kidney Calculi,Kidney Calculi: physiopathology,Research,Ureter,Ureter: physiology,Urinary Diversion,Urinary Tract Physiological Phenomena,Urodynamics,Urology,Urology: trends,Vesico-Ureteral Reflux,Vesico-Ureteral Reflux: physiopathology},
month = {jan},
number = {1},
pages = {1--7},
pmid = {8966835},
title = {{Progress in urodynamic research on the upper urinary tract: implications for practical urology.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8966835},
volume = {24},
year = {1996}
}
@article{Bonin2012,
author = {Bonin, Muriel Mercier and Boulbene, Benjamin and F-, Toulouse and Lafont, Frank and Schmitz, Philippe},
doi = {10.1002/aic},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bonin et al. - A Combined Computational Fluid Dynamics ( CFD ) and Experimental Approach to Quantify the Adhesion Force of Bacterial Cel.pdf:pdf},
journal = {AIChE Journal},
keywords = {bacterial adhesion,hydrodynamics,model,shear flow},
number = {0},
pages = {1--11},
title = {{A Combined Computational Fluid Dynamics ( CFD ) and Experimental Approach to Quantify the Adhesion Force of Bacterial Cells Attached to a Plane Surface}},
volume = {00},
year = {2012}
}
@article{Donlan2002,
abstract = {Microorganisms attach to surfaces and develop biofilms. Biofilm-associated cells can be differentiated from their suspended counterparts by generation of an extracellular polymeric substance (EPS) matrix, reduced growth rates, and the up- and down- regulation of specific genes. Attachment is a complex process regulated by diverse characteristics of the growth medium, substratum, and cell surface. An established biofilm structure comprises microbial cells and EPS, has a defined architecture, and provides an optimal environment for the exchange of genetic material between cells. Cells may also communicate via quorum sensing, which may in turn affect biofilm processes such as detachment. Biofilms have great importance for public health because of their role in certain infectious diseases and importance in a variety of device-related infections. A greater understanding of biofilm processes should lead to novel, effective control strategies for biofilm control and a resulting improvement in patient management.},
author = {Donlan, Rodney M.},
doi = {10.3201/eid0809.020063},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Donlan - Biofilms Microbial life on surfaces - 2002.pdf:pdf},
isbn = {1080-6040 (Print)$\backslash$r1080-6040 (Linking)},
issn = {10806040},
journal = {Emerging Infectious Diseases},
number = {9},
pages = {881--890},
pmid = {12194761},
title = {{Biofilms: Microbial life on surfaces}},
volume = {8},
year = {2002}
}
@techreport{Nature2005,
abstract = {Nature guide to authors: Summary paragraph for Letters},
author = {Nature},
booktitle = {Nature},
doi = {10.1107/S0365110X59001529},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nature - How to construct a Nature summary paragraph - 2005.pdf:pdf},
issn = {0365110X},
number = {May},
pages = {2005},
title = {{How to construct a Nature summary paragraph}},
volume = {118},
year = {2005}
}
@article{Cherukat1994,
abstract = {An expression which predicts the inertial lift, to lowest order, on a rigid sphere translating in a linear shear flow field near a flat infinite wall has been derived. This expression may be used when the wall lies within the inner region of the sphere's disturbance flow. It is valid even when the gap is small compared to the radius of the sphere. When the sphere is far from the wall, the lift force predicted by the present analysis converges to the value predicted by earlier analyses which consider the sphere as a point force or a force doublet singularity. The effect of rotation of the sphere on the lift has also been analysed.},
annote = {ISI Document Delivery No.: NG420
Times Cited: 94
Cited Reference Count: 20
Cherukat, p mclaughlin, jb
Cambridge univ press
New york},
author = {Cherukat, P and McLaughlin, J B},
doi = {10.1017/s0022112094004015},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
keywords = {lateral migration,particle,plane},
language = {English},
pages = {1--18},
title = {{The inertial lift on a rigid sphere in a linear shear-flow field near a flat wall}},
url = {<Go to ISI>://WOS:A1994NG42000001},
volume = {263},
year = {1994}
}
@article{Tinoco2002,
abstract = {The usual variables chemists use to affect a chemical reaction are temperature and pressure. We consider here an additional variable: force, F. By attaching a molecule to the tip of a cantilever of an atomic force microscope, or to a bead in a laser light trap, we can control the force on a single molecule. This mechanical force can drive a reaction to completion, or stabilize the reactants. Force changes the thermodynamic stability of a molecule; it can thus increase or decrease the free energy change for the reaction. Force can also speed or slow rates of reactions; it changes the free energy of activation of the reaction.},
author = {Tinoco, Ignacio and Bustamante, Carlos},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tinoco, Bustamante - The effect of force on thermodynamics and kinetics of single molecule reactions. - 2002.pdf:pdf},
issn = {0301-4622},
journal = {Biophysical chemistry},
keywords = {Kinetics,Pressure,Temperature,Thermodynamics},
month = {dec},
pages = {513--33},
pmid = {12488024},
title = {{The effect of force on thermodynamics and kinetics of single molecule reactions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12488024},
volume = {101-102},
year = {2002}
}
@article{Bewes2008,
abstract = {We present an automated cell colony counting method that is flexible, robust and capable of providing more in-depth clonogenic analysis than existing manual and automated approaches. The full form of the Hough transform without approximation has been implemented, for the first time. Improvements in computing speed have facilitated this approach. Colony identification was achieved by pre-processing the raw images of the colonies in situ in the flask, including images of the flask edges, by erosion, dilation and Gaussian smoothing processes. Colony edges were then identified by intensity gradient field discrimination. Our technique eliminates the need for specialized hardware for image capture and enables the use of a standard desktop scanner for distortion-free image acquisition. Additional parameters evaluated included regional colony counts, average colony area, nearest neighbour distances and radial distribution. This spatial and qualitative information extends the utility of the clonogenic assay, allowing analysis of spatially-variant cytotoxic effects. To test the automated system, two flask types and three cell lines with different morphology, cell size and plating density were examined. A novel Monte Carlo method of simulating cell colony images, as well as manual counting, were used to quantify algorithm accuracy. The method was able to identify colonies with unusual morphology, to successfully resolve merged colonies and to correctly count colonies adjacent to flask edges.},
author = {Bewes, J M and Suchowerska, N and McKenzie, D R},
doi = {10.1088/0031-9155/53/21/007},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bewes, Suchowerska, McKenzie - Automated cell colony counting and analysis using the circular Hough image transform algorithm (CHiTA). -.pdf:pdf},
issn = {0031-9155},
journal = {Physics in medicine and biology},
month = {nov},
number = {21},
pages = {5991--6008},
pmid = {18836215},
title = {{Automated cell colony counting and analysis using the circular Hough image transform algorithm (CHiTA).}},
volume = {53},
year = {2008}
}
@article{Gross2011a,
author = {Gross, Peter and Laurens, Niels and Oddershede, Lene B. and Bockelmann, Ulrich and Peterman, Erwin J. G. and Wuite, Gijs J. L.},
doi = {10.1038/nphys2002},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gross et al. - Quantifying how DNA stretches, melts and changes twist under tension - 2011(2).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Gross et al. - Quantifying how DNA stretches, melts and changes twist under tension - 2011.pdf:pdf},
issn = {1745-2473},
journal = {Nature Physics},
month = {may},
number = {9},
pages = {1--16},
publisher = {Nature Publishing Group},
title = {{Quantifying how DNA stretches, melts and changes twist under tension}},
url = {http://www.nature.com/doifinder/10.1038/nphys2002},
volume = {7},
year = {2011}
}
@article{Cuche1999,
abstract = {We present a digital method for holographic microscopy involving a CCD camera as a recording device. Off-axis holograms recorded with a magnified image of microscopic objects are numerically reconstructed in amplitude and phase by calculation of scalar diffraction in the Fresnel approximation. For phase-contrast imaging the reconstruction method involves the computation of a digital replica of the reference wave. A digital method for the correction of the phase aberrations is presented. We present a detailed description of the reconstruction procedure and show that the transverse resolution is equal to the diffraction limit of the imaging system.},
author = {Cuche, E and Marquet, P and Depeursinge, C},
doi = {10.1364/AO.38.006994},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Cuche, Marquet, Depeursinge - Simultaneous amplitude-contrast and quantitative phase-contrast microscopy by numerical reconstruction of.pdf:pdf},
isbn = {0003-6935},
issn = {0003-6935},
journal = {Applied optics},
number = {34},
pages = {6994--7001},
pmid = {18324243},
title = {{Simultaneous amplitude-contrast and quantitative phase-contrast microscopy by numerical reconstruction of Fresnel off-axis holograms.}},
volume = {38},
year = {1999}
}
@article{Bustamante2011,
abstract = {The faithful relay and timely expression of genetic information depend on specialized molecular machines, many of which function as nucleic acid translocases. The emergence over the last decade of single-molecule fluorescence detection and manipulation techniques with nm and {\AA} resolution and their application to the study of nucleic acid translocases are painting an increasingly sharp picture of the inner workings of these machines, the dynamics and coordination of their moving parts, their thermodynamic efficiency, and the nature of their transient intermediates. Here we present an overview of the main results arrived at by the application of single-molecule methods to the study of the main machines of the central dogma.},
author = {Bustamante, Carlos and Cheng, Wei and Mejia, Yara X and Meija, Yara X},
doi = {10.1016/j.cell.2011.01.033},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bustamante et al. - Revisiting the central dogma one molecule at a time. - 2011.pdf:pdf},
issn = {1097-4172},
journal = {Cell},
keywords = {Chromosomes,Chromosomes: metabolism,DNA Helicases,DNA Helicases: metabolism,DNA Replication,Enzymes,Enzymes: metabolism,Nucleic Acids,Nucleic Acids: metabolism,Protein Biosynthesis,Thermodynamics,Transcription, Genetic,Virus Assembly},
month = {feb},
number = {4},
pages = {480--97},
pmid = {21335233},
publisher = {Elsevier Inc.},
title = {{Revisiting the central dogma one molecule at a time.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3063003{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {144},
year = {2011}
}
@article{Jones1992a,
author = {Jones, C H and Jacob-Dubuisson, F and Dodson, Karen and Kuehn, M and Slonim, L and Striker, R and Hultgren, Scott J},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Jones et al. - Adhesin presentation in bacteria requires molecular chaperones and ushers. - 1992.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
keywords = {Adhesins,Bacterial,Bacterial Adhesion,Bacterial Outer Membrane Proteins,Bacterial Outer Membrane Proteins: metabolism,Bacterial Outer Membrane Proteins: ultrastructure,Bacterial Proteins,Bacterial Proteins: genetics,Bacterial: physiology,Cell Surface,Chaperonins,Epithelium,Epithelium: microbiology,Escherichia coli,Escherichia coli: pathogenicity,Escherichia coli: ultrastructure,Fimbriae,Galactosides,Galactosides: metabolism,Genes,Macromolecular Substances,Models,Molecular,Protein Conformation,Proteins,Proteins: metabolism,Receptors},
month = {nov},
number = {11},
pages = {4445--51},
pmid = {1356928},
title = {{Adhesin presentation in bacteria requires molecular chaperones and ushers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=258187{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {60},
year = {1992}
}
@article{Umansky2012,
author = {Umansky, Moti and Weihs, Daphne},
doi = {10.1016/j.cpc.2012.03.001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Umansky, Weihs - Novel algorithm and MATLAB-based program for automated power law analysis of single particle, time-dependent mean-squar.pdf:pdf},
issn = {00104655},
journal = {Computer Physics Communications},
keywords = {single-particle trajectory analysis,time-dependent mean-square displacemen},
month = {aug},
number = {8},
pages = {1783--1792},
publisher = {Elsevier B.V.},
title = {{Novel algorithm and MATLAB-based program for automated power law analysis of single particle, time-dependent mean-square displacement}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0010465512001063},
volume = {183},
year = {2012}
}
@article{Svoboda1994a,
abstract = {On SciFinder (R)},
author = {Svoboda, K and Block, S M},
doi = {10.1146/annurev.bb.23.060194.001335},
isbn = {1056-8700},
issn = {1056-8700},
journal = {Annual review of biophysics and biomolecular structure},
pages = {247--285},
pmid = {7919782},
title = {{Biological applications of optical forces.}},
volume = {23},
year = {1994}
}
@article{Jaume-i-Capo2012,
author = {Jaume-i-Capó, Antoni and Varona, Javier and González-Hidalgo, Manuel and Mas, Ramon and Perales, Francisco J.},
doi = {10.1117/1.OE.51.2.020501},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jaume-i-Capó et al. - Automatic human body modeling for vision-based motion capture system using B-spline parameterization of the silho.pdf:pdf},
issn = {00913286},
journal = {Optical Engineering},
number = {2},
pages = {020501},
title = {{Automatic human body modeling for vision-based motion capture system using B-spline parameterization of the silhouette}},
url = {http://link.aip.org/link/OPEGAR/v51/i2/p020501/s1{\&}Agg=doi},
volume = {51},
year = {2012}
}
@article{Neuert2006,
abstract = {Small ligands and their receptors are widely used non-covalent couplers in various biotech applications. One prominent example, the digoxigenin-antibody complex, was often used to immobilize samples for single molecule force measurements by optical trap or AFM. Here, we employed dynamic AFM spectroscopy to demonstrate that a single digoxigenin-antibody bond is likely to fail even under moderate loading rates. This effect potentially could lower the yield of measurements or even obscure the unbinding data of the sample by the rupture events of the coupler. Immobilization by multiple antibody-antigen bonds, therefore, is highly recommended. The analysis of our data revealed a pronounced loading rate dependence of the rupture force, which we analyzed based on the well-established Bell-Evans-model with two subsequent unbinding barriers. We could show that the first barrier has a width of Deltax(1)=1.15 nm and a spontaneous rate of k(off1)=0.015 s(-1) and the second has a width of Deltax(2)=0.35 nm and a spontaneous rate of k(off2)=4.56 s(-1). In the crossover region between the two regimes, we found a marked discrepancy between the predicted bond rupture probability density and the measured rupture force histograms, which we discuss as non-Markovian contribution to the unbinding process.},
author = {Neuert, G and Albrecht, C and Pamir, E and Gaub, H E},
doi = {10.1016/j.febslet.2005.12.052},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Neuert et al. - Dynamic force spectroscopy of the digoxigenin-antibody complex. - 2006.pdf:pdf},
issn = {0014-5793},
journal = {FEBS letters},
keywords = {Antibodies,Antibodies: chemistry,Antibodies: metabolism,Digoxigenin,Digoxigenin: chemistry,Digoxigenin: metabolism,Ligands,Microscopy, Atomic Force,Microscopy, Atomic Force: instrumentation,Microscopy, Atomic Force: methods,Models, Molecular,Molecular Structure,Protein Binding,Protein Conformation},
month = {jan},
number = {2},
pages = {505--9},
pmid = {16388805},
title = {{Dynamic force spectroscopy of the digoxigenin-antibody complex.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16388805},
volume = {580},
year = {2006}
}
@article{Urban2007,
author = {Urban, Constantin and Zychlinsky, Arturo},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Urban, Zychlinsky - Netting bacteria in sepsis Providing AID to p53 mutagenesis - 2007.pdf:pdf},
journal = {Nature Medicine},
number = {4},
pages = {403--404},
title = {{Netting bacteria in sepsis Providing AID to p53 mutagenesis}},
volume = {13},
year = {2007}
}
@article{Brodin2014,
author = {Brodin, T and Fick, M and Jonsson, M and Klaminder, J},
doi = {10.1126/science.1226850},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Brodin et al. - Dilute Concentrations of a Psychiatric - 2014.pdf:pdf},
journal = {Science},
keywords = {writing science},
mendeley-tags = {writing science},
number = {2013},
pages = {814--815},
title = {{Dilute Concentrations of a Psychiatric}},
volume = {814},
year = {2014}
}
@article{Sauer2000,
author = {Sauer, FG and Mulvey, MA and Schilling, JD and Martinez, JJ and Hultgren, Scott J},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sauer et al. - Bacterial pili molecular mechanisms of pathogenesis - 2000.pdf:pdf},
journal = {Current opinion in {\ldots}},
pages = {65--72},
title = {{Bacterial pili: molecular mechanisms of pathogenesis}},
url = {http://www.sciencedirect.com/science/article/pii/S1369527499000533},
volume = {3},
year = {2000}
}
@article{Zakrisson 2015,
archivePrefix = {arXiv},
arxivId = {1411.4416},
author = {Zakrisson, Johan and Wiklund, Krister and Servin, Martin and Axner, Ove and Lacoursi{\`{e}}re, Claude and Andersson, Magnus},
doi = {10.1007/s00249-015-1021-1},
eprint = {1411.4416},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zakrisson et al. - Rigid multibody simulation of a helix-like structure – The dynamics of bacterial adhesion pili - 2015(2).pdf:pdf},
journal = {European biophysics journal},
pages = {10.1007/s00249--015--1021--1},
title = {{Rigid multibody simulation of a helix-like structure – The dynamics of bacterial adhesion pili}},
year = {2015}
}
@article{Forero2004,
author = {Forero, Manu and Thomas, Wendy E and Bland, Clint and Nilsson, Lina M and Sokurenko, Evgeni V and Vogel, Viola},
doi = {10.1021/nl049329z},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Forero et al. - A Catch-Bond Based Nanoadhesive Sensitive to Shear Stress - 2004.pdf:pdf},
issn = {1530-6984},
journal = {Nano Letters},
month = {sep},
number = {9},
pages = {1593--1597},
title = {{A Catch-Bond Based Nanoadhesive Sensitive to Shear Stress}},
url = {http://pubs.acs.org/doi/abs/10.1021/nl049329z},
volume = {4},
year = {2004}
}
@article{Andersson2007,
abstract = {Uropathogenic Escherichia coli express pili that mediate binding to host tissue cells. We demonstrate with in situ force measuring optical tweezers that the ability of P and type 1 pili to elongate by unfolding under exposure to stress is a shared property with some differences. The unfolding force of the quaternary structures under equilibrium conditions is similar, 28 +/- 2 and 30 +/- 2 pN for P pili and type 1 pili, respectively. However, type 1 pili are found to be more rigid than P pili through their stronger layer-to-layer bonds. It was found that type 1 pili enter a dynamic regime at elongation speeds of 6 nm/s, compared to 400 nm/s for P pili; i.e., it responds faster to an external force. This possibly helps type 1 to withstand the irregular urine flow in the urethra as compared to the more constant urine flow in the upper urinary tract. Also, it was found that type 1 pili refold during retraction at two different levels that possibly could be related to several possible configurations. Our findings highlight functions that are believed to be of importance for the bacterial ability to sustain a basic antimicrobial mechanism of the host and for bacterial colonization.},
annote = {From Duplicate 2 ( The biomechanical properties of E. coli pili for urinary tract attachment reflect the host environment. - Andersson, Magnus; Uhlin, Bernt Eric; F{\"{a}}llman, Erik )},
author = {Andersson, Magnus and Uhlin, Bernt Eric and F{\"{a}}llman, Erik},
doi = {10.1529/biophysj.107.110643},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson, Uhlin, F{\"{a}}llman - The biomechanical properties of E. coli pili for urinary tract attachment reflect the host environment. - 20.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Atomic Force,Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: chemistry,Bacterial: physiology,Biomechanics,Escherichia coli,Escherichia coli: physiology,Fimbriae,Humans,Microscopy,Optical Tweezers,Urinary Tract Infections,Urinary Tract Infections: microbiology,Urinary Tract Physiological Phenomena},
number = {9},
pages = {3008--14},
pmid = {17675342},
title = {{The biomechanical properties of E. coli pili for urinary tract attachment reflect the host environment.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17675342},
volume = {93},
year = {2007}
}
@article{Morelli2009,
abstract = {The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. Despite extensive characterization of this regulatory network, the origin of the extreme stability of the lysogenic state remains unclear. We have constructed a stochastic model for this switch. Using Forward Flux Sampling simulations, we show that this model predicts an extremely low rate of spontaneous prophage induction in a recA mutant, in agreement with experimental observations. In our model, the DNA loop formed by octamerization of CI bound to the O(L) and O(R) operator regions is crucial for stability, allowing the lysogenic state to remain stable even when a large fraction of the total CI is depleted by nonspecific binding to genomic DNA. DNA looping also ensures that the switch is robust to mutations in the order of the O(R) binding sites. Our results suggest that DNA looping can provide a mechanism to maintain a stable lysogenic state in the face of a range of challenges including noisy gene expression, nonspecific DNA binding, and operator site mutations.},
author = {Morelli, Marco J and {Ten Wolde}, Pieter Rein and Allen, Rosalind J},
doi = {10.1073/pnas.0810399106},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Morelli, Ten Wolde, Allen - DNA looping provides stability and robustness to the bacteriophage lambda switch. - 2009.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Bacteriophage lambda,Bacteriophage lambda: genetics,Binding Sites,DNA, Viral,DNA, Viral: chemistry,DNA, Viral: physiology,Gene Expression Regulation, Viral,Genes, Switch,Genomic Instability,Lysogeny,Lysogeny: genetics,Models, Genetic,Mutation,Nucleic Acid Conformation,Operator Regions, Genetic,Stochastic Processes},
month = {may},
number = {20},
pages = {8101--6},
pmid = {19416825},
title = {{DNA looping provides stability and robustness to the bacteriophage lambda switch.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2686219{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {106},
year = {2009}
}
@article{Thalhammer2011,
author = {Thalhammer, G and Steiger, R and Bernet, S and Ritsch-Marte, M},
doi = {10.1088/2040-8978/13/4/044024},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Thalhammer et al. - Optical macro-tweezers trapping of highly motile micro-organisms - 2011.pdf:pdf},
issn = {2040-8978},
journal = {Journal of Optics},
month = {apr},
number = {4},
pages = {044024},
title = {{Optical macro-tweezers: trapping of highly motile micro-organisms}},
url = {http://stacks.iop.org/2040-8986/13/i=4/a=044024?key=crossref.8da94b2c69fcbd60d1e89bc9544ce230},
volume = {13},
year = {2011}
}
@article{Svedberg2006a,
abstract = {We use optical tweezers to move single silver nanoparticles into near-field contact with immobilized particles, forming isolated surface-enhanced Raman spectroscopy (SERS) active Ag particle dimers. The surface-averaged SERS intensity increases by a factor approximately 20 upon dimerization. Electrodynamics calculations indicate that the final approach between the particles is due to "optical binding". The described methodology may facilitate controlled single molecule SERS analysis.},
author = {Svedberg, Fredrik and Li, Zhipeng and Xu, Hongxing and K{\"{a}}ll, Mikael},
doi = {10.1021/nl062101m},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Svedberg et al. - Creating hot nanoparticle pairs for surface-enhanced Raman spectroscopy through optical manipulation. - 2006.pdf:pdf},
issn = {1530-6984},
journal = {Nano letters},
keywords = {Metal Nanoparticles,Optical Tweezers,Silver,Silver: chemistry,Spectrum Analysis, Raman,Spectrum Analysis, Raman: methods},
month = {dec},
number = {12},
pages = {2639--41},
pmid = {17163680},
title = {{Creating hot nanoparticle pairs for surface-enhanced Raman spectroscopy through optical manipulation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17163680},
volume = {6},
year = {2006}
}
@article{Andersson2006b,
abstract = {Surface organelles (so-called pili) expressed on the bacterial membrane mediate the adhesion of Escherichia coli causing urinary tract infection. These pili possess some extraordinary elongation properties that are assumed to allow a close bacterium-to-host contact even in the presence of shear forces caused by urine flow. The elongation properties of P pili have therefore been assessed for low elongation speeds (steady-state conditions). This work reports on the behavior of P pili probed by dynamic force spectroscopy. A kinetic model for the unfolding of a helixlike chain structure is derived and verified. It is shown that the unfolding of the quaternary structure of the PapA rod takes place at a constant force that is almost independent of elongation speed for slow elongations (up to approximately 0.4 mum/s), whereas it shows a dynamic response with a logarithmic dependence for fast elongations. The results provide information about the energy landscape and reaction rates. The bond length and thermal bond opening and closure rates for the layer-to-layer bond have been assessed to approximately 0.76 nm, approximately 0.8 Hz, and approximately 8 GHz, respectively. The results also support a previously constructed sticky-chain model for elongation of the PapA rod that until now had been experimentally verified only under steady-state conditions.},
annote = {From Duplicate 1 ( Dynamic force spectroscopy of E. coli P pili. - Andersson, Magnus; F{\"{a}}llman, Erik; Uhlin, Bernt Eric; Axner, Ove )
},
author = {Andersson, Magnus and F{\"{a}}llman, Erik and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1529/biophysj.106.087429},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - Dynamic force spectroscopy of E. coli P pili. - 2006.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Bacterial,Bacterial: physiology,Biological,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: physiology,Escherichia coli: physiology,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: physiology,Models,Protein Folding,Shear Strength},
number = {7},
pages = {2717--25},
pmid = {16844748},
title = {{Dynamic force spectroscopy of E. coli P pili.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16844748},
volume = {91},
year = {2006}
}
@article{Persat2015,
author = {Persat, Alexandre and Nadell, Carey D. and Kim, Minyoung Kevin and Ingremeau, Francois and Siryaporn, Albert and Drescher, Knut and Wingreen, Ned S. and Bassler, Bonnie L. and Gitai, Zemer and Stone, Howard A.},
doi = {10.1016/j.cell.2015.05.005},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Persat et al. - The Mechanical World of Bacteria - 2015.pdf:pdf},
issn = {00928674},
journal = {Cell},
number = {5},
pages = {988--997},
publisher = {Elsevier Inc.},
title = {{The Mechanical World of Bacteria}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867415005528},
volume = {161},
year = {2015}
}
@article{Andersson2006,
abstract = {Optical tweezers have previously been used to characterize the force-vs. -elongation dependence of the PapA rod of uropathogenic E. coli P pili. It was found that the PapA rod elongates in several elongation regions. In the two first, the elongation originates from an elastic stretching and a sequential unfolding of the layer-to-layer bonds (and thereby of the helical structure). Region III is characterized by an elongation that originates from an elastic stretching and an opening of the head-to-tail bonds in the linearized PapA rod. The opening of these bonds takes place in a random order, wherefore the response in this region is affected by entropy. Since the entropic softening of a macromolecule depends on the number of units, the shape of this region can be used to assess the number of PapA units. We provide in this work a recipe for how this can be done solely from the form of region III. An advantage with this technique is that it does not require a continuous monitoring of the elongation of a single PapA rod from unstretched conditions, which often is difficult because of simultaneous multi-pili binding; it suffices to detect it in the third region at which binding often is mediated by only one pilus. Another advantage is that it does not require any prior knowledge about (or assessment of) any physical entity of the PapA rod; the number of PapA units can be assessed solely from the shape of the curve in the third elongation region.},
author = {Andersson, Magnus and F{\"{a}}llman, Erik and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1117/12.642261},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - Technique for determination of the number of PapA units in an - 2006.pdf:pdf},
issn = {0277786X},
journal = {Proceedings of SPIE},
keywords = {ATOMIC-FORCE MICROSCOPY,BACTERIAL ADHESION PILI,BIOLOGICAL APPLICATIONS,DNA MECHANICS,E. coli,EXTRAINTESTINAL INFECTIONS,FLAGELLAR MOTOR,FLUCTUATION ANALYSIS,OPTICAL TWEEZERS,SINGLE KINESIN MOLECULE,SPECTROSCOPY,coli,e,force measuring optical tweezers,macromolecules,p pili,papa,refolding,sticky chain,unfolding,unfolding/refolding},
pages = {608814--608814--12},
publisher = {SPIE},
title = {{Technique for determination of the number of PapA units in an}},
url = {http://link.aip.org/link/PSISDG/v6088/i1/p608814/s1{\&}Agg=doi},
year = {2006}
}
@article{Kultanen1990,
abstract = {A method is developed for calculating the Hough transform (HT) and
completing the task of finding global features from binary edge images.
The method is based on the fact that a single parameter space point can
be determined uniquely with a pair, triple, or generally
<e1>n</e1>-tuple of points from the original picture. Such
<e1>n</e1>-tuples of points can be chosen randomly from the edge image,
giving the method the name randomized Hough transform (RHT). The new
algorithm reduces the computation time and memory use of the HT
drastically. In the standard HT one must calculate one parameter curve
in the parameter space for one pixel, whereas in the RHT only one
parameter point has to be solved for one <e1>n</e1>-tuple of points, and
the presence of a specific curve in the image is quickly revealed by the
accumulation of a small number of parameter points},
author = {Kultanen, P. and Xu, L. and Oja, E.},
doi = {10.1109/ICPR.1990.118177},
isbn = {0-8186-2062-5},
journal = {[1990] Proceedings. 10th International Conference on Pattern Recognition},
title = {{Randomized Hough transform (RHT)}},
volume = {i},
year = {1990}
}
@article{Habenstein2015,
author = {Habenstein, Birgit and Loquet, Antoine and Hwang, Songhwan and Giller, Karin and Vasa, Suresh Kumar and Becker, Stefan and Habeck, Michael and Lange, Adam},
doi = {10.1002/ange.201505065},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Habenstein et al. - Hybrid Structure of the Type 1 Pilus of Uropathogenic Escherichia coli - 2015.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Habenstein et al. - Hybrid Structure of the Type 1 Pilus of Uropathogenic Escherichia coli - 2015(2).pdf:pdf},
issn = {00448249},
journal = {Angewandte Chemie},
keywords = {Type 1},
mendeley-tags = {Type 1},
pages = {n/a--n/a},
title = {{Hybrid Structure of the Type 1 Pilus of Uropathogenic Escherichia coli}},
url = {http://doi.wiley.com/10.1002/ange.201505065},
year = {2015}
}
@article{Levine1979,
author = {Levine, Myron M and Nalin, David R and Hoover, David L and Bergquist, Erick J and Hornick, Richard B and Charles, R},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Levine et al. - Enterotoxigenic Immunity to Enterotoxigenic Escherichia coli - 1979.pdf:pdf},
title = {{Enterotoxigenic Immunity to Enterotoxigenic Escherichia coli}},
year = {1979}
}
@article{Wang2006,
author = {Wang, H.-H. and Liu, C.-Y. and Wu, S.-B. and Liu, N.-W. and Peng, C.-Y. and Chan, T.-H. and Hsu, C.-F. and Wang, J.-K. and Wang, Y.-L.},
doi = {10.1002/adma.200501875},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wang et al. - Highly Raman-Enhancing Substrates Based on Silver Nanoparticle Arrays with Tunable Sub-10nm Gaps - 2006.pdf:pdf},
issn = {0935-9648},
journal = {Advanced Materials},
month = {feb},
number = {4},
pages = {491--495},
title = {{Highly Raman-Enhancing Substrates Based on Silver Nanoparticle Arrays with Tunable Sub-10nm Gaps}},
url = {http://doi.wiley.com/10.1002/adma.200501875},
volume = {18},
year = {2006}
}
@article{Smyth1982,
author = {Smyth, C J},
doi = {10.1099/00221287-128-9-2081},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Smyth - Two mannose-resistant haemagglutinins on enterotoxigenic Escherichia coli of serotype O6K15H16 or H-isolated from travellers' an.pdf:pdf},
isbn = {0022-1287 (Print)},
issn = {1350-0872},
journal = {Journal of general microbiology},
pages = {2081--2096},
pmid = {6816903},
title = {{Two mannose-resistant haemagglutinins on enterotoxigenic Escherichia coli of serotype O6:K15:H16 or H-isolated from travellers' and infantile diarrhoea.}},
volume = {128},
year = {1982}
}
@article{Lansdorp2012,
abstract = {Single-molecule manipulation instruments, such as optical traps and magnetic tweezers, frequently use video tracking to measure the position of a force-generating probe. The instruments are calibrated by comparing the measured probe motion to a model of Brownian motion in a harmonic potential well; the results of calibration are estimates of the probe drag, $\alpha$, and spring constant, $\kappa$. Here, we present both time- and frequency-domain methods to accurately and precisely extract $\alpha$ and $\kappa$ from the probe trajectory. In the frequency domain, we discuss methods to estimate the power spectral density (PSD) from data (including windowing and blocking), and we derive an analytical formula for the PSD which accounts both for aliasing and the filtering intrinsic to video tracking. In the time domain, we focus on the Allan variance (AV): we present a theoretical equation for the AV relevant to typical single-molecule setups and discuss the optimal manner for computing the AV from experimental data using octave-sampled overlapping bins. We show that, when using maximum-likelihood methods to fit to the data, both the PSD and AV approaches can extract $\alpha$ and $\kappa$ in an unbiased and low-error manner, though the AV approach is simpler and more robust.},
author = {Lansdorp, Bob M and Saleh, Omar a},
doi = {10.1063/1.3687431},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lansdorp, Saleh - Power spectrum and Allan variance methods for calibrating single-molecule video-tracking instruments. - 2012.pdf:pdf},
issn = {1089-7623},
journal = {The Review of scientific instruments},
keywords = {Calibration,Likelihood Functions,Models, Theoretical,Spectrum Analysis,Spectrum Analysis: instrumentation},
month = {mar},
number = {2},
pages = {025115},
pmid = {22380133},
title = {{Power spectrum and Allan variance methods for calibrating single-molecule video-tracking instruments.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22380133},
volume = {83},
year = {2012}
}
@article{Norregaard2013b,
author = {Norregaard, Kamilla and Andersson, Magnus and Sneppen, Kim and Nielsen, Peter Eigil and Brown, Stanley and Oddershede, Lene Broeng},
doi = {10.1073/pnas.1215907110},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Norregaard et al. - DNA supercoiling enhances cooperativity and ef fi ciency of an epigenetic switch - 2013.pdf:pdf},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
title = {{DNA supercoiling enhances cooperativity and ef fi ciency of an epigenetic switch}},
year = {2013}
}
@book{Lamb1945,
address = {New York},
author = {Lamb, Horace},
edition = {Sixth edit},
keywords = {Fluid},
publisher = {Dover Publications},
title = {{Hydrodynamics}},
year = {1945}
}
@article{Cox2014,
abstract = {Acquisition of the intestinal microbiota begins at birth, and a stable microbial community develops from a succession of key organisms. Disruption of the microbiota during maturation by low-dose antibiotic exposure can alter host metabolism and adiposity. We now show that low-dose penicillin (LDP), delivered from birth, induces metabolic alterations and affects ileal expression of genes involved in immunity. LDP that is limited to early life transiently perturbs the microbiota, which is sufficient to induce sustained effects on body composition, indicating that microbiota interactions in infancy may be critical determinants of long-term host metabolic effects. In addition, LDP enhances the effect of high-fat diet induced obesity. The growth promotion phenotype is transferrable to germ-free hosts by LDP-selected microbiota, showing that the altered microbiota, not antibiotics per se, play a causal role. These studies characterize important variables in early-life microbe-host metabolic interaction and identify several taxa consistently linked with metabolic alterations.},
author = {Cox, Laura M. and Yamanishi, Shingo and Sohn, Jiho and Alekseyenko, Alexander V. and Leung, Jacqueline M. and Cho, Ilseung and Kim, Sungheon G. and Li, Huilin and Gao, Zhan and Mahana, Douglas and {Z{\'{a}}rate Rodriguez}, Jorge G. and Rogers, Arlin B. and Robine, Nicolas and Loke, P’ng and Blaser, Martin J.},
doi = {10.1016/j.cell.2014.05.052},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Cox et al. - Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences. - 2014.pdf:pdf},
isbn = {1097-4172 (Electronic)$\backslash$r0092-8674 (Linking)},
issn = {1097-4172},
journal = {Cell},
number = {4},
pages = {705--721},
pmid = {25126780},
title = {{Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences.}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867414008216$\backslash$nhttp://www.ncbi.nlm.nih.gov/pubmed/25126780},
volume = {158},
year = {2014}
}
@article{Marshall2005,
abstract = {Receptor-ligand bonds that mediate cell adhesion are often subjected to forces that regulate their dissociation via modulating off-rates. Off-rates control how long receptor-ligand bonds last and how much force they withstand. One should therefore be able to determine off-rates from either bond lifetime or unbinding force measurements. However, substantial discrepancies exist between the force dependence of off-rates derived from the two types of measurements even for the same interactions, e.g., selectins dissociating from their ligands, which mediate the tethering and rolling of leukocytes on vascular surfaces during inflammation and immune surveillance. We used atomic force microscopy to measure survival times of P-selectin dissociating from P-selectin glycoprotein ligand 1 or from an antibody in both bond lifetime and unbinding force experiments. By a new method of data analysis, we showed that the discrepancies resulted from the assumption that off-rates were functions of force only. The off-rates derived from forced dissociation data depended not only on force but also on the history of force application. This finding provides a new paradigm for understanding how force regulates receptor-ligand interactions.},
author = {Marshall, Bryan T and Sarangapani, Krishna K and Lou, Jizhong and McEver, Rodger P and Zhu, Cheng},
doi = {10.1529/biophysj.104.050567},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Marshall et al. - Force history dependence of receptor-ligand dissociation. - 2005.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Algorithms,Computer Simulation,Elasticity,Image Interpretation, Computer-Assisted,Image Interpretation, Computer-Assisted: methods,Kinetics,Membrane Glycoproteins,Membrane Glycoproteins: chemistry,Membrane Glycoproteins: ultrastructure,Micromanipulation,Micromanipulation: methods,Models, Chemical,Multiprotein Complexes,Multiprotein Complexes: chemistry,Multiprotein Complexes: ultrastructure,P-Selectin,P-Selectin: chemistry,P-Selectin: ultrastructure,Protein Binding,Stress, Mechanical},
month = {feb},
number = {2},
pages = {1458--66},
pmid = {15556978},
title = {{Force history dependence of receptor-ligand dissociation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15556978},
volume = {88},
year = {2005}
}
@article{Gong2006,
author = {Gong, Z and Chen, H and Xu, S and Li, Y and Lou, L},
doi = {10.1016/j.optcom.2006.01.052},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gong et al. - Monte-Carlo simulation of optical trap stiffness measurement - 2006.pdf:pdf},
issn = {00304018},
journal = {Optics Communications},
keywords = {bandwidth,monte-carlo simulation,optical tweezers,trap stiffness},
month = {jul},
number = {2},
pages = {229--234},
title = {{Monte-Carlo simulation of optical trap stiffness measurement}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0030401806001118},
volume = {263},
year = {2006}
}
@article{Hacker1985,
abstract = {The uropathogenic Escherichia coli strain 536 (O6:K15:H31) exhibits a mannose-resistant hemagglutination phenotype (Mrh) with bovine erythrocytes and delayed Mrh with human and guinea pig erythrocytes. Neuraminidase treatment of the erythrocytes abolishes mannose resistant hemagglutination, which is typical for X fimbriae. E. coli strain 536 synthesizes two different fimbriae (Fim phenotype) protein subunits, 16.5 and 22 kilodaltons in size. In addition the strain shows mannose-sensitive hemagglutination and common type I (F1) fimbriae. The cosmid clone E. coli K-12(pANN801) and another nine independently isolated Mrh+ cosmid clones derived from a cosmid gene bank of strain 536 express the 16.5-kilodalton protein band, but not the 22-kilodalton protein, indicating an association of the Mrh+ property with the "16.5-kilodalton fimbriae." All cosmid clones were fimbriated, and they reacted with antiserum produced against Mrh+ fimbriae of the E. coli strain HB101(pANN801) and lacked mannose-sensitive hemagglutination (F1) fimbriae. From the Mrh fim cosmid DNA pANN801, several subclones coding for hemagglutination and X fimbriae were constructed. Subclones that express both hemagglutination and fimbriae and subclones that only code for the hemagglutination antigen were isolated; subclones that only produce fimbriae were not detected. By transposon Tn5 mutagenesis we demonstrated that about 6.5 kilobases of DNA is required for the Mrh+ Fim+ phenotype, and the 1.5- to 2-kilobase DNA region coding for the structural protein of the fimbriae has been mapped adjacent to the region responsible for the Mrh+ phenotype. Two different regions can thus be distinguished in the adhesion determinant, one coding for hemagglutination and the other coding for fimbria formation. Transformation of plasmid DNA from these subclones into a Mrh- Fim- mutant of E. coli 536 and into a galE (rough) strain of Salmonella typhimurium yielded transformants that expressed both hemagglutination and fimbria production.},
author = {Hacker, J and Schmidt, G and Hughes, C and Knapp, S and Marget, M and Goebel, W},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hacker et al. - Cloning and characterization of genes involved in production of mannose-resistant, neuraminidase-susceptible (X) fimbria.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
keywords = {Animals,Cattle,Cloning, Molecular,Escherichia coli,Escherichia coli: genetics,Escherichia coli: isolation {\&} purification,Escherichia coli: ultrastructure,Fimbriae, Bacterial,Fimbriae, Bacterial: drug effects,Genes, Bacterial,Guinea Pigs,Hemagglutination Tests,Humans,Mannose,Mannose: pharmacology,Neuraminidase,Neuraminidase: metabolism,Plasmids,Recombination, Genetic,Urinary Tract Infections,Urinary Tract Infections: microbiology},
month = {feb},
number = {2},
pages = {434--40},
pmid = {2857153},
title = {{Cloning and characterization of genes involved in production of mannose-resistant, neuraminidase-susceptible (X) fimbriae from a uropathogenic O6:K15:H31 Escherichia coli strain.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=263188{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {47},
year = {1985}
}
@article{Holmgren2013,
abstract = {A first-generation oral inactivated whole-cell enterotoxigenic Escherichia coli (ETEC) vaccine, comprising formalin-killed ETEC bacteria expressing different colonization factor (CF) antigens combined with cholera toxin B subunit (CTB), when tested in phase III studies did not significantly reduce overall (generally mild) ETEC diarrhea in travelers or children although it reduced more severe ETEC diarrhea in travelers by almost 80{\%}. We have now developed a novel more immunogenic ETEC vaccine based on recombinant non-toxigenic E. coli strains engineered to express increased amounts of CF antigens, including CS6 as well as an ETEC-based B subunit protein (LCTBA), and the optional combination with a nontoxic double-mutant heat-labile toxin (LT) molecule (dmLT) as an adjuvant. Two test vaccines were prepared under GMP: (1) A prototype E. coli CFA/I-only formalin-killed whole-cell+LCTBA vaccine, and (2) A "complete" inactivated multivalent ETEC-CF (CFA/I, CS3, CS5 and CS6 antigens) whole-cell+LCTBA vaccine. These vaccines, when given intragastrically alone or together with dmLT in mice, were well tolerated and induced strong intestinal-mucosal IgA antibody responses as well as serum IgG and IgA responses to each of the vaccine CF antigens as well as to LT B subunit (LTB). Both mucosal and serum responses were further enhanced (adjuvanted) when the vaccines were co-administered with dmLT. We conclude that the new multivalent oral ETEC vaccine, both alone and especially in combination with the dmLT adjuvant, shows great promise for further testing in humans.},
author = {Holmgren, J and Bourgeois, L and Carlin, N and Clements, J and Gustafsson, B and Lundgren, A and Nygren, E and Tobias, J and Walker, R and Svennerholm, Ann-Mari},
doi = {10.1016/j.vaccine.2013.03.027},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Holmgren et al. - Development and preclinical evaluation of safety and immunogenicity of an oral ETEC vaccine containing inactivated E..pdf:pdf},
issn = {1873-2518},
journal = {Vaccine},
keywords = {Adjuvants,Administration,Animals,Antibody Formation,Antibody Formation: immunology,Antigens,Bacterial,Bacterial Toxins,Bacterial Toxins: administration {\&} dosage,Bacterial Toxins: genetics,Bacterial Toxins: immunology,Bacterial: genetics,Bacterial: immunology,Cholera Toxin,Cholera Toxin: administration {\&} dosage,Cholera Toxin: genetics,Cholera Toxin: immunology,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: immunology,Enterotoxins,Enterotoxins: administration {\&} dosage,Enterotoxins: genetics,Enterotoxins: immunology,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli Infections: microbiology,Escherichia coli Infections: prevention {\&} control,Escherichia coli Proteins,Escherichia coli Proteins: administration {\&} dosage,Escherichia coli Proteins: genetics,Escherichia coli Proteins: immunology,Escherichia coli Vaccines,Escherichia coli Vaccines: administration {\&} dosage,Escherichia coli Vaccines: adverse effects,Escherichia coli Vaccines: genetics,Escherichia coli Vaccines: immunology,Female,Fimbriae Proteins,Fimbriae Proteins: genetics,Fimbriae Proteins: immunology,Immunity,Immunoglobulin A,Immunoglobulin A: analysis,Immunoglobulin A: blood,Immunoglobulin A: immunology,Immunoglobulin G,Immunoglobulin G: analysis,Immunoglobulin G: blood,Immunoglobulin G: immunology,Immunologic,Immunologic: administration {\&} dosage,Inactivated,Inactivated: administration {\&} dosage,Inactivated: adverse effects,Inactivated: genetics,Inactivated: immunology,Inbred BALB C,Intestines,Intestines: immunology,Mice,Mucosal,Mucosal: immunology,Mutant Proteins,Mutant Proteins: administration {\&} dosage,Mutant Proteins: immunology,Oral,Vaccines},
month = {may},
number = {20},
pages = {2457--64},
pmid = {23541621},
publisher = {Elsevier Ltd},
title = {{Development and preclinical evaluation of safety and immunogenicity of an oral ETEC vaccine containing inactivated E. coli bacteria overexpressing colonization factors CFA/I, CS3, CS5 and CS6 combined with a hybrid LT/CT B subunit antigen, administered al}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23541621},
volume = {31},
year = {2013}
}
@article{Govender2014,
abstract = {Adhesion to host cells is a precursor to host colonization and the evasion of the host immune response. Conversely, it triggers the induction of the immune response, a process vital to the host's defence against infection. Adhesins are microbial cell surface molecules or structures that mediate the attachment of the microbe to host cells and, thus, the host-pathogen interaction. They also play a crucial role in bacterial aggregation and biofilm formation. In this review, we discuss the role of adhesins in the pathogenesis of the etiological agent of tuberculosis, Mycobacterium tuberculosis. We also provide insight into the structure and characteristics of some of the characterized and putative M. tuberculosis adhesins. Finally, we examine the potential of adhesins as targets for the development of TB control strategies.},
author = {Govender, Viveshree S and Ramsugit, Saiyur and Pillay, Manormoney},
doi = {10.1099/mic.0.082206-0},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Govender, Ramsugit, Pillay - Mycobacterium tuberculosis adhesins potential biomarkers as anti-tuberculosis therapeutic and diagnostic ta.pdf:pdf},
issn = {1465-2080},
journal = {Microbiology (Reading, England)},
month = {jul},
pages = {1821--1831},
pmid = {25009234},
title = {{Mycobacterium tuberculosis adhesins: potential biomarkers as anti-tuberculosis therapeutic and diagnostic targets.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25009234},
year = {2014}
}
@article{Schwan2002,
author = {Schwan, W.R. and Lee, J.L. and Lenard, F.A. and Matthews, B.T. and Beck, M.T.},
doi = {10.1128/IAI.70.3.1391},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schwan et al. - Osmolarity and pH growth conditions regulate fim gene transcription and type 1 pilus expression in uropathogenic Escheri.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
number = {3},
pages = {1391},
publisher = {Am Soc Microbiol},
title = {{Osmolarity and pH growth conditions regulate fim gene transcription and type 1 pilus expression in uropathogenic Escherichia coli}},
url = {http://iai.asm.org/cgi/content/abstract/70/3/1391},
volume = {70},
year = {2002}
}
@article{Petrov2006,
author = {Petrov, E. and Ohrt, T. and Winkler, R. and Schwille, P.},
doi = {10.1103/PhysRevLett.97.258101},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Petrov et al. - Diffusion and Segmental Dynamics of Double-Stranded DNA - 2006.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {dec},
number = {25},
pages = {1--4},
title = {{Diffusion and Segmental Dynamics of Double-Stranded DNA}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.97.258101},
volume = {97},
year = {2006}
}
@book{CastroSantos2005,
abstract = {The field of biomechanics tends focuses on suborganismal processes. Muscle kinetics, body and fin morphologies, and sensory systems characterize the mechanical interactions between fishes and their habitat. These in turn define the fishes' ability to exploit their environment, influencing not only home range, but also reproductive success, energetics, trophic interactions, and the scope of available habitats. Fisheries managers must take into account more than ecology and life history theory when developing policy: physiology, energetics, behavior, and stochastic habitat and ecosystem‐level processes must all be considered. The chapter discusses the current state of the field of fish biomechanics in a management context, identifying advances and gaps in knowledge that may both aid the development of sound management policies and provide helpful directions for future research. When developing conservation policy, managers often focus on critical life history stages: those parts of the life cycle that determine population-level processes. Many factors influence whether and in what condition fishes progress through these life stages. The chapter also presents a summary of gaps in current knowledge, with suggestions to how future biomechanics research might help to improve practices in both fisheries management and conservation.},
author = {Castro‐Santos, Theodore and Haro, Alex},
booktitle = {Fish Physiology},
doi = {10.1016/S1546-5098(05)23012-1},
isbn = {9780123504470},
issn = {15465098},
pages = {469--523},
title = {{Fish Biomechanics}},
volume = {23},
year = {2005}
}
@article{Zakrisson2013a,
author = {Zakrisson, Johan and Wiklund, Krister and Axner, Ove and Andersson, Magnus},
doi = {10.1016/j.bpj.2013.03.059},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Zakrisson et al. - The shaft of the type 1 fimbriae regulates an externalforce to match the FimH catch bond - 2013.pdf:pdf},
issn = {00063495},
journal = {Biophysical Journal},
month = {may},
number = {10},
pages = {2137--2148},
publisher = {Biophysical Society},
title = {{The Shaft of the Type 1 Fimbriae Regulates an External Force to Match the FimH Catch Bond}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349513004438},
volume = {104},
year = {2013}
}
@article{Andersson2008,
abstract = {Bacterial adhesion to surfaces mediated by specific adhesion organelles that promote infections, as exemplified by the pili of uropathogenic E. coli, is studied mostly at the level of cell-cell interactions and thereby reflects the averaged behavior of multiple pili. The role of pilus rod structure has therefore only been estimated from the outcome of experiments involving large numbers of organelles at the same time. It has, however, lately become clear that the biomechanical behavior of the pilus shafts play an important, albeit hitherto rather unrecognized, role in the adhesion process. For example, it has been observed that shafts from two different strains, even though they are similar in structure, result in large differences in the ability of the bacteria to adhere to their host tissue. However, in order to identify all properties of pilus structures that are of importance in the adhesion process, the biomechanical properties of pili must be assessed at the single-molecule level. Due to the low range of forces of these structures, until recently it was not possible to obtain such information. However, with the development of force-measuring optical tweezers (FMOT) with force resolution in the low piconewton range, it has lately become possible to assess forces mediated by individual pili on single living bacteria in real time. FMOT allows for a more or less detailed mapping of the biomechanical properties of individual pilus shafts, in particular those that are associated with their elongation and contraction under stress. This Mi- nireview presents the FMOT technique, the biological model system, and results from assessment of the biomechanical properties of bacterial pili. The information retrieved is also compared with that obtained by atomic force microscopy.},
author = {Andersson, Magnus and Axner, Ove and Almqvist, Fredrik and Uhlin, Bernt Eric and F{\"{a}}llman, Erik},
doi = {10.1002/cphc.200700389},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Andersson et al. - Physical properties of biopolymers assessed by optical tweezers analysis of folding and refolding of bacterial pili..pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - Physical properties of biopolymers assessed by optical tweezers analysis of folding and refolding of bacterial pil(2).pdf:pdf},
issn = {1439-7641},
journal = {ChemPhysChem},
keywords = {Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: chemistry,Bacterial: genetics,Biological,Biopolymers,Biopolymers: chemistry,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: pathogenicity,Escherichia coli: physiology,Fimbriae,Hydrogen-Ion Concentration,Mechanical,Models,Optical Tweezers,Protein Folding,Stress,Surface Properties},
month = {feb},
number = {2},
pages = {221--35},
pmid = {18181116},
title = {{Physical properties of biopolymers assessed by optical tweezers: analysis of folding and refolding of bacterial pili.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18181116},
volume = {9},
year = {2008}
}
@article{CenterforDiseaseControlandPreventionCDC2014,
author = {{Center for Disease Control and Prevention (CDC)}},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Center for Disease Control and Prevention (CDC) - Principles of Vaccination - 2014.pdf:pdf},
issn = {0003-1488},
journal = {Pink Book},
pages = {1--8},
pmid = {11549079},
title = {{Principles of Vaccination}},
year = {2014}
}
@article{Leake2004,
abstract = {Titin is responsible for the passive elasticity of the muscle sarcomere. The mechanical properties of skeletal and cardiac muscle titin were characterized in single molecules using a novel dual optical tweezers assay. Antibody pairs were attached to beads and used to select the whole molecule, I-band, A-band, a tandem-immunoglobulin (Ig) segment, and the PEVK region. A construct from the PEVK region expressing >25{\%} of the full-length skeletal muscle isoform was chemically conjugated to beads and similarly characterized. By elucidating the elasticity of the different regions, we showed directly for the first time, to our knowledge, that two entropic components act in series in the skeletal muscle titin I-band (confirming previous speculations), one associated with tandem-immunoglobulin domains and the other with the PEVK region, with persistence lengths of 2.9 nm and 0.76 nm, respectively (150 mM ionic strength, 22 degrees C). Novel findings were: the persistence length of the PEVK component rose (0.4-2.7 nm) with an increase in ionic strength (15-300 mM) and fell (3.0-0.3 nm) with a temperature increase (10-60 degrees C); stress-relaxation in 10-12-nm steps was observed in the PEVK construct and hysteresis in the native PEVK region. The region may not be a pure random coil, as previously thought, but contains structured elements, possibly with hydrophobic interactions.},
author = {Leake, Mark C and Wilson, David and Gautel, Mathias and Simmons, Robert M},
doi = {10.1529/biophysj.103.033571},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Leake et al. - The elasticity of single titin molecules using a two-bead optical tweezers assay. - 2004.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Animals,Elasticity,Hydrogen-Ion Concentration,Mechanical,Micromanipulation,Micromanipulation: methods,Molecular Motor Proteins,Molecular Motor Proteins: chemistry,Muscle,Muscle Proteins,Muscle Proteins: analysis,Muscle Proteins: chemistry,Myocardium,Myocardium: chemistry,Optics and Photonics,Physical Stimulation,Physical Stimulation: methods,Protein Kinases,Protein Kinases: analysis,Protein Kinases: chemistry,Rabbits,Sarcomeres,Sarcomeres: chemistry,Skeletal,Skeletal: chemistry,Stress,Temperature,isomerization,proline},
mendeley-tags = {isomerization,proline},
month = {aug},
number = {2},
pages = {1112--35},
pmid = {15298915},
publisher = {Elsevier},
title = {{The elasticity of single titin molecules using a two-bead optical tweezers assay.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1304451{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {87},
year = {2004}
}
@article{Evans2007,
abstract = {Adhesion of a biological cell to another cell or the extracellular matrix involves complex couplings between cell biochemistry, structural mechanics, and surface bonding. The interactions are dynamic and act through association and dissociation of bonds between very large molecules at rates that change considerably under stress. Combining molecular cell biology with single-molecule force spectroscopy provides a powerful tool for exploring the complexity of cell adhesion, that is, how cell signaling processes strengthen adhesion bonds and how forces applied to cell-surface bonds act on intracellular sites to catalyze chemical processes or switch molecular interactions on and off. Probing adhesion receptors on strategically engineered cells with force during functional stimulation can reveal key nodes of communication between the mechanical and chemical circuitry of a cell.},
author = {Evans, Evan and Calderwood, David},
doi = {10.1126/science.1137592},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans, Calderwood - Forces and bond dynamics in cell adhesion. - 2007.pdf:pdf},
issn = {1095-9203},
journal = {Science (New York, N.Y.)},
keywords = {Biomechanics,Cell Adhesion,Cell Adhesion: physiology,Humans,Integrins,Integrins: chemistry,Integrins: physiology,Selectins,Selectins: chemistry,Selectins: physiology,Signal Transduction,Spectrum Analysis},
month = {may},
number = {5828},
pages = {1148--53},
pmid = {17525329},
title = {{Forces and bond dynamics in cell adhesion.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17525329},
volume = {316},
year = {2007}
}
@article{Eom,
author = {Eom, Namsoon and Sedev, Rossen and Wedding, Bruce and Connor, Jason},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Eom et al. - Probing Fluid Flow Using the Force Measurement Capability of Optical Trapping - Unknown.pdf:pdf},
keywords = {-optical trapping,fluid flow,mapping,microfluidics,trap stiffness,viscous friction},
pages = {1--6},
title = {{Probing Fluid Flow Using the Force Measurement Capability of Optical Trapping}}
}
@article{Steadman2014,
abstract = {The rise of multidrug resistant bacteria is a major worldwide health concern. There is currently an unmet need for the development of new and selective antibacterial drugs. Therapies that target and disarm the crucial virulence factors of pathogenic bacteria, while not actually killing the cells themselves, could prove to be vital for the treatment of numerous diseases. This article discusses the main surface architectures of pathogenic Gram-negative bacteria and the small molecules that have been discovered, which target their specific biogenesis pathways and/or actively block their virulence. The future perspective for the use of antivirulence compounds is also assessed.},
author = {Steadman, David and Lo, Alvin and Waksman, Gabriel and Remaut, Han},
doi = {10.2217/fmb.14.46},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Steadman et al. - Bacterial surface appendages as targets for novel antibacterial therapeutics. - 2014.pdf:pdf},
issn = {1746-0921},
journal = {Future microbiology},
month = {jul},
pages = {887--900},
pmid = {25156378},
title = {{Bacterial surface appendages as targets for novel antibacterial therapeutics.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25156378},
volume = {9},
year = {2014}
}
@article{Loth2008,
abstract = {The drag of a non-spherical particle was reviewed and investigated for a variety of shapes (regular and irregular) and particle Reynolds numbers (Rep). Point-force models for the trajectory-averaged drag were discussed for both the Stokes regime (Rep ??? 1) and Newton regime (Rep ??? 1 and sub-critical with approximately constant drag coefficient) for a particular particle shape. While exact solutions were often available for the Stokes regime, the Newton regime depended on: aspect ratio for spheroidal particles, surface area ratio for other regularly-shaped particles, and min-med-max area for irregularly shaped particles. The combination of the Stokes and Newton regimes were well integrated using a general method by Ganser (developed for isometric shapes and disks). In particular, a modified Clift-Gauvin expression was developed for particles with approximately cylindrical cross-sections relative to the flow, e.g. rods, prolate spheroids, and oblate spheroids with near-unity aspect ratios. However, particles with non-circular cross-sections exhibited a weaker dependence on Reynolds number, which is attributed to the more rapid transition to flow separation and turbulent boundary layer conditions. Their drag coefficient behavior was better represented by a modified Dallavalle drag model, by again integrating the Stokes and Newton regimes. This paper first discusses spherical particle drag and classification of particle shapes, followed by the main body which discusses drag in Stokes and Newton regimes and then combines these results for the intermediate regimes. ?? 2007 Elsevier B.V. All rights reserved.},
author = {Loth, E.},
doi = {10.1016/j.powtec.2007.06.001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Loth - Drag of non-spherical solid particles of regular and irregular shape - 2008.pdf:pdf},
isbn = {0032-5910},
issn = {00325910},
journal = {Powder Technology},
keywords = {Drag non-spherical,Irregular risk,Reynolds sphericity,Spheroid},
number = {3},
pages = {342--353},
title = {{Drag of non-spherical solid particles of regular and irregular shape}},
volume = {182},
year = {2008}
}
@article{Kiss2006,
abstract = {Desmin intermediate filaments play important role in the mechanical integrity and elasticity of muscle cells. The mechanisms of how desmin contributes to cellular mechanics are little understood. Here, we explored the nanomechanics of desmin by manipulating individual filaments with atomic force microscopy. In complex, hierarchical force responses we identified recurring features which likely correspond to distinct properties and structural transitions related to desmin's extensibility and elasticity. The most frequently observed feature is an initial unbinding transition that corresponds to the removal of ∼45-nm-long coiled-coil dimers from the filament surface with 20-60 pN forces in usually two discrete steps. In tethers longer than 60 nm we most often observed force plateaus studded with bumps spaced ∼16 nm apart, which are likely caused by a combination of protofilament unzipping, dimer-dimer sliding and coiled-coil-domain unfolding events. At high stresses and strains non-linear, entropic elasticity was dominant, and sometimes repetitive sawtooth force transitions were seen which might arise because of slippage within the desmin protofilament. A model is proposed in which mechanical yielding is caused by coiled-coil domain unfolding and dimer-dimer sliding/slippage, and strain hardening by the entropic elasticity of partially unfolded protofilaments. © 2006 Elsevier Inc. All rights reserved.},
author = {Kiss, B. and Karsai, {\'{A}} and Kellermayer, M. S Z},
doi = {10.1016/j.jsb.2006.03.020},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kiss, Karsai, Kellermayer - Nanomechanical properties of desmin intermediate filaments - 2006.pdf:pdf},
issn = {10478477},
journal = {Journal of Structural Biology},
keywords = {Atomic force microscopy,Desmin,Elasticity,Force spectroscopy,Sliding,Unzipping,Wormlike chain},
number = {2},
pages = {327--339},
pmid = {16714122},
title = {{Nanomechanical properties of desmin intermediate filaments}},
volume = {155},
year = {2006}
}
@article{Nuccio2007,
abstract = {Many Proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. These filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). This article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. Based on usher amino acid sequence comparisons, our analysis shows that the chaperone/usher assembly class is subdivided into six major phylogenetic clades, which we have termed alpha-, beta-, gamma-, kappa-, pi-, and sigma-fimbriae. Members of each clade share related operon structures and encode fimbrial subunits with similar protein domains. The proposed classification system offers a simple and convenient method for assigning newly discovered chaperone/usher systems to one of the six major phylogenetic groups.},
author = {Nuccio, Sean-Paul and B{\"{a}}umler, Andreas J},
doi = {10.1128/MMBR.00014-07},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nuccio, B{\"{a}}umler - Evolution of the chaperoneusher assembly pathway fimbrial classification goes Greek. - 2007.pdf:pdf},
issn = {1092-2172},
journal = {Microbiology and molecular biology reviews : MMBR},
keywords = {Bacterial Proteins,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,Evolution, Molecular,Fimbriae, Bacterial,Fimbriae, Bacterial: classification,Fimbriae, Bacterial: genetics,Fimbriae, Bacterial: metabolism,Genes, Bacterial,Molecular Chaperones,Molecular Chaperones: genetics,Molecular Chaperones: metabolism,Multigene Family,Operon,Phylogeny,Proteobacteria,Proteobacteria: genetics,Proteobacteria: metabolism},
month = {dec},
number = {4},
pages = {551--75},
pmid = {18063717},
title = {{Evolution of the chaperone/usher assembly pathway: fimbrial classification goes Greek.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2168650{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {71},
year = {2007}
}
@article{VanMameren2009,
abstract = {Single-molecule manipulation studies have revealed that double-stranded DNA undergoes a structural transition when subjected to tension. At forces that depend on the attachment geometry of the DNA (65 pN or 110 pN), it elongates approximately 1.7-fold and its elastic properties change dramatically. The nature of this overstretched DNA has been under debate. In one model, the DNA cooperatively unwinds, while base pairing remains intact. In a competing model, the hydrogen bonds between base pairs break and two single DNA strands are formed, comparable to thermal DNA melting. Here, we resolve the structural basis of DNA overstretching using a combination of fluorescence microscopy, optical tweezers, and microfluidics. In DNA molecules undergoing the transition, we visualize double- and single-stranded segments using specific fluorescent labels. Our data directly demonstrate that overstretching comprises a gradual conversion from double-stranded to single-stranded DNA, irrespective of the attachment geometry. We found that these conversions favorably initiate from nicks or free DNA ends. These discontinuities in the phosphodiester backbone serve as energetically favorable nucleation points for melting. When both DNA strands are intact and no nicks or free ends are present, the overstretching force increases from 65 to 110 pN and melting initiates throughout the molecule, comparable to thermal melting. These results provide unique insights in the thermodynamics of DNA and DNA-protein interactions.},
author = {van Mameren, Joost and Gross, Peter and Farge, Geraldine and Hooijman, Pleuni and Modesti, Mauro and Falkenberg, Maria and Wuite, Gijs J L and Peterman, Erwin J G},
doi = {10.1073/pnas.0904322106},
file = {:E$\backslash$:/Mina Dokument/Mendeley/van Mameren et al. - Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging. -.pdf:pdf},
isbn = {1091-6490 (Electronic)$\backslash$n0027-8424 (Linking)},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {43},
pages = {18231--18236},
pmid = {19841258},
title = {{Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging.}},
volume = {106},
year = {2009}
}
@phdthesis{Yang2006,
author = {Yang, Fu-ling},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yang - Interaction Law for a Collision Between Two Solid Particles in a Viscous Liquid - 2006.pdf:pdf},
school = {California Institute of Technology},
title = {{Interaction Law for a Collision Between Two Solid Particles in a Viscous Liquid}},
type = {PhD thesis},
url = {http://resolver.caltech.edu/CaltechETD:etd-05262006-120244},
volume = {2006},
year = {2006}
}
@article{Ashkin1998,
abstract = {We calculate the forces of single-beam gradient radiation pressure laser traps, also called "optical tweezers," on micron-sized dielectric spheres in the ray optics regime. This serves as a simple model system for describing laser trapping and manipulation of living cells and organelles within cells. The gradient and scattering forces are defined for beams of complex shape in the ray-optics limit. Forces are calculated over the entire cross-section of the sphere using TEM00 and TEM*00 mode input intensity profiles and spheres of varying index of refraction. Strong uniform traps are possible with force variations less than a factor of 2 over the sphere cross-section. For a laser power of 10 mW and a relative index of refraction of 1.2, we compute trapping forces as high as approximately 1.2 x 10(-6) dynes in the weakest (backward) direction of the gradient trap. It is shown that good trapping requires high convergence beams from a high numerical aperture objective. A comparison is given of traps made using bright field or differential interference contrast optics and phase contrast optics.},
author = {Ashkin, A},
doi = {10.1016/S0006-3495(92)81860-X},
isbn = {0006349519210},
issn = {00063495},
journal = {Methods in cell biology},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
number = {2},
pages = {1--27},
pmid = {9352508},
publisher = {Elsevier},
title = {{Forces of a single-beam gradient laser trap on a dielectric sphere in the ray optics regime.}},
volume = {55},
year = {1998}
}
@article{Shusterman2004,
abstract = {We present the first measurements of the kinetics of random motion of individual monomers within large polymer coils. We use double- and single-stranded DNA (dsDNA and ssDNA) as models of semiflexible and flexible polymers, respectively. Fluorescence fluctuations of DNA fragments labeled specifically at a single position reveal the time dependence of the DNA monomer's mean-square displacement <r(2)(t)>. The monomer motions within dsDNA and ssDNA coils are characterized by two qualitatively different kinetic regimes: close to <r(2)(t)> proportional to t(2/3) for ssDNA and <r(2)(t)> proportional to sqrt[t] for dsDNA. While the kinetic behavior of ssDNA is consistent with the generally accepted Zimm theory of polymer dynamics, the kinetic behavior of dsDNA monomers is in good agreement with the Rouse model.},
author = {Shusterman, Roman and Alon, Sergey and Gavrinyov, Tatyana and Krichevsky, Oleg},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Shusterman et al. - Monomer dynamics in double- and single-stranded DNA polymers. - 2004.pdf:pdf},
issn = {0031-9007},
journal = {Physical review letters},
keywords = {DNA,DNA, Single-Stranded,DNA, Single-Stranded: chemistry,DNA: chemistry,Fluorescent Dyes,Fluorescent Dyes: chemistry,Kinetics,Models, Chemical,Molecular Weight,Nucleic Acid Conformation,Spectrometry, Fluorescence,Thermodynamics},
month = {jan},
number = {4},
pages = {048303},
pmid = {14995414},
title = {{Monomer dynamics in double- and single-stranded DNA polymers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14995414},
volume = {92},
year = {2004}
}
@article{Hancock2011,
abstract = {Biofilm formation is involved in the majority of bacterial infections. Comparing six Escherichia coli and Klebsiella pneumoniae isolates revealed significant differences in biofilm formation depending on the growth medium. Fimbriae are known to be involved in biofilm formation, and type 1, F1C and P fimbriae were seen to influence biofilm formation significantly different depending on strain background, growth media and aeration as well as surface material. Altogether, this report clearly demonstrates that biofilm formation of a given strain is highly dependent on experimental design and that specific mechanisms involved in biofilm formation such as fimbrial expression only play a role under certain environmental conditions. This study underscores the importance of careful selection of experimental conditions when investigating bacterial biofilm formation and to take great precaution/care when comparing results from different biofilm studies.},
author = {Hancock, Viktoria and Wits{\o}, Ingun Lund and Klemm, Per},
doi = {10.1016/j.ijmm.2011.04.018},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hancock, Wits{\o}, Klemm - Biofilm formation as a function of adhesin, growth medium, substratum and strain type. - 2011.pdf:pdf},
issn = {1618-0607},
journal = {International journal of medical microbiology : IJMM},
keywords = {Bacterial,Bacterial: metabolism,Biofilms,Biofilms: growth {\&} development,Culture Media,Culture Media: chemistry,Escherichia coli,Escherichia coli: growth {\&} development,Escherichia coli: metabolism,Escherichia coli: physiology,Female,Fimbriae,Human Experimentation,Humans,Klebsiella pneumoniae,Klebsiella pneumoniae: growth {\&} development,Klebsiella pneumoniae: metabolism,Klebsiella pneumoniae: physiology,Urine,Urine: chemistry,Urine: microbiology,biofilm},
mendeley-tags = {biofilm},
month = {nov},
number = {7},
pages = {570--6},
pmid = {21646046},
publisher = {Elsevier GmbH.},
title = {{Biofilm formation as a function of adhesin, growth medium, substratum and strain type.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21646046},
volume = {301},
year = {2011}
}
@article{Kotze2007,
author = {Kotz{\'{e}}, Theuns},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kotz{\'{e}} - Guidelines on Writing a First Quantitative Academic Article - 2007.pdf:pdf},
isbn = {0250-0868 (Print)$\backslash$r0250-0868 (Linking)},
issn = {0250-0868},
journal = {University of Pretoria},
keywords = {6,7,introduction},
pages = {11--79},
pmid = {15573690},
title = {{Guidelines on Writing a First Quantitative Academic Article}},
year = {2007}
}
@article{Griffiths1987a,
author = {Griffiths, Derek J.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Griffiths - Dynamics of the upper urinary tract I. Peristaltic flow through a distensible tube of limited length - 1987.pdf:pdf},
journal = {Physics in medicine and biology},
number = {7},
pages = {813--822},
title = {{Dynamics of the upper urinary tract: I. Peristaltic flow through a distensible tube of limited length}},
volume = {32},
year = {1987}
}
@article{Tees2002,
author = {Tees, David F. J. and Chang, Kai-Chien and Rodgers, Stephen D. and Hammer, Daniel a.},
doi = {10.1021/ie010383p},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tees et al. - Simulation of Cell Adhesion to Bioreactive Surfaces in Shear The Effect of Cell Size - 2002.pdf:pdf},
issn = {0888-5885},
journal = {Industrial {\&} Engineering Chemistry Research},
keywords = {paper3},
mendeley-tags = {paper3},
month = {feb},
number = {3},
pages = {486--493},
title = {{Simulation of Cell Adhesion to Bioreactive Surfaces in Shear: The Effect of Cell Size}},
url = {http://pubs.acs.org/doi/abs/10.1021/ie010383p},
volume = {41},
year = {2002}
}
@article{Evans1988b,
abstract = {The human erythrocyte receptor which mediates mannose-resistant hemagglutination by enterotoxigenic Escherichia coli possessing colonization factor antigen II is not universally distributed among donors. Mannose-resistant hemagglutination-positive erythrocytes are more common among black donors than nonblack donors; tests with erythrocytes of known antigenic makeup confirm this correlation. Colonization factor antigen II receptor activity of mannose-resistant hemagglutination-positive erythrocytes is unstable when whole blood is stored at 4 degrees C. Also, screening of donors is best performed with enterotoxigenic E. coli possessing colonization factor antigen II composed of the coli surface antigen 1 (CS1) plus CS3, since these consistently produce stronger hemagglutination reactions than strains with colonization factor antigen II composed of either CS2 plus CS3 or CS3 only.},
author = {Evans, D. G. J. and Evans, D. G. J. and Diaz, S. R. and Graham, D. Y.},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Evans et al. - Mannose-resistant hemagglutination of human erythrocytes by enterotoxigenic Escherichia coli with colonization factor ant.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Evans et al. - Mannose-resistant hemagglutination of human erythrocytes by enterotoxigenic Escherichia coli with colonization factor ant.pdf:pdf},
issn = {00951137},
journal = {Journal of Clinical Microbiology},
number = {9},
pages = {1626--1629},
pmid = {3053770},
title = {{Mannose-resistant hemagglutination of human erythrocytes by enterotoxigenic Escherichia coli with colonization factor antigen II}},
volume = {26},
year = {1988}
}
@article{Yi2013,
abstract = {We present a method to automatically segment red blood cells (RBCs) visualized by digital holographic microscopy (DHM), which is based on the marker-controlled watershed algorithm. Quantitative phase images of RBCs can be obtained by using off-axis DHM along to provide some important information about each RBC, including size, shape, volume, hemoglobin content, etc. The most important process of segmentation based on marker-controlled watershed is to perform an accurate localization of internal and external markers. Here, we first obtain the binary image via Otsu algorithm. Then, we apply morphological operations to the binary image to get the internal markers. We then apply the distance transform algorithm combined with the watershed algorithm to generate external markers based on internal markers. Finally, combining the internal and external markers, we modify the original gradient image and apply the watershed algorithm. By appropriately identifying the internal and external markers, the problems of oversegmentation and undersegmentation are avoided. Furthermore, the internal and external parts of the RBCs phase image can also be segmented by using the marker-controlled watershed combined with our method, which can identify the internal and external markers appropriately. Our experimental results show that the proposed method achieves good performance in terms of segmenting RBCs and could thus be helpful when combined with an automated classification of RBCs.},
author = {Yi, Faliu and Moon, Inkyu and Javidi, Bahram and Boss, Daniel and Marquet, Pierre},
doi = {10.1117/1.JBO.18.2.026006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yi et al. - Automated segmentation of multiple red blood cells with digital holographic microscopy. - 2013.pdf:pdf},
issn = {1560-2281},
journal = {Journal of biomedical optics},
keywords = {Algorithms,Cell Shape,Cell Size,Erythrocytes,Erythrocytes: cytology,Erythrocytes: metabolism,Hemoglobins,Hemoglobins: metabolism,Holography,Holography: instrumentation,Holography: statistics {\&} numerical data,Humans,Imaging, Three-Dimensional,Microscopy,Microscopy: instrumentation,Microscopy: statistics {\&} numerical data,Optical Phenomena,Signal Processing, Computer-Assisted},
month = {feb},
number = {2},
pages = {26006},
pmid = {23370481},
title = {{Automated segmentation of multiple red blood cells with digital holographic microscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23370481},
volume = {18},
year = {2013}
}
@article{Chan2012,
abstract = {The Klebsiella pneumoniae type 3 fimbriae are mainly composed of MrkA pilins that assemble into a helixlike filament. This study determined the biomechanical properties of the fimbriae and analyzed 11 site-directed MrkA mutants to identify domains that are critical for the properties. Escherichia coli strains expressing type 3 fimbriae with an Ala substitution at either F34, V45, C87, G189, T196, or Y197 resulted in a significant reduction in biofilm formation. The E. coli strain expressing MrkAG189A remained capable of producing a normal number of fimbriae. Although F34A, V45A, T196A, and Y197A substitutions expressed on E. coli strains produced sparse quantities of fimbriae, no fimbriae were observed on the cells expressing MrkAC87A. Further investigations of the mechanical properties of the MrkAG189A fimbriae with optical tweezers revealed that, unlike the wild-type fimbriae, the uncoiling force for MrkAG189A fimbriae was not constant. The MrkAG189A fimbriae also exhibited a lower enthalpy in the differential scanning calorimetry analysis. Together, these findings indicate that the mutant fimbriae are less stable than the wild-type. This study has demonstrated that the C-terminal $\beta$ strands of MrkA are required for the assembly and structural stability of fimbriae.},
author = {Chan, Chia-Han and Chen, Feng-Jung and Huang, Ying-Jung and Chen, Shin-Yu and Liu, Kuo-Liang and Wang, Zhe-Chong and Peng, Hwei-Ling and Yew, Tri-Rung and Liu, Cheng-Hsien and Liou, Gunn-Guang and Hsu, Ken Y and Chang, Hwan-You and Hsu, Long},
doi = {10.1021/la300224w},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chan et al. - Identification of Protein Domains on Major Pilin MrkA That Affects the Mechanical Properties of Klebsiella pneumoniae Type.pdf:pdf},
issn = {1520-5827},
journal = {Langmuir : the ACS journal of surfaces and colloids},
month = {may},
number = {19},
pages = {7428--35},
pmid = {22524463},
title = {{Identification of Protein Domains on Major Pilin MrkA That Affects the Mechanical Properties of Klebsiella pneumoniae Type 3 Fimbriae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22524463},
volume = {28},
year = {2012}
}
@article{Raucher1999,
abstract = {When membrane-attached beads are pulled vertically by a laser tweezers, a membrane tube of constant diameter (tether) is formed. We found that the force on the bead (tether force) did not depend on tether length over a wide range of tether lengths, which indicates that a previously unidentified reservoir of membrane and not stretch of the plasma membrane provides the tether membrane. Plots of tether force vs. tether length have an initial phase, an elongation phase, and an exponential phase. During the major elongation phase, tether force is constant, buffered by the "membrane reservoir." Finally, there is an abrupt exponential rise in force that brings the tether out of the trap, indicating depletion of the membrane reservoir. In chick embryo fibroblasts and 3T3 fibroblasts, the maximum tether lengths that can be pulled at a velocity of 4 microm/s are 5.1 +/- 0. 3 and 5.0 +/- 0.2 microm, respectively. To examine the importance of the actin cytoskeleton, we treated cells with cytochalasin B or D and found that the tether lengths increased dramatically to 13.8 +/- 0.8 and 12.0 +/- 0.7 microm, respectively. Similarly, treatment of the cells with colchicine and nocodazole results in more than a twofold increase in tether length. We found that elevation of membrane tension (through osmotic pressure, a long-term elevation of tether force, or a number of transitory increases) increased reservoir size over the whole cell. Using a tracking system to hold tether force on the bead constant near its maximal length in the exponential phase, the rate of elongation of the tethers was measured as a function of tether force (membrane tension). The rate of elongation of tethers was linearly dependent on the tether force and reflected an increase in size of the reservoir. Increases in the reservoir caused by tension increases on one side of the cell caused increases in reservoir size on the other side of the cell. Thus, we suggest that cells maintain a plasma membrane reservoir to buffer against changes in membrane tension and that the reservoir is increased with membrane tension or disruption of the cytoskeleton.},
author = {Raucher, D and Sheetz, M P},
doi = {10.1016/S0006-3495(99)77040-2},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Raucher, Sheetz - Characteristics of a membrane reservoir buffering membrane tension. - 1999.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {3T3 Cells,Actins,Actins: physiology,Animals,Cell Membrane,Cell Membrane: drug effects,Cell Membrane: metabolism,Cell Membrane: physiology,Cell Size,Cell Size: drug effects,Chick Embryo,Colchicine,Colchicine: pharmacology,Cytochalasins,Cytochalasins: pharmacology,Cytoskeleton,Cytoskeleton: drug effects,Cytoskeleton: physiology,Fibroblasts,Fibroblasts: cytology,Fibroblasts: drug effects,Hypotonic Solutions,Kinetics,Lasers,Mice,Microspheres,Nocodazole,Nocodazole: pharmacology,Osmolar Concentration,Osmotic Pressure,Physical Stimulation},
month = {oct},
number = {4},
pages = {1992--2002},
pmid = {10512819},
title = {{Characteristics of a membrane reservoir buffering membrane tension.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300480{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {77},
year = {1999}
}
@phdthesis{Lacoursiere2007,
author = {Lacoursi{\`{e}}re, Claude},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lacoursi{\`{e}}re - Ghosts and Machines Regularized Variational Methods for Interactive Simulations of Multibodies with Dry Frictional Contac.pdf:pdf},
isbn = {9789172643338},
title = {{Ghosts and Machines : Regularized Variational Methods for Interactive Simulations of Multibodies with Dry Frictional Contacts}},
year = {2007}
}
@article{Melican2011,
abstract = {The progression of a natural bacterial infection is a dynamic process influenced by the physiological characteristics of the target organ. Recent developments in live animal imaging allow for the study of the dynamic microbe-host interplay in real-time as the infection progresses within an organ of a live host. Here we used multiphoton microscopy-based live animal imaging, combined with advanced surgical procedures, to investigate the role of uropathogenic Escherichia coli (UPEC) attachment organelles P and Type 1 fimbriae in renal bacterial infection. A GFP+ expressing variant of UPEC strain CFT073 and genetically well-defined isogenic mutants were microinfused into rat glomerulus or proximal tubules. Within 2 h bacteria colonized along the flat squamous epithelium of the Bowman's capsule despite being exposed to the primary filtrate. When facing the challenge of the filtrate flow in the proximal tubule, the P and Type 1 fimbriae appeared to act in synergy to promote colonization. P fimbriae enhanced early colonization of the tubular epithelium, while Type 1 fimbriae mediated colonization of the center of the tubule via a mechanism believed to involve inter-bacterial binding and biofilm formation. The heterogeneous bacterial community within the tubule subsequently affected renal filtration leading to total obstruction of the nephron within 8 h. Our results reveal the importance of physiological factors such as filtration in determining bacterial colonization patterns, and demonstrate that the spatial resolution of an infectious niche can be as small as the center, or periphery, of a tubule lumen. Furthermore, our data show how secondary physiological injuries such as obstruction contribute to the full pathophysiology of pyelonephritis.},
annote = {From Duplicate 2 ( Uropathogenic Escherichia coli P and Type 1 fimbriae act in synergy in a living host to facilitate renal colonization leading to nephron obstruction. - Melican, Keira; Sandoval, Ruben M; Kader, Abdul; Josefsson, Lina; Tanner, George a; Molitoris, Bruce a; Richter-Dahlfors, Agneta )
},
author = {Melican, Keira and Sandoval, Ruben M and Kader, Abdul and Josefsson, Lina and Tanner, George a and Molitoris, Bruce a and Richter-Dahlfors, Agneta},
doi = {10.1371/journal.ppat.1001298},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Melican et al. - Uropathogenic Escherichia coli P and Type 1 fimbriae act in synergy in a living host to facilitate renal colonization l.pdf:pdf},
issn = {1553-7374},
journal = {PLoS pathogens},
keywords = {Animals,Bacterial,Bacterial Adhesion,Bacterial: physiology,Escherichia coli Infections,Escherichia coli Infections: microbiology,Female,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: metabolism,Kidney,Kidney: microbiology,Kidney: physiopathology,Nephrons,Nephrons: microbiology,Nephrons: physiopathology,Rats,Sprague-Dawley,Ureteral Obstruction,Ureteral Obstruction: pathology,Uropathogenic Escherichia coli,Uropathogenic Escherichia coli: physiology},
month = {feb},
number = {2},
pages = {e1001298},
pmid = {21383970},
title = {{Uropathogenic Escherichia coli P and Type 1 fimbriae act in synergy in a living host to facilitate renal colonization leading to nephron obstruction.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3044688{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {7},
year = {2011}
}
@article{Duval2014,
author = {Duval, J{\'{e}}r{\^{o}}me F L and Francius, G.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Unknown - J Biomed Nanotechno{\_}Jacquot et al.pdf - Unknown.pdf:pdf},
journal = {Journal of Biomedical Nanotechnology},
number = {11},
pages = {3361--3372},
title = {{Dynamic Modulation of Fimbrail Extension and FimH-Mannose Binding Force on Live Bacteria Under pH Changes: A Molecular Atomic Force Microscopy Analysis}},
volume = {10},
year = {2014}
}
@article{Volpe2011,
author = {Volpe, Giovanni and Singh, Gajendra Pratap},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Volpe, Singh - Optical Tweezers Raman Spectroscopy - 2011.pdf:pdf},
journal = {Optics {\&} Photonics News},
pages = {2011--2011},
title = {{Optical Tweezers Raman Spectroscopy}},
year = {2011}
}
@article{Judd1998,
author = {Judd, A L I and Walters, Kate and Street, Rowland Hill},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Judd, Walters, Street - Hospice-at-home - 1998.pdf:pdf},
number = {February},
pages = {1005--1006},
title = {{Hospice-at-home}},
year = {1998}
}
@phdthesis{Andersson2007a,
address = {Ume{\aa}},
author = {Andersson, Magnus},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Andersson - Construction of force measuring optical tweezers instrumentation and investigations of biophysical properties of bacterial a.pdf:pdf},
isbn = {978-91-7264-435-9},
keywords = {Optical Tweezers,Thesis,bacterial adhesion,fimbriae,optical tweezers,pili},
mendeley-tags = {Thesis,optical tweezers,pili},
pages = {79},
school = {Ume{\aa} University},
title = {{Construction of force measuring optical tweezers instrumentation and investigations of biophysical properties of bacterial adhesion organelles}},
type = {Doctoral thesis},
url = {http://www.diva-portal.org/umu/theses/abstract.xsql?dbid=1425 http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1425},
year = {2007}
}
@inproceedings{Topal2010,
abstract = {We propose a new edge detection algorithm that works by computing a set of anchor edge points in an image and then linking these anchor points by drawing edges between them. The resulting edge map consists of perfect contiguous, one-pixel wide edges. The performance tests show that our algorithm is up to 16{\%} faster than the fastest known edge detection algorithm, i.e., OpenCV implementation of the Canny edge detector. We believe that our edge detector is a novel step in edge detection and would be very suitable for the next generation real-time image processing and computer vision applications.},
author = {Topal, Cihan and Akinlar, Cuneyt and Genc, Yakup},
booktitle = {2010 20th International Conference on Pattern Recognition},
doi = {10.1109/ICPR.2010.593},
isbn = {978-1-4244-7542-1},
issn = {10514651},
pages = {2424--2427},
pmid = {5595747},
title = {{Edge Drawing: A Heuristic Approach to Robust Real-Time Edge Detection}},
year = {2010}
}
@article{Brinkers2009b,
abstract = {The wormlike chain model describes the micromechanics of semiflexible polymers by introducing the persistence length. We propose a method of measuring the persistence length of DNA in a controllable near-native environment. Using a dark field microscope, the projected positions of a gold nanoparticle undergoing constrained Brownian motion are captured. The nanoparticle is tethered to a substrate using a single double stranded DNA (dsDNA) molecule and immersed in buffer. No force is exerted on the DNA. We carried out Monte Carlo simulations of the experiment, which give insight into the micromechanics of the DNA and can be used to interpret the motion of the nanoparticle. Our simulations and experiments demonstrate that, unlike other similar experiments, the use of nanometer instead of micrometer sized particles causes particle-substrate and particle-DNA interactions to be of negligible effect on the position distribution of the particle. We also show that the persistence length of the tethering DNA can be estimated with a statistical error of 2 nm, by comparing the statistics of the projected position distribution of the nanoparticle to the Monte Carlo simulations. The persistence lengths of 45 single molecules of four different lengths of dsDNA were measured under the same environmental conditions at high salt concentration. The persistence lengths we found had a mean value of 35 nm (standard error of 2.8 nm), which compares well to previously found values using similar salt concentrations. Our method can be used to directly study the effect of the environmental conditions (e.g., buffer and temperature) on the persistence length.},
author = {Brinkers, Sanneke and Dietrich, Heidelinde R C and de Groote, Frederik H and Young, Ian T and Rieger, Bernd},
doi = {10.1063/1.3142699},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Brinkers et al. - The persistence length of double stranded DNA determined using dark field tethered particle motion. - 2009.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Brinkers et al. - The persistence length of double stranded DNA determined using dark field tethered particle motion. - 2009(2).pdf:pdf},
issn = {1089-7690},
journal = {The Journal of chemical physics},
keywords = {Base Sequence,Biomechanics,DNA,DNA: chemistry,DNA: genetics,DNA: metabolism,Gold,Gold: chemistry,Metal Nanoparticles,Metal Nanoparticles: chemistry,Models,Molecular,Monte Carlo Method,Motion,Nucleic Acid Conformation,Surface Properties},
month = {jun},
number = {21},
pages = {215105},
pmid = {19508104},
title = {{The persistence length of double stranded DNA determined using dark field tethered particle motion.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19508104},
volume = {130},
year = {2009}
}
@article{Thomas2002c,
abstract = {Surface adhesion of bacteria generally occurs in the presence of shear stress, and the lifetime of receptor bonds is expected to be shortened in the presence of external force. However, by using Escherichia coli expressing the lectin-like adhesin FimH and guinea pig erythrocytes in flow chamber experiments, we show that bacterial attachment to target cells switches from loose to firm upon a 10-fold increase in shear stress applied. Steered molecular dynamics simulations of tertiary structure of the FimH receptor binding domain and subsequent site-directed mutagenesis studies indicate that shear-enhancement of the FimH-receptor interactions involves extension of the interdomain linker chain under mechanical force. The ability of FimH to function as a force sensor provides a molecular mechanism for discrimination between surface-exposed and soluble receptor molecules.},
author = {Thomas, Wendy E and Trintchina, Elena and Forero, Manu and Vogel, Viola and Sokurenko, Evgeni V},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Thomas et al. - Bacterial adhesion to target cells enhanced by shear force. - 2002.pdf:pdf},
issn = {0092-8674},
journal = {Cell},
keywords = {Adhesins,Animals,Bacterial,Bacterial Adhesion,Bacterial: chemistry,Bacterial: genetics,Bacterial: metabolism,Biomechanics,Cell Aggregation,Computer Simulation,Erythrocytes,Erythrocytes: cytology,Erythrocytes: microbiology,Escherichia coli,Escherichia coli: genetics,Escherichia coli: physiology,Fimbriae Proteins,Guinea Pigs,Models,Molecular,Mutation,Protein Structure,Structure-Activity Relationship,Tertiary},
month = {jun},
number = {7},
pages = {913--23},
pmid = {12110187},
title = {{Bacterial adhesion to target cells enhanced by shear force.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12110187},
volume = {109},
year = {2002}
}
@article{Leid2009,
author = {Leid, Jeff G},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Leid - Bacterial Biofilms Resist Key Host Defenses - 2009.pdf:pdf},
journal = {Micro},
number = {2},
pages = {66--70},
title = {{Bacterial Biofilms Resist Key Host Defenses}},
volume = {4},
year = {2009}
}
@article{Kau2005,
abstract = {Investigation into the pathogenesis of Escherichia coli urinary tract infection has provided numerous insights into the mechanisms by which bacteria adhere, grow and persist in association with host tissue. Many molecular details concerning the interaction of these bacteria with their host have been elucidated, and the murine model of cystitis has generated a new paradigm by which acute and recurrent urinary tract infections may proceed. These advances could potentially result in the development of novel vaccines and therapies for this very costly disease.},
author = {Kau, Andrew L and Hunstad, David a and Hultgren, Scott J},
doi = {10.1016/j.mib.2004.12.001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kau, Hunstad, Hultgren - Interaction of uropathogenic Escherichia coli with host uroepithelium. - 2005.pdf:pdf},
issn = {1369-5274},
journal = {Current opinion in microbiology},
keywords = {Animals,Epithelium,Epithelium: immunology,Epithelium: microbiology,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli Infections: physiopathology,Escherichia coli: pathogenicity,Female,Humans,Mice,Urinary Bladder,Urinary Bladder: immunology,Urinary Bladder: microbiology,Urinary Tract Infections,Urinary Tract Infections: immunology,Urinary Tract Infections: microbiology,Urinary Tract Infections: physiopathology,Virulence},
month = {feb},
number = {1},
pages = {54--9},
pmid = {15694857},
title = {{Interaction of uropathogenic Escherichia coli with host uroepithelium.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15694857},
volume = {8},
year = {2005}
}
@article{Girardeau2000,
author = {Girardeau, J. and Bertin, Y and Callebaut, I},
journal = {Journal of Molecular Evolution},
pages = {424--442},
title = {{Conserved structural features in class I major fimbrial subunits (pilin) in Gram-negative bacteria. Molecular basis of classification in seven subfamilies and identification of intrasubfamily sequence signature motifs which might be implicated in quaterna}},
volume = {50},
year = {2000}
}
@article{Sirinakis2011,
abstract = {ATP-dependent chromatin remodelling complexes use the energy of ATP hydrolysis to reposition and reconfigure nucleosomes. Despite their diverse functions, all remodellers share highly conserved ATPase domains, many shown to translocate DNA. Understanding remodelling requires biophysical knowledge of the DNA translocation process: how the ATPase moves DNA and generates force, and how translocation and force generation are coupled on nucleosomes. Here, we characterize the real-time activity of a minimal RSC translocase 'motor' on bare DNA, using high-resolution optical tweezers and a 'tethered' translocase system. We observe on dsDNA a processivity of ∼35 bp, a speed of ∼25 bp/s, and a step size of 2.0 (±0.4, s.e.m.) bp. Surprisingly, the motor is capable of moving against high force, up to 30 pN, making it one of the most force-resistant motors known. We also provide evidence for DNA 'buckling' at initiation. These observations reveal the ATPase as a powerful DNA translocating motor capable of disrupting DNA-histone interactions by mechanical force.},
author = {Sirinakis, George and Clapier, Cedric R and Gao, Ying and Viswanathan, Ramya and Cairns, Bradley R and Zhang, Yongli},
doi = {10.1038/emboj.2011.141},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sirinakis et al. - The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. - 2011.pdf:pdf},
isbn = {1460-2075 (Electronic)$\backslash$n0261-4189 (Linking)},
issn = {0261-4189},
journal = {The EMBO journal},
keywords = {atp-dependent chromatin remodelling complex,dna translocase,optical tweezers,step size},
number = {12},
pages = {2364--2372},
pmid = {21552204},
publisher = {Nature Publishing Group},
title = {{The RSC chromatin remodelling ATPase translocates DNA with high force and small step size.}},
url = {http://dx.doi.org/10.1038/emboj.2011.141},
volume = {30},
year = {2011}
}
@article{Kumagai2001,
author = {Kumagai, Izumi and Tsumoto, Kouhei},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kumagai, Tsumoto - Antigen – Antibody Binding - 2001.pdf:pdf},
title = {{Antigen – Antibody Binding}},
year = {2001}
}
@article{Shitamichi2009a,
annote = {        From Duplicate 1 (                   Mechanical properties of a giant liposome studied using optical tweezers                 - Shitamichi, Yoko; Ichikawa, Masatoshi; Kimura, Yasuyuki )
                
        
        
      },
author = {Shitamichi, Yoko and Ichikawa, Masatoshi and Kimura, Yasuyuki},
doi = {10.1016/j.cplett.2009.08.018},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Shitamichi, Ichikawa, Kimura - Mechanical properties of a giant liposome studied using optical tweezers - 2009.pdf:pdf},
issn = {00092614},
journal = {Chemical Physics Letters},
month = {sep},
number = {4-6},
pages = {274--278},
publisher = {Elsevier B.V.},
title = {{Mechanical properties of a giant liposome studied using optical tweezers}},
url = {http://dx.doi.org/10.1016/j.cplett.2009.08.018 http://linkinghub.elsevier.com/retrieve/pii/S0009261409009804},
volume = {479},
year = {2009}
}
@article{Berg-Sorensen2003a,
abstract = {We characterize the frequency-dependent response of a photo detection system based on a Si-PIN photodiode and a laser with wavelength 1064 nm, a system commonly used with optical tweezers. We chopped the laser beam with chopper frequencies from 200 Hz to 14 kHz, and found an exponentially delayed response of the detection system with a characteristic delay time of similar to20 mus. The physical mechanism causing this time delay is silicon's transparency to 1064 nm light: Photons are absorbed and create charge carriers not only in the diode's depletion layer, where they are detected within nano-seconds, but predominantly in the n-layer, where they remain undetected till transported out by thermal diffusion. The diode's response is dominated by this delay which can be characterized as a first-order low-pass filter with a 3dB-frequency of 8-9 kHz, depending on laser intensity. Measurements exploiting frequencies near or above this 3dB-frequency must be corrected for this unintended filter effect. We describe how to do this, and how to diagnose other systems which may or may not have the same problem. Explanations are intended for users of photo detection systems, and present the little semi-conductor physics needed to make sense. (C) 2003 American Institute of Physics.},
author = {Berg-Sorensen, K and Oddershede, Lene B. and Florin, E L and Flyvbjerg, H},
doi = {10.1063/1.1554755},
journal = {J Appl Phys},
keywords = {Dna-Molecules,Force Microscopy,Membrane,Motor,calibration,optical tweezers},
mendeley-tags = {calibration,optical tweezers},
number = {6},
pages = {3167--3176},
title = {{Unintended filtering in a typical photodiode detection system for optical tweezers}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=000181376400006 http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal{\&}id=JAPIAU000093000006003167000001{\&}idtype=cvips{\&}gifs=yes},
volume = {93},
year = {2003}
}
@article{Clausen2009,
abstract = {Type IV pili are major bacterial virulence factors supporting adhesion, surface motility, and gene transfer. The polymeric pilus fiber is a highly dynamic molecular machine that switches between elongation and retraction. We used laser tweezers to investigate the dynamics of individual pili of Neisseria gonorrheae at clamped forces between 8 pN and 100 pN and at varying concentration of the retraction ATPase PilT. The elongation probability of individual pili increased with increasing mechanical force. Directional switching occurred on two distinct timescales, and regular stepping was absent on a scale > 3 nm. We found that the retraction velocity is bimodal and that the bimodality depends on force and on the concentration of PilT proteins. We conclude that the pilus motor is a multistate system with at least one polymerization mode and two depolymerization modes with the dynamics fine-tuned by force and PilT concentration.},
author = {Clausen, Martin and Koomey, Michael and Maier, Berenike},
doi = {10.1016/j.bpj.2008.10.017},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Clausen, Koomey, Maier - Dynamics of type IV pili is controlled by switching between multiple states. - 2009.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {Adenosine Triphosphatases,Adenosine Triphosphatases: metabolism,Biomechanics,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Fimbriae, Bacterial: metabolism,Movement,Neisseria gonorrhoeae,Neisseria gonorrhoeae: cytology,Probability,Thermodynamics,Time Factors},
month = {feb},
number = {3},
pages = {1169--77},
pmid = {19186152},
publisher = {Biophysical Society},
title = {{Dynamics of type IV pili is controlled by switching between multiple states.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2716576{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {96},
year = {2009}
}
@article{Peterman2003,
abstract = {In an optical tweezers experiment intense laser light is tightly focused to intensities of MW/cm(2) in order to apply forces to submicron particles or to measure mechanical properties of macromolecules. It is important to quantify potentially harmful or misleading heating effects due to the high light intensities in biophysical experiments. We present a model that incorporates the geometry of the experiment in a physically correct manner, including heat generation by light absorption in the neighborhood of the focus, balanced by outward heat flow, and heat sinking by the glass surfaces of the sample chamber. This is in contrast to the earlier simple models assuming heat generation in the trapped particle only. We find that in the most common experimental circumstances, using micron-sized polystyrene or silica beads, absorption of the laser light in the solvent around the trapped particle, not in the particle itself, is the most important contribution to heating. To validate our model we measured the spectrum of the Brownian motion of trapped beads in water and in glycerol as a function of the trapping laser intensity. Heating both increases the thermal motion of the bead and decreases the viscosity of the medium. We measured that the temperature in the focus increased by 34.2 +/- 0.1 K/W with 1064-nm laser light for 2200-nm-diameter polystyrene beads in glycerol, 43.8 +/- 2.2 K/W for 840-nm polystyrene beads in glycerol, 41.1 +/- 0.7 K/W for 502-nm polystyrene beads in glycerol, and 7.7 +/- 1.2 K/W for 500-nm silica beads and 8.1 +/- 2.1 K/W for 444-nm silica beads in water. Furthermore, we observed that in glycerol the heating effect increased when the bead was trapped further away from the cover glass/glycerol interface as predicted by the model. We show that even though the heating effect in water is rather small it can have non-negligible effects on trap calibration in typical biophysical experimental circumstances and should be taken into consideration when laser powers of more than 100 mW are used.},
author = {Peterman, Erwin J G and Gittes, Frederick and Schmidt, Christoph F},
doi = {10.1016/S0006-3495(03)74946-7},
isbn = {0006-3495},
issn = {00063495},
journal = {Biophysical journal},
number = {2 Pt 1},
pages = {1308--1316},
pmid = {12547811},
publisher = {Elsevier},
title = {{Laser-induced heating in optical traps.}},
volume = {84},
year = {2003}
}
@article{Box,
author = {Box, Sail and Avenue, York and York, New},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Box, Avenue, York - Comparative protein modeling by satisfaction of spatial restraints - Unknown.pdf:pdf},
pages = {270--277},
title = {{Comparative protein modeling by satisfaction of spatial restraints}},
volume = {2}
}
@article{Hospenthal2015,
abstract = {Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher pathway, are polymers of pilus subunits assembling into two parts: a thin, short tip fibrillum at the top, mounted on a long pilus rod. The rod adopts a helical quaternary structure and is thought to play essential roles: its formation may drive pilus extrusion by preventing backsliding of the nascent growing pilus within the secretion pore; the rod also has striking spring-like properties, being able to uncoil and recoil depending on the intensity of shear forces generated by urine flow. Here, we present an atomic model of the P pilus generated from a 3.8 {\AA} resolution cryo-electron microscopy reconstruction. This structure provides the molecular basis for the rod's remarkable mechanical properties and illuminates its role in pilus secretion. An atomic model of the P pilus rod generated from a 3.8 {\AA} resolution cryo-EM reconstruction provides the molecular basis for its remarkable mechanical properties that allow bacteria to maintain adhesion to the urinary tract.},
author = {Hospenthal, Manuela K. and Redzej, Adam and Dodson, Karen and Ukleja, Marta and Frenz, Brandon and Rodrigues, Catarina and Hultgren, Scott J. and DiMaio, Frank and Egelman, Edward H. and Waksman, Gabriel},
doi = {10.1016/j.cell.2015.11.049},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hospenthal et al. - Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling - 2015.pdf:pdf},
issn = {10974172},
journal = {Cell},
keywords = {Pili},
mendeley-tags = {Pili},
number = {1-2},
pages = {269--278},
pmid = {26724865},
publisher = {The Authors},
title = {{Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling}},
url = {http://dx.doi.org/10.1016/j.cell.2015.11.049},
volume = {164},
year = {2015}
}
@article{Servin2007,
abstract = {The present paper addresses real-time simulation of cables for virtual environments. A faithful physical model based on constrained rigid bodies is introduced and discretized. The performance and stability of the numerical method are analyzed in details and found to meet the requirements of interactive heavy hoisting simulations. The physical model is well behaved in the limit of infinite stiffness as well as in the elastic regime, and the tuning parameters correspond directly to conventional material constants. The integration scheme mixes the well known St{\"{o}}rmer-Verlet method for the dynamics equations with the linearly implicit Euler method for the constraint equations and enables physical constraint relaxation and stabilization terms. The technique is shown to have superior numerical stability properties in comparison with either chain link systems, or spring and damper models. Experimental results are presented to show that the method results in stable, real-time simulations. Stability persists for moderately large fixed integration step of Delta t = 1/60 s, with hoisting loads of up to 10(5) times heavier than the elements of the cable. Further numerical experiments validating the physical model are also presented.},
author = {Servin, Martin and Lacoursi{\`{e}}re, Claude},
doi = {10.1109/TVCG.2007.70629},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Servin, Lacoursi{\`{e}}re - Rigid body cable for virtual environments. - 2007.pdf:pdf},
issn = {1077-2626},
journal = {IEEE transactions on visualization and computer graphics},
keywords = {Algorithms,Computer Graphics,Computer Simulation,Computer-Assisted,Models,Motion,Numerical Analysis,Theoretical,User-Computer Interface},
number = {4},
pages = {783--96},
pmid = {18467754},
title = {{Rigid body cable for virtual environments.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18467754},
volume = {14},
year = {2007}
}
@article{Nilsson2006a,
author = {Nilsson, Lina M and Thomas, Wendy E and Sokurenko, Evgeni V and Vogel, Viola},
doi = {10.1128/AEM.72.4.3005},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nilsson et al. - Elevated shear stress protects Escherichia coli cells adhering to surfaces via catch bonds from detachment by soluble i.pdf:pdf},
issn = {0099-2240},
journal = {Applied and environmental microbiology},
number = {4},
pages = {3005},
publisher = {Am Soc Microbiol},
title = {{Elevated shear stress protects Escherichia coli cells adhering to surfaces via catch bonds from detachment by soluble inhibitors}},
url = {http://aem.asm.org/cgi/content/abstract/72/4/3005},
volume = {72},
year = {2006}
}
@article{Creely2005,
abstract = {We describe the use of dual optical tweezers to manipulate micron-size particles in and out of the focus of a confocal Raman microscope. One of the beams excites the Raman spectrum while the second tweezers improves the sensitivity of the technique and also allows for the manipulation of the environment of the trapped objects. We concentrated on optimising the alignment of both trapping and Raman excitation beams and on the background subtraction method. Even at the low trapping/excitation powers used a single living cell could be trapped and monitored for over 2 h without incurring damage. ?? 2004 Elsevier B.V. All rights reserved.},
author = {Creely, C. M. and Singh, G. P. and Petrov, D.},
doi = {10.1016/j.optcom.2004.10.011},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Creely, Singh, Petrov - Dual wavelength optical tweezers for confocal Raman spectroscopy - 2005.pdf:pdf},
isbn = {0030-4018},
issn = {00304018},
journal = {Optics Communications},
keywords = {Microspectroscopy,Optical tweezers,Raman spectroscopy},
number = {1-6},
pages = {465--470},
title = {{Dual wavelength optical tweezers for confocal Raman spectroscopy}},
volume = {245},
year = {2005}
}
@article{Rothbaum1982,
abstract = {Fifteen infants (age 3-28 wk) suffered from severe diarrhea with acute dehydration and poor growth. Persistent watery stools and suboptimal nutrition necessitated central venous alimentation with prolonged hospitalization. Repeated stool and small intestinal fluid cultures yielded the classical enteropathogenic Escherichia coli serotype 0119:B14. In all patients, biopsy of the jejunum or rectal mucosa, or both, showed moderate to severe damage, irregular atrophy of surface epithelium, and subnuclear vacuolization of crypt epithelium. Ultrastructural studies revealed bacteria adherent to mucosal cells with flattening of microvilli, loss of the cellular terminal web, and cupping of the plasma membrane around individual bacteria. Heavily colonized cells had marked intracellular damage. Assays for heat-labile, heat-stable, and vero cell toxins were negative for these Escherichia coli isolates. Oral neomycin and nutritional support resulted in clearing of Escherichia coli 0119:B14 from stool and small bowel with improvement in histologic characteristics. Damage to enterocytes and villi by adherent nontoxigenic Escherichia coli 0119:B14 results in protracted diarrhea in infants.},
author = {Rothbaum, R and McAdams, a J and Giannella, R and Partin, J C},
doi = {S0016508582001541 [pii]},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rothbaum et al. - A clinicopathologic study of enterocyte-adherent Escherichia coli a cause of protracted diarrhea in infants. - 1982.pdf:pdf},
isbn = {0016-5085 (Print)$\backslash$r0016-5085 (Linking)},
issn = {00165085},
journal = {Gastroenterology},
number = {2},
pages = {441--454},
pmid = {7044882},
publisher = {American Gastroenterological Association},
title = {{A clinicopathologic study of enterocyte-adherent Escherichia coli: a cause of protracted diarrhea in infants.}},
url = {http://dx.doi.org/10.1016/S0016-5085(82)80342-9},
volume = {83},
year = {1982}
}
@article{Mandlik2007,
abstract = {Adherence to host tissues mediated by pili is pivotal in the establishment of infection by many bacterial pathogens. Corynebacterium diphtheriae assembles on its surface three distinct pilus structures. The function and the mechanism of how various pili mediate adherence, however, have remained poorly understood. Here we show that the SpaA-type pilus is sufficient for the specific adherence of corynebacteria to human pharyngeal epithelial cells. The deletion of the spaA gene, which encodes the major pilin forming the pilus shaft, abolishes pilus assembly but not adherence to pharyngeal cells. In contrast, adherence is greatly diminished when either minor pilin SpaB or SpaC is absent. Antibodies directed against either SpaB or SpaC block bacterial adherence. Consistent with a direct role of the minor pilins, latex beads coated with SpaB or SpaC protein bind specifically to pharyngeal cells. Therefore, tissue tropism of corynebacteria for pharyngeal cells is governed by specific minor pilins. Importantly, immunoelectron microscopy and immunofluorescence studies reveal clusters of minor pilins that are anchored to cell surface in the absence of a pilus shaft. Thus, the minor pilins may also be cell wall anchored in addition to their incorporation into pilus structures that could facilitate tight binding to host cells during bacterial infection.},
author = {Mandlik, Anjali and Swierczynski, Arlene and Das, Asis and Ton-That, Hung},
doi = {10.1111/j.1365-2958.2007.05630.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mandlik et al. - Corynebacterium diphtheriae employs specific minor pilins to target human pharyngeal epithelial cells - 2007.pdf:pdf},
isbn = {0950-382X (Print)$\backslash$n0950-382X (Linking)},
issn = {0950382X},
journal = {Molecular Microbiology},
number = {1},
pages = {111--124},
pmid = {17376076},
title = {{Corynebacterium diphtheriae employs specific minor pilins to target human pharyngeal epithelial cells}},
volume = {64},
year = {2007}
}
@article{Duda1972,
author = {Duda, Richard O. and Hart, Peter E.},
doi = {10.1145/361237.361242},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Duda, Hart - Use of the Hough transformation to detect lines and curves in pictures - 1972.pdf:pdf},
issn = {00010782},
journal = {Communications of the ACM},
month = {jan},
number = {1},
pages = {11--15},
title = {{Use of the Hough transformation to detect lines and curves in pictures}},
volume = {15},
year = {1972}
}
@article{Dreyer2004,
abstract = {We investigate the axial position detection of a trapped microsphere in an optical trap by using a quadrant photodiode. By replacing the photodiode with a CCD camera, we obtain detailed information on the light scattered by the microsphere. The correlation of the interference pattern with the axial position displays complex behavior with regions of positive and negative interference. By analyzing the scattered light intensity as a function of the axial position of the trapped sphere, we propose a simple method to increase the sensitivity and control the linear range of axial position detection.},
author = {Dreyer, Jakob Kisbye and Berg-S{\o}rensen, Kirstine and Oddershede, Lene B.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dreyer, Berg-S{\o}rensen, Oddershede - Improved axial position detection in optical tweezers measurements. - 2004.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
month = {apr},
number = {10},
pages = {1991--5},
pmid = {15074403},
title = {{Improved axial position detection in optical tweezers measurements.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15074403},
volume = {43},
year = {2004}
}
@article{Heras2015,
abstract = {New antibacterials need new approaches to overcome the problem of rapid antibiotic resistance. Here we review the development of potential new antibacterial drugs that do not kill bacteria or inhibit their growth, but combat disease instead by targeting bacterial virulence.},
author = {Heras, Bego{\~{n}}a and Scanlon, Martin J and Martin, Jennifer L},
doi = {10.1111/bcp.12356},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Heras, Scanlon, Martin - Targeting virulence not viability in the search for future antibacterials. - 2015.pdf:pdf},
issn = {1365-2125},
journal = {British journal of clinical pharmacology},
keywords = {--------------------------------------------------,antibacterial,antivirulence,bacterial,infection,pilicide,quorum sensing},
number = {2},
pages = {208--15},
pmid = {24552512},
title = {{Targeting virulence not viability in the search for future antibacterials.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24552512},
volume = {79},
year = {2015}
}
@article{Yakovenko2008a,
abstract = {The bacterial adhesive protein, FimH, is the most common adhesin of Escherichia coli and mediates weak adhesion at low flow but strong adhesion at high flow. There is evidence that this occurs because FimH forms catch bonds, defined as bonds that are strengthened by tensile mechanical force. Here, we applied force to single isolated FimH bonds with an atomic force microscope in order to test this directly. If force was loaded slowly, most of the bonds broke up at low force (<60 piconewtons of rupture force). However, when force was loaded rapidly, all bonds survived until much higher force (140-180 piconewtons of rupture force), behavior that indicates a catch bond. Structural mutations or pretreatment with a monoclonal antibody, both of which allosterically stabilize a high affinity conformation of FimH, cause all bonds to survive until high forces regardless of the rate at which force is applied. Pretreatment of FimH bonds with intermediate force has the same strengthening effect on the bonds. This demonstrates that FimH forms catch bonds and that tensile force induces an allosteric switch to the high affinity, strong binding conformation of the adhesin. The catch bond behavior of FimH, the amount of force needed to regulate FimH, and the allosteric mechanism all provide insight into how bacteria bind and form biofilms in fluid flow. Additionally, these observations may provide a means for designing antiadhesive mechanisms.},
author = {Yakovenko, Olga and Sharma, Shivani and Forero, Manu and Tchesnokova, Veronika and Aprikian, Pavel and Kidd, Brian and Mach, Albert and Vogel, Viola and Sokurenko, Evgeni V and Thomas, Wendy E},
doi = {10.1074/jbc.M707815200},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yakovenko et al. - FimH forms catch bonds that are enhanced by mechanical force due to allosteric regulation. - 2008(2).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Yakovenko et al. - FimH forms catch bonds that are enhanced by mechanical force due to allosteric regulation - 2008.pdf:pdf},
isbn = {0021-9258 (Print)$\backslash$r0021-9258 (Linking)},
issn = {00219258},
journal = {Journal of Biological Chemistry},
keywords = {Adhesins,Allosteric Regulation,Allosteric Site,Atomic Force,Bacterial,Bacterial Adhesion,Bacterial: chemistry,Biological,Chemical,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: metabolism,Escherichia coli: physiology,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: physiology,Gene Expression Regulation,Kinetics,Mechanical,Microscopy,Models,Molecular Conformation,Protein Conformation,Stress},
month = {apr},
number = {17},
pages = {11596--11605},
pmid = {18292092},
title = {{FimH forms catch bonds that are enhanced by mechanical force due to allosteric regulation}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18292092},
volume = {283},
year = {2008}
}
@article{Rene1982,
abstract = {Antipili antibody (APA) was quantitated by enzyme-linked immunosorbent assay in the serum, urine, and vaginal secretions of 12 women with cystitis due to Escherichia coli. Pili were purified from the strain infecting each patient. The geometric mean titers of APA in serum taken at the initial visit were: immunoglobulin G (IgG), 23.7 +/- 3.9; IgA, 4.1 +/- 4.0; and IgM, 4.4 +/- 5.7. No consistent change was observed between samples obtained at 3 and 6 weeks. APA in serum from 10 control patients was assayed against a pool of pili assembled from the 12 infecting isolates. The geometric mean titers of the control sera were: IgG, 8.4 +/- 3.2; IgA, 9.6 +/- 2.4; and IgM, 0. Antipili IgG and IgM were significantly greater in the infected than in the control sera (P less than 0.05). APA was not detected in the urine or vaginal secretions from any infected or control patient. Antigenic relationships between the 12 infecting strains were investigated by indirect immune electron microscopy. All but 1 of 12 infecting strains shared antigenic determinants. Two patients had a second E. coli infection during the study. The pili of the reinfecting isolates showed partial antigenic cross-reactivity with the pili of the initial infecting bacteria. These observations indicate that although cystitis stimulates the development of serum APAs, it fails to stimulate local APA and thus may not engender any immunological barrier to subsequent recolonization.},
author = {Rene, P and Dinolfo, M and Silverblatt, F J},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rene, Dinolfo, Silverblatt - Serum and urogenital antibody responses to Escherichia coli pili in cystitis. - 1982.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
keywords = {Adult,Antibodies, Bacterial,Antibodies, Bacterial: analysis,Antibodies, Bacterial: urine,Cystitis,Cystitis: etiology,Cystitis: immunology,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli: immunology,Female,Fimbriae, Bacterial,Fimbriae, Bacterial: immunology,Humans,Immunoglobulin G,Immunoglobulin G: analysis,Immunoglobulin M,Immunoglobulin M: analysis,Vagina,Vagina: immunology,Vagina: secretion},
month = {nov},
number = {2},
pages = {542--7},
pmid = {6128309},
title = {{Serum and urogenital antibody responses to Escherichia coli pili in cystitis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=347772{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {38},
year = {1982}
}
@article{Oyofo2001,
abstract = {Infection caused by enterotoxigenic Escherichia coli (ETEC) poses a serious health problem among children and adults in developing countries. Colonization of the small intestinal mucosa by ETEC strains is mediated by antigenically specific fimbriae, also known as colonization factor antigens (CFA). The significance of this study arises from reports that active and passive immunization with ETEC strains harboring CFAs has previously been shown to induce protective immunity against diarrhea in animal models. The aim of this study was to determine toxin-associated CFAs of ETEC isolated from a diarrheal disease case-control study in Jakarta, Indonesia. Thirteen hundred and twenty-three diarrheic and control patients with lactose-fermenting colonies were screened by ganglioside GM1-enzyme-linked immunosorbent assay (GM1-ELISA) for heat-labile (LT) and heat-stable (ST) toxins. Two hundred and forty-six (19{\%}) ETEC isolates identified by GM1-ELISA for the LT/ST toxins were screened for CFAs by Dot blot assay using monoclonal antibodies against CFA/I, II, and IV and against the putative colonization antigens (PCF) PCFO159, PCFO166, CS7, and CS17. Of the 246 ETEC isolates, 177 (72{\%}) elaborated ST, 56 (23{\%}) produced LT, while 13 (5{\%}) elicited both the ST and LT toxins. CFA testing of the 246 ETEC isolates showed that 21 (8{\%}) expressed CFA/I, 3 (1{\%}) exhibited CFA/II, 14 (6{\%}) elaborated CFA/IV, while 7 (3{\%}) expressed PCFO159 and PCFO159 plus CS5. No CFAs or PCFs could be associated with 201 (82{\%}) of the ETEC strains. This report documents the types of CFAs associated with ETEC strains in Jakarta, Indonesia. These data may help current research efforts on the development of CFA-based vaccines for humans against ETEC and provide additional information for future ETEC vaccine trials in Southeast Asia.},
author = {Oyofo, B. a. and Subekti, D. S. and Svennerholm, Ann-Mari and Machpud, N. N. and Tjaniadi, P. and Komalarini, S. and Setiawan, B. and Campbell, J. R. and Corwin, a. L. and Lesmana, M.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Oyofo et al. - Toxins and colonization factor antigens of enterotoxigenic Escherichia coli among residents of Jakarta, Indonesia - 2001.pdf:pdf},
isbn = {0002-9637 (Print)$\backslash$n0002-9637 (Linking)},
issn = {00029637},
journal = {American Journal of Tropical Medicine and Hygiene},
number = {2},
pages = {120--124},
pmid = {11508385},
title = {{Toxins and colonization factor antigens of enterotoxigenic Escherichia coli among residents of Jakarta, Indonesia}},
volume = {65},
year = {2001}
}
@article{Evans2004,
abstract = {Many biomolecular bonds exhibit a mechanical strength that increases in proportion to the logarithm of the rate of force application. Consistent with exponential decrease in bond lifetime under rising force, this kinetically limited failure reflects dissociation along a single thermodynamic pathway impeded by a sharp free energy barrier. Using a sensitive force probe to test the leukocyte adhesion bond P-selectin glycoprotein ligand 1 (PSGL-1)-P-selectin, we observed a linear increase of bond strength with each 10-fold increase in the rate of force application from 300 to 30,000 pN/sec, implying a single pathway for failure. However, the strength and lifetime of PSGL-1-P-selectin bonds dropped anomalously when loaded below 300 pN/sec, demonstrating unexpectedly faster dissociation and a possible second pathway for failure. Remarkably, if first loaded by a "jump" in force to 20-30 pN, the bonds became strong when subjected to a force ramp as slow as 30 pN/sec and exhibited the same single-pathway kinetics under all force rates. Applied in this way, a new "jump/ramp" mode of force spectroscopy was used to show that the PSGL-1-P-selectin bond behaves as a mechanochemical switch where force history selects between two dissociation pathways with markedly different properties. Furthermore, replacing PSGL-1 by variants of its 19-aa N terminus and by the crucial tetrasaccharide sialyl LewisX produces dramatic changes in the failure kinetics, suggesting a structural basis for the two pathways. The two-pathway switch seems to provide a mechanism for the "catch bond" response observed recently with PSGL-1-P-selectin bonds subjected to small-constant forces.},
annote = {        From Duplicate 1 (                   Mechanical switching and coupling between two dissociation pathways in a P-selectin adhesion bond.                 - Evans, Evan; Leung, Andrew; Heinrich, Volkmar; Zhu, Cheng )
                
        
        
      },
author = {Evans, Evan and Leung, Andrew and Heinrich, Volkmar and Zhu, Cheng},
doi = {10.1073/pnas.0401870101},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans et al. - Mechanical switching and coupling between two dissociation pathways in a P-selectin adhesion bond. - 2004.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Evans et al. - Mechanical switching and coupling between two dissociation pathways in a P-selectin adhesion bond. - 2004.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Chemical,Gangliosides,Gangliosides: metabolism,Ligands,Membrane Glycoproteins,Membrane Glycoproteins: metabolism,Models,P-Selectin,P-Selectin: chemistry,P-Selectin: metabolism,Protein Binding,Protein Binding: physiology,Protein Structure,Tertiary,Tissue Adhesions},
month = {aug},
number = {31},
pages = {11281--6},
pmid = {15277675},
title = {{Mechanical switching and coupling between two dissociation pathways in a P-selectin adhesion bond.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=509195{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {101},
year = {2004}
}
@article{Steffen2005a,
author = {Steffen, Robert},
journal = {Clinical Infectious Diseases},
number = {Suppl 8},
pages = {536--540},
title = {{Epidemiology of Traveler’s Diarrhea}},
volume = {41},
year = {2005}
}
@article{Fischer2010,
abstract = {In order to use optical tweezers as a force measuring tool inside a viscoelastic medium such as the cytoplasm of a living cell, it is crucial to perform an exact force calibration within the complex medium. This is a nontrivial task, as many of the physical characteristics of the medium and probe, e.g., viscosity, elasticity, shape, and density, are often unknown. Here, we suggest how to calibrate single beam optical tweezers in a complex viscoelastic environment. At the same time, we determine viscoelastic characteristics such as friction retardation spectrum and elastic moduli of the medium. We apply and test a method suggested [M. Fischer and K. Berg-S{\o}rensen, J. Opt. A, Pure Appl. Opt. 9, S239 (2007)], a method which combines passive and active measurements. The method is demonstrated in a simple viscous medium, water, and in a solution of entangled F-actin without cross-linkers.},
author = {Fischer, Mario and Richardson, Andrew C and Reihani, S Nader S and Oddershede, Lene B. and Berg-S{\o}rensen, Kirstine},
doi = {10.1063/1.3280222},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Fischer et al. - Active-passive calibration of optical tweezers in viscoelastic media. - 2010.pdf:pdf},
issn = {1089-7623},
journal = {The Review of scientific instruments},
keywords = {Actins,Actins: chemistry,Algorithms,Calibration,Elastic Modulus,Friction,Linear Models,Optical Tweezers,Periodicity,Viscoelastic Substances,Viscoelastic Substances: chemistry,Water,Water: chemistry},
month = {jan},
number = {1},
pages = {015103},
pmid = {20113125},
title = {{Active-passive calibration of optical tweezers in viscoelastic media.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20113125},
volume = {81},
year = {2010}
}
@article{Pereverzev2005,
author = {Pereverzev, Yuriy V and Prezhdo, Oleg V and Forero, Manu and Sokurenko, Evgeni V and Thomas, Wendy E},
doi = {10.1529/biophysj.105.062158},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Pereverzev et al. - The Two-Pathway Model for the Catch-Slip Transition in Biological Adhesion - 2005.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical Journal},
number = {3},
pages = {1446--1454},
publisher = {Elsevier},
title = {{The Two-Pathway Model for the Catch-Slip Transition in Biological Adhesion}},
url = {http://dx.doi.org/10.1529/biophysj.105.062158},
volume = {89},
year = {2005}
}
@article{Jacquot2014,
abstract = {Self-associating auto-transporter (SAAT) adhesins are two-domain cell surface proteins involved in bacteria auto-aggregation and biofilm formation. Antigen 43 (Ag43) is a SAAT adhesin commonly found in Escherichia coli whose variant Ag43a has been shown to promote persistence of uropathogenic E. coli within the bladder. The recent resolution of the tri-dimensional structure of the 499 amino-acids' $\beta$-domain in Ag43a has shed light on the possible mechanism governing the self-recognition of SAAT adhesins, in particular the importance of trans-interactions between the L shaped $\beta$-helical scaffold of two $\alpha$-domains of neighboring adhesins. In this study, we use single-molecule force spectroscopy (SMFS) and dynamic force spectroscopy (DFS) to unravel the dynamics of Ag43-self association under various pH and molecular elongation rate conditions that mimic the situations encountered by E. coli in its natural environment. Results evidenced an important stretchability of Ag43$\alpha$ with unfolding of sub-domains leading to molecular extension as long as 150 nm. Nanomechanical analysis of molecular stretching data suggested that self-association of Ag43 can lead to the formation of dimers and tetramers driven by rapid and weak cis- as well as slow but strong trans-interaction forces with a magnitude as large as 100-250 pN. The dynamics of cis- and trans-interactions were demonstrated to be strongly influenced by pH and applied shear force, thus suggesting that environmental conditions can modulate Ag43-mediated aggregation of bacteria at the molecular level.},
author = {Jacquot, Adrien and Sakamoto, Chizuko and Razafitianamarahavo, Angelina and Caillet, C{\'{e}}line and Merlin, Jenny and Fahs, Ahmad and Ghigo, Jean-Marc and Duval, J{\'{e}}r{\^{o}}me F L and Beloin, Christophe and Francius, Gr{\'{e}}gory},
doi = {10.1039/c4nr03312d},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jacquot et al. - The dynamics and pH-dependence of Ag43 adhesins' self-association probed by atomic force spectroscopy. - 2014.pdf:pdf},
issn = {2040-3372},
journal = {Nanoscale},
month = {sep},
pages = {16--18},
pmid = {25208582},
title = {{The dynamics and pH-dependence of Ag43 adhesins' self-association probed by atomic force spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25208582},
year = {2014}
}
@article{Klauke2006,
abstract = {This paper demonstrates the use of micron sized beads, modified with fluorescent dyes, as non-invasive sensors to probe the local changes in pH, within a microfluidic channel. To achieve this, amine modified polystyrene spheres (either 3 microm or 6 microm in diameter) were functionalised with the pH sensitive fluorochrome SNARF-1 to produce point sensors. The modified beads were trapped at defined positions close to a pair of integrated planar gold microelectrodes within the channel, using optical tweezers. Both transient and steady-state electrochemical potentials were applied to the microelectrode pair in order to generate changes in the local pH, associated with electrolysis. The functionalised beads indicated the pH changes in the channel, measured as a change in the fluorescence signal, generated by the immobilised pH sensitive dye. Responses were measured with temporal resolutions of between 1 and 200 ms, whilst the spatial resolution of the pH gradients was limited by the size of the beads to 3 microm.},
author = {Klauke, Norbert and Monaghan, Paul and Sinclair, Gavin and Padgett, Miles and Cooper, Jon},
doi = {10.1039/b517237c},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Klauke et al. - Characterisation of spatial and temporal changes in pH gradients in microfluidic channels using optically trapped fluore.pdf:pdf},
issn = {1473-0197},
journal = {Lab on a chip},
keywords = {Benzopyrans,Benzopyrans: chemistry,Electrochemistry,Electrochemistry: methods,Fluorescent Dyes,Fluorescent Dyes: chemistry,Hydrogen-Ion Concentration,Microelectrodes,Microfluidic Analytical Techniques,Microfluidic Analytical Techniques: instrumentatio,Microfluidic Analytical Techniques: methods,Naphthols,Naphthols: chemistry,Optics and Photonics,Optics and Photonics: instrumentation,Polystyrenes,Polystyrenes: chemistry,Rhodamines,Rhodamines: chemistry},
month = {jun},
number = {6},
pages = {788--93},
pmid = {16738732},
title = {{Characterisation of spatial and temporal changes in pH gradients in microfluidic channels using optically trapped fluorescent sensors.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16738732},
volume = {6},
year = {2006}
}
@article{Busscher2012,
abstract = {Why Do Bacteria Adhere to Surfaces and Why Is Adhesion Considered a Virulence Factor?},
author = {Busscher, Henk J. and van der Mei, Henny C.},
doi = {10.1371/journal.ppat.1002440},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Busscher, van der Mei - How do bacteria know they are on a surface and regulate their response to an adhering state - 2012.pdf:pdf},
isbn = {1553-7374 (Electronic)$\backslash$n1553-7366 (Linking)},
issn = {15537366},
journal = {PLoS Pathogens},
number = {1},
pages = {1--3},
pmid = {22291589},
title = {{How do bacteria know they are on a surface and regulate their response to an adhering state?}},
volume = {8},
year = {2012}
}
@article{Connell1996,
author = {Connell, H and Agace, W and Klemm, P and Schembri, M and M{\aa}rild, S and Svanborg, C},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Connell et al. - Type 1 fimbrial expression enhances Escherichia coli virulence for the urinary tract - 1996.pdf:pdf},
journal = {PNAS},
number = {September},
pages = {9827--9832},
title = {{Type 1 fimbrial expression enhances Escherichia coli virulence for the urinary tract}},
volume = {93},
year = {1996}
}
@article{Hung2013,
author = {Hung, Chia and Zhou, Yizhou and Pinkner, Jerome S},
doi = {10.1128/mBio.00645-13.Editor},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hung, Zhou, Pinkner - Escherichia coli Biofilms Have an Organized and Complex Extracellular Matrix Structure - 2013.pdf:pdf},
title = {{Escherichia coli Biofilms Have an Organized and Complex Extracellular Matrix Structure}},
year = {2013}
}
@article{Singh2015,
author = {Singh, Bhupender and Mortezaei, Narges and Uhlin, Bernt Eric and Savarino, Stephen J. and Bullitt, Esther and Andersson, Magnus},
doi = {10.1038/srep13678},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Singh et al. - Antibody-mediated disruption of the mechanics of CS20 fimbriae of enterotoxigenic Escherichia coli - 2015.pdf:pdf},
issn = {2045-2322},
journal = {Scientific Reports},
pages = {13678},
publisher = {Nature Publishing Group},
title = {{Antibody-mediated disruption of the mechanics of CS20 fimbriae of enterotoxigenic Escherichia coli}},
url = {http://www.nature.com/doifinder/10.1038/srep13678},
volume = {5},
year = {2015}
}
@article{Lee2007a,
author = {Lee, Sang-hyuk and Roichman, Yohai and Yi, Gi-ra and Kim, Shin-hyun and Yang, Seung-man and Blaaderen, Alfons Van and Oostrum, Peter Van and Grier, David G},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lee et al. - Characterizing and tracking single colloidal particles with video holographic microscopy - 2007.pdf:pdf},
journal = {Optics express},
number = {26},
pages = {18275--18282},
title = {{Characterizing and tracking single colloidal particles with video holographic microscopy}},
volume = {15},
year = {2007}
}
@article{Kim2010,
abstract = {Digital holography is an emerging field of new paradigm in general imaging applications. We present a review of a subset of the research and development activities in digital holography, with emphasis on microscopy techniques and applications. First, the basic results from the general theory of holography, based on the scalar diffraction theory, are summarized, and a general description of the digital holographic microscopy process is given, including quantitative phase microscopy. Several numerical diffraction methods are described and compared, and a number of representative configurations used in digital holography are described, including off-axis Fresnel, Fourier, image plane, in-line, Gabor, and phase-shifting digital holographies. Then we survey numerical techniques that give rise to unique capabilities of digital holography, including suppression of dc and twin image terms, pixel resolution control, optical phase unwrapping, aberration compensation, and others. A survey is also given of representative application areas, including biomedical microscopy, particle field holography, micrometrology, and holographic tomography, as well as some of the special techniques, such as holography of total internal reflection, optical scanning holography, digital interference holography, and heterodyne holography. The review is intended for students and new researchers interested in developing new techniques and exploring new applications of digital holography.},
author = {Kim, Myung K.},
doi = {10.1117/6.0000006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kim - Principles and techniques of digital holographic microscopy - 2010.pdf:pdf},
issn = {19463251},
journal = {SPIE Reviews},
keywords = {17,2 010,2009,2010,5,accepted for publication mar,biomedical imaging,diffraction,digital holography,numerical,online may 1 4,paper sr090109 received dec,phase microscopy,published,three-dimensional microscopy},
number = {1},
pages = {018005},
pmid = {16330029},
title = {{Principles and techniques of digital holographic microscopy}},
volume = {1},
year = {2010}
}
@article{Hansen2006a,
author = {Hansen, P and Tolicnorrelykke, I and Flyvbjerg, H and Bergsorensen, K},
doi = {10.1016/j.cpc.2006.07.009},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Hansen et al. - tweezercalib 2.1 Faster version of MatLab package for precise calibration of optical tweezers☆ - 2006.pdf:pdf},
journal = {Computer Physics Communications},
keywords = {calibration},
mendeley-tags = {calibration},
number = {8},
pages = {572--573},
title = {{tweezercalib 2.1: Faster version of MatLab package for precise calibration of optical tweezers☆}},
volume = {175},
year = {2006}
}
@book{Gonzalez2007,
abstract = {THE leader in the field for more than twenty years, this introduction to basic concepts and methodologies for digital image processing continues its cutting-edge focus on contemporary developments in all mainstream areas of image processing. Completely self-contained, heavily illustrated, and mathematically accessible, it has a scope of application that is not limited to the solution of specialized problems. Digital Image Fundamentals. Image Enhancement in the Spatial Domain. Image Enhancement in the Frequency Domain. Image Restoration. Color Image Processing. Wavelets and Multiresolution Processing. Image Compression. Morphological Image Processing. Image Segmentation. Representation and Description. Object Recognition. For technicians interested in the fundamentals and contemporary applications of digital imaging processing},
author = {Gonzalez, Rafael C and Woods, Richard E},
booktitle = {3nd edition},
isbn = {013168728X},
pages = {976},
title = {{Digital Image Processing (3rd Edition)}},
year = {2007}
}
@article{Clauvelin2008,
author = {Clauvelin, N. and Audoly, B. and Neukirch, S.},
doi = {10.1021/ma702713x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Clauvelin, Audoly, Neukirch - Mechanical Response of Plectonemic DNA An Analytical Solution - 2008.pdf:pdf},
issn = {0024-9297},
journal = {Macromolecules},
month = {jun},
number = {12},
pages = {4479--4483},
title = {{Mechanical Response of Plectonemic DNA: An Analytical Solution}},
url = {http://pubs.acs.org/doi/abs/10.1021/ma702713x},
volume = {41},
year = {2008}
}
@article{Pel2007b,
abstract = {A novel, non-invasive method to diagnose bladder outlet obstruction involves the recording of noise with a contact microphone pressed against the perineum (between anus and scrotum). This noise results from flow-generated vortices caused by prostatic obstruction. We developed a computational fluid dynamic (CFD) urethral model including urethral geometry to study the relation between generated noise and the degree of obstruction. This model comprised a bladder, bladder neck, prostate and urethra. Calculations were carried out at four bladder pressures, five degrees of obstruction and three obstruction shapes. For each of the sixty simulations, the velocity and pressure distributions along the urethra were calculated including wall shear stresses to localize flow transition from disturbed to normal. Negative pressures at the obstruction outlet induced recirculation of flow. The location of transition was independent of the applied bladder pressure, but it depended primarily on the degree and secondarily on the shape of the obstruction. Based on the presented results, we hypothesize that the location of the maximum amplitude of perineal noise mainly depends on the degree and shape of the prostatic obstruction. Our future aim is to test our hypothesis in male patients and to extend the presented model to 3D with a viscoelastic urethral wall to calculate the fluid-wall interaction.},
annote = {From Duplicate 1 ( Development of a CFD urethral model to study flow-generated vortices under different conditions of prostatic obstruction. - Pel, Johan J M; van Mastrigt, Ron )
},
author = {Pel, Johan J M and van Mastrigt, Ron},
doi = {10.1088/0967-3334/28/1/002},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Pel, van Mastrigt - Development of a CFD urethral model to study flow-generated vortices under different conditions of prostatic obstruc.pdf:pdf},
issn = {0967-3334},
journal = {Physiological measurement},
keywords = {Biological,Humans,Male,Models,Prostatic Diseases,Prostatic Diseases: pathology,Prostatic Diseases: physiopathology,Shear Strength,Urethra,Urethra: physiology,Urinary Bladder,Urinary Bladder: physiology,paper3},
mendeley-tags = {paper3},
month = {jan},
number = {1},
pages = {13--23},
pmid = {17151416},
title = {{Development of a CFD urethral model to study flow-generated vortices under different conditions of prostatic obstruction.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17151416},
volume = {28},
year = {2007}
}
@article{Golding2005,
abstract = {Protein levels have been shown to vary substantially between individual cells in clonal populations. In prokaryotes, the contribution to such fluctuations from the inherent randomness of gene expression has largely been attributed to having just a few transcripts of the corresponding mRNAs. By contrast, eukaryotic studies tend to emphasize chromatin remodeling and burst-like transcription. Here, we study single-cell transcription in Escherichia coli by measuring mRNA levels in individual living cells. The results directly demonstrate transcriptional bursting, similar to that indirectly inferred for eukaryotes. We also measure mRNA partitioning at cell division and correlate mRNA and protein levels in single cells. Partitioning is approximately binomial, and mRNA-protein correlations are weaker earlier in the cell cycle, where cell division has recently randomized the relative concentrations. Our methods further extend protein-based approaches by counting the integer-valued number of transcript with single-molecule resolution. This greatly facilitates kinetic interpretations in terms of the integer-valued random processes that produce the fluctuations.},
author = {Golding, Ido and Paulsson, Johan and Zawilski, Scott M and Cox, Edward C},
doi = {10.1016/j.cell.2005.09.031},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Golding et al. - Real-time kinetics of gene activity in individual bacteria. - 2005.pdf:pdf},
issn = {0092-8674},
journal = {Cell},
keywords = {Algorithms,Bacterial Proteins,Bacterial Proteins: analysis,Bacterial Proteins: biosynthesis,Binding Sites,Binding Sites: genetics,Binomial Distribution,Capsid Proteins,Capsid Proteins: genetics,Cell Division,Cell Division: genetics,Escherichia coli,Escherichia coli: genetics,Escherichia coli: metabolism,Gene Expression Regulation, Bacterial,Gene Expression Regulation, Bacterial: genetics,Green Fluorescent Proteins,Green Fluorescent Proteins: genetics,Green Fluorescent Proteins: metabolism,Kinetics,Levivirus,Levivirus: genetics,Luminescent Proteins,Luminescent Proteins: genetics,Microscopy, Fluorescence,Models, Genetic,Operator Regions, Genetic,Operator Regions, Genetic: genetics,Plasmids,Plasmids: genetics,Poisson Distribution,RNA, Bacterial,RNA, Bacterial: analysis,RNA, Bacterial: genetics,RNA, Messenger,RNA, Messenger: analysis,RNA, Messenger: genetics,Stochastic Processes,Transcription, Genetic,Transcription, Genetic: genetics},
month = {dec},
number = {6},
pages = {1025--36},
pmid = {16360033},
title = {{Real-time kinetics of gene activity in individual bacteria.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16360033},
volume = {123},
year = {2005}
}
@article{Tense2005,
author = {Tense, a Present and Tense, B Simple Past},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tense, Tense - A Brief Guide To Verb Tense And Voice In Scientific Writing - 2005.pdf:pdf},
pages = {2005--2007},
title = {{A Brief Guide To Verb Tense And Voice In Scientific Writing}},
year = {2005}
}
@article{Asadi2012,
abstract = {Urinary tract infection (UTI) is one of the most common infections in the world. The majority of UTIs are caused by Uropathogenic Escherichia coli (UPEC) strains. FimH and FliC are the most important virulence factors of UPEC. To date, any ideal vaccine against UTI has not been approved for human use and we need to test new targets to develop an ideal vaccine against UTI. In this study, we constructed fusion fimH/fliC of UPEC as a novel vaccine candidate against UTI.},
author = {Asadi, Karam Mr and Oloomi, M and Habibi, M and Bouzari, S},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Asadi et al. - Cloning of fimH and fliC and expression of the fusion protein FimHFliC from Uropathogenic Escherichia coli (UPEC) isolate.pdf:pdf},
isbn = {9821669533118},
issn = {2008-4447},
journal = {Iranian journal of microbiology},
keywords = {fimh,flic,fusion protein expression,urinary tract infection,uropathogenic escherichia coli},
month = {jun},
number = {2},
pages = {55--62},
pmid = {22973470},
title = {{Cloning of fimH and fliC and expression of the fusion protein FimH/FliC from Uropathogenic Escherichia coli (UPEC) isolated in Iran.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3434642{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {4},
year = {2012}
}
@article{Shusterman2008,
author = {Shusterman, Roman and Gavrinyov, Tatyana and Krichevsky, Oleg},
doi = {10.1103/PhysRevLett.100.098102},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Shusterman, Gavrinyov, Krichevsky - Internal Dynamics of Superhelical DNA - 2008.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {mar},
number = {9},
pages = {22--25},
title = {{Internal Dynamics of Superhelical DNA}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.100.098102},
volume = {100},
year = {2008}
}
@article{Alteri2012,
abstract = {Bacterial growth in the host is required for pathogenesis. To successfully grow in vivo, pathogens have adapted their metabolism to replicate in specific host microenvironments. These adaptations reflect the nutritional composition of their host niches, inter-bacterial competition for carbon and energy sources, and survival in the face of bactericidal defense mechanisms. A subgroup of Escherichia coli, which cause urinary tract infection, bacteremia, sepsis, and meningitis, have adapted to grow as a harmless commensal in the nutrient-replete, carbon-rich human intestine but rapidly transition to pathogenic lifestyle in the nutritionally poorer, nitrogen-rich urinary tract. We discuss bacterial adaptations that allow extraintestinal pathogenic E. coli to establish both commensal associations and virulence as the bacterium transits between disparate microenvironments within the same individual.},
author = {Alteri, Christopher J and Mobley, Harry L T},
doi = {10.1016/j.mib.2011.12.004},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Alteri, Mobley - Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments. - 2012.pdf:pdf},
issn = {1879-0364},
journal = {Current opinion in microbiology},
keywords = {Adaptation, Physiological,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli Infections: pathology,Gastrointestinal Tract,Gastrointestinal Tract: microbiology,Host-Pathogen Interactions,Humans,Urinary Tract,Urinary Tract Infections,Urinary Tract Infections: microbiology,Urinary Tract Infections: pathology,Urinary Tract: microbiology,Uropathogenic Escherichia coli,Uropathogenic Escherichia coli: metabolism,Uropathogenic Escherichia coli: pathogenicity,Uropathogenic Escherichia coli: physiology,Virulence Factors,Virulence Factors: metabolism},
month = {feb},
number = {1},
pages = {3--9},
pmid = {22204808},
publisher = {Elsevier Ltd},
title = {{Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3265668{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {15},
year = {2012}
}
@article{Giatrellis,
author = {Giatrellis, Sarantis and Koutris, Efstratios and Castelain, Micka{\"{e}}l and Lundmark, Richard and Andersson, Magnus and Axner, Ove and Lindblom, G{\"{o}}ran and Carlsson, Sven},
journal = {In manuscript},
title = {{Membrane-to-tubule transformation: insights from the interaction and active membrane remodeling by clathrin-mediated endocytosis component Sorting Nexin 9}}
}
@article{Janshoff2001,
author = {Janshoff, Andreas and Steinem, Claudia},
doi = {10.1002/1439-7641(20011015)2:10<577::AID-CPHC577>3.0.CO;2-W},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Janshoff, Steinem - Energy Landscapes of Ligand-Receptor Couples Probed by Dynamic Force Spectroscopy - 2001.pdf:pdf},
issn = {1439-4235},
journal = {ChemPhysChem},
keywords = {and,antibodies,binding strength,biophysics,covalent bonds between proteins,dynamic force spectroscopy,the dynamic properties of,weak non-},
month = {oct},
number = {10},
pages = {577--579},
title = {{Energy Landscapes of Ligand-Receptor Couples Probed by Dynamic Force Spectroscopy}},
url = {http://doi.wiley.com/10.1002/1439-7641{\%}2820011015{\%}292{\%}3A10{\%}3C577{\%}3A{\%}3AAID-CPHC577{\%}3E3.0.CO{\%}3B2-W},
volume = {2},
year = {2001}
}
@article{Dorobantu2009,
abstract = {Microbial adhesion to surfaces and interfaces is strongly influenced by their structure and physicochemical properties. We used atomic force microscopy (AFM) to measure the forces between chemically functionalized AFM tips and two bacterial species exhibiting different cell surface hydrophobicities, measured as the oil/water contact angle (theta): Acinetobacter venetianus RAG-1 (theta = 56.4 degrees ) and Rhodococcus erythropolis 20S-E1-c (theta = 152.9 degrees ). The forces were measured as the AFM tips, coated with either hydrophobic (octadecane) or hydrophilic (undecanol) groups, approached the bacterial cells in aqueous buffer. The experimental force curves between the two microbial cells and functionalized AFM probes were not successfully described by the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloid stability. To reconcile the discrepancy between theory and experiments, two types of extended DLVO models were proposed. The first modification considers an additional acid-base component that accounts for attractive hydrophobic interactions and repulsive hydration effects. The second model considers an additional exponentially decaying steric interaction between polymeric brushes in addition to the acid-base interactions. These extended DLVO predictions agreed well with AFM experimental data for both A. venetianus RAG-1, whose surface consists of an exopolymeric capsule and pili, and R. erythropolis 20S-E1-c, whose surface is covered by an exopolymeric capsule. The extended models for the bacteria-AFM tip force-distance curves were consistent with the effects of steric interactions.},
author = {Dorobantu, Loredana S and Bhattacharjee, Subir and Foght, Julia M and Gray, Murray R},
doi = {10.1021/la9001237},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dorobantu et al. - Analysis of force interactions between AFM tips and hydrophobic bacteria using DLVO theory. - 2009.pdf:pdf},
issn = {0743-7463},
journal = {Langmuir : the ACS journal of surfaces and colloids},
keywords = {Acinetobacter,Acinetobacter: ultrastructure,Microscopy, Atomic Force,Rhodococcus,Rhodococcus: ultrastructure},
month = {jun},
number = {12},
pages = {6968--76},
pmid = {19334745},
title = {{Analysis of force interactions between AFM tips and hydrophobic bacteria using DLVO theory.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19334745},
volume = {25},
year = {2009}
}
@article{Saffman1968,
annote = {ISI Document Delivery No.: A7106
Times Cited: 318
Cited Reference Count: 1
Saffman, pg
Cambridge univ press
New york
Part 3},
author = {Saffman, P G},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
language = {English},
pages = {624},
title = {{Correction}},
url = {<Go to ISI>://WOS:A1968A710600014},
volume = {31},
year = {1968}
}
@article{Dopheide2002,
author = {Dopheide, S. M.},
doi = {10.1182/blood.V99.1.159},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dopheide - Shear-dependent tether formation during platelet translocation on von Willebrand factor - 2002.pdf:pdf},
issn = {00064971},
journal = {Blood},
month = {jan},
number = {1},
pages = {159--167},
title = {{Shear-dependent tether formation during platelet translocation on von Willebrand factor}},
url = {http://www.bloodjournal.org/cgi/doi/10.1182/blood.V99.1.159},
volume = {99},
year = {2002}
}
@article{Moffitt2008,
abstract = {It has been over 20 years since the pioneering work of Arthur Ashkin, and in the intervening years, the field of optical tweezers has grown tremendously. Optical tweezers are now being used in the investigation of an increasing number of biochemical and biophysical processes, from the basic mechanical properties of biological polymers to the multitude of molecular machines that drive the internal dynamics of the cell. Innovation, however, continues in all areas of instrumentation and technique, with much of this work focusing on the refinement of established methods and on the integration of this tool with other forms of single-molecule manipulation or detection. Although technical in nature, these developments have important implications for the expanded use of optical tweezers in biochemical research and thus should be of general interest. In this review, we address these recent advances and speculate on possible future developments.},
author = {Moffitt, Jeffrey R and Chemla, Yann R and Smith, Steven B and Bustamante, Carlos},
doi = {10.1146/annurev.biochem.77.043007.090225},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Moffitt et al. - Recent advances in optical tweezers. - 2008.pdf:pdf},
issn = {0066-4154},
journal = {Annual review of biochemistry},
keywords = {Animals,Biochemistry,Biochemistry: methods,Biophysics,Biophysics: methods,DNA,DNA: chemistry,Equipment Design,Humans,Micromanipulation,Micromanipulation: methods,Molecular Biology,Molecular Biology: methods,Molecular Motor Proteins,Molecular Motor Proteins: chemistry,Optical Tweezers,Polymers,Polymers: chemistry,Reproducibility of Results,Spectrometry, Fluorescence,Spectrometry, Fluorescence: methods,Time Factors},
month = {jan},
number = {February},
pages = {205--28},
pmid = {18307407},
title = {{Recent advances in optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18307407},
volume = {77},
year = {2008}
}
@article{Bjornham2009b,
abstract = {In dynamic force spectroscopy, access to the characteristic parameters of single molecular bonds requires nontrivial measurements and data processing as the rupture forces are found not only to be distributed over a wide range, but are also dependent on the loading rate. The choice of measurement procedure and data processing methods has a considerable impact on the accuracy and precision of the final results. We analyze, by means of numerical simulations, methods to minimize and assess the magnitude of the expected errors for different combinations of experimental and evaluation methods. It was found that the choice of fitting function is crucial to extract correct parameter values. Applying a Gaussian function, which is a common practice, is equivalent to introducing a systematic error, and leads to a consequent overestimation of the thermal off-rate by more than 30{\%}. We found that the precision of the bond length and the thermal off-rate, in presence of unbiased noise, were improved by reducing the number of loading rates for a given number of measurements. Finally, the results suggest that the minimum number of measurements needed to obtain the bond strength, with acceptable precision, exceeds the common number of approximately 100 reported in literature.},
author = {Bj{\"{o}}rnham, Oscar and Schedin, Staffan},
doi = {10.1007/s00249-009-0471-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bj{\"{o}}rnham, Schedin - Methods and estimations of uncertainties in single-molecule dynamic force spectroscopy - 2009.pdf:pdf},
isbn = {0024900904718},
issn = {01757571},
journal = {European Biophysics Journal},
keywords = {Bond length,DFS,Error propagation,Monte Carlo simulation,Receptor-ligand,Specific binding,Thermal off-rate},
number = {7},
pages = {911--922},
pmid = {19462167},
title = {{Methods and estimations of uncertainties in single-molecule dynamic force spectroscopy}},
volume = {38},
year = {2009}
}
@article{Thomas2006,
abstract = {High shear enhances the adhesion of Escherichia coli bacteria binding to mannose coated surfaces via the adhesin FimH, raising the question as to whether FimH forms catch bonds that are stronger under tensile mechanical force. Here, we study the length of time that E. coli pause on mannosylated surfaces and report a double exponential decay in the duration of the pauses. This double exponential decay is unlike previous single molecule or whole cell data for other catch bonds, and indicates the existence of two distinct conformational states. We present a mathematical model, derived from the common notion of chemical allostery, which describes the lifetime of a catch bond in which mechanical force regulates the transitions between two conformational states that have different unbinding rates. The model explains these characteristics of the data: a double exponential decay, an increase in both the likelihood and lifetime of the high-binding state with shear stress, and a biphasic effect of force on detachment rates. The model parameters estimated from the data are consistent with the force-induced structural changes shown earlier in FimH. This strongly suggests that FimH forms allosteric catch bonds. The model advances our understanding of both catch bonds and the role of allostery in regulating protein activity.},
author = {Thomas, Wendy E and Forero, Manu and Yakovenko, Olga and Nilsson, Lina M and Vicini, Paolo and Sokurenko, Evgeni V and Vogel, Viola},
doi = {10.1529/biophysj.105.066548},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Thomas et al. - Catch-bond model derived from allostery explains force-activated bacterial adhesion. - 2006.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Adhesins,Allosteric Site,Bacterial,Bacterial Adhesion,Bacterial: chemistry,Biological,Biophysics,Biophysics: methods,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: metabolism,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: chemistry,Ligands,Mannose,Mannose: chemistry,Mechanical,Microscopy,Models,Protein Binding,Protein Conformation,Statistical,Stress,Temperature,Theoretical,Time Factors,Video},
month = {feb},
number = {3},
pages = {753--64},
pmid = {16272438},
title = {{Catch-bond model derived from allostery explains force-activated bacterial adhesion.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1367101{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {90},
year = {2006}
}
@article{Takemura2002,
author = {Takemura, Fumio and Takagi, Shu and Magnaudet, Jacques and Matsumoto, Yoichiro},
doi = {10.1017/S0022112002008388},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Takemura et al. - Drag and lift forces on a bubble rising near a vertical wall in a viscous liquid - 2002.pdf:pdf},
issn = {0022-1120},
journal = {Journal of Fluid Mechanics},
month = {jul},
pages = {277--300},
title = {{Drag and lift forces on a bubble rising near a vertical wall in a viscous liquid}},
url = {http://www.journals.cambridge.org/abstract{\_}S0022112002008388},
volume = {461},
year = {2002}
}
@article{DiStasio2010,
abstract = {Macromolecules and cells exposed to blood flow in the circulatory tree experience hydrodynamic forces that affect their structure and function. After introducing the general theory of the effects of shear forces on protein conformation, selected examples are presented in this review for biological macromolecules sensitive to shear stress. In particular, the biochemical effects of shear stress in controlling the von Willebrand Factor (VWF) conformation are extensively described. This protein, together with blood platelets, is the main actor of the early steps of primary haemostasis. Under the effect of shear forces >30 dyn/cm², VWF unfolding occurs and the protein exhibits an extended chain conformation oriented in the general direction of the shear stress field. The stretched VWF conformation favors also a process of self aggregation, responsible for the formation of a spider web network, particularly efficient in the trapping process of flowing platelets. Thus, the effect of shear stress on conformational changes in VWF shows a close structure-function relationship in VWF for platelet adhesion and thrombus formation in arterial circulation, where high shear stress is present. The investigation of biophysical effects of shear forces on VWF conformation contributes to unraveling the molecular interaction mechanisms involved in arterial thrombosis.},
author = {{Di Stasio}, Enrico and {De Cristofaro}, Raimondo},
doi = {10.1016/j.bpc.2010.07.002},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Di Stasio, De Cristofaro - The effect of shear stress on protein conformation Physical forces operating on biochemical systems The case.pdf:pdf},
issn = {1873-4200},
journal = {Biophysical chemistry},
keywords = {Platelet Adhesiveness,Protein Multimerization,Protein Structure, Tertiary,Protein Unfolding,Stress, Mechanical,von Willebrand Factor,von Willebrand Factor: chemistry,von Willebrand Factor: physiology},
month = {dec},
number = {1},
pages = {1--8},
pmid = {20797815},
publisher = {Elsevier B.V.},
title = {{The effect of shear stress on protein conformation: Physical forces operating on biochemical systems: The case of von Willebrand factor.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20797815},
volume = {153},
year = {2010}
}
@article{Rohrbach2005,
abstract = {An experiment is described, where an ultra-weak force of 25 femtoNewtons (fN = 10-15 N) displaces a 0.53microm latex bead captured in a soft optical trap. The displacement is measured by exploiting the phase anomaly of the trapping beam, resulting in a small phase shift of the scattered light. The 25fN force stems from the radiation pressure of a nearly collimated second laser beam, which is switched by an accousto-optical modulator. To the best of my knowledge, this is the smallest switchable force which has ever been directly measured.},
author = {Rohrbach, Alexander},
doi = {10.1364/OPEX.13.009695},
isbn = {1094-4087},
issn = {1094-4087},
journal = {Optics express},
number = {24},
pages = {9695--9701},
pmid = {19503175},
title = {{Switching and measuring a force of 25 femtoNewtons with an optical trap.}},
volume = {13},
year = {2005}
}
@article{Darsley2012,
abstract = {An oral, live attenuated, three-strain recombinant bacterial vaccine, ACE527, was demonstrated to generate strong immune responses to colonization factor and toxin antigens of enterotoxigenic Escherichia coli (ETEC) in human volunteers. The vaccine was safe and well tolerated at doses of up to 10(11) CFU, administered in each of two doses given 21 days apart. These observations have now been extended in a phase 2b study with a total of 70 subjects. Fifty-six of these subjects were challenged 28 days after the second dose of vaccine with the highly virulent ETEC strain H10407 to obtain preliminary indicators of efficacy against disease and to support further development of the vaccine for both travelers and infants in countries where ETEC is endemic. The vaccine had a significant impact on intestinal colonization by the challenge strain, as measured by quantitative fecal culture 2 days after challenge, demonstrating the induction of a functional immune response to the CFA/I antigen. The incidence and severity of diarrhea were also reduced in vaccinees as measured by a number of secondary and ad hoc endpoints, although the 27{\%} reduction seen in the primary endpoint, moderate to severe diarrhea, was not statistically significant. Together, these observations support the hypothesis that the ACE527 vaccine has a dual mode of action, targeting both colonization factors and the heat-labile enterotoxin (LT), and suggest that it should be further developed for more advanced trials to evaluate its impact on the burden of ETEC disease in field settings.},
author = {Darsley, Michael J and Chakraborty, Subhra and DeNearing, Barbara and Sack, David a and Feller, Andrea and Buchwaldt, Charlotte and Bourgeois, a Louis and Walker, Richard and Harro, Clayton D},
doi = {10.1128/CVI.00364-12},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Darsley et al. - The oral, live attenuated enterotoxigenic Escherichia coli vaccine ACE527 reduces the incidence and severity of diarrhe.pdf:pdf},
issn = {1556-679X},
journal = {Clinical and vaccine immunology : CVI},
keywords = {Administration, Oral,Adolescent,Adult,Bacterial Load,Diarrhea,Diarrhea: microbiology,Diarrhea: pathology,Diarrhea: prevention {\&} control,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: immunology,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli Infections: pathology,Escherichia coli Infections: prevention {\&} control,Escherichia coli Vaccines,Escherichia coli Vaccines: administration {\&} dosage,Escherichia coli Vaccines: adverse effects,Escherichia coli Vaccines: immunology,Feces,Feces: microbiology,Human Experimentation,Humans,Incidence,Male,Middle Aged,Severity of Illness Index,Vaccination,Vaccination: methods,Vaccines, Attenuated,Vaccines, Attenuated: administration {\&} dosage,Vaccines, Attenuated: adverse effects,Vaccines, Attenuated: immunology,Young Adult},
month = {dec},
number = {12},
pages = {1921--31},
pmid = {23035175},
title = {{The oral, live attenuated enterotoxigenic Escherichia coli vaccine ACE527 reduces the incidence and severity of diarrhea in a human challenge model of diarrheal disease.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3535858{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {19},
year = {2012}
}
@article{Bidhendi2007,
abstract = {Presence of fimbriae on Escherichia coli isolated from the urine of patients with urinary tract infection was related to the ability of the bacteria to attach to human uroepithelial cells. One of the 50 isolates that expresses high MRHA p-fimbriae, selected and antibody against p-fimbriae from it, showed blocking of attachment of bacteria to HEP-2 cell in 1:1024 titer. Also, 1:512 titer of this antiserum to blocking of attachment in bladder tissue of mice is significant.},
author = {Bidhendi, S Moradi and Sattari, M and Pourbakhsh, S a and Mobarez, a and Vandyousefi, J and Khaki, P and Heidari, M H and Kazemnejad, a},
doi = {10.1016/j.biologicals.2006.03.012},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bidhendi et al. - Blocking adherence of uropathogenic Escherichia coli isolate to HEP-2 cells and bladder of mice in the presence of ant.pdf:pdf},
issn = {1045-1056},
journal = {Biologicals : journal of the International Association of Biological Standardization},
keywords = {Animals,Antibodies,Antibodies: pharmacology,Bacterial Adhesion,Bacterial Adhesion: immunology,Cells, Cultured,Epithelial Cells,Epithelial Cells: immunology,Epithelial Cells: microbiology,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli Infections: urine,Escherichia coli: immunology,Escherichia coli: isolation {\&} purification,Female,Fimbriae Proteins,Fimbriae Proteins: immunology,Fimbriae Proteins: isolation {\&} purification,Fimbriae Proteins: urine,Fimbriae, Bacterial,Fimbriae, Bacterial: immunology,Humans,Larynx,Larynx: immunology,Larynx: microbiology,Mice,Mice, Inbred Strains,Microscopy, Electron, Scanning,Microscopy, Electron, Transmission,Rabbits,Urinary Bladder,Urinary Bladder: immunology,Urinary Bladder: microbiology,Urinary Tract Infections,Urinary Tract Infections: microbiology,Urinary Tract Infections: urine},
month = {may},
number = {2},
pages = {99--105},
pmid = {16879977},
title = {{Blocking adherence of uropathogenic Escherichia coli isolate to HEP-2 cells and bladder of mice in the presence of antibody against p-fimbriae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16879977},
volume = {35},
year = {2007}
}
@article{Williams2013,
author = {Williams, Z T and Macklin, K S},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Williams, Macklin - Stratification of bacterial concentrations , from upper to lower , in broiler litter - 2013.pdf:pdf},
keywords = {10,2012-00705,2013 j,22,3382,492,498,appl,bacteria stratification,description of problem,doi,dx,http,japr,litter,litter , bacteria stratification , management,management,org,poult,res},
title = {{Stratification of bacterial concentrations , from upper to lower , in broiler litter}},
year = {2013}
}
@article{Goldman1967b,
annote = {From Duplicate 2 ( Slow Viscous Motion of a Sphere Parallel to a Plane Wall, Chem - Goldman, A.J; Cox, R.G.; Brenner, H. )

From Duplicate 2 ( Slow viscous motion of a sphere parallel to a plane wall.pdf - Goldman, A.J; Cox, R.G.; Brenner, H. )

From Duplicate 1 ( Slow viscous motion of a sphere parallel to a plane wall.pdf - Goldman, A.J; Cox, R.G.; Brenner, H. )
},
author = {Goldman, A.J and Cox, R.G. and Brenner, H.},
doi = {http://dx.doi.org/10.1016/0009-2509(67)80047-2},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Goldman, Cox, Brenner - Slow Viscous Motion of a Sphere Parallel to a Plane Wall - II Couette flow, Chem - 1967.pdf:pdf},
journal = {Chemical Engineering Science},
keywords = {Flow,shear force,sphere},
mendeley-tags = {Flow,shear force,sphere},
number = {4},
pages = {653--660},
title = {{Slow Viscous Motion of a Sphere Parallel to a Plane Wall - II Couette flow, Chem}},
url = {http://scholar.google.com/scholar?hl=en{\&}btnG=Search{\&}q=intitle:Slow+viscous+motion+of+a+sphere+parallel+to+a+plane+wall{\#}5},
volume = {22},
year = {1967}
}
@article{Messina2011,
author = {Messina, E and Cavallaro, E and Cacciola, A and Saija, R and Borghese, F and Denti, P and Fazio, B and Andrea, C D and Meneghetti, M and Compagnini, G and Amendola, V and Marag, O M and Gucciardi, P G and Iati, M A and Catania, I- and Messina, I-},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Messina et al. - Manipulation and Raman Spectroscopy with Optically Trapped Metal Nanoparticles Obtained by Pulsed Laser Ablation in Liq.pdf:pdf},
pages = {5115--5122},
title = {{Manipulation and Raman Spectroscopy with Optically Trapped Metal Nanoparticles Obtained by Pulsed Laser Ablation in Liquids}},
year = {2011}
}
@article{Anderson2007,
abstract = {Bacterial adhesion to and subsequent colonization of surfaces are the first steps toward forming biofilms, which are a major concern for implanted medical devices and in many diseases. It has generally been assumed that strong irreversible adhesion is a necessary step for biofilm formation. However, some bacteria, such as Escherichia coli when binding to mannosylated surfaces via the adhesive protein FimH, adhere weakly in a mode that allows them to roll across the surface. Since single-point mutations or even increased shear stress can switch this FimH-mediated adhesion to a strong stationary mode, the FimH system offers a unique opportunity to investigate the role of the strength of adhesion independently from the many other factors that may affect surface colonization. Here we compare levels of surface colonization by E. coli strains that differ in the strength of adhesion as a result of flow conditions or point mutations in FimH. We show that the weak rolling mode of surface adhesion can allow a more rapid spreading during growth on a surface in the presence of fluid flow. Indeed, an attempt to inhibit the adhesion of strongly adherent bacteria by blocking mannose receptors with a soluble inhibitor actually increased the rate of surface colonization by allowing the bacteria to roll. This work suggests that (i) a physiological advantage to the weak adhesion demonstrated by commensal variants of FimH bacteria may be to allow rapid surface colonization and (ii) antiadhesive therapies intended to prevent biofilm formation can have the unintended effect of enhancing the rate of surface colonization.},
author = {Anderson, Brett N and Ding, Albert M and Nilsson, Lina M and Kusuma, Kaoru and Tchesnokova, Veronika and Vogel, Viola and Sokurenko, Evgeni V and Thomas, Wendy E},
doi = {10.1128/JB.00899-06},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Anderson et al. - Weak rolling adhesion enhances bacterial surface colonization. - 2007.pdf:pdf},
issn = {0021-9193},
journal = {Journal of bacteriology},
keywords = {Adhesins,Bacterial Adhesion,Biofilms,Escherichia coli,Escherichia coli: physiology,Fimbriae Proteins,Fimbriae Proteins: physiology,biofilm},
mendeley-tags = {biofilm},
month = {mar},
number = {5},
pages = {1794--802},
pmid = {17189376},
title = {{Weak rolling adhesion enhances bacterial surface colonization.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1855705{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {189},
year = {2007}
}
@article{Sali1993,
author = {Sali, A and Blundell, TL},
journal = {Journal of molecular biology},
pages = {779--815},
title = {{Comparative protein modelling by satisfaction of spatial restraints}},
volume = {234},
year = {1993}
}
@article{Soriani2010,
abstract = {A common mechanism used by bacteria to initiate adhesion to host tissues during colonization is the expression of long filamentous structures extending from their surface. These structures, known as pili or fimbriae, were initially identified in Gram-negative bacteria, and are typically formed by noncovalent interactions between pilin subunits. Pili have only recently been described in Gram-positive bacteria. In particular, in pathogenic streptococci the proteinaceous components of pili are covalently polymerized by the action of sortase enzymes similar to those involved in the covalent attachment of Gram-positive surface proteins to the peptidoglycan cell wall. With great relevance to the development of strategies to combat Gram-positive-associated infections, pilus components from pathogenic streptococci have been shown to induce protective immunity in mouse models of streptococcal disease. In addition, recent papers have created new perspectives on the role of such organelles in streptococcal pathogenesis, from the involvement in colonization and biofilm formation to translocation of tissue barriers. All this information makes the characterization of pili a hot scientific issue that we believe will lead to important future developments in understanding bacterial dynamics that lead to successful occupation of microbial niches.},
author = {Soriani, M and Telford, JL},
journal = {Future microbiology},
number = {5},
pages = {735--747},
title = {{Relevance of pili in pathogenic streptococci pathogenesis and vaccine development}},
volume = {5},
year = {2010}
}
@phdthesis{Wallin2011,
author = {Wallin, Anders and Science, Faculty},
booktitle = {Control},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wallin, Science - OPTICAL TWEEZERS FOR SINGLE - 2011.pdf:pdf},
isbn = {9789521068799},
number = {February},
school = {Helsinki},
title = {{OPTICAL TWEEZERS FOR SINGLE}},
year = {2011}
}
@article{Bullerjahn2016,
author = {Bullerjahn, J. T. and Kroy, K.},
doi = {10.1103/PhysRevE.93.012404},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bullerjahn, Kroy - Analytical catch-slip bond model for arbitrary forces and loading rates - 2016.pdf:pdf},
issn = {2470-0045},
journal = {Physical Review E},
number = {1},
pages = {012404},
title = {{Analytical catch-slip bond model for arbitrary forces and loading rates}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.93.012404},
volume = {93},
year = {2016}
}
@article{Gouy1890,
author = {Gouy, L. G.},
journal = {C. R. Acad. Sci. Paris},
pages = {1251--1253},
title = {{Sur une propriet{\'{e}} nouvelle des ondes lumineuses}},
volume = {110},
year = {1890}
}
@article{Caron1989b,
abstract = {To be virulent, enterotoxigenic Escherichia coli (ETEC) must produce a toxin and a pilus-like structure that mediates specific attachment to host tissue. Expression of two of these specific adherence structures, CS1 and CS2, requires the presence of a plasmid in an ETEC strain of a particular serotype and biotype. We show here that this plasmid does not contain the structural gene for a pilin protein, as previously believed. Instead we have identified a plasmid-encoded gene called rns that is required for expression of CS1 or CS2 colonization factor antigens and for adhesion. The rns gene, defined by two separately isolated insertion mutations, produces a 26-kDa protein when transcribed and translated in vitro. At the protein level the rns gene product is homologous to AraC, a positive regulator of the arabinose operon of enteric bacteria, and to RhaR and RhaS, which regulate the rhamnose operon of E. coli. The homology of the Rns protein to AraC is localized to regions that are believed to bind to DNA. Moreover, the sequence of one of these homologous regions is consistent with a DNA binding helix-turn-helix motif. The average G + C content of E. coli DNA is 50{\%}; yet the rns gene contains only 28{\%} G + C, suggesting that it was acquired from some other organism.},
author = {Caron, J and Coffield, L M and Scott, J R},
doi = {10.1073/pnas.86.3.963},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Caron, Coffield, Scott - A plasmid-encoded regulatory gene, rns, required for expression of the CS1 and CS2 adhesins of enterotoxigenic.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Caron, Coffield, Scott - A plasmid-encoded regulatory gene, rns, required for expression of the CS1 and CS2 adhesins of enterotoxigen(2).pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {February},
pages = {963--967},
pmid = {2563591},
title = {{A plasmid-encoded regulatory gene, rns, required for expression of the CS1 and CS2 adhesins of enterotoxigenic Escherichia coli.}},
volume = {86},
year = {1989}
}
@article{Ermak1978,
author = {Ermak, Donald L. and McCammon, J. a.},
doi = {10.1063/1.436761},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ermak, McCammon - Brownian dynamics with hydrodynamic interactions - 1978.pdf:pdf},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {4},
pages = {1352},
title = {{Brownian dynamics with hydrodynamic interactions}},
url = {http://link.aip.org/link/JCPSA6/v69/i4/p1352/s1{\&}Agg=doi},
volume = {69},
year = {1978}
}
@article{Biais2010,
author = {Biais, N. and Higashi, D. L. and Brujic, J. and So, M. and Sheetz, M. P.},
doi = {10.1073/pnas.0911328107},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Biais et al. - Force-dependent polymorphism in type IV pili reveals hidden epitopes - 2010.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = {jun},
number = {25},
title = {{Force-dependent polymorphism in type IV pili reveals hidden epitopes}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0911328107},
volume = {107},
year = {2010}
}
@article{Martelli2010,
abstract = {The results of a theoretical and experimental investigation of the Gouy effect in Bessel beams are presented. We point out that the peculiar feature of the Bessel beams of being nondiffracting is related to the accumulation of an extra axial phase shift (i.e., the Gouy phase shift) linearly dependent on the propagation distance. The constant spatial rate of variation of the Gouy phase shift is independent of the order of the Bessel beam, while it is a growing function of the transverse component of the angular spectrum wave-vectors, originated by the transverse confinement of the beam. A free-space Mach-Zehnder interferometer has been set-up for measuring the transverse intensity distribution of the interference between holographically-produced finite-aperture Bessel beams of order from zero up to three and a reference Gaussian beam, at a wavelength of 633 nm. The interference patterns have been registered for different propagation distances and show a spatial periodicity, in agreement with the expected period due to the linear increase of the Gouy phase shift of the realized Bessel beams.},
author = {Martelli, Paolo and Tacca, Matteo and Gatto, Alberto and Moneta, Giorgio and Martinelli, Mario},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Martelli et al. - Gouy phase shift in nondiffracting Bessel beams. - 2010.pdf:pdf},
issn = {1094-4087},
journal = {Optics express},
keywords = {Algorithms,Computer Simulation,Equipment Design,Holography,Holography: methods,Interferometry,Interferometry: methods,Light,Models, Statistical,Normal Distribution,Optics and Photonics,Physical Processes},
month = {mar},
number = {7},
pages = {7108--20},
pmid = {20389732},
title = {{Gouy phase shift in nondiffracting Bessel beams.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20389732},
volume = {18},
year = {2010}
}
@article{Putkiranta2010,
author = {Putkiranta, M. and Manninen, a. and Rostedt, a. and Saarela, J. and Sorvaj{\"{a}}rvi, T. and Marjam{\"{a}}ki, M. and Hernberg, R. and Keskinen, J.},
doi = {10.1007/s00340-010-4073-z},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Putkiranta et al. - Fluorescence properties of biochemicals in dry NaCl composite aerosol particles and in solutions - 2010.pdf:pdf},
issn = {0946-2171},
journal = {Applied Physics B},
month = {may},
number = {4},
pages = {841--851},
title = {{Fluorescence properties of biochemicals in dry NaCl composite aerosol particles and in solutions}},
url = {http://www.springerlink.com/index/10.1007/s00340-010-4073-z},
volume = {99},
year = {2010}
}
@article{Brisson2010,
abstract = {A set of methods has been developed to study the adhesion between four Lactobacillus reuteri strains and the milk fat globule membrane (MFGM) components in dairy products. By combining sucrose density gradient (SDG) centrifugation and bacterial DNA quantification it was found which strains of L. reuteri were more strongly associated with the dairy products, and the results were corroborated by direct binding rate and force measurements made with optical tweezers. It was determined that strong binding was associated with hydrophobicity of the bacteria and that this hydrophobicity is correlated with the presence of LiCl-extractable protein on the surface of the bacteria. Confocal laser scanning microscopy (CLSM) allowed for the visualization of interactions between bacteria and MFGM. This study demonstrates that these methods can be used in combination to characterize, both qualitatively and quantitatively, the adhesion of lactic acid bacteria strains in dairy products.},
author = {Brisson, Guillaume and Payken, Hannah F and Sharpe, John P and Jim{\'{e}}nez-Flores, Rafael},
doi = {10.1021/jf904381s},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Brisson et al. - Characterization of Lactobacillus reuteri interaction with milk fat globule membrane components in dairy products. - 20.pdf:pdf},
issn = {1520-5118},
journal = {Journal of agricultural and food chemistry},
keywords = {Animals,Dairy Products,Fats,Fats: metabolism,Lactobacillus reuteri,Lactobacillus reuteri: physiology,Microscopy, Confocal,Milk,Milk: metabolism},
month = {may},
number = {9},
pages = {5612--9},
pmid = {20377223},
title = {{Characterization of Lactobacillus reuteri interaction with milk fat globule membrane components in dairy products.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20377223},
volume = {58},
year = {2010}
}
@article{Kallestinova2011,
abstract = {Writing a research manuscript is an intimidating process for many novice writers in the sciences. One of the stumbling blocks is the beginning of the process and creating the first draft. This paper presents guidelines on how to initiate the writing process and draft each section of a research manuscript. The paper discusses seven rules that allow the writer to prepare a well-structured and comprehensive manuscript for a publication submission. In addition, the author lists different strategies for successful revision. Each of those strategies represents a step in the revision process and should help the writer improve the quality of the manuscript. The paper could be considered a brief manual for publication.},
author = {Kallestinova, Elena D.},
doi = {10.1016/j.paed.2011.05.009},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kallestinova - How to write your first research paper - 2011.pdf:pdf},
isbn = {1751-7222},
issn = {00440086},
journal = {Yale Journal of Biology and Medicine},
keywords = {Revision,Scientific paper,Writing process},
number = {3},
pages = {181--190},
pmid = {21966034},
title = {{How to write your first research paper}},
volume = {84},
year = {2011}
}
@article{Xia1999,
author = {Xia, Yan and Uhlin, Bernt Eric},
doi = {10.1074/jbc.274.28.19723},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Xia, Uhlin - Mutational Analysis of the PapB Transcriptional Regulator in Escherichia coli. REGIONS IMPORTANT FOR DNA BINDING AND OLIGOM.pdf:pdf},
isbn = {4690772630},
issn = {00219258},
journal = {Journal of Biological Chemistry},
month = {jul},
number = {28},
pages = {19723--19730},
title = {{Mutational Analysis of the PapB Transcriptional Regulator in Escherichia coli. REGIONS IMPORTANT FOR DNA BINDING AND OLIGOMERIZATION}},
url = {http://www.jbc.org/cgi/doi/10.1074/jbc.274.28.19723},
volume = {274},
year = {1999}
}
@article{Nishiyama2005,
abstract = {Adhesive type 1 pili from uropathogenic Escherichia coli are filamentous protein complexes that are attached to the assembly platform FimD in the outer membrane. During pilus assembly, FimD binds complexes between the chaperone FimC and type 1 pilus subunits in the periplasm and mediates subunit translocation to the cell surface. Here we report nuclear magnetic resonance and X-ray protein structures of the N-terminal substrate recognition domain of FimD (FimD(N)) before and after binding of a chaperone-subunit complex. FimD(N) consists of a flexible N-terminal segment of 24 residues, a structured core with a novel fold, and a C-terminal hinge segment. In the ternary complex, residues 1-24 of FimD(N) specifically interact with both FimC and the subunit, acting as a sensor for loaded FimC molecules. Together with in vivo complementation studies, we show how this mechanism enables recognition and discrimination of different chaperone-subunit complexes by bacterial pilus assembly platforms.},
author = {Nishiyama, Mireille and Horst, Reto and Eidam, Oliv and Herrmann, Torsten and Ignatov, Oleksandr and Vetsch, Michael and Bettendorff, Pascal and Jelesarov, Ilian and Gr{\"{u}}tter, Markus G and W{\"{u}}thrich, Kurt and Glockshuber, Rudi and Capitani, Guido},
doi = {10.1038/sj.emboj.7600693},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nishiyama et al. - Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD. - 2005.pdf:pdf},
issn = {0261-4189},
journal = {The EMBO journal},
keywords = {Adhesins, Escherichia coli,Adhesins, Escherichia coli: chemistry,Amino Acid Sequence,Crystallography, X-Ray,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: metabolism,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Fimbriae, Bacterial: metabolism,Magnetic Resonance Spectroscopy,Molecular Chaperones,Molecular Chaperones: chemistry,Molecular Chaperones: metabolism,Molecular Sequence Data,Peptide Fragments,Peptide Fragments: chemistry,Peptide Fragments: metabolism,Protein Structure, Tertiary},
month = {jun},
number = {12},
pages = {2075--86},
pmid = {15920478},
title = {{Structural basis of chaperone-subunit complex recognition by the type 1 pilus assembly platform FimD.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15920478},
volume = {24},
year = {2005}
}
@article{Yusko2014,
author = {Yusko, E. C. and Asbury, C. L.},
doi = {10.1091/mbc.E13-12-0707},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yusko, Asbury - Force is a signal that cells cannot ignore - 2014.pdf:pdf},
issn = {1059-1524},
journal = {Molecular Biology of the Cell},
month = {nov},
number = {23},
pages = {3717--3725},
title = {{Force is a signal that cells cannot ignore}},
url = {http://www.molbiolcell.org/cgi/doi/10.1091/mbc.E13-12-0707},
volume = {25},
year = {2014}
}
@article{Rognoni2014,
author = {Rognoni, Lorenz and M{\"{o}}st, Tobias and Gabriel, {\v{Z}} and Rief, Matthias},
doi = {10.1073/pnas.1319448111},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rognoni et al. - Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of fila.pdf:pdf},
number = {15},
title = {{Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin}},
volume = {111},
year = {2014}
}
@article{Clements2012,
abstract = {Enteric Escherichia coli (E. coli) are both natural flora of humans and important pathogens causing significant morbidity and mortality worldwide. Traditionally enteric E. coli have been divided into 6 pathotypes, with further pathotypes often proposed. In this review we suggest expansion of the enteric E. coli into 8 pathotypes to include the emerging pathotypes of adherent invasive E. coli (AIEC) and Shiga-toxin producing enteroaggregative E. coli (STEAEC). The molecular mechanisms that allow enteric E. coli to colonize and cause disease in the human host are examined and for two of the pathotypes that express a type 3 secretion system (T3SS) we discuss the complex interplay between translocated effectors and manipulation of host cell signaling pathways that occurs during infection.},
author = {Clements, Abigail and Young, Joanna C. and Constantinou, Nicholas and Frankel, Gad},
doi = {10.4161/gmic.19182},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Clements et al. - Infection strategies of enteric pathogenic Escherichia coli - 2012.pdf:pdf},
issn = {19490976},
journal = {Gut Microbes},
keywords = {Enteric E. coli,Gut microbes,Host-pathogen interactions,Molecular mechanisms of pathogenesis,T3SS},
number = {2},
pages = {71--87},
pmid = {22555463},
title = {{Infection strategies of enteric pathogenic Escherichia coli}},
volume = {3},
year = {2012}
}
@article{Davies1987,
address = {New York},
author = {Davies, E R},
doi = {10.1016/0167-8655(87)90014-6},
issn = {0167-8655},
journal = {Pattern Recogn. Lett.},
month = {dec},
number = {5},
pages = {315--322},
publisher = {Elsevier Science Inc.},
title = {{The Effect of Noise on Edge Orientation Computations}},
volume = {6},
year = {1987}
}
@article{Rzhepishevska2013,
abstract = {Bacterial biofilms affect many areas of human activity including food
processing{\{},{\}} transportation{\{},{\}} public infrastructure{\{},{\}} and most
importantly healthcare. This study addresses the prevention of biofilms
and shows that the surface charge of an abiotic substrate influences
bacterial motility as well as the morphology and physiology of the
biofilm. Grafting-from polymerisation was used to create polymer
brush surfaces with different characteristics{\{},{\}} and the development
of Pseudomonas aeruginosa biofilms was followed using confocal microscopy.
Interestingly{\{},{\}} two types of biofilms developed on these surfaces:
mushroom structures with high levels of cyclic diguanylate (c-di-GMP)
were found on negatively charged poly (3-sulphopropylmethacrylate)
(SPM) and zwitterionic poly (2-(methacryloyloxy)ethyl)dimethyl-3-sulphoproyl)
ammonium hydroxide) (MEDSAH){\{},{\}} while flat biofilms developed on
glass{\{},{\}} positively charged poly (2-(methacryloyloxy)-ethyl trimethyl
ammonium chloride) (METAC){\{},{\}} protein-repellent poly oligo(ethylene
glycol methyl ether methacrylate) (POEGMA) and hydrophobic polymethylmethacrylate
(PMMA). The results show that of all the surfaces studied{\{},{\}} overall
the negatively charged polymer brushes were most efficient in reducing
bacterial adhesion and biofilm formation. However{\{},{\}} the increased
level of regulatory c-di-GMP in mushroom structures suggests that
bacteria are capable of a quick physiological response when exposed
to surfaces with varying physicochemical characteristics enabling
some bacterial colonization also on negatively charged surfaces.},
author = {Rzhepishevska, Olena and Hakobyan, Shoghik and Ruhal, Rohit and Gautrot, Julien and Barbero, David and Ramstedt, Madeleine},
doi = {10.1039/C3BM00197K},
journal = {Biomater. Sci.},
number = {6},
pages = {589--602},
publisher = {The Royal Society of Chemistry},
title = {{The surface charge of anti-bacterial coatings alters motility and biofilm architecture}},
volume = {1},
year = {2013}
}
@article{Jeffrey2003c,
abstract = {The guinea pig ileum responds to distension with characteristic wall movements, luminal pressure gradients, and outflow (the peristaltic reflex). To date, little is known about whether the peristaltic reflex generates flow events other than laminar flow. Here we used a numerical method to solve for the flow generated by moving walls to assess occlusive contractions (case 1), nonocclusive contractions (case 2), and contractions with steep shoulders (case 3) for which visual parameters of wall movements are published. We found that all three contraction cases produced pressure differentials across the coapting segment, downstream and reverse flow, and vortical flow patterns that redistributed particles and mixed liquids. Contractions generated pressures and shear stresses, particularly along the moving section of the wall. The nonocclusive contraction was much less effective than the occlusive contraction with the steep shoulders; the occlusive contraction with flat shoulders had an intermediate effect. Our analysis shows that even peristaltic contractions produce not only laminar flow but also many flow events likely to promote digestion and absorption. The visual patterns of contractions impact the patterns of luminal flow, and precise definition of wall movements is critical to quantify the fluid mechanical consequences of intestinal contractions.},
annote = {From Duplicate 2 ( Flow fields generated by peristaltic reflex in isolated guinea pig ileum: impact of contraction depth and shoulders. - Jeffrey, Brian; Udaykumar, Holavanahalli S; Schulze, Konrad S )
},
author = {Jeffrey, Brian and Udaykumar, Holavanahalli S and Schulze, Konrad S},
doi = {10.1152/ajpgi.00062.2003},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jeffrey, Udaykumar, Schulze - Flow fields generated by peristaltic reflex in isolated guinea pig ileum impact of contraction depth an(2).pdf:pdf},
issn = {0193-1857},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
keywords = {Animals,Biological,Gastrointestinal Motility,Gastrointestinal Motility: physiology,Gastrointestinal Transit,Gastrointestinal Transit: physiology,Guinea Pigs,Ileum,Ileum: physiology,Models,Peristalsis,Peristalsis: physiology,Reflex,Reflex: physiology},
month = {nov},
number = {5},
pages = {G907--18},
pmid = {14561588},
title = {{Flow fields generated by peristaltic reflex in isolated guinea pig ileum: impact of contraction depth and shoulders.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14561588},
volume = {285},
year = {2003}
}
@article{Soto1999,
author = {Soto, G E and Hultgren, Scott J},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Soto, Hultgren - Bacterial adhesins common themes and variations in architecture and assembly. - 1999.pdf:pdf},
issn = {0021-9193},
journal = {Journal of bacteriology},
keywords = {Adhesins,Amino Acid,Amino Acid Sequence,Bacteria,Bacteria: pathogenicity,Bacterial,Bacterial Adhesion,Bacterial: biosynthesis,Bacterial: chemistry,Bacterial: metabolism,Biological,Fimbriae,Models,Molecular,Molecular Sequence Data,Sequence Homology},
month = {feb},
number = {4},
pages = {1059--71},
pmid = {9973330},
title = {{Bacterial adhesins: common themes and variations in architecture and assembly.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93481{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {181},
year = {1999}
}
@article{Ochoa2011,
author = {Ochoa, Theresa J and Rivera, Fulton P and Bernal, Maria and Meza, Rina and Ecker, Lucie and Ana, I and Cepeda, David and Mosquito, Susan and Mercado, Erik and Maves, Ryan C and Hall, Eric R and Svennerholm, Mari and Mcveigh, Annette and Savarino, Stephen J and Lanata, Claudio F},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ochoa et al. - NIH Public Access - 2011.pdf:pdf},
keywords = {children,coli,colonization factor antigens,colonization factors,diarrhea,diarrhea in,diarrheagenic e,diffusely adherent e,enterotoxigenic e,enterotoxigenic escherichia coli,etec,is one of the,main causes of pediatric},
pages = {1--5},
title = {{NIH Public Access}},
year = {2011}
}
@article{Formenti2015,
author = {Formenti, Federico and Minetti, Alberto E. and Borrani, Fabio},
doi = {10.14814/phy2.12500},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Formenti, Minetti, Borrani - Pedaling rate is an important determinant of human oxygen uptake during exercise on the cycle ergometer - 2.pdf:pdf},
issn = {2051-817X},
journal = {Physiological Reports},
keywords = {biomechanics,exercise physiology,oxygen},
number = {9},
pages = {e12500},
title = {{Pedaling rate is an important determinant of human oxygen uptake during exercise on the cycle ergometer}},
url = {http://physreports.physiology.org/lookup/doi/10.14814/phy2.12500},
volume = {3},
year = {2015}
}
@article{Rene1982a,
author = {Rene, Pierre and Silverblatt, Fredric J},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rene, Silverblatt - Serological response to Escherichia coli pili in Serological Response to Escherichia coli Pili in Pyelonephritis - 1.pdf:pdf},
journal = {Infection},
number = {2},
pages = {749},
title = {{Serological response to Escherichia coli pili in Serological Response to Escherichia coli Pili in Pyelonephritis}},
volume = {37},
year = {1982}
}
@article{Kang2009a,
abstract = {The pili expressed by Streptococcus pyogenes and certain other Gram-positive bacterial pathogens are based on a polymeric backbone in which individual pilin subunits are joined end-to-end by covalent isopeptide bonds through the action of sortase enzymes. The crystal structure of the major pilin of S. pyogenes, Spy0128, revealed that each domain of the two domain protein contained an intramolecular isopeptide bond cross-link joining a Lys side chain to an Asn side chain. In the present work, mutagenesis was used to create mutant proteins that lacked either one isopeptide bond (E117A, N168A, and E258A mutants) or both isopeptide bonds (E117A/E258A). Both the thermal stability and proteolytic stability of Spy0128 were severely compromised by loss of the isopeptide bonds. Unfolding experiments, monitored by circular dichroism, revealed a transition temperature T(m) of 85 degrees C for the wild type protein. In contrast, mutants with only one isopeptide bond showed biphasic unfolding, with the domain lacking an isopeptide bond having a T(m) that was approximately 30 degrees C lower than the unaltered domain. High resolution crystal structures of the E117A and N168A mutants showed that the loss of an isopeptide bond did not change the overall pilin structure but caused local disturbance of the protein core that was greater for E117A than for N168A. These effects on stability appear also to be important for pilus assembly.},
author = {Kang, Hae Joo and Baker, Edward N},
doi = {10.1074/jbc.M109.014514},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kang, Baker - Intramolecular isopeptide bonds give thermodynamic and proteolytic stability to the major pilin protein of Streptococcus p.pdf:pdf},
issn = {1083-351X},
journal = {The Journal of biological chemistry},
keywords = {Amino Acid Substitution,Circular Dichroism,Crystallography, X-Ray,Fimbriae Proteins,Fimbriae Proteins: chemistry,Mutant Proteins,Mutant Proteins: chemistry,Peptides,Peptides: chemistry,Protein Denaturation,Protein Processing, Post-Translational,Protein Stability,Protein Structure, Secondary,Spectrometry, Mass, Electrospray Ionization,Static Electricity,Streptococcus pyogenes,Streptococcus pyogenes: chemistry,Thermodynamics},
month = {jul},
number = {31},
pages = {20729--37},
pmid = {19497855},
title = {{Intramolecular isopeptide bonds give thermodynamic and proteolytic stability to the major pilin protein of Streptococcus pyogenes.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2742838{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {284},
year = {2009}
}
@article{Flores-Mireles2015,
author = {Flores-Mireles, Ana L. and Walker, Jennifer N. and Caparon, Michael and Hultgren, Scott J.},
doi = {10.1038/nrmicro3432},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Flores-Mireles et al. - Urinary tract infections epidemiology, mechanisms of infection and treatment options - 2015.pdf:pdf},
issn = {1740-1526},
journal = {Nature Reviews Microbiology},
number = {5},
pages = {269--284},
publisher = {Nature Publishing Group},
title = {{Urinary tract infections: epidemiology, mechanisms of infection and treatment options}},
url = {http://www.nature.com/doifinder/10.1038/nrmicro3432},
volume = {13},
year = {2015}
}
@article{Nezu2004,
author = {Nezu, Iehisa and Asce, M and Azuma, Ryoukei},
doi = {10.1061/(ASCE)0733-9429(2004)130},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nezu, Asce, Azuma - Turbulence Characteristics and Interaction between Particles and Fluid in Particle-Laden Open Channel Flows - 2004.pdf:pdf},
number = {October},
title = {{Turbulence Characteristics and Interaction between Particles and Fluid in Particle-Laden Open Channel Flows}},
year = {2004}
}
@article{Andersson2011,
author = {Andersson, Magnus and Czerwinski, Fabian and Oddershede, Lene B.},
doi = {10.1088/2040-8978/13/4/044020},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson, Czerwinski, Oddershede - Optimizing active and passive calibration of optical tweezers - 2011.pdf:pdf},
issn = {2040-8978},
journal = {Journal of Optics},
keywords = {active calibration,allan variance,article are in colour,drift,laser,noise,only in the electronic,optical tweezers,passive calibration,power,some figures in this,spectrum,version},
month = {apr},
number = {4},
pages = {044020},
title = {{Optimizing active and passive calibration of optical tweezers}},
url = {http://stacks.iop.org/2040-8986/13/i=4/a=044020?key=crossref.9524dc48dfe1e0de2811f4536d4f75d2},
volume = {13},
year = {2011}
}
@article{Qjlqhhulqj2012,
author = {Qjlqhhulqj, Rpsxwhu and Qdgrox, Hsduwphqw and Yduldqwv, P D Q and Ehhq, Kdyh and Lqfoxglqj, Sursrvhg},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Qjlqhhulqj et al. - FDNLQODU FLKDQW ` {\#} DQDGROX HGX WU - 2012.pdf:pdf},
isbn = {9781467300469},
pages = {1309--1312},
title = {{{\^{}} FDNLQODU FLKDQW ` {\#} DQDGROX HGX WU}},
volume = {5},
year = {2012}
}
@article{Tolic-Nørrelykke2006,
abstract = {The TATA-box binding protein (TBP) is required by all three eukaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called "TATA-boxes" in the DNA. We present results from the study of individual Saccharomyces cerevisiae TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we observed the Brownian motion of beads tethered by short surface-bound DNA. When TBP binds to and bends the DNA, the conformation of the DNA changes and the amplitude of Brownian motion of the tethered bead is reduced compared to that of unbent DNA. We detected individual binding and dissociation events and derived kinetic parameters for the process. Dissociation was induced by increasing the salt concentration or by directly pulling on the tethered bead using optical tweezers. In addition to the well-defined free and bound classes of Brownian motion, we observed another two classes of motion. These extra classes were identified with intermediate states on a three-step, linear-binding pathway. Biological implications of the intermediate states are discussed.},
author = {Tolić-N{\o}rrelykke, Simon F. and Rasmussen, Mette B. and Pavone, Francesco S. and Berg-S{\o}rensen, Kirstine and Oddershede, Lene B.},
doi = {10.1529/biophysj.105.074856},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tolić-N{\o}rrelykke et al. - Stepwise bending of DNA by a single TATA-box binding protein. - 2006.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Binding Sites,Chemical,Computer Simulation,DNA,DNA: chemistry,DNA: ultrastructure,Elasticity,Mechanical,Models,Nucleic Acid Conformation,Protein Binding,Stress,TATA-Box Binding Protein,TATA-Box Binding Protein: chemistry,TATA-Box Binding Protein: ultrastructure},
month = {may},
number = {10},
pages = {3694--703},
pmid = {16500964},
title = {{Stepwise bending of DNA by a single TATA-box binding protein.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1440750{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {90},
year = {2006}
}
@article{Snyder2005,
author = {Snyder, Jennifer A and Haugen, Brian J and Lockatell, C Virginia and Maroncle, Nathalie and Hagan, Erin C and Johnson, David E and Welch, Rodney A and Mobley, Harry L T},
doi = {10.1128/IAI.73.11.7588},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Snyder et al. - Coordinate Expression of Fimbriae in Uropathogenic Escherichia coli Coordinate Expression of Fimbriae in Uropathogenic E.pdf:pdf},
title = {{Coordinate Expression of Fimbriae in Uropathogenic Escherichia coli Coordinate Expression of Fimbriae in Uropathogenic Escherichia coli}},
year = {2005}
}
@article{Huttner2001,
annote = {        From Duplicate 1 (                   Implications of lipid microdomains for membrane curvature , budding and fission Commentary                 - Huttner, Wieland B; Zimmerberg, Joshua )
                
        
        
      },
author = {Huttner, Wieland B and Zimmerberg, Joshua},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Huttner, Zimmerberg - Implications of lipid microdomains for membrane curvature , budding and fission Commentary - 2001.pdf:pdf},
journal = {Human Molecular Genetics},
pages = {478--484},
title = {{Implications of lipid microdomains for membrane curvature , budding and fission Commentary}},
year = {2001}
}
@article{Dreyer2006,
abstract = {In a nanoscale system out of thermodynamic equilibrium, it is important to account for thermal fluctuations. Typically, the thermal noise contributes fluctuations, e.g., of distances that are substantial in comparison to the size of the system and typical distances measured. If the thermal fluctuations are ignored, misinterpretation of measured quantities such as interaction forces, potentials, and constants may result. Here, we consider a particle moving in a time-dependent landscape, as, e.g., in an optical tweezers or atomic force nanoscopic measurement. Based on the Kramers equation [H. A. Kramers, Physica 7, 284 (1940)], we propose an approximate but quantitative way of dealing with such an out-of-equilibrium system. The limits of this approximate description of the escape process are determined through optical tweezers experiments and comparison to simulations. Also, this serves as a recipe for how to use the proposed method to obtain knowledge about the underlying energy landscape from a set of experimental measurements. Finally, we perform estimates of the error made if thermal fluctuations are ignored.},
author = {Dreyer, Jakob Kisbye and Berg-S{\o}rensen, Kirstine and Oddershede, Lene B.},
journal = {Phys Rev E},
number = {5 Pt 1},
pages = {51110},
title = {{Quantitative approach to small-scale nonequilibrium systems}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=16802921 http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal{\&}id=PLEEE8000073000005051110000001{\&}idtype=cvips{\&}gifs=yes},
volume = {73},
year = {2006}
}
@article{Yakovenko2015,
author = {Yakovenko, Olga and Tchesnokova, Veronika and Sokurenko, Evgeni V. and Thomas, Wendy E},
doi = {10.1073/pnas.1503160112},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yakovenko et al. - Inactive conformation enhances binding function in physiological conditions - 2015.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {32},
pages = {9884--9889},
title = {{Inactive conformation enhances binding function in physiological conditions}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1503160112},
volume = {112},
year = {2015}
}
@article{Rief2002,
abstract = {Many processes in the body are effected and regulated by highly specialized protein molecules: These molecules certainly deserve the name "biochemical nanomachines". Recent progress in single-molecule experiments and corresponding simulations with supercomputers enable us to watch these "nanomachines" at work, revealing a host of astounding mechanisms. Examples are the fine-tuned movements of the binding pocket of a receptor protein locking into its ligand molecule and the forced unfolding of titin, which acts as a molecular shock absorber to protect muscle cells. At present, we are not capable of designing such high precision machines, but we are beginning to understand their working principles and to simulate and predict their function.},
author = {Rief, Matthias and Grubm{\"{u}}ller, Helmut},
doi = {10.1002/1439-7641(20020315)3:3<255::AID-CPHC255>3.0.CO;2-M},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rief, Grubm{\"{u}}ller - Force spectroscopy of single biomolecules. - 2002.pdf:pdf},
issn = {1439-4235},
journal = {Chemphyschem : a European journal of chemical physics and physical chemistry},
keywords = {Ligands,Microscopy, Atomic Force,Polysaccharides,Polysaccharides: chemistry,Protein Denaturation,Proteins,Proteins: chemistry},
month = {mar},
number = {3},
pages = {255--61},
pmid = {12503171},
title = {{Force spectroscopy of single biomolecules.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12503171},
volume = {3},
year = {2002}
}
@article{Mantis2011,
abstract = {Secretory IgA (SIgA) serves as the first line of defense in protecting the intestinal epithelium from enteric toxins and pathogenic microorganisms. Through a process known as immune exclusion, SIgA promotes the clearance of antigens and pathogenic microorganisms from the intestinal lumen by blocking their access to epithelial receptors, entrapping them in mucus, and facilitating their removal by peristaltic and mucociliary activities. In addition, SIgA functions in mucosal immunity and intestinal homeostasis through mechanisms that have only recently been revealed. In just the past several years, SIgA has been identified as having the capacity to directly quench bacterial virulence factors, influence composition of the intestinal microbiota by Fab-dependent and Fab-independent mechanisms, promote retro-transport of antigens across the intestinal epithelium to dendritic cell subsets in gut-associated lymphoid tissue, and, finally, to downregulate proinflammatory responses normally associated with the uptake of highly pathogenic bacteria and potentially allergenic antigens. This review summarizes the intrinsic biological activities now associated with SIgA and their relationships with immunity and intestinal homeostasis.},
author = {Mantis, N J and Rol, N and Corth{\'{e}}sy, B},
doi = {10.1038/mi.2011.41},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mantis, Rol, Corth{\'{e}}sy - Secretory IgA's complex roles in immunity and mucosal homeostasis in the gut. - 2011.pdf:pdf},
issn = {1935-3456},
journal = {Mucosal immunology},
keywords = {Animals,Antigen Presentation,Antigen-Antibody Complex,Antigen-Antibody Complex: immunology,Dendritic Cells,Dendritic Cells: immunology,Homeostasis,Humans,Immunity, Mucosal,Immunoglobulin A, Secretory,Immunoglobulin A, Secretory: immunology,Immunomodulation,Intestinal Mucosa,Intestinal Mucosa: immunology,Metagenome,Mucociliary Clearance},
month = {nov},
number = {6},
pages = {603--11},
pmid = {21975936},
title = {{Secretory IgA's complex roles in immunity and mucosal homeostasis in the gut.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3774538{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {4},
year = {2011}
}
@article{Schedin2006,
author = {Schedin, Staffan},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schedin - Digital Holographic Interferometry - 2006.pdf:pdf},
journal = {Journal of Holography and Speckle},
pages = {1--17},
title = {{Digital Holographic Interferometry}},
volume = {3},
year = {2006}
}
@article{Wong2008,
abstract = {At many promoters, transcription is regulated by simultaneous binding of a protein to multiple sites on DNA, but the structures and dynamics of such transcription factor-mediated DNA loops are poorly understood. We directly examined in vitro loop formation mediated by Escherichia coli lactose repressor using single-molecule structural and kinetics methods. Small ( approximately 150 bp) loops form quickly and stably, even with out-of-phase operator spacings. Unexpectedly, repeated spontaneous transitions between two distinct loop structures were observed in individual protein-DNA complexes. The results imply a dynamic equilibrium between a novel loop structure with the repressor in its crystallographic "V" conformation and a second structure with a more extended linear repressor conformation that substantially lessens the DNA bending strain. The ability to switch between different loop structures may help to explain how robust transcription regulation is maintained even though the mechanical work required to form a loop may change substantially with metabolic conditions.},
author = {Wong, Oi Kwan and Guthold, Martin and Erie, Dorothy a and Gelles, Jeff},
doi = {10.1371/journal.pbio.0060232},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wong et al. - Interconvertible lac repressor-DNA loops revealed by single-molecule experiments. - 2008.pdf:pdf},
issn = {1545-7885},
journal = {PLoS biology},
keywords = {DNA,DNA: chemistry,DNA: metabolism,DNA: ultrastructure,Gene Expression Regulation, Bacterial,Lac Operon,Macromolecular Substances,Macromolecular Substances: chemistry,Macromolecular Substances: metabolism,Mathematics,Microscopy, Atomic Force,Models, Molecular,Nucleic Acid Conformation,Operator Regions, Genetic,Promoter Regions, Genetic,Protein Structure, Quaternary,Repressor Proteins,Repressor Proteins: chemistry,Repressor Proteins: genetics,Repressor Proteins: metabolism,Repressor Proteins: ultrastructure,Transcription, Genetic},
month = {sep},
number = {9},
pages = {e232},
pmid = {18828671},
title = {{Interconvertible lac repressor-DNA loops revealed by single-molecule experiments.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2553838{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {6},
year = {2008}
}
@article{Caitriona2005,
abstract = {Raman imaging can yield spatially resolved biochemical information from living cells. To date there have been no Raman images published of cells in suspension because of the problem of immobilising them suitably to acquire space-resolved spectra. In this paper in order to overcome this problem the use of holographic optical tweezers is proposed and implemented, and data is shown for spatially resolved Raman spectroscopy of a live cell in suspension.},
author = {Caitriona, M and Volpe, Giovanni and Singh, Gajendra P and Soler, Marta and Petrov, Dmitri},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Caitriona et al. - Raman imaging of ﬂoating cells.pdf - 2005.pdf:pdf},
journal = {Optics express},
keywords = {Raman,cells,optical tweezers},
mendeley-tags = {Raman,cells,optical tweezers},
number = {16},
title = {{Raman imaging of ﬂoating cells.pdf}},
volume = {12},
year = {2005}
}
@article{Townes2012,
author = {Townes, C.L. and Ali, a. and Lanz, M. and Gross, N. and Robson, C.N. and Hall, J. and Pickard, R.S.},
doi = {10.1016/S1569-9056(12)60040-2},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Townes et al. - 41 The protective antimicrobial effect of raised prostate specific antigen levels during male urinary tract infection -.pdf:pdf},
issn = {15699056},
journal = {European Urology Supplements},
month = {feb},
number = {1},
pages = {e41--e41a},
title = {{41 The protective antimicrobial effect of raised prostate specific antigen levels during male urinary tract infection}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1569905612600402},
volume = {11},
year = {2012}
}
@article{Gaastra2002,
abstract = {Colonization factor antigens (CFAs) of human enterotoxigenic Escherichia coli can be divided in groups based on the N-terminal amino acid sequence of their major subunit protein. One of the groups that has been distinguished in this way, is the CFA/I group of fimbriae. The sequence of the fimbrial subunit genes in the operons encoding the antigens CS4, CS14 and CS17, all members of this group, was determined. A duplication of the fimbrial subunit gene (csuA) was found in the CS14 operon, both genes encoding very similar proteins. Purified CS14 fimbriae consist of two proteins with different molecular masses (15.5 and 17.0 kDa) but identical N-terminal amino acid sequences, which strongly suggests that both csuA genes are transcribed. A phylogenetic tree derived from the amino acid sequences of the CFA/I, CS1, CS2, CS4, CS14, CS17 and CS19 subunit proteins shows that CS1, CS17 and CS19 belong to the same subgroup. CFA/I, CS4 and CS14 belong to a second subgroup, while CS2 is distinct within the CFA/I group of fimbriae. The genetic similarity between CS1, CS17 and CS19 is reflected in the substantial immunological cross-reactivity observed, both between their protein subunits and intact fimbriae.},
author = {Gaastra, Wim and Sommerfelt, Halvor and van Dijk, Linda and Kusters, Johannes G and Svennerholm, Ann-Mari and Grewal, Harleen M S},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gaastra et al. - Antigenic variation within the subunit protein of members of the colonization factor antigen I group of fimbrial protei.pdf:pdf},
issn = {14384221},
journal = {International journal of medical microbiology : IJMM},
keywords = {31 30 253 4755,31 30 254 0874,3584 cl utrecht,and,coli,colonization factors,corresponding author,department of bacteriology,division of infectious diseases,dr,e-mail,fax,gaastra,human enterotoxigenic e,immunology,nl,phone,prof,the netherlands,utrecht university,uu,vet,w,yalelaan 1},
pages = {43--50},
pmid = {12139428},
title = {{Antigenic variation within the subunit protein of members of the colonization factor antigen I group of fimbrial proteins in human enterotoxigenic Escherichia coli.}},
volume = {292},
year = {2002}
}
@article{Thomas2008b,
abstract = {Receptor-ligand bonds strengthened by tensile mechanical force are referred to as catch bonds. This review examines experimental data and biophysical theory to analyze why mechanical force prolongs the lifetime of these bonds rather than shortens the lifetime by pulling the ligand out of the binding pocket. Although many mathematical models can explain catch bonds, experiments using structural variants have been more helpful in determining how catch bonds work. The underlying mechanism has been worked out so far only for the bacterial adhesive protein FimH. This protein forms catch bonds because it is allosterically activated when mechanical force pulls an inhibitory domain away from the ligand-binding domain. Other catch bond-forming proteins, including blood cell adhesion proteins called selectins and the motor protein myosin, show evidence of allosteric regulation between two domains, but it remains unclear if this is related to their catch bond behavior.},
author = {Thomas, Wendy E and Vogel, Viola and Sokurenko, Evgeni V},
doi = {10.1146/annurev.biophys.37.032807.125804},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Thomas, Vogel, Sokurenko - Biophysics of catch bonds. - 2008.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Thomas, Vogel, Sokurenko - Biophysics of catch bonds. - 2008.pdf:pdf},
issn = {1936-122X},
journal = {Annual review of biophysics},
keywords = {Binding Sites,Biological,Biophysics: methods,Cell Surface,Cell Surface: chemistry,Cell Surface: physiology,Chemical,Computer Simulation,Ligands,Models,Protein Binding,Receptors,adhesion,allostery,biophysics,force,molecular,molecular biomechanics,protein regulation,shear stress},
month = {jan},
pages = {399--416},
pmid = {18573088},
title = {{Biophysics of catch bonds.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18573088},
volume = {37},
year = {2008}
}
@article{Janshoff2000,
abstract = {How do molecules interact with each other? What happens if a neurotransmitter binds to a ligand-operated ion channel? How do antibodies recognize their antigens? Molecular recognition events play a pivotal role in nature: in enzymatic catalysis and during the replication and transcription of the genome; it is also important for the cohesion of cellular structures and in numerous metabolic reactions that molecules interact with each other in a specific manner. Conventional methods such as calorimetry provide very precise values of binding enthalpies; these are, however, average values obtained from a large ensemble of molecules without knowledge of the dynamics of the molecular recognition event. Which forces occur when a single molecular couple meets and forms a bond? Since the development of the scanning force microscope and force spectroscopy a couple of years ago, tools have now become available for measuring the forces between interfaces with high precision-starting from colloidal forces to the interaction of single molecules. The manipulation of individual molecules using force spectroscopy is also possible. In this way, the mechanical properties on a molecular scale are measurable. The study of single molecules is not an exclusive domain of force spectroscopy; it can also be performed with a surface force apparatus, laser tweezers, or the micropipette technique. Regardless of these techniques, force spectroscopy has been proven as an extraordinary versatile tool. The intention of this review article is to present a critical evaluation of the actual development of static force spectroscopy. The article mainly focuses on experiments dealing with inter- and intramolecular forces-starting with "simple" electrostatic forces, then ligand-receptor systems, and finally the stretching of individual molecules.},
author = {Janshoff, a and Neitzert, M and Oberd{\"{o}}rfer, Y and Fuchs, H},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Janshoff et al. - Force Spectroscopy of Molecular Systems-Single Molecule Spectroscopy of Polymers and Biomolecules. - 2000.pdf:pdf},
issn = {1521-3773},
journal = {Angewandte Chemie (International ed. in English)},
month = {sep},
number = {18},
pages = {3212--3237},
pmid = {11028062},
title = {{Force Spectroscopy of Molecular Systems-Single Molecule Spectroscopy of Polymers and Biomolecules.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11028062},
volume = {39},
year = {2000}
}
@article{Wizemann1999,
abstract = {Blocking the primary stages of infection, namely bacterial attachment to host cell receptors and colonization of the mucosal surface, may be the most effective strategy to prevent bacterial infections. Bacterial attachment usually involves an interaction between a bacterial surface protein called an adhesin and the host cell receptor. Recent preclinical vaccine studies with the FimH adhesin (derived from uropathogenic Escherichia coli) have confirmed that antibodies elicited against an adhesin can impede colonization, block infection, and prevent disease. The studies indicate that prophylactic vaccination with adhesins can block bacterial infections. With recent advances in the identification, characterization, and isolation of other adhesins, similar approaches are being explored to prevent infections, from otitis media and dental caries to pneumonia and sepsis.},
author = {Wizemann, Theresa M. and Adamou, John E. and Langermann, Solomon},
doi = {10.3201/eid0503.990310},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wizemann, Adamou, Langermann - Adhesins as targets for vaccine development - 1999.pdf:pdf},
isbn = {1080-6040},
issn = {10806040},
journal = {Emerging Infectious Diseases},
number = {3},
pages = {395--403},
pmid = {10341176},
title = {{Adhesins as targets for vaccine development}},
volume = {5},
year = {1999}
}
@article{Francius2011,
abstract = {The physicochemical properties and dynamics of bacterial envelope, play a major role in bacterial activity. In this study, the morphological, nanomechanical and electrohydrodynamic properties of Escherichia coli K-12 mutant cells were thoroughly investigated as a function of bulk medium ionic strength using atomic force microscopy (AFM) and electrokinetics (electrophoresis). Bacteria were differing according to genetic alterations controlling the production of different surface appendages (short and rigid Ag43 adhesins, longer and more flexible type 1 fimbriae and F pilus). From the analysis of the spatially resolved force curves, it is shown that cells elasticity and turgor pressure are not only depending on bulk salt concentration but also on the presence/absence and nature of surface appendage. In 1 mM KNO(3), cells without appendages or cells surrounded by Ag43 exhibit large Young moduli and turgor pressures (∼700-900 kPa and ∼100-300 kPa respectively). Under similar ionic strength condition, a dramatic ∼50{\%} to ∼70{\%} decrease of these nanomechanical parameters was evidenced for cells with appendages. Qualitatively, such dependence of nanomechanical behavior on surface organization remains when increasing medium salt content to 100 mM, even though, quantitatively, differences are marked to a much smaller extent. Additionally, for a given surface appendage, the magnitude of the nanomechanical parameters decreases significantly when increasing bulk salt concentration. This effect is ascribed to a bacterial exoosmotic water loss resulting in a combined contraction of bacterial cytoplasm together with an electrostatically-driven shrinkage of the surface appendages. The former process is demonstrated upon AFM analysis, while the latter, inaccessible upon AFM imaging, is inferred from electrophoretic data interpreted according to advanced soft particle electrokinetic theory. Altogether, AFM and electrokinetic results clearly demonstrate the intimate relationship between structure/flexibility and charge of bacterial envelope and propensity of bacterium and surface appendages to contract under hypertonic conditions.},
author = {Francius, Gr{\'{e}}gory and Polyakov, Pavel and Merlin, Jenny and Abe, Yumiko and Ghigo, Jean-Marc and Merlin, Christophe and Beloin, Christophe and Duval, J{\'{e}}r{\^{o}}me F L},
doi = {10.1371/journal.pone.0020066},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Francius et al. - Bacterial surface appendages strongly impact nanomechanical and electrokinetic properties of Escherichia coli cells su.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
keywords = {Biomechanical Phenomena,Electrophoresis,Escherichia coli,Escherichia coli: physiology,Microscopy, Atomic Force,Osmosis,Osmosis: physiology},
month = {jan},
number = {5},
pages = {e20066},
pmid = {21655293},
title = {{Bacterial surface appendages strongly impact nanomechanical and electrokinetic properties of Escherichia coli cells subjected to osmotic stress.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3105017{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {6},
year = {2011}
}
@article{Eckmann2015a,
author = {Eckmann, Lars and Stappenbeck, Thaddeus S. S.},
doi = {10.1016/j.chom.2015.05.001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Eckmann, Stappenbeck - IgG “Detoxes” the Intestinal Mucosa - 2015.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Eckmann, Stappenbeck - IgG “Detoxes” the Intestinal Mucosa - 2015(2).pdf:pdf},
issn = {19313128},
journal = {Cell Host {\&} Microbe},
keywords = {IgG,antibodies},
mendeley-tags = {IgG,antibodies},
number = {5},
pages = {538--539},
publisher = {Elsevier Inc.},
title = {{IgG “Detoxes” the Intestinal Mucosa}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1931312815001754},
volume = {17},
year = {2015}
}
@article{Ling2010,
author = {Ling, Lin and Zhou, Fei and Huang, Lu and Li, Zhi-Yuan},
doi = {10.1063/1.3484045},
issn = {00218979},
journal = {Journal of Applied Physics},
number = {7},
pages = {073110},
title = {{Optical forces on arbitrary shaped particles in optical tweezers}},
volume = {108},
year = {2010}
}
@article{Sulchek2005,
abstract = {We used atomic force microscopy to measure the binding forces between Mucin1 (MUC1) peptide and a single-chain variable fragment (scFv) antibody selected from a scFv library screened against MUC1. This binding interaction is central to the design of molecules used for targeted delivery of radioimmunotherapeutic agents for prostate and breast cancer treatment. Our experiments separated the specific binding interaction from nonspecific interactions by tethering the antibody and MUC1 molecules to the atomic force microscope tip and sample surface with flexible polymer spacers. Rupture force magnitude and elastic characteristics of the spacers allowed identification of the rupture events corresponding to different numbers of interacting proteins. We used dynamic force spectroscopy to estimate the intermolecular potential widths and equivalent thermodynamic off rates for monovalent, bivalent, and trivalent interactions. Measured interaction potential parameters agree with the results of molecular docking simulation. Our results demonstrate that an increase of the interaction valency leads to a precipitous decline in the dissociation rate. Binding forces measured for monovalent and multivalent interactions match the predictions of a Markovian model for the strength of multiple uncorrelated bonds in a parallel configuration. Our approach is promising for comparison of the specific effects of molecular modifications as well as for determination of the best configuration of antibody-based multivalent targeting agents.},
author = {Sulchek, Todd a and Friddle, Raymond W and Langry, Kevin and Lau, Edmond Y and Albrecht, Huguette and Ratto, Timothy V and DeNardo, Sally J and Colvin, Michael E and Noy, Aleksandr},
doi = {10.1073/pnas.0505208102},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sulchek et al. - Dynamic force spectroscopy of parallel individual Mucin1-antibody bonds. - 2005.pdf:pdf},
isbn = {0027-8424},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {46},
pages = {16638--16643},
pmid = {16269547},
title = {{Dynamic force spectroscopy of parallel individual Mucin1-antibody bonds.}},
volume = {102},
year = {2005}
}
@article{Fallman1997,
abstract = {A design for complete beam steering (in three dimensions) of one or two optical tweezers traps is presented. The two most important requirements for efficient and stable movement of an optical trap are identified. A detailed recipe for the construction of a movable optical tweezers trap that fulfills these requirements is given (exemplified with an inverted microscope). The system has been found to allow for precise and free movements of both traps in all three dimensions in a dual-trap optical tweezers configuration and to be robust and reliable, as well as forgiving of small misalignments in the optical system.},
author = {Fallman, Erik and Axner, Ove},
doi = {10.1364/AO.36.002107},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Fallman, Axner - Design for fully steerable dual-trap optical tweezers. - 1997.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
keywords = {beam steering,dual trap,micromanipulation,optical tweezers},
number = {10},
pages = {2107--2113},
pmid = {18253180},
title = {{Design for fully steerable dual-trap optical tweezers.}},
volume = {36},
year = {1997}
}
@article{LeTrong2010,
abstract = {The Escherichia coli fimbrial adhesive protein, FimH, mediates shear-dependent binding to mannosylated surfaces via force-enhanced allosteric catch bonds, but the underlying structural mechanism was previously unknown. Here we present the crystal structure of FimH incorporated into the multiprotein fimbrial tip, where the anchoring (pilin) domain of FimH interacts with the mannose-binding (lectin) domain and causes a twist in the beta sandwich fold of the latter. This loosens the mannose-binding pocket on the opposite end of the lectin domain, resulting in an inactive low-affinity state of the adhesin. The autoinhibition effect of the pilin domain is removed by application of tensile force across the bond, which separates the domains and causes the lectin domain to untwist and clamp tightly around the ligand like a finger-trap toy. Thus, beta sandwich domains, which are common in multidomain proteins exposed to tensile force in vivo, can undergo drastic allosteric changes and be subjected to mechanical regulation.},
annote = {From Duplicate 1 ( Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like beta sheet twisting. - Le Trong, Isolde; Aprikian, Pavel; Kidd, Brian a; Forero-Shelton, Manu; Tchesnokova, Veronika; Rajagopal, Ponni; Rodriguez, Victoria; Interlandi, Gianluca; Klevit, Rachel; Vogel, Viola; Stenkamp, Ronald E; Sokurenko, Evgeni V; Thomas, Wendy E )
},
author = {{Le Trong}, Isolde and Aprikian, Pavel and Kidd, Brian a and Forero-Shelton, Manu and Tchesnokova, Veronika and Rajagopal, Ponni and Rodriguez, Victoria and Interlandi, Gianluca and Klevit, Rachel and Vogel, Viola and Stenkamp, Ronald E and Sokurenko, Evgeni V and Thomas, Wendy E},
doi = {10.1016/j.cell.2010.03.038},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Le Trong et al. - Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like beta sheet twisting. - 2010.pdf:pdf},
issn = {1097-4172},
journal = {Cell},
keywords = {Adhesins,Allosteric Regulation,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Models,Molecular,Protein Structure,Secondary,Tertiary},
month = {may},
number = {4},
pages = {645--55},
pmid = {20478255},
publisher = {Elsevier Ltd},
title = {{Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like beta sheet twisting.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2905812{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {141},
year = {2010}
}
@article{Proft2009,
abstract = {Many bacterial species possess long filamentous structures known as pili or fimbriae extending from their surfaces. Despite the diversity in pilus structure and biogenesis, pili in Gram-negative bacteria are typically formed by non-covalent homopolymerization of major pilus subunit proteins (pilins), which generates the pilus shaft. Additional pilins may be added to the fiber and often function as host cell adhesins. Some pili are also involved in biofilm formation, phage transduction, DNA uptake and a special form of bacterial cell movement, known as 'twitching motility'. In contrast, the more recently discovered pili in Gram-positive bacteria are formed by covalent polymerization of pilin subunits in a process that requires a dedicated sortase enzyme. Minor pilins are added to the fiber and play a major role in host cell colonization.This review gives an overview of the structure, assembly and function of the best-characterized pili of both Gram-negative and Gram-positive bacteria.},
author = {Proft, T and Baker, E N},
doi = {10.1007/s00018-008-8477-4},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Proft, Baker - Pili in Gram-negative and Gram-positive bacteria - structure, assembly and their role in disease. - 2009.pdf:pdf},
isbn = {0001800884},
issn = {1420-9071},
journal = {Cellular and molecular life sciences : CMLS},
keywords = {Animals,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial Infections,Bacterial Infections: physiopathology,Bacterial Vaccines,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: genetics,Fimbriae Proteins: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: metabolism,Fimbriae, Bacterial: ultrastructure,Gram-Negative Bacteria,Gram-Negative Bacteria: metabolism,Gram-Negative Bacteria: pathogenicity,Gram-Negative Bacteria: ultrastructure,Gram-Positive Bacteria,Gram-Positive Bacteria: metabolism,Gram-Positive Bacteria: pathogenicity,Gram-Positive Bacteria: ultrastructure,Humans,Models, Molecular,Molecular Chaperones,Molecular Chaperones: metabolism,Protein Conformation},
month = {feb},
number = {4},
pages = {613--35},
pmid = {18953686},
title = {{Pili in Gram-negative and Gram-positive bacteria - structure, assembly and their role in disease.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18953686},
volume = {66},
year = {2009}
}
@article{DeRee1987,
abstract = {Uropathogenic Escherichia coli strains isolated from four patients with pyelonephritis were characterized by their O:K serotype, hemolysin production, mannose-resistant hemagglutination, and the serotype of the P fimbriae. These P fimbriae were serotyped with specific monoclonal antibodies. Serum samples from the patients were analyzed for the presence of specific antibodies to the P fimbriae. In all cases antifimbrial antibodies were found, strongly suggesting that these P fimbriae are expressed in vivo. However, the antibodies in the patient sera were not able to inhibit the mannose-resistant hemagglutination. This finding suggests that these antibodies react with the fimbrial components and not with the minor components which are responsible for adhesion.},
author = {de Ree, J M and van den Bosch, J F},
file = {:E$\backslash$:/Mina Dokument/Mendeley/de Ree, van den Bosch - Serological response to the P fimbriae of uropathogenic Escherichia coli in pyelonephritis. - 1987.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
keywords = {Antibodies, Bacterial,Antibodies, Bacterial: biosynthesis,Antibodies, Monoclonal,Antibodies, Monoclonal: diagnostic use,Bacterial Adhesion,Cross Reactions,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli: immunology,Female,Fimbriae, Bacterial,Fimbriae, Bacterial: immunology,Hemolysin Proteins,Hemolysin Proteins: biosynthesis,Humans,Pyelonephritis,Pyelonephritis: immunology,Pyelonephritis: microbiology,Serotyping},
month = {sep},
number = {9},
pages = {2204--7},
pmid = {2887515},
title = {{Serological response to the P fimbriae of uropathogenic Escherichia coli in pyelonephritis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=260679{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {55},
year = {1987}
}
@article{Sandin2004,
abstract = {In contrast to averaging methods of determining structure, such as X-ray diffraction, NMR, and single-particle tomography, cryo-electron tomography allows three-dimensional imaging of an individual object in solution. The method has previously been used to study cells and very large macromolecules. We have used cryo-electron tomography to analyze a monoclonal IgG, with a molecular weight of only 150 kDa. Tomograms reveal y-shaped IgG molecules with three protruding subunits. Docking X-ray structures enabled us to recognize the three subunits as two ellipsoidal Fab arms and a heart-shaped Fc stem. Each subunit has a similar structure in the tomograms and in the X-ray map. Notably, the positions of the Fab arms relative to the Fc stem differed greatly from one molecule to another. The large flexibility of IgG in solution is most likely of functional significance in antigen recognition. This distribution of individual structures provides a qualitative insight into the system dynamics.},
author = {Sandin, Sara and Ofverstedt, Lars-G{\"{o}}ran and Wikstr{\"{o}}m, Ann-Charlotte and Wrange, Orjan and Skoglund, Ulf},
doi = {10.1016/j.str.2004.02.011},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sandin et al. - Structure and flexibility of individual immunoglobulin G molecules in solution. - 2004.pdf:pdf},
issn = {0969-2126},
journal = {Structure (London, England : 1993)},
keywords = {Animals,Cryoelectron Microscopy,Crystallography,Immunoglobulin G,Immunoglobulin G: chemistry,Mice,Models,Molecular,X-Ray,antibodies},
mendeley-tags = {antibodies},
month = {mar},
number = {3},
pages = {409--15},
pmid = {15016357},
title = {{Structure and flexibility of individual immunoglobulin G molecules in solution.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15016357},
volume = {12},
year = {2004}
}
@article{Isidean2011,
abstract = {INTRODUCTION: Vaccine development for enterotoxigenic Escherichia coli (ETEC) is dependent on in-depth understanding of toxin and colonization factor (CF) distribution. We sought to describe ETEC epidemiology across regions and populations, focusing on CF and toxin prevalence. METHODS: We conducted a systematic review of the published literature, including studies reporting data on ETEC CF and toxin distributions among those with ETEC infection. Point estimates and confidence intervals were calculated using random effects models. RESULTS: Data on 17,205 ETEC isolates were abstracted from 136 included studies. Approximately half of the studies (49{\%}) involved endemic populations, and an additional 17{\%} involved only travel populations. Globally, 60{\%} of isolates expressed LT either alone (27{\%}) or in combination with ST (33{\%}). CFA/I-expressing strains were common in all regions (17{\%}), as were ETEC expressing CFA/II (9{\%}) and IV (18{\%}). Marked variation in toxins and CFs across regions and populations was observed. DISCUSSION/CONCLUSIONS: These results demonstrate the relative importance of specific CFs in achieving target product profiles for a future ETEC vaccine. However, heterogeneity across time, population, and region, confounded by variability in CF and toxin detection methodologies, obfuscates rational estimates for valency requirements.},
author = {Isidean, S D and Riddle, M S and Savarino, Stephen J and Porter, C K},
doi = {10.1016/j.vaccine.2011.06.084},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Isidean et al. - A systematic review of ETEC epidemiology focusing on colonization factor and toxin expression. - 2011.pdf:pdf},
issn = {1873-2518},
journal = {Vaccine},
keywords = {Bacterial Toxins,Bacterial Toxins: biosynthesis,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: classification,Enterotoxigenic Escherichia coli: immunology,Enterotoxigenic Escherichia coli: isolation {\&} puri,Enterotoxins,Enterotoxins: biosynthesis,Escherichia coli Infections,Escherichia coli Infections: epidemiology,Escherichia coli Proteins,Escherichia coli Proteins: biosynthesis,Escherichia coli Vaccines,Fimbriae Proteins,Fimbriae Proteins: biosynthesis,Humans},
month = {aug},
number = {37},
pages = {6167--78},
pmid = {21723899},
publisher = {Elsevier Ltd},
title = {{A systematic review of ETEC epidemiology focusing on colonization factor and toxin expression.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21723899},
volume = {29},
year = {2011}
}
@article{Rao2009a,
author = {Rao, Satish and B{\'{a}}lint, {\v{S}}tefan and L{\o}vhaugen, P{\aa}l and Kreuzer, Mark and Petrov, Dmitri},
doi = {10.1103/PhysRevLett.102.087401},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rao et al. - Measurement of Mechanical Forces Acting on Optically Trapped Dielectric Spheres Induced by Surface-Enhanced Raman Scatterin.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {feb},
number = {8},
pages = {100--103},
title = {{Measurement of Mechanical Forces Acting on Optically Trapped Dielectric Spheres Induced by Surface-Enhanced Raman Scattering}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.102.087401},
volume = {102},
year = {2009}
}
@article{Uni1998,
author = {Uni, Melbourne},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Uni - Verb Tenses in Scientific Writing - 1998.pdf:pdf},
pages = {1998},
title = {{Verb Tenses in Scientific Writing}},
year = {1998}
}
@article{Laverty2014,
abstract = {Pseudomonas aeruginosa and Escherichia coli are the most prevalent $\backslash$nGram-negative biofilm forming medical device associated pathogens, particularly with respect to catheter associated urinary tract infections. In a similar manner to Gram-positive bacteria, Gram-negative biofilm formation is fundamentally determined by a series of steps outlined more fully in this review, namely adhesion, cellular aggregation, and the production of an extracellular polymeric matrix. More specifically this review will explore the biosynthesis and role of pili and flagella in Gram-negative adhesion and accumulation on surfaces in Pseudomonas aeruginosa and Escherichia coli. The process of biofilm maturation is compared and contrasted in both species, namely the production of the exopolysaccharides via the polysaccharide synthesis locus (Psl), pellicle Formation (Pel) and alginic acid synthesis in Pseudomonas aeruginosa, and UDP-4-amino-4-deoxy-L-arabinose and colonic acid synthesis in Escherichia coli. An emphasis is placed on the importance of the LuxR homologue sdiA; the luxS/autoinducer-II; an autoinducer-III/epinephrine/norepinephrine and indole mediated Quorum sensing systems in enabling Gram-negative bacteria to adapt to their environments. The majority of Gram-negative biofilms consist of polysaccharides of a simple sugar structure (either homo- or heteropolysaccharides) that provide an optimum environment for the survival and maturation of bacteria, allowing them to display increased resistance to antibiotics and predation.},
author = {Laverty, Garry and Gorman, Sean and Gilmore, Brendan},
doi = {10.3390/pathogens3030596},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Laverty, Gorman, Gilmore - Biomolecular Mechanisms of Pseudomonas aeruginosa and Escherichia coli Biofilm Formation - 2014.pdf:pdf},
issn = {2076-0817},
journal = {Pathogens},
keywords = {Gram-negative,bacteria,biofilm,biomaterial,infection,quorum sensing},
number = {3},
pages = {596--632},
pmid = {25438014},
title = {{Biomolecular Mechanisms of Pseudomonas aeruginosa and Escherichia coli Biofilm Formation}},
url = {http://www.mdpi.com/2076-0817/3/3/596/},
volume = {3},
year = {2014}
}
@article{Zakrisson2013,
annote = {From Duplicate 1 ( 









































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































The shaft of the type 1 fimbriae regulates an externalforce to match the FimH catch bond












































































































































































































































































































































































































































































































































































































































































































































































},
author = {Zakrisson, Johan and Wiklund, Krister and Axner, Ove and Andersson, Magnus},
doi = {10.1016/j.bpj.2013.03.059},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Zakrisson et al. - The shaft of the type 1 fimbriae regulates an externalforce to match the FimH catch bond - 2013.pdf:pdf},
issn = {00063495},
journal = {Biophysical journal},
month = {may},
number = {10},
pages = {2137--2148},
publisher = {Biophysical Society},
title = {{The shaft of the type 1 fimbriae regulates an externalforce to match the FimH catch bond}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349513004438},
volume = {104},
year = {2013}
}
@article{Leith1987,
author = {Leith, David},
doi = {10.1080/02786828708959128},
isbn = {0278682870895},
issn = {0278-6826},
journal = {Aerosol Science and Technology},
number = {2},
pages = {153--161},
title = {{Drag on Nonspherical Objects}},
volume = {6},
year = {1987}
}
@article{Ettema2009,
abstract = {We focus on the effect of cadence and work rate on energy expenditure and efficiency in cycling, and present arguments to support the contention that gross efficiency can be considered to be the most relevant expression of efficiency. A linear relationship between work rate and energy expenditure appears to be a rather consistent outcome among the various studies considered in this review, irrespective of subject performance level. This relationship is an example of the Fenn effect, described more than 80 years ago for muscle contraction. About 91{\%} of all variance in energy expenditure can be explained by work rate, with only about 10{\%} being explained by cadence. Gross efficiency is strongly dependent on work rate, mainly because of the diminishing effect of the (zero work-rate) base-line energy expenditure with increasing work rate. The finding that elite athletes have a higher gross efficiency than lower-level performers may largely be explained by this phenomenon. However, no firm conclusions can be drawn about the energetically optimal cadence for cycling because of the multiple factors associated with cadence that affect energy expenditure.},
author = {Ettema, Gertjan and Lor{\aa}s, H{\aa}vard Wuttudal},
doi = {10.1007/s00421-009-1008-7},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ettema, Lor{\aa}s - Efficiency in cycling a review. - 2009.pdf:pdf},
isbn = {0042100910087},
issn = {1439-6327},
journal = {European journal of applied physiology},
keywords = {Activity Cycles,Activity Cycles: physiology,Athletic Performance,Athletic Performance: physiology,Basal Metabolism,Basal Metabolism: physiology,Efficiency,Efficiency: physiology,Energy Metabolism,Energy Metabolism: physiology,Humans,Models, Biological,Task Performance and Analysis,Thermodynamics},
number = {1},
pages = {1--14},
pmid = {19229554},
title = {{Efficiency in cycling: a review.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19229554},
volume = {106},
year = {2009}
}
@article{Klinth2012a,
abstract = {Adhesion to host tissues is an initiating step in a majority of bacterial infections. In the case of Gram-negative bacteria this adhesion is often mediated by a specific interaction between an adhesin, positioned at the distal end of bacterial pili, and its receptor on the surface of the host tissue. Furthermore, the rod of the pilus, and particularly its biomechanical properties, is believed to be crucial for the ability of bacteria to withstand external forces caused by, for example, (in the case of urinary tract infections) urinary rinsing flows by redistributing the force to several pili. In this work, the adhesion properties of P-piliated E. coli and their dependence of pH have been investigated in a broad pH range by both the surface plasmon resonance technique and force measuring optical tweezers. We demonstrate that P piliated bacteria have an adhesion ability throughout the entire physiologically relevant pH range (pH 4.5 - 8). We also show that pH has a higher impact on the binding rate than on the binding stability or the biomechanical properties of pili; the binding rate was found to have a maximum around pH 5 while the binding stability was found to have a broader distribution over pH and be significant over the entire physiologically relevant pH range. Force measurements on a single organelle level show that the biomechanical properties of P pili are not significantly affected by pH.},
author = {Klinth, Jeanna E and Castelain, Micka{\"{e}}l and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1371/journal.pone.0038548},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Klinth et al. - The influence of pH on the specific adhesion of P piliated Escherichia coli. - 2012.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
month = {jan},
number = {6},
pages = {e38548},
pmid = {22679512},
title = {{The influence of pH on the specific adhesion of P piliated Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3367954{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {7},
year = {2012}
}
@article{Moisan2000,
author = {Moisan, Lionel and Morel, Jean-michel},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Moisan, Morel - Meaningful Alignments - 2000.pdf:pdf},
keywords = {alignment,gestalt,helmholtz,principle,probability},
number = {1},
pages = {7--23},
title = {{Meaningful Alignments}},
volume = {40},
year = {2000}
}
@article{Evans1997,
abstract = {In biology, molecular linkages at, within, and beneath cell interfaces arise mainly from weak noncovalent interactions. These bonds will fail under any level of pulling force if held for sufficient time. Thus, when tested with ultrasensitive force probes, we expect cohesive material strength and strength of adhesion at interfaces to be time- and loading rate-dependent properties. To examine what can be learned from measurements of bond strength, we have extended Kramers' theory for reaction kinetics in liquids to bond dissociation under force and tested the predictions by smart Monte Carlo (Brownian dynamics) simulations of bond rupture. By definition, bond strength is the force that produces the most frequent failure in repeated tests of breakage, i.e., the peak in the distribution of rupture forces. As verified by the simulations, theory shows that bond strength progresses through three dynamic regimes of loading rate. First, bond strength emerges at a critical rate of loading (> or = 0) at which spontaneous dissociation is just frequent enough to keep the distribution peak at zero force. In the slow-loading regime immediately above the critical rate, strength grows as a weak power of loading rate and reflects initial coupling of force to the bonding potential. At higher rates, there is crossover to a fast regime in which strength continues to increase as the logarithm of the loading rate over many decades independent of the type of attraction. Finally, at ultrafast loading rates approaching the domain of molecular dynamics simulations, the bonding potential is quickly overwhelmed by the rapidly increasing force, so that only naked frictional drag on the structure remains to retard separation. Hence, to expose the energy landscape that governs bond strength, molecular adhesion forces must be examined over an enormous span of time scales. However, a significant gap exists between the time domain of force measurements in the laboratory and the extremely fast scale of molecular motions. Using results from a simulation of biotin-avidin bonds (Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K. Schulten. 1997. Molecular dynamics study of unbinding of the avidin-biotin complex. Biophys. J., this issue), we describe how Brownian dynamics can help bridge the gap between molecular dynamics and probe tests.},
author = {Evans, Evan and Ritchie, K},
doi = {10.1016/S0006-3495(97)78802-7},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans, Ritchie - Dynamic strength of molecular adhesion bonds. - 1997.pdf:pdf},
isbn = {0006-3495},
issn = {00063495},
journal = {Biophysical journal},
number = {4},
pages = {1541--1555},
pmid = {9083660},
title = {{Dynamic strength of molecular adhesion bonds.}},
volume = {72},
year = {1997}
}
@article{Lane2007,
abstract = {P fimbria, a mannose-resistant adhesin of uropathogenic Escherichia coli (UPEC), has been shown to be associated with acute pyelonephritis. The pap gene cluster encodes the proteins required for P-fimbrial biogenesis, including papG, which encodes the tip adhesin. The three most studied PapG molecular variants, which are shown to bind distinct isoreceptors, are PapGI, -II, and -III. PapGII preferentially binds globoside, or GbO4, a glycolipid isoreceptor of the human kidney. Studies using different animal models of ascending urinary tract infection (UTI) have demonstrated a variable role for P fimbriae, and specifically PapGII-mediated adherence, in renal colonization. The disparities in the results obtained from those studies are likely to be attributed to the differences in animal models and UPEC strains utilized. One explanation that is discussed in detail is the contribution of multiple fimbriae of UPEC that potentially mediate adherence to the mammalian kidney. Overall, P fimbriae appear to play some role in mediating adherence to uroepithelial cells in vivo and establishing an inflammatory response during renal colonization, thus contributing to kidney damage during acute pyelonephritis. To verify that P fimbriae contribute to the pathogenesis of UPEC during ascending UTI (and in particular acute pyelonephritis), future studies should be conducted to satisfy fully all three tenets of the molecular Koch's postulates, including complementation of a mutated allele.},
author = {Lane, M C and Mobley, H L T},
doi = {10.1038/sj.ki.5002230},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lane, Mobley - Role of P-fimbrial-mediated adherence in pyelonephritis and persistence of uropathogenic Escherichia coli (UPEC) in the m.pdf:pdf},
issn = {0085-2538},
journal = {Kidney international},
keywords = {Adhesins, Escherichia coli,Adhesins, Escherichia coli: analysis,Adhesins, Escherichia coli: physiology,Amino Acid Sequence,Animals,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: pathology,Escherichia coli Infections: physiopathology,Escherichia coli: pathogenicity,Fimbriae Proteins,Fimbriae Proteins: analysis,Fimbriae Proteins: physiology,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Humans,Kidney,Kidney: microbiology,Kidney: pathology,Kidney: physiopathology,Molecular Sequence Data,Pyelonephritis,Pyelonephritis: physiopathology},
month = {jul},
number = {1},
pages = {19--25},
pmid = {17396114},
title = {{Role of P-fimbrial-mediated adherence in pyelonephritis and persistence of uropathogenic Escherichia coli (UPEC) in the mammalian kidney.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17396114},
volume = {72},
year = {2007}
}
@article{Derenyi2002b,
annote = {        From Duplicate 1 (                   Formation and Interaction of Membrane Tubes                 - Der{\'{e}}nyi, Imre; J{\"{u}}licher, Frank; Prost, Jacques )
                
        
        
      },
author = {Der{\'{e}}nyi, Imre and J{\"{u}}licher, Frank and Prost, Jacques},
doi = {10.1103/PhysRevLett.88.238101},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Der{\'{e}}nyi, J{\"{u}}licher, Prost - Formation and Interaction of Membrane Tubes - 2002.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {may},
number = {23},
pages = {23--26},
title = {{Formation and Interaction of Membrane Tubes}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.88.238101},
volume = {88},
year = {2002}
}
@article{Katsikogianni2004,
abstract = {This article reviews the mechanisms of bacterial adhesion to biomaterial surfaces, the factors affecting the adhesion, the techniques used in estimating bacteria-material interactions and the models that have been developed in order to predict adhesion. The process of bacterial adhesion includes an initial physicochemical interaction phase and a late molecular and cellular one. It is a complicated process influenced by many factors, including the bacterial properties, the material surface characteristics, the environmental factors, such as the presence of serum proteins and the associated flow conditions. Two categories of techniques used in estimating bacteria-material interactions are described: those that utilize fluid flowing against the adhered bacteria and counting the percentage of bacteria that detach, and those that manipulate single bacteria in various configurations which lend themselves to more specific force application and provide the basis for theoretical analysis of the receptor-ligand interactions. The theories that are reviewed are the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, the thermodynamic approach and the extended DLVO theory. Over the years, significant work has been done to investigate the process of bacterial adhesion to biomaterial surfaces, however a lot of questions still remain unanswered.},
author = {Katsikogianni, M and Missirlis, Y F},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Katsikogianni, Missirlis - Concise review of mechanisms of bacterial adhesion to biomaterials and of techniques used in estimating bacte.pdf:pdf},
issn = {1473-2262},
journal = {European cells {\&} materials},
keywords = {Bacteria,Bacteria: cytology,Bacteria: pathogenicity,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial Physiological Phenomena,Biocompatible Materials,Biocompatible Materials: chemistry,Biocompatible Materials: metabolism,Chemistry,Physical,Physical: methods,biofilm},
mendeley-tags = {biofilm},
month = {dec},
pages = {37--57},
pmid = {15593018},
title = {{Concise review of mechanisms of bacterial adhesion to biomaterials and of techniques used in estimating bacteria-material interactions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15593018},
volume = {8},
year = {2004}
}
@article{Holz2010,
author = {Holz, Claudia and Opitz, Dirk and Greune, Lilo and Kurre, Rainer and Koomey, Michael and Schmidt, M. Alexander and Maier, Berenike},
doi = {10.1103/PhysRevLett.104.178104},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Holz et al. - Multiple Pilus Motors Cooperate for Persistent Bacterial Movement in Two Dimensions - 2010.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {apr},
number = {17},
pages = {1--4},
title = {{Multiple Pilus Motors Cooperate for Persistent Bacterial Movement in Two Dimensions}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.104.178104},
volume = {104},
year = {2010}
}
@article{Gineste2011,
abstract = {The forward scattering of light in a conventional inverted optical microscope by nanoparticles ranging in diameter from 10 to 50nm has been used to automatically and quantitatively identify and track their location in three-dimensions with a temporal resolution of 200ms. The standard deviation of the location of nominally stationary 50-nm-diameter nanoparticles was found to be about 50nm along the light path and about 5nm in the plane perpendicular to the light path. The method is based on oscillating the microscope objective along the light path using a piezo actuator and acquiring images with the condenser aperture closed to a minimum to enhance the effects of diffraction. Data processing in the time and spatial domains allowed the location of particles to be obtained automatically so that the technique has potential applications both in the processing of nanoparticles and in their use in a variety of fields including nanobiotechnology, pharmaceuticals and food processing where a simple optical microscope maybe preferred for a variety of reasons.},
author = {Gineste, J-M and Macko, P and Patterson, E a and Whelan, M P},
doi = {10.1111/j.1365-2818.2011.03491.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gineste et al. - Three-dimensional automated nanoparticle tracking using Mie scattering in an optical microscope. - 2011.pdf:pdf},
issn = {1365-2818},
journal = {Journal of microscopy},
keywords = {Algorithms,Imaging, Three-Dimensional,Imaging, Three-Dimensional: methods,Light,Microscopy,Microscopy: instrumentation,Microscopy: methods,Nanoparticles,Nanoparticles: chemistry,Nanoparticles: radiation effects,Scattering, Radiation},
month = {aug},
number = {2},
pages = {172--8},
pmid = {21375530},
title = {{Three-dimensional automated nanoparticle tracking using Mie scattering in an optical microscope.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21375530},
volume = {243},
year = {2011}
}
@article{Keren2011,
author = {Keren, Kinneret},
doi = {10.1073/pnas.1111671108},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Keren - Membrane tension leads the way. - 2011.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Actomyosin,Actomyosin: physiology,Animals,Cell Membrane,Cell Membrane: metabolism,Cell Movement,Exocytosis},
month = {aug},
number = {35},
pages = {14379--80},
pmid = {21873200},
title = {{Membrane tension leads the way.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3167539{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {108},
year = {2011}
}
@article{Pontes2011,
abstract = {We perform a detailed investigation of the force × deformation curve in tether extraction from 3T3 cells by optical tweezers. Contrary to conventional wisdom about tethers extracted from cells, we find that actin filaments are present within them, so that a revised theory of tether pulling from cells is called for. We also measure steady and maximum tether force values significantly higher than previously published ones for 3T3 cells. Possible explanations for these differences are investigated. Further experimental support of the theory of force barriers for membrane tube extension is obtained. The potential of studies on tether pulling force × deformation for retrieving information on membrane-cytoskeleton interaction is emphasized.},
author = {Pontes, B and Viana, N B and Salgado, L T and Farina, M and Neto, V Moura and Nussenzveig, H M},
doi = {10.1016/j.bpj.2011.05.044},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Pontes et al. - Cell cytoskeleton and tether extraction. - 2011.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
month = {jul},
number = {1},
pages = {43--52},
pmid = {21723813},
publisher = {Biophysical Society},
title = {{Cell cytoskeleton and tether extraction.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21723813},
volume = {101},
year = {2011}
}
@article{NalbantEsenturk2009,
author = {{Nalbant Esenturk}, E.},
doi = {10.1002/jrs.2084},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nalbant Esenturk - Surface-enhanced Raman scattering spectroscopy via gold nanostars - 2009.pdf:pdf},
journal = {Journal of Raman Spectroscopy},
month = {jan},
number = {1},
pages = {2444--91},
title = {{Surface-enhanced Raman scattering spectroscopy via gold nanostars}},
volume = {76},
year = {2009}
}
@article{Jin2010,
author = {Jin, Qinghua and Zhang, Xiaojun and Li, Xiaoyang and Wang, Jianliu},
doi = {10.1007/s11465-010-0027-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jin et al. - Dynamics analysis of bladder-urethra system based on CFD - 2010.pdf:pdf},
issn = {1673-3479},
journal = {Frontiers of Mechanical Engineering in China},
keywords = {bladder-urethra system,cfd,computational fluid dynamics,paper3,stress urinary incon-,sui,tinence},
mendeley-tags = {paper3},
month = {may},
number = {3},
pages = {336--340},
title = {{Dynamics analysis of bladder-urethra system based on CFD}},
url = {http://www.springerlink.com/index/10.1007/s11465-010-0027-8},
volume = {5},
year = {2010}
}
@article{Duncan2005,
abstract = {Type 1 fimbriae of enterobacteria are heteropolymeric organelles of adhesion composed of FimH, a mannose-binding lectin, and a shaft composed primarily of FimA. We compared the binding activities of recombinant clones expressing type 1 fimbriae from Escherichia coli, Klebsiella pneumoniae, and Salmonella typhimurium for gut and uroepithelial cells and for various soluble mannosylated proteins. Each fimbria was characterized by its capacity to bind particular epithelial cells and to aggregate mannoproteins. However, when each respective FimH subunit was cloned and expressed in the absence of its shaft as a fusion protein with MalE, each FimH bound a wide range of mannose-containing compounds. In addition, we found that expression of FimH on a heterologous fimbrial shaft, e.g. K. pneumoniae FimH on the E. coli fimbrial shaft or vice versa, altered the binding specificity of FimH such that it closely resembled that of the native heterologous type 1 fimbriae. Furthermore, attachment to and invasion of bladder epithelial cells, which were mediated much better by native E. coli type 1 fimbriae compared with native K. pneumoniae type 1 fimbriae, were found to be dependent on the background of the fimbrial shaft (E. coli versus K. pneumoniae) rather than the background of the FimH expressed. Thus, the distinct binding specificities of different enterobacterial type 1 fimbriae cannot be ascribed solely to the primary structure of their respective FimH subunits, but are also modulated by the fimbrial shaft on which each FimH subunit is presented, possibly through conformational constraints imposed on FimH by the fimbrial shaft. The capacity of type 1 fimbrial shafts to modulate the tissue tropism of different enterobacterial species represents a novel function for these highly organized structures.},
author = {Duncan, Matthew J and Mann, Elena L and Cohen, Michael S and Ofek, Itzhak and Sharon, Nathan and Abraham, Soman N},
doi = {10.1074/jbc.M501249200},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Duncan et al. - The distinct binding specificities exhibited by enterobacterial type 1 fimbriae are determined by their fimbrial shafts..pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Animals,Bacterial Adhesion,Cells, Cultured,Epithelial Cells,Epithelial Cells: metabolism,Epithelial Cells: microbiology,Escherichia coli,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Fimbriae, Bacterial: classification,Fimbriae, Bacterial: metabolism,Gastrointestinal Tract,Gastrointestinal Tract: cytology,Gastrointestinal Tract: microbiology,Gene Expression,Klebsiella pneumoniae,Klebsiella pneumoniae: metabolism,Mice,Molecular Sequence Data,Protein Binding,Recombinant Proteins,Salmonella typhimurium,Salmonella typhimurium: metabolism,Species Specificity,Substrate Specificity,Urinary Bladder,Urinary Bladder: cytology,Urinary Bladder: microbiology},
month = {nov},
number = {45},
pages = {37707--16},
pmid = {16118220},
title = {{The distinct binding specificities exhibited by enterobacterial type 1 fimbriae are determined by their fimbrial shafts.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16118220},
volume = {280},
year = {2005}
}
@article{Krishnan1995,
author = {Krishnan, Gokul P. and Leighton, David T.},
doi = {10.1063/1.868755},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Krishnan, Leighton - Inertial lift on a moving sphere in contact with a plane wall in a shear flow - 1995.pdf:pdf},
issn = {10706631},
journal = {Physics of Fluids},
number = {11},
pages = {2538},
title = {{Inertial lift on a moving sphere in contact with a plane wall in a shear flow}},
url = {http://scitation.aip.org/content/aip/journal/pof2/7/11/10.1063/1.868755},
volume = {7},
year = {1995}
}
@article{Thomas1999,
author = {Thomas, N and Thornhill, R a},
doi = {10.1088/0022-3727/31/3/002},
issn = {0022-3727},
journal = {Journal of Physics D: Applied Physics},
number = {3},
pages = {253--266},
title = {{The physics of biological molecular motors}},
volume = {31},
year = {1999}
}
@article{Neutra2006,
abstract = {Most infectious agents enter the body at mucosal surfaces and therefore mucosal immune responses function as a first line of defence. Protective mucosal immune responses are most effectively induced by mucosal immunization through oral, nasal, rectal or vaginal routes, but the vast majority of vaccines in use today are administered by injection. As discussed in this Review, current research is providing new insights into the function of mucosal tissues and the interplay of innate and adaptive immune responses that results in immune protection at mucosal surfaces. These advances promise to accelerate the development and testing of new mucosal vaccines against many human diseases including HIV/AIDS.},
author = {Neutra, Marian R and Kozlowski, Pamela A},
doi = {10.1038/nri1777},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Neutra, Kozlowski - Mucosal vaccines the promise and the challenge. - 2006.pdf:pdf},
issn = {1474-1733},
journal = {Nature reviews. Immunology},
keywords = {Animals,Cellular,Humans,Immunity,Innate,Mucosal,Vaccines,Vaccines: immunology},
month = {feb},
number = {2},
pages = {148--58},
pmid = {16491139},
title = {{Mucosal vaccines: the promise and the challenge.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16491139},
volume = {6},
year = {2006}
}
@article{Ayala-Ramirez2006,
author = {Ayala-Ramirez, Victor and Garcia-Capulin, Carlos H. and Perez-Garcia, Arturo and Sanchez-Yanez, Raul E.},
doi = {10.1016/j.patrec.2005.10.003},
issn = {01678655},
journal = {Pattern Recognition Letters},
month = {apr},
number = {6},
pages = {652--657},
title = {{Circle detection on images using genetic algorithms}},
volume = {27},
year = {2006}
}
@article{Ganic2004,
abstract = {There has been an interest to understand the trapping performance produced by a laser beam with a complex wavefront structure because the current methods for calculating trapping force ignore the effect of diffraction by a vectorial electromagnetic wave. In this letter, we present a method for determining radiation trapping force on a micro-particle, based on the vectorial diffraction theory and the Maxwell stress tensor approach. This exact method enables one to deal with not only complex apodization, phase, and polarization structures of trapping laser beams but also the effect of spherical aberration present in the trapping system.},
author = {Ganic, Djenan and Gan, Xiaosong and Gu, Min},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Ganic, Gan, Gu - Exact radiation trapping force calculation based on vectorial diffraction theory. - 2004.pdf:pdf},
issn = {1094-4087},
journal = {Optics express},
month = {jun},
number = {12},
pages = {2670--5},
pmid = {19475108},
title = {{Exact radiation trapping force calculation based on vectorial diffraction theory.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19475108},
volume = {12},
year = {2004}
}
@article{Whitfield2014a,
abstract = {Many bacteria and eukaryotic cells express adhesive proteins at the end of tethers that elongate reversibly at constant or near constant force, which we refer to as yielding elasticity. Here we address the function of yielding elastic adhesive tethers with Escherichia coli bacteria as a model for cell adhesion, using a combination of experiments and simulations. The adhesive bond kinetics and tether elasticity was modeled in the simulations with realistic biophysical models that were fit to new and previously published single molecule force spectroscopy data. The simulations were validated by comparison to experiments measuring the adhesive behavior of E. coli in flowing fluid. Analysis of the simulations demonstrated that yielding elasticity is required for the bacteria to remain bound in high and variable flow conditions, because it allows the force to be distributed evenly between multiple bonds. In contrast, strain-hardening and linear elastic tethers concentrate force on the most vulnerable bonds, which leads to failure of the entire adhesive contact. Load distribution is especially important to noncovalent receptor-ligand bonds, because they become exponentially shorter lived at higher force above a critical force, even if they form catch bonds. The advantage of yielding is likely to extend to any blood cells or pathogens adhering in flow, or to any situation where bonds are stretched unequally due to surface roughness, unequal native bond lengths, or conditions that act to unzip the bonds.},
author = {Whitfield, Matt J. and Luo, Jonathon P. and Thomas, Wendy E},
doi = {10.1371/journal.pcbi.1003971},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Whitfield, Luo, Thomas - Yielding Elastic Tethers Stabilize Robust Cell Adhesion - 2014.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Whitfield, Luo, Thomas - Yielding Elastic Tethers Stabilize Robust Cell Adhesion - 2014.pdf:pdf},
issn = {1553-7358},
journal = {PLoS Computational Biology},
month = {dec},
number = {12},
pages = {e1003971},
pmid = {25473833},
title = {{Yielding Elastic Tethers Stabilize Robust Cell Adhesion}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25473833 http://dx.plos.org/10.1371/journal.pcbi.1003971},
volume = {10},
year = {2014}
}
@article{Pettersen2004,
abstract = {The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.},
author = {Pettersen, Eric F and Goddard, Thomas D and Huang, Conrad C and Couch, Gregory S and Greenblatt, Daniel M and Meng, Elaine C and Ferrin, Thomas E},
doi = {10.1002/jcc.20084},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Pettersen et al. - UCSF Chimera--a visualization system for exploratory research and analysis. - 2004.pdf:pdf},
issn = {0192-8651},
journal = {Journal of computational chemistry},
keywords = {Amino Acid Sequence,Computer Graphics,Models,Molecular,Molecular Conformation,Molecular Sequence Data,Research,Sequence Alignment,Software,Thermodynamics},
month = {oct},
number = {13},
pages = {1605--12},
pmid = {15264254},
title = {{UCSF Chimera--a visualization system for exploratory research and analysis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15264254},
volume = {25},
year = {2004}
}
@article{Boyer1969,
author = {Boyer, Herbert W. and Roulland-Dussoix, Daisy},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Boyer, Roulland-Dussoix - A complementation analysis of the restriction and modification of DNA in Escherichia coli - 1969.pdf:pdf},
journal = {Journal of molecular biology},
number = {3},
pages = {459--472},
title = {{A complementation analysis of the restriction and modification of DNA in Escherichia coli}},
volume = {41},
year = {1969}
}
@article{Chang2000a,
abstract = {Selectin-mediated leukocyte rolling is crucial for the proper function of the immune response. Recently, selectin-mediated rolling was recreated in a cell-free system (Biophysical Journal 71:2902-2907 (1996)); it was shown that sialyl Lewis(x) (sLe(x))-coated microspheres roll over E-selectin-coated surfaces under hydrodynamic flow. The cell-free system removes many confounding cellular features, such as cell deformability and signaling, allowing us to focus on the role of carbohydrate/selectin physical chemistry in mediating rolling. In this paper, we use adhesive dynamics, a computational method that allows us to simulate adhesion, to analyze the experimental data produced in the cell-free system. We simulate the effects of shear rate, ligand density, and number of receptors per particle on rolling velocity and compare them with experimental results obtained with the cell-free system. If we assume the population of particles is homogeneous in receptor density, we predict that particle rolling velocity calculated in simulations is more sensitive to shear rate than found in experiments. Also, the calculated rolling velocity is more sensitive to the number of receptors on the microspheres than to the ligand density on the surface, again in contrast to experiment. We argue that heterogeneity in the distribution of receptors throughout the particle population causes these discrepancies. We improve the agreement between experiment and simulation by calculating the average rolling velocity of a population whose receptors follow a normal distribution, suggesting heterogeneity among particles significantly affects the experimental results. Further comparison between theory and experiment yields an estimate of the reactive compliance of sLe(x)/E-selectin interactions of 0.25 A, close to that reported in the literature for E-selectin and its natural ligand (0.3 A). We also provide an estimate of the value of the intrinsic association rate (between 10(4) and 10(5) s(-1)) for the formation of sLe(x)/E-selectin bonds.},
author = {Chang, K C and Hammer, D a},
doi = {10.1016/S0006-3495(00)76439-3},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chang, Hammer - Adhesive dynamics simulations of sialyl-Lewis(x)E-selectin-mediated rolling in a cell-free system. - 2000.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Biophysical Phenomena,Biophysics,Cell Adhesion,Cell Adhesion: physiology,Cell Movement,Cell Movement: physiology,Cell-Free System,E-Selectin,E-Selectin: physiology,Humans,Leukocytes,Leukocytes: physiology,Microspheres,Models, Biological,Oligosaccharides,Oligosaccharides: physiology},
month = {oct},
number = {4},
pages = {1891--902},
pmid = {11023895},
publisher = {Elsevier},
title = {{Adhesive dynamics simulations of sialyl-Lewis(x)/E-selectin-mediated rolling in a cell-free system.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1301081{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {79},
year = {2000}
}
@article{Ruer2015,
abstract = {In view of the relentless increase in antibiotic resistance in human pathogens, efforts are needed to safeguard our future therapeutic options against infectious diseases. In addition to regulatory changes in our antibiotic use, this will have to include the development of new therapeutic compounds. One area that has received growing attention in recent years is the possibility to treat or prevent infections by targeting the virulence mechanisms that render bacteria pathogenic. Antivirulence targets include bacterial adherence, secretion of toxic effector molecules, bacterial persistence through biofilm formation, quorum sensing and immune evasion. Effective small-molecule compounds have already been identified that suppress such processes. In this review, we discuss the susceptibility of such compounds to the development of resistance, by comparison with known resistance mechanisms observed for classical bacteriostatic or bacteriolytic antibiotics, and by review of available experimental case studies. Unfortunately, appearance of resistance mechanisms has already been demonstrated for some, showing that the quest of new, lasting drugs remains complicated.},
author = {Ruer, S{\'{e}}gol{\`{e}}ne and Pinotsis, Nikos and Steadman, David and Waksman, Gabriel and Remaut, Han},
doi = {10.1111/cbdd.12517},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ruer et al. - Virulence-targeted Antibacterials Concept, Promise, and Susceptibility to Resistance Mechanisms - 2015.pdf:pdf},
isbn = {1747-0285},
issn = {17470277},
journal = {Chemical Biology {\&} Drug Design},
keywords = {antibiotic resistance,bacterial virulence,drug discovery,mechanism-based drug design,molecular recognition,therapeutic target},
pages = {n/a--n/a},
pmid = {25589217},
title = {{Virulence-targeted Antibacterials: Concept, Promise, and Susceptibility to Resistance Mechanisms}},
url = {http://dx.doi.org/10.1111/cbdd.12517},
year = {2015}
}
@article{King2005,
abstract = {Transient capture of cells or model microspheres from flow over substrates sparsely coated with adhesive ligands has provided significant insight into the unbinding kinetics of leukocyte:endothelium adhesion complexes under external force. Whenever a cell is stopped by a point attachment, the full hydrodynamic load is applied to the adhesion site within an exceptionally short time-less than the reciprocal of the hydrodynamic shear rate (e.g., typically <0.01 s). The decay in numbers of cells or beads that remain attached to a surface has been used as a measure of the kinetics of molecular bond dissociation under constant force, revealing a modest increase in detachment rate at growing applied shear stresses. On the other hand, when detached under steady ramps of force with mechanical probes (e.g., the atomic force microscope and biomembrane force probe), P-selectin:PSGL-1 adhesion bonds break at rates that increase enormously under rising force, yielding 100-fold faster off rates at force levels comparable to high shear. The comparatively weak effect of force on tether survival in flow chamber experiments could be explained by a possible partition of the load amongst several bonds. However, a comprehensive understanding of the difference in kinetic behavior requires us to also inspect other factors affecting the dynamics of attachment-force buildup, such as the interfacial compliance of all linkages supporting the adhesion complex. Here, combining the mechanical properties of the leukocyte interface measured in probe tests with single-bond kinetics and the kinetics of cytoskeletal dissociation, we show that for the leukocyte adhesion complex P-selectin:PSGL-1, a detailed adhesive dynamics simulation accurately reproduces the tethering behavior of cells observed in flow chambers. Surprisingly, a mixture of 10{\%} single bonds and 90{\%} dimeric bonds is sufficient to fully match the data of the P-selectin:PSGL-1 experiments, with the calculated decay in fraction of attached cells still appearing exponential.},
author = {King, M R and Heinrich, Volkmar and Evans, Evan and Hammer, D a},
doi = {10.1529/biophysj.104.051805},
file = {:E$\backslash$:/Mina Dokument/Mendeley/King et al. - Nano-to-micro scale dynamics of P-selectin detachment from leukocyte interfaces. III. Numerical simulation of tethering un.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Binding Sites,Blood Flow Velocity,Blood Flow Velocity: physiology,Cardiovascular,Cell Adhesion,Cell Adhesion: physiology,Computer Simulation,Cytoskeleton,Cytoskeleton: physiology,Leukocytes,Leukocytes: physiology,Leukocytes: ultrastructure,Microspheres,Models,Nanotechnology,Nanotechnology: methods,P-Selectin,P-Selectin: metabolism,Protein Binding,Shear Strength,flow,shear force,stokes},
mendeley-tags = {flow,shear force,stokes},
month = {mar},
number = {3},
pages = {1676--83},
pmid = {15574709},
title = {{Nano-to-micro scale dynamics of P-selectin detachment from leukocyte interfaces. III. Numerical simulation of tethering under flow.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1305224{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {88},
year = {2005}
}
@article{Kokubo2013,
abstract = {BACKGROUND AND PURPOSE: Few prospective studies have examined the impact of both green tea and coffee consumption on strokes. We investigated the association of the combination of those consumption with stroke incidence in a general population. METHODS: We studied 82 369 Japanese (aged 45-74 years; without cardiovascular disease [CVD] or cancer in 1995 and 1998 for Cohort I and II, respectively) who received 13 years of mean follow-up through the end of 2007. Green tea and coffee consumption was assessed by self-administered food frequency questionnaire at baseline. RESULTS: In the 1 066 718 person-years of follow-up, we documented the incidence of strokes (n=3425) and coronary heart disease (n=910). Compared with seldom drinking green tea, the multivariable-adjusted hazard ratios (95{\%} confidence intervals) of all strokes were 0.86 (0.78-0.95) and 0.80 (0.73-0.89) in green tea 2 to 3 and ≥ 4 cups/d, respectively. Higher green tea consumption was associated with inverse risks of CVD and strokes subtypes. Compared with seldom drinking coffee, the multivariable-adjusted hazard ratios (95{\%} confidence intervals) of all strokes were 0.89 (0.80-0.99), 0.80 (0.72-0.90), and 0.81 (0.72-0.91) for coffee 3 to 6 times/week and 1 and ≥ 2 times/day, respectively. Coffee consumption was associated with an inverse risk of CVD and cerebral infarction. Higher green tea or coffee consumption reduced the risks of CVD and stroke subtypes (especially in intracerebral hemorrhage, P for interaction between green tea and coffee=0.04). None of the significant association was observed in coronary heart disease. CONCLUSIONS: Higher green tea and coffee consumption were inversely associated with risk of CVD and stroke in general population.},
author = {Kokubo, Yoshihiro and Iso, Hiroyasu and Saito, Isao and Yamagishi, Kazumasa and Yatsuya, Hiroshi and Ishihara, Junko and Inoue, Manami and Tsugane, Shoichiro},
doi = {10.1161/STROKEAHA.111.677500},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kokubo et al. - The impact of green tea and coffee consumption on the reduced risk of stroke incidence in japanese population The Japan.pdf:pdf},
isbn = {1524-4628 (Electronic)$\backslash$r0039-2499 (Linking)},
issn = {00392499},
journal = {Stroke},
keywords = {coffee,cohort study,coronary heart disease,green tea,stroke},
number = {5},
pages = {1369--1374},
pmid = {23493733},
title = {{The impact of green tea and coffee consumption on the reduced risk of stroke incidence in japanese population: The Japan public health center-based study cohort}},
volume = {44},
year = {2013}
}
@article{Green2009,
abstract = {Microfluidic channels coated with ligands are a versatile platform for the separation or enrichment of cells from small sample volumes. This adhesion-based mode of separation is mediated by ligand-receptor bonds between the cells and channel surface and also by fluid shear stress. This paper demonstrates how aspects of microchannel geometry can play an additional role in controlling cell adhesion. With a combination of computational fluid dynamics modeling and cell adhesion experiments, channels with sharp turns are shown to have regions with near-zero velocity at the turn regions where large numbers of cells adhere or become collected. The lack of uniform adhesion in the turn regions compared to other regions of these channels, together with the large variability in observed cell adhesion indicates that channels with sharp turns are not optimal for cell-capture applications where predictable cell adhesion is desired. Channels with curved turns, on the other hand are shown to provide more uniform and predictable cell adhesion provided the gap between parallel arms of the channels is sufficiently wide. The magnitude of cell adhesion in these curved channels is comparable to that in straight channels with no turns.},
author = {Green, James V and Kniazeva, Tatiana and Abedi, Mehdi and Sokhey, Darshan S and Taslim, Mohammad E and Murthy, Shashi K},
doi = {10.1039/b813516a},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Green et al. - Effect of channel geometry on cell adhesion in microfluidic devices. - 2009.pdf:pdf},
issn = {1473-0197},
journal = {Lab on a chip},
keywords = {Cell Adhesion,Cell Adhesion: physiology,Cell Line,Cells, Cultured,Equipment Design,Humans,Kinetics,Ligands,Microfluidics,Peptides,Peptides: chemistry,Shear Strength},
month = {mar},
number = {5},
pages = {677--85},
pmid = {19224017},
title = {{Effect of channel geometry on cell adhesion in microfluidic devices.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19224017},
volume = {9},
year = {2009}
}
@article{Hess2004,
abstract = {Explaining the meaning of the results to the reader is the purpose of the discussion section of a research paper. There are elements of the discussion that should be included and other things that should be avoided. Always write the discussion for the reader; remember that the focus should be to help the reader understand the study and that the highlight should be on the study data.},
author = {Hess, Dean R},
doi = {10.1365/s35131-011-0274-y},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hess - How to write an effective discussion. - 2004.pdf:pdf},
isbn = {0020-1324 (Print)$\backslash$n0020-1324 (Linking)},
issn = {1438-471X},
journal = {Respiratory care},
number = {10},
pages = {1238--1241},
pmid = {15447810},
title = {{How to write an effective discussion.}},
volume = {49},
year = {2004}
}
@article{Oram1997,
abstract = {To determine how distant sites on supercoiled DNA communicate with each other, the mechanism of site-specific recombination by resolvase was analysed by using a rapid-reaction quench-flow device to study the kinetics of individual steps in the reaction pathway. Three sets of measurements revealed the rates for: (1) the initial binding of the protein to its target sites on the DNA; (2) the synapsis of the two DNA-protein complexes; (3) the overall process of recombination. The binding of the protein to the DNA was complete within 50 milliseconds while recombination required 500 seconds. Surprisingly, synapsis spanned this entire time range: some DNA molecules gave synaptic complexes within ten milliseconds after the initial binding, while others took over 100 seconds. The departure from exponential behaviour may be due to each molecule of DNA having to undergo different conformational fluctuations in order to juxtapose the recombinational sites. From polymer physics theory, the rate of synapsis ought to vary with either the size of the DNA molecule or the length of DNA between the recombinational sites, depending on the nature of the fluctuations, but plasmids of different sizes and with different spacings between the sites all gave the same rates for synapsis. This observation cannot be reconciled with current models for encounters of distant sites on supercoiled DNA. However, the superhelical axis in the DNA molecules used here will be branched at one or more positions and the encounters may arise from the motion of a single branch relative to the remainder of the chain. Alternatively, the non-exponential kinetics for synapsis may be due to multiple re-arrangements of non-productive complexes following DNA juxtaposition.},
author = {Oram, M and Marko, J F and Halford, S E},
doi = {10.1006/jmbi.1997.1109},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Oram, Marko, Halford - Communications between distant sites on supercoiled DNA from non-exponential kinetics for DNA synapsis by resolva.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Buffers,DNA Nucleotidyltransferases,DNA Nucleotidyltransferases: metabolism,DNA, Superhelical,DNA, Superhelical: chemistry,DNA, Superhelical: metabolism,DNA-Binding Proteins,DNA-Binding Proteins: metabolism,Glutamic Acid,Glutamic Acid: pharmacology,Kinetics,Models, Genetic,Nucleic Acid Conformation,Osmolar Concentration,Recombination, Genetic,Recombination, Genetic: physiology,Sodium Chloride,Sodium Chloride: pharmacology,Transposases},
month = {jul},
number = {3},
pages = {396--412},
pmid = {9237906},
title = {{Communications between distant sites on supercoiled DNA from non-exponential kinetics for DNA synapsis by resolvase.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9237906},
volume = {270},
year = {1997}
}
@article{Oddershede2002,
abstract = {Using optical tweezers and single particle tracking, we have revealed the motion of a single protein, the lambda-receptor, in the outer membrane of living Escherichia coli bacteria. We genetically modified the lambda-receptor placing a biotin on an extracellular site of the receptor in vivo. The efficiency of this in vivo biotinylation is very low, thus enabling the attachment of a streptavidin-coated bead binding specifically to a single biotinylated lambda-receptor. The bead was used as a handle for the optical tweezers and as a marker for the single particle tracking routine. We propose a model that allows extraction of the motion of the protein from measurements of the mobility of the bead-molecule complex; these results are equally applicable to analyze bead-protein complexes in other membrane systems. Within a domain of radius approximately 25 nm, the receptor diffuses with a diffusion constant of (1.5 +/- 1.0) x 10(-9) cm(2)/s and sits in a harmonic potential as if it were tethered by an elastic spring of spring constant of {\~{}}1.0 x 10(-2) pN/nm to the bacterial membrane. The purpose of the protein motion might be to facilitate transport of maltodextrins through the outer bacterial membrane.},
author = {Oddershede, Lene B. and Dreyer, Jakob Kisbye and Grego, Sonia and Brown, Stanley and Berg-S{\o}rensen, Kirstine},
doi = {10.1016/S0006-3495(02)75318-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Oddershede et al. - The motion of a single molecule, the lambda-receptor, in the bacterial outer membrane. - 2002.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Bacterial Outer Membrane Proteins,Bacterial Outer Membrane Proteins: chemistry,Bacterial Outer Membrane Proteins: physiology,Biological,Biotin,Biotin: chemistry,Biotin: genetics,Biotinylation,Biotinylation: methods,Chemical,Computer Simulation,Elasticity,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: physiology,Escherichia coli: ultrastructure,Lasers,Mechanical,Micromanipulation,Micromanipulation: instrumentation,Micromanipulation: methods,Microspheres,Models,Motion,Nanotechnology,Nanotechnology: instrumentation,Nanotechnology: methods,Optics and Photonics,Optics and Photonics: instrumentation,Particle Size,Porins,Protein Conformation,Receptors,Recombinant Proteins,Recombinant Proteins: chemistry,Recombinant Proteins: metabolism,Streptavidin,Streptavidin: chemistry,Stress,Virus,Virus: chemistry,Virus: genetics,Virus: physiology},
month = {dec},
number = {6},
pages = {3152--61},
pmid = {12496085},
title = {{The motion of a single molecule, the lambda-receptor, in the bacterial outer membrane.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302393{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {83},
year = {2002}
}
@article{Liebesny2010,
author = {Liebesny, Paul and Goyal, Sachin and Dunlap, David and Family, Fereydoon and Finzi, Laura},
doi = {10.1088/0953-8984/22/41/414104},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Liebesny et al. - Determination of the number of proteins bound non-specifically to DNA - 2010.pdf:pdf},
issn = {0953-8984},
journal = {Journal of Physics: Condensed Matter},
month = {oct},
number = {41},
pages = {414104},
title = {{Determination of the number of proteins bound non-specifically to DNA}},
url = {http://stacks.iop.org/0953-8984/22/i=41/a=414104?key=crossref.cebe71b7b87af53a4f2e3715e1122a8d},
volume = {22},
year = {2010}
}
@article{Brenner1961,
annote = {Brenner, h},
author = {Brenner, H},
doi = {10.1016/0009-2509(61)80035-3},
isbn = {0009-2509},
journal = {Chemical Engineering Science},
number = {3-4},
pages = {242--251},
title = {{The slow motion of a sphere through a viscous fluid towards a plane surface}},
url = {<Go to ISI>://WOS:A1961XG76500009},
volume = {16},
year = {1961}
}
@article{Strunz2000,
abstract = {We discuss models for the force-induced dissociation of a ligand-receptor bond, occurring in the context of cell adhesion or single molecule unbinding force measurements. We consider a bond with a structured energy landscape which is modeled by a network of force dependent transition rates between intermediate states. The behavior of a model with only one intermediate state and a model describing a molecular zipper is studied. We calculate the bond lifetime as a function of an applied force and unbinding forces under an increasing applied load and determine the relationship between both quantities. The dissociation via an intermediate state can lead to distinct functional relations of the bond lifetime on force. One possibility is the occurrence of three force regimes where the lifetime of the bond is determined by different transitions within the energy landscape. This case can be related to recent experimental observations of the force-induced dissociation of single avidin-biotin bonds.},
author = {Strunz, T and Oroszlan, K and Schumakovitch, I and G{\"{u}}ntherodt, H and Hegner, M},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Strunz et al. - Model energy landscapes and the force-induced dissociation of ligand-receptor bonds. - 2000.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {DNA,DNA: chemistry,Kinetics,Ligands,Models, Theoretical,Nucleic Acid Conformation,Protein Binding,Protein Conformation,Receptors, Cell Surface,Receptors, Cell Surface: chemistry,Receptors, Cell Surface: metabolism,Stress, Mechanical,Thermodynamics},
month = {sep},
number = {3},
pages = {1206--12},
pmid = {10968985},
title = {{Model energy landscapes and the force-induced dissociation of ligand-receptor bonds.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1301017{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {79},
year = {2000}
}
@article{Li2004,
abstract = {Metal oxides can increase the adhesion of negatively-charged bacteria to surfaces primarily due to their positive charge. However, the hydrophobicity of a metal-oxide surface can also increase adhesion of bacteria. In order to understand the relative contribution of charge and hydrophobicity to bacterial adhesion, we measured the adhesion of 8 strains of bacteria, under conditions of low and high-ionic strength (1 and 100 mM, respectively) to 11 different surfaces and examined adhesion as a function of charge, hydrophobicity (water contact angle) and surface energy. Inorganic surfaces included three uncoated glass surfaces and eight metal-oxide thin films prepared on the upper (non-tin-exposed) side of float glass by chemical vapor deposition. The Gram-negative bacteria differed in lengths of lipopolysaccharides on their outer surface (three Escherichia coli strains), the amounts of exopolysaccharides (two Pseudomonas aeruginosa strains), and their known relative adhesion to sand grains (two Burkholderia cepacia strains). One Gram positive bacterium was also used that had a lower adhesion to glass than these other bacteria (Bacillus subtilis). For all eight bacteria, there was a consistent increase in adhesion between with the type of inorganic surface in the order: float glass exposed to tin (coded here as Si-Sn), glass microscope slide (Si-m), uncoated air-side float glass surface (Si-a), followed by thin films of (Co(1-y-z)Fe(y)Cr(z))3O4, Ti/Fe/O, TiO2, SnO2, SnO2:F, SnO2:Sb, A1(2)O3, and Fe2O3 (the colon indicates metal doping, a slash indicates that the metal is a major component, while the dash is used to distinguish surfaces). Increasing the ionic strength from 1 to 100 mM increased adhesion by a factor of 2.0 +/- 0.6 (73{\%} of the sample results were within the 95{\%} CI) showing electrostatic charge was important in adhesion. However, adhesion was not significantly correlated with bacterial charge and contact angle. Adhesion (A) of the eight strains was significantly (P < 10(-25)) correlated with total adhesion free energy (U) between the bacteria and surface (A = 2162e(-1.8U)). Although the correlation was significant, agreement between the model and data was poor for the low energy surfaces (R2 = 0.68), indicating that better models or additional methods to characterize bacteria and surfaces are still needed to more accurately describe initial bacterial adhesion to inorganic surfaces.},
author = {Li, Baikun and Logan, Bruce E},
doi = {10.1016/j.colsurfb.2004.05.006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Li, Logan - Bacterial adhesion to glass and metal-oxide surfaces. - 2004.pdf:pdf},
issn = {0927-7765},
journal = {Colloids and surfaces. B, Biointerfaces},
keywords = {Bacillus subtilis,Bacillus subtilis: drug effects,Bacillus subtilis: physiology,Bacterial Adhesion,Bacterial Adhesion: drug effects,Bacterial Adhesion: physiology,Burkholderia cepacia,Burkholderia cepacia: drug effects,Burkholderia cepacia: physiology,Coated Materials, Biocompatible,Coated Materials, Biocompatible: pharmacology,Escherichia coli,Escherichia coli: drug effects,Escherichia coli: physiology,Gram-Negative Bacteria,Gram-Negative Bacteria: drug effects,Gram-Negative Bacteria: physiology,Gram-Positive Bacteria,Gram-Positive Bacteria: drug effects,Gram-Positive Bacteria: physiology,Hydrophobicity,Metals,Metals: chemistry,Metals: pharmacology,Oxides,Oxides: chemistry,Oxides: pharmacology,Pseudomonas aeruginosa,Pseudomonas aeruginosa: drug effects,Pseudomonas aeruginosa: physiology,Silicon Dioxide,Silicon Dioxide: pharmacology,Surface Properties,Water,Water: chemistry},
month = {jul},
number = {2},
pages = {81--90},
pmid = {15261011},
title = {{Bacterial adhesion to glass and metal-oxide surfaces.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15261011},
volume = {36},
year = {2004}
}
@article{Lee2005,
author = {Lee, J.R.J. and Smith, M.L. and Smith, L.N. and Midha, P.S.},
doi = {10.1016/j.compind.2005.05.006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lee et al. - Robust and efficient automated detection of tooling defects in polished stone - 2005.pdf:pdf},
issn = {01663615},
journal = {Computers in Industry},
keywords = {circle detection,circle hough transform,polished stone,randomised algorithm,surface inspection},
month = {dec},
number = {8-9},
pages = {787--801},
title = {{Robust and efficient automated detection of tooling defects in polished stone}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0166361505001193},
volume = {56},
year = {2005}
}
@article{Lewis2011a,
abstract = {The prophage state of bacteriophage $\lambda$ is extremely stable and is maintained by a highly regulated level of $\lambda$ repressor protein, CI, which represses lytic functions. CI regulates its own synthesis in a lysogen by activating and repressing its promoter, P(RM). CI participates in long-range interactions involving two regions of widely separated operator sites by generating a loop in the intervening DNA. We investigated the roles of each individual site under conditions that permitted DNA loop formation by using in vitro transcription assays for the first time on supercoiled DNA that mimics in vivo situation. We confirmed that DNA loops generated by oligomerization of CI bound to its operators influence the autoactivation and autorepression of P(RM) regulation. We additionally report that different configurations of DNA loops are central to this regulation--one configuration further enhances autoactivation and another is essential for autorepression of P(RM).},
author = {Lewis, Dale and Le, Phuoc and Zurla, Chiara and Finzi, Laura and Adhya, Sankar},
doi = {10.1073/pnas.1111221108},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lewis et al. - Multilevel autoregulation of $\lambda$ repressor protein CI by DNA looping in vitro. - 2011.pdf:pdf},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Bacteriophage lambda,Bacteriophage lambda: chemistry,Bacteriophage lambda: metabolism,DNA, Superhelical,DNA, Superhelical: chemistry,DNA, Superhelical: metabolism,DNA, Viral,DNA, Viral: chemistry,DNA, Viral: metabolism,Lysogeny,Lysogeny: physiology,Repressor Proteins,Repressor Proteins: chemistry,Repressor Proteins: metabolism,Viral Proteins,Viral Proteins: chemistry,Viral Proteins: metabolism},
month = {sep},
number = {36},
pages = {14807--12},
pmid = {21873207},
title = {{Multilevel autoregulation of $\lambda$ repressor protein CI by DNA looping in vitro.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3169136{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {108},
year = {2011}
}
@article{Powers2002b,
annote = {        From Duplicate 1 (                   Fluid-membrane tethers: Minimal surfaces and elastic boundary layers                 - Powers, Thomas; Huber, Greg; Goldstein, Raymond )
                
        
        
      },
author = {Powers, Thomas and Huber, Greg and Goldstein, Raymond},
doi = {10.1103/PhysRevE.65.041901},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Powers, Huber, Goldstein - Fluid-membrane tethers Minimal surfaces and elastic boundary layers - 2002.pdf:pdf},
issn = {1063-651X},
journal = {Physical Review E},
month = {mar},
number = {4},
pages = {1--11},
title = {{Fluid-membrane tethers: Minimal surfaces and elastic boundary layers}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.65.041901},
volume = {65},
year = {2002}
}
@article{Bockelmann2002,
abstract = {Force measurements are performed on single DNA molecules with an optical trapping interferometer that combines subpiconewton force resolution and millisecond time resolution. A molecular construction is prepared for mechanically unzipping several thousand-basepair DNA sequences in an in vitro configuration. The force signals corresponding to opening and closing the double helix at low velocity are studied experimentally and are compared to calculations assuming thermal equilibrium. We address the effect of the stiffness on the basepair sensitivity and consider fluctuations in the force signal. With respect to earlier work performed with soft microneedles, we obtain a very significant increase in basepair sensitivity: presently, sequence features appearing at a scale of 10 basepairs are observed. When measured with the optical trap the unzipping force exhibits characteristic flips between different values at specific positions that are determined by the base sequence. This behavior is attributed to bistabilities in the position of the opening fork; the force flips directly reflect transitions between different states involved in the time-averaging of the molecular system.},
author = {Bockelmann, U and Thomen, Ph and Essevaz-Roulet, B and Viasnoff, V and Heslot, F},
doi = {10.1016/S0006-3495(02)75506-9},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bockelmann et al. - Unzipping DNA with optical tweezers high sequence sensitivity and force flips. - 2002.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Calibration,DNA,DNA: chemistry,Interferometry,Interferometry: instrumentation,Interferometry: methods,Lasers,Polymerase Chain Reaction,Sensitivity and Specificity},
month = {mar},
number = {3},
pages = {1537--53},
pmid = {11867467},
title = {{Unzipping DNA with optical tweezers: high sequence sensitivity and force flips.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1301953{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {82},
year = {2002}
}
@article{Marchioli2002b,
abstract = {Particle transfer in the wall region of turbulent boundary layers is dominated by the coherent structures which control the turbulence regeneration cycle. Coherent structures bring particles toward and away from the wall and favour particle segregation in the viscous region, giving rise to non-uniform particle. distribution profiles which peak close to the wall. The object of this work is to understand the reasons for higher particle concentration in the wall region by examining turbulent transfer of heavy particles to and away from the wall in connection with the coherent structures of the boundary layer. We will examine the behaviour of a dilute dispersion of heavy particles - flyashes in air - in a vertical channel flow, using pseudo-spectral direct numerical simulation to calculate the turbulent flow field at a shear Reynolds number Re-tau = 150, and Lagrangian tracking to describe the dynamics of particles. Drag force, gravity and Saffman lift are used in the equation of motion for the particles, which are assumed to have no influence on the flow field. Particle interaction with the wall is fully elastic. As reported in several previous investigations, we found that particles are transferred by sweeps - Q2 type events - in the wall region, where they preferentially accumulate in the low-speed streak environments, whereas ejections - Q4 type events - transfer particles from the wall region to the outer flow. We quantify the efficiency of the instantaneous realizations of the Reynolds stresses events in transferring different size particles to the wall and away from the wall, respectively. Our findings confirm that sweeps and ejections are efficient transfer mechanisms for particles. In particular, we find that only those sweep and ejection events with substantial spatial coherence are effective in transferring particles. However, the efficiency of the transfer mechanisms is conditioned by the presence of particles to be transferred. In the case of ejections, particles are more rarely available since, when in the viscous wall layer, they are concentrated under the low-speed streaks. Even though the low-speed streaks are ejection-like environments, particles remain trapped for a long time. This phenomenon, which causes accumulation of particles in the near-wall region, can be interpreted in terms of overall fluxes toward and away from the wall by the theory of turbophoresis. This theory, proposed initially by Caporaloni et al. (1975) and re-examined later by Reeks (1983), can help to explain the existence of net particle fluxes toward the wall as a manifestation of the skewness in the velocity distribution of the particles (Reeks 1983). To understand the local and instantaneous mechanisms which give rise to the phenomenon of turbophoresis, we focus on the near-wall region of the turbulent boundary layer. We examine the role of the rear-end of a quasistreamwise vortex very near to the wall in preventing particles in the proximity of the wall from being re-entrained by the pumping action of the large, farther from the wall, forward-end of a following quasi-streamwise vortex. We examine several mechanisms for turbulence structures near the wall and we find that the mechanism based on the archetypal quasi-streamwise structures identified by Schoppa {\&} Hussain (1997), the parent-offspring regeneration cycle for near-wall quasi-streamwise vortices discussed by Brooke {\&} Hanratty (1993), and the mechanism based on coherent packets of hairpin vortices, the fundamental super-structure characterized by Adrian, Meinhart {\&} Tomkins (2000), all depict the same characteristic pattern whic},
annote = {Marchioli, C Soldati, A},
author = {Marchioli, C and Soldati, A},
doi = {10.1017/s0022112002001738},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Marchioli, Soldati - Mechanisms for particle transfer and segregation in a turbulent boundary layer - 2002.pdf:pdf},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
pages = {283--315},
title = {{Mechanisms for particle transfer and segregation in a turbulent boundary layer}},
url = {<Go to ISI>://WOS:000178731400011},
volume = {468},
year = {2002}
}
@article{Froehlich1995,
author = {Froehlich, Barbara J and Karakashian, Alexander and Sakellaris, Harry and Scott, June R and Froehlich, Barbara J and Karakashian, Alexander and Sakellaris, Harry and Scott, June R},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Froehlich et al. - Genes for CS2 pili of enterotoxigenic Escherichia coli and their interchangeability with those for CS1 pili . These i.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Froehlich et al. - Genes for CS2 pili of enterotoxigenic Escherichia coli and their interchangeability with those for CS1 pili . Thes(2).pdf:pdf},
number = {12},
pages = {4849--4856},
title = {{Genes for CS2 pili of enterotoxigenic Escherichia coli and their interchangeability with those for CS1 pili . These include : Genes for CS2 Pili of Enterotoxigenic Escherichia coli and Their Interchangeability with Those for CS1 Pili}},
volume = {63},
year = {1995}
}
@article{Whitfield2010c,
abstract = {Escherichia coli exhibit both shear-stabilized rolling and a transition to stationary adhesion while adhering in fluid flow. Understanding the mechanism by which this shear-enhanced adhesion occurs is an important step in understanding bacterial pathogenesis. In this work, simulations are used to investigate the relative contributions of fimbrial deformation and bond transitions to the rolling and stationary adhesion of E. coli. Each E. coli body is surrounded by many long, thin fimbriae terminating in a single FimH receptor that is capable of forming a catch bond with mannose. As simulated cells progress along a mannosylated surface under flow, the fimbriae bend and buckle as they interact with the surface, and FimH-mannose bonds form and break according to a two-state, allosteric catch-bond model. In simulations, shear-stabilized rolling resulted from an increase in the low-affinity bond number due to increased fimbrial deformation with shear. Catch-bond formation did not occur during cell rolling, but instead led to the transition to stationary adhesion. In contrast, in leukocyte and platelet systems, catch bonds appear to be involved in the stabilization of rolling, and integrin activation is required for stationary adhesion.},
annote = {From Duplicate 1 ( Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )

From Duplicate 2 ( Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )

From Duplicate 2 ( Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )







From Duplicate 2 ( Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )

From Duplicate 1 ( Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )

From Duplicate 2 ( Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )

From Duplicate 2 ( Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )
},
author = {Whitfield, Matthew and Ghose, Tia and Thomas, Wendy E},
doi = {10.1016/j.bpj.2010.08.045},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Whitfield, Ghose, Thomas - Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - 2010(3).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Whitfield, Ghose, Thomas - Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - 2010.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
month = {oct},
number = {8},
pages = {2470--8},
pmid = {20959087},
publisher = {Biophysical Society},
title = {{Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20959087},
volume = {99},
year = {2010}
}
@article{WorldHealthOrganization2006,
author = {{World Health Organization}},
journal = {Weekly epidemiological record},
number = {11},
pages = {97--104},
title = {{Future directions for research on enterotoxigenic Escherichia coli vaccines for developing countries}},
year = {2006}
}
@article{Kucharzik2006,
author = {Kucharzik, T. and L{\"{u}}gering, N. and Rautenberg, K. and L{\"{u}}gering, a. and Schmidt, M. a. and Stoll, R. and Domschke, W.},
doi = {10.1111/j.1749-6632.2000.tb05240.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kucharzik et al. - Role of M Cells in Intestinal Barrier Function - 2006.pdf:pdf},
issn = {00778923},
journal = {Annals of the New York Academy of Sciences},
month = {jan},
number = {1},
pages = {171--183},
title = {{Role of M Cells in Intestinal Barrier Function}},
url = {http://doi.wiley.com/10.1111/j.1749-6632.2000.tb05240.x},
volume = {915},
year = {2006}
}
@phdthesis{Nicklasson,
author = {Nicklasson, Matilda},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nicklasson - Studies on the Expression and Regulation of Enterotoxins and Colonization Factors in Enterotoxigenic Escherichia coli ( ETE.pdf:pdf},
school = {Gotenburg},
title = {{Studies on the Expression and Regulation of Enterotoxins and Colonization Factors in Enterotoxigenic Escherichia coli ( ETEC )}}
}
@article{Yuan2000,
abstract = {The dissociation of ligand and receptor involves multiple transitions between intermediate states formed during the unbinding process. In this paper, we explored the energy landscape of the streptavidin-biotin interaction by using the atomic force microscope (AFM) to measure the unbinding dynamics of individual ligand-receptor complexes. The rupture force of the streptavidin-biotin bond increased more than 2-fold over a range of loading rates between 100 and 5000 pN/s. Moreover, the force measurements showed two regimes of loading in the streptavidin-biotin force spectrum, revealing the presence of two activation barriers in the unbinding process. Parallel experiments carried out with a streptavidin mutant (W120F) were used to investigate the molecular determinants of the activation barriers. From these experiments, we attributed the outer activation barrier in the energy landscape to the molecular interaction of the '3-4' loop of streptavidin that closes behind biotin.},
author = {Yuan, C. and Chen, a. and Kolb, P. and Moy, V. T.},
doi = {10.1021/bi992715o},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yuan et al. - Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy - 2000.pdf:pdf},
isbn = {0006-2960 (Print)},
issn = {00062960},
journal = {Biochemistry},
number = {33},
pages = {10219--10223},
pmid = {10956011},
title = {{Energy landscape of streptavidin-biotin complexes measured by atomic force microscopy}},
volume = {39},
year = {2000}
}
@article{Nakao2012,
abstract = {Lipopolysaccharide (LPS) is the major component of the surface of Gram-negative bacteria and its polysaccharide portion is situated at the outermost region. We investigated the relationship between the polysaccharide portion of LPS and biofilm formation using a series of Escherichia coli mutants defective in genes earlier shown to affect the LPS sugar compositions. Biofilm formation by a deep rough LPS mutant, the hldE strain, was strongly enhanced in comparison with the parental strain and other LPS mutants. The hldE strain also showed a phenotype of increased auto-aggregation and stronger cell surface hydrophobicity compared to the wild-type. Similar results were obtained with another deep rough LPS mutant, the waaC strain whose LPS showed same molecular mass as that of the hldE strain. Confocal laser scanning microscopy (CLSM) analysis and biofilm formation assay using DNase I revealed that biofilm formation by the hldE strain was dependent on extracellular DNA. Furthermore, a loss of flagella and an increase in amount of outer membrane vesicles in case of the hldE strain were also observed by transmission electron microscopy and atomic force microscopy, respectively. In addition, we demonstrated that a mutation in the hldE locus, which alters the LPS structure, caused changes in both expression and properties of several surface bacterial factors involved in biofilm formation and virulence. We suggest that the implication of these results should be considered in the context of biofilm formation on abiotic surfaces, which is frequently associated with nosocominal infections such as the catheter-associated infections.},
author = {Nakao, Ryoma and Ramstedt, Madeleine and Wai, Sun Nyunt and Uhlin, Bernt Eric},
doi = {10.1371/journal.pone.0051241},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nakao et al. - Enhanced Biofilm Formation by Escherichia coli LPS Mutants Defective in Hep Biosynthesis. - 2012.pdf:pdf},
issn = {1932-6203},
journal = {PloS one},
month = {jan},
number = {12},
pages = {e51241},
pmid = {23284671},
title = {{Enhanced Biofilm Formation by Escherichia coli LPS Mutants Defective in Hep Biosynthesis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3532297{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {7},
year = {2012}
}
@article{Fallman2003,
abstract = {A systematic study of the influence of a glass-water interface on the on-axis trapping of micrometer-sized spherical objects by optical tweezers is presented. The ways in which the escape force and the trapping position, as well as the stiffness of the trap, depend on the focusing depth, the numerical aperture, and the degree of overfilling of the objective entrance pupil are investigated. It is concluded, among other things, that objectives with the highest numerical aperture and the use of large degrees of overfilling do not always provide the optimum trapping conditions at finite depths.},
author = {F{\"{a}}llman, Erik and Axner, Ove},
doi = {10.1364/AO.42.003915},
file = {:E$\backslash$:/Mina Dokument/Mendeley/F{\"{a}}llman, Axner - Influence of a Glass-Water Interface on the On-Axis Trapping of Micrometer-Sized Spherical Objects by Optical Tweezers.pdf:pdf},
issn = {0003-6935},
journal = {Applied Optics},
number = {19},
pages = {3915--3926},
pmid = {12868831},
title = {{Influence of a Glass-Water Interface on the On-Axis Trapping of Micrometer-Sized Spherical Objects by Optical Tweezers}},
url = {http://www.opticsinfobase.org/abstract.cfm?id=72824$\backslash$nhttp://www.opticsinfobase.org/abstract.cfm?URI=AO-42-19-3915},
volume = {42},
year = {2003}
}
@article{Samadi2014,
author = {Samadi, Akbar and Zhang, Chensong and Chen, Joseph and Reihani, S. N. S. and Chen, Zhigang},
doi = {10.1364/BOE.6.000112},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Samadi et al. - Evaluating the toxic effect of an antimicrobial agent on single bacterial cells with optical tweezers - 2014.pdf:pdf},
issn = {2156-7085},
journal = {Biomedical Optics Express},
month = {dec},
number = {1},
pages = {112},
title = {{Evaluating the toxic effect of an antimicrobial agent on single bacterial cells with optical tweezers}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=boe-6-1-112},
volume = {6},
year = {2014}
}
@article{Hammermann1997,
abstract = {Using laser light scattering, we have measured the static and dynamic structure factor of two different superhelical DNAs, p1868 (1868 bp) and simian virus 40 (SV40) (5243 bp), in dilute aqueous solution at salt concentrations between 1 mM and 3 M NaCl. For both DNA molecules, Brownian dynamics (BD) simulations were also performed, using a previously described model. A Fourier mode decomposition procedure was used to compute theoretical light scattering autocorrelation functions (ACFs) from the BD trajectories. Both measured and computed autocorrelation functions were then subjected to the same multiexponential decomposition procedure. Simulated and measured relaxation times as a function of scattering angle were in very good agreement. Similarly, computed and measured static structure factors and radii of gyration agreed within experimental error. One main result of this study is that the amplitudes of the fast-relaxing component in the ACF show a peak at 1 M salt concentration. This nonmonotonic behavior might be caused by an initial increase in the amplitudes of internal motions due to diminishing long-range electrostatic repulsions, followed by a decrease at higher salt concentration due to a compaction of the structure.},
author = {Hammermann, M and Steinmaier, C and Merlitz, H and Kapp, U and Waldeck, W and Chirico, G and Langowski, J},
doi = {10.1016/S0006-3495(97)78296-1},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hammermann et al. - Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dy.pdf:pdf},
isbn = {4962214233},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Biophysical Phenomena,Biophysics,Computer Simulation,DNA, Superhelical,DNA, Superhelical: chemistry,DNA, Viral,DNA, Viral: chemistry,Diffusion,Lasers,Light,Models, Molecular,Nucleic Acid Conformation,Plasmids,Scattering, Radiation,Simian virus 40,Simian virus 40: chemistry,Sodium Chloride,Sodium Chloride: pharmacology},
month = {nov},
number = {5},
pages = {2674--87},
pmid = {9370461},
title = {{Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1181169{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {73},
year = {1997}
}
@article{DeLaFuente2007,
abstract = {Xylella fastidiosa, a bacterium responsible for Pierce's disease in grapevines, possesses both type I and type IV pili at the same cell pole. Type IV pili facilitate twitching motility, and type I pili are involved in biofilm development. The adhesiveness of the bacteria and the roles of the two pili types in attachment to a glass substratum were evaluated using a microfluidic flow chamber in conjunction with pilus-defective mutants. The average adhesion force necessary to detach wild-type X. fastidiosa cells was 147 +/- 11 pN. Mutant cells possessing only type I pili required a force of 204 +/- 22 pN for removal, whereas cells possessing only type IV pili required 119 +/- 8 pN to dislodge these cells. The experimental results demonstrate that microfluidic flow chambers are useful and convenient tools for assessing the drag forces necessary for detaching bacterial cells and that with specific pilus mutants, the role of the pilus type can be further assessed.},
author = {{De La Fuente}, Leonardo and Montanes, Emilie and Meng, Yizhi and Li, Yaxin and Burr, Thomas J and Hoch, H C and Wu, Mingming},
doi = {10.1128/AEM.02649-06},
file = {:E$\backslash$:/Mina Dokument/Mendeley/De La Fuente et al. - Assessing adhesion forces of type I and type IV pili of Xylella fastidiosa bacteria by use of a microfluidic flow.pdf:pdf},
issn = {0099-2240},
journal = {Applied and environmental microbiology},
keywords = {Bacterial Adhesion,Colony Count, Microbial,Fimbriae, Bacterial,Fimbriae, Bacterial: genetics,Fimbriae, Bacterial: physiology,Glass,Image Processing, Computer-Assisted,Microfluidic Analytical Techniques,Xylella,Xylella: genetics,Xylella: physiology},
month = {apr},
number = {8},
pages = {2690--6},
pmid = {17293518},
title = {{Assessing adhesion forces of type I and type IV pili of Xylella fastidiosa bacteria by use of a microfluidic flow chamber.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1855618{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {73},
year = {2007}
}
@phdthesis{Yongning2011,
author = {Yongning, Lu},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yongning - Uropathogenic Escherichia coli ( UPEC ) cause impairment of spermatogenesis by inducing programmed necrosis - 2011.pdf:pdf},
title = {{Uropathogenic Escherichia coli ( UPEC ) cause impairment of spermatogenesis by inducing programmed necrosis}},
year = {2011}
}
@article{Zakrisson2012,
abstract = {Biopolymers are vital structures for many living organisms; for a variety of bacteria, adhesion polymers play a crucial role for the initiation of colonization. Some bacteria express, on their surface, attachment organelles (pili) that comprise subunits formed into stiff helix-like structures that possess unique biomechanical properties. These helix-like structures possess a high degree of flexibility that gives the biopolymers a unique extendibility. This has been considered beneficial for piliated bacteria adhering to host surfaces in the presence of a fluid flow. We show in this work that helix-like pili have the ability to act as efficient dampers of force that can, for a limited time, lower the load on the force-mediating adhesin-receptor bond on the tip of an individual pilus. The model presented is applied to bacteria adhering with a single pilus of either of the two most common types expressed by uropathogenic Escherichia coli, P or type 1 pili, subjected to realistic flows. The results indicate that for moderate flows ({\~{}}25 mm/s) the force experienced by the adhesin-receptor interaction at the tip of the pilus can be reduced by a factor of {\~{}}6 and {\~{}}4, respectively. The uncoiling ability provides a bacterium with a "go with the flow" possibility that acts as a damping. It is surmised that this can be an important factor for the initial part of the adhesion process, in particular in turbulent flows, and thereby be of use for bacteria in their striving to survive a natural defense such as fluid rinsing actions.},
author = {Zakrisson, Johan and Wiklund, Krister and Axner, Ove and Andersson, Magnus},
doi = {10.1007/s00249-012-0814-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Zakrisson et al. - Helix-like biopolymers can act as dampers of force for bacteria in flows. - 2012.pdf:pdf},
issn = {0175-7571},
journal = {European biophysics journal},
keywords = {Bacteria,Bacteria: metabolism,Bacterial,Bacterial Adhesion: physiology,Bacterial Physiological Phenomena,Bacterial: physiology,Biological,Biomechanics,Biopolymers,Biopolymers: chemistry,Biopolymers: metabolism,Computer Simulation,Mechanical,Models,Stress,bacterial adhesion,damping,fimbriae,pili,uncoiling},
month = {may},
number = {6},
pages = {551--60},
pmid = {22562139},
title = {{Helix-like biopolymers can act as dampers of force for bacteria in flows.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22562139 http://www.springerlink.com/content/34050071l5021655/},
volume = {41},
year = {2012}
}
@article{Pereira2013,
abstract = {Escherichia coli colonizes the human intestine shortly after birth, with most strains engaging in a commensal relationship. However, some E. coli strains have evolved toward acquiring genetic traits associated with virulence. Currently, five categories of enteroadherent E. coli strains are well-recognized, and are classified in regard to expressed adhesins and the strategy used during the colonization. The high morbidity associated with diarrhea has motivated investigations focusing on E. coli adhesins, as well on factors that inhibit bacterial adherence. Breastfeeding has proved to be the most effective strategy for preventing diarrhea in children. Aside from the immunoglobulin content, glycocompounds and oligosaccharides in breast milk play a critical role in the innate immunity against diarrheagenic E. coli strains. This review summarizes the colonization factors and virulence strategies exploited by diarrheagenic E. coli strains, addressing the inhibitory effects that oligosaccharides and glycocompounds, such as lactoferrin and free secretory components, exert on the adherence and virulence of these strains. This review thus provides an overview of experimental data indicating that human milk glycocompounds are responsible for the universal protective effect of breastfeeding against diarrheagenic E. coli pathotypes.},
author = {Pereira, Alex L and Giugliano, Loreny G},
doi = {10.3390/biology2020810},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Pereira, Giugliano - Adhesion of Diarrheagenic Escherichia coli and Inhibition by Glycocompounds Engaged in the Mucosal Innate Immunity..pdf:pdf},
issn = {2079-7737},
journal = {Biology},
pages = {810--31},
pmid = {24832810},
title = {{Adhesion of Diarrheagenic Escherichia coli and Inhibition by Glycocompounds Engaged in the Mucosal Innate Immunity.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3960885{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {2},
year = {2013}
}
@article{Schmidtke2000,
abstract = {Adhesion and subsequent aggregation between neutrophils and platelets is dependent upon the initial binding of P-selectin on activated platelets to P-selectin glycoprotein ligand 1 (PSGL-1) on the microvilli of neutrophils. High speed, high resolution videomicroscopy of flowing neutrophils interacting with spread platelets demonstrated that thin membrane tethers were pulled from neutrophils in 32 +/- 4{\%} of the interactions. After capture by spread platelets, neutrophil membrane tethers (length of 5.9 +/- 4.1 microm, n = 63) were pulled at an average rate of 6-40 microm/s as the wall shear rate was increased from 100-250 s(-1). The average tether lifetime decreased significantly (P < 0.001) from 630 to 133 ms as the shear rate was increased from 100 s(-1) (F(bond) = 86 pN) to 250 s(-1) (F(bond) = 172 pN), which is consistent with P-selectin/PSGL-1 bond dynamics under stress. Tether formation was blocked by antibodies against P-selectin or PSGL-1, but not by anti-CD18 antibodies. During neutrophil rolling on P-selectin at 150 s(-1), thin membrane tethers were also pulled from the neutrophils. The characteristic jerking motion of the neutrophil coexisted with tether growth (8.9 +/- 8.8 microm long), whereas tether breakage (average lifetime of 3.79 +/- 3.32 s) caused an acute jump in the rolling velocity, proving multiple bonding in the cell surface and the tether surface contact area. Extremely long membrane tethers (>40 microm) were sometimes pulled, which detached in a flow-dependent mechanism of microparticle formation. Membrane tethers were also formed when neutrophils were perfused over platelet monolayers. These results are the first visualization of the often hypothesized tethers that shield the P-selectin/PSGL-1 bond from force loading to regulate neutrophil rolling during inflammation and thrombosis.},
author = {Schmidtke, D W and Diamond, S L},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schmidtke, Diamond - Direct observation of membrane tethers formed during neutrophil attachment to platelets or P-selectin under physiol.pdf:pdf},
issn = {0021-9525},
journal = {The Journal of cell biology},
keywords = {Antibodies,Antibodies: pharmacology,Blood Platelets,Blood Platelets: metabolism,Cell Adhesion,Cell Movement,Humans,Membrane Glycoproteins,Membrane Glycoproteins: metabolism,Microscopy, Video,Neutrophils,Neutrophils: metabolism,P-Selectin,P-Selectin: metabolism,Platelet Activation,Rheology,Stress, Mechanical,Surface Properties},
month = {may},
number = {3},
pages = {719--30},
pmid = {10791984},
title = {{Direct observation of membrane tethers formed during neutrophil attachment to platelets or P-selectin under physiological flow.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2174847{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {149},
year = {2000}
}
@article{Valvatne2002,
abstract = {A considerable proportion of enterotoxigenic Escherichia coli (ETEC) do not possess identifiable colonization factors (CFs). Genetic fingerprint analyses based on repetitive sequence-based polymerase chain reaction (rep-PCR) showed that 9 of 10 such CF-negative isolates which produced the thermolabile and the porcine thermostabile enterotoxin could be divided into three clusters. Following transformation with a plasmid harbouring the gene encoding CfaR, a positive regulator for several ETEC adhesins, three of the six strains in the first cluster expressed coli surface antigen 20 (CS20). No CFs were identified on the two transformed strains in the second cluster while the transformants of the two strains in the last cluster expressed CS12, the N-terminal amino acid sequence of which was deciphered. The study illustrates the potential of using genetic fingerprinting to group ETEC into clusters of strains with genes encoding different CFs and confirms the ability of CfaR to induce the expression of several different CFs.},
author = {Valvatne, H{\aa}vard and Steinsland, Hans and Sommerfelt, Halvor},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Valvatne, Steinsland, Sommerfelt - Clonal clustering and colonization factors among thermolabile and porcine thermostable enterotoxin-pr.pdf:pdf},
issn = {0903-4641},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
keywords = {Amino Acid Sequence,Bacterial Toxins,Bacterial Toxins: biosynthesis,DNA Fingerprinting,Enterotoxins,Enterotoxins: biosynthesis,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: analysis,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Escherichia coli Proteins: metabolism,Escherichia coli: classification,Escherichia coli: genetics,Escherichia coli: immunology,Fimbriae Proteins,Fimbriae Proteins: analysis,Fimbriae Proteins: genetics,Fimbriae, Bacterial,Fimbriae, Bacterial: genetics,Fimbriae, Bacterial: metabolism,Fimbriae, Bacterial: ultrastructure,Genes, Bacterial,Humans,Molecular Sequence Data,Molecular Weight,Multigene Family,Plasmids,Repetitive Sequences, Nucleic Acid},
month = {sep},
number = {9},
pages = {665--72},
pmid = {12529021},
title = {{Clonal clustering and colonization factors among thermolabile and porcine thermostable enterotoxin-producing Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12529021},
volume = {110},
year = {2002}
}
@article{Ruan2014,
abstract = {Diarrhea is the second leading cause of death in children younger than 5 years and continues to be a major threat to global health. Enterotoxigenic Escherichia coli (ETEC) strains are the most common bacteria causing diarrhea in developing countries. ETEC strains are able to attach to host small intestinal epithelial cells by using bacterial colonization factor antigen (CFA) adhesins. This attachment helps to initiate the diarrheal disease. Vaccines that induce antiadhesin immunity to block adherence of ETEC strains that express immunologically heterogeneous CFA adhesins are expected to protect against ETEC diarrhea. In this study, we created a CFA multiepitope fusion antigen (MEFA) carrying representative epitopes of CFA/I, CFA/II (CS1, CS2, and CS3), and CFA/IV (CS4, CS5, and CS6), examined its immunogenicity in mice, and assessed the potential of this MEFA as an antiadhesin vaccine against ETEC. Mice intraperitoneally immunized with this CFA MEFA exhibited no adverse effects and developed immune responses to CFA/I, CFA/II, and CFA/IV adhesins. Moreover, after incubation with serum of the immunized mice, ETEC or E. coli strains expressing CFA/I, CFA/II, or CFA/IV adhesins were significantly inhibited in adherence to Caco-2 cells. Our results indicated this CFA MEFA elicited antibodies that not only cross-reacted to CFA/I, CFA/II and CFA/IV adhesins but also broadly inhibited adherence of E. coli strains expressing these seven adhesins and suggested that this CFA MEFA could be a candidate to induce broad-spectrum antiadhesin protection against ETEC diarrhea. Additionally, this antigen construction approach (creating an MEFA) may be generally used in vaccine development against heterogenic pathogens.},
author = {Ruan, Xiaosai and Knudsen, David E. and Wollenberg, Katie M. and Sack, David a. and Zhang, Weiping},
doi = {10.1128/CVI.00652-13},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ruan et al. - Multiepitope fusion antigen induces broadly protective antibodies that prevent adherence of Escherichia coli strains expre.pdf:pdf},
issn = {15566811},
journal = {Clinical and Vaccine Immunology},
number = {2},
pages = {243--249},
pmid = {24351757},
title = {{Multiepitope fusion antigen induces broadly protective antibodies that prevent adherence of Escherichia coli strains expressing colonization factor antigen I (CFA/I), CFA/II, and CFA/IV}},
volume = {21},
year = {2014}
}
@article{Mu2006b,
abstract = {High-resolution structures of macromolecular complexes offer unparalleled insight into the workings of biological systems and hence the interplay of these systems in health and disease. We have adopted a multifaceted approach to understanding the pathogenically important structure of P-pili, the class I adhesion pili from pyelonephritic Escherichia coli. Our approach combines electron cryomicroscopy, site-directed mutagenesis, homology modeling, and energy calculations, resulting in a high-resolution model of PapA, the major structural element of these pili. Fitting of the modeled PapA subunit into the electron cryomicroscopy data provides a detailed view of these pilins within the supramolecular architecture of the pilus filament. A structural hinge in the N-terminal region of the subunit is located at the site of a newly resolved electron density that protrudes from the P-pilus surface. The structural flexibility provided by this hinge is necessary for assembly of P-pili, illustrating one solution to construction of large macromolecular complexes from small repeating units. These data support our hypothesis that domain-swapped pilin subunits transit the outer cell membrane vertically and rotate about the hinge for final positioning into the pilus filament. Our data confirm and supply a structural basis for much previous genetic, biochemical, and structural data. This model of the P-pilus filament provides an insight into the mechanism of assembly of a macromolecular complex essential for initiation of kidney infection by these bacteria.},
author = {Mu, Xiang-Qi and Bullitt, Esther},
doi = {10.1073/pnas.0509620103},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Mu, Bullitt - Structure and assembly of P-pili a protruding hinge region used for assembly of a bacterial adhesion filament. - 2006.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Bacterial Adhesion,Cryoelectron Microscopy,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Escherichia coli: pathogenicity,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: genetics,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Fimbriae, Bacterial: genetics,Fimbriae, Bacterial: ultrastructure,Models, Molecular,Mutagenesis, Site-Directed,Protein Conformation},
month = {jun},
number = {26},
pages = {9861--6},
pmid = {16782819},
title = {{Structure and assembly of P-pili: a protruding hinge region used for assembly of a bacterial adhesion filament.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1502544{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {103},
year = {2006}
}
@article{Silverblatt1983,
abstract = {Since Duguid and Guilles first described the ability of piliated bacteria to bind to leukocytes, much has been learned about the nature of this interaction. Mannose-sensitive (MS) pili bind to specific mannose-containing receptors on the leukocyte surface. While MS pili are responsible for attachment, the relative hydrophobicity of the bacterial surface determines whether the organism is internalized. Both binding and ingestion trigger the leukocyte to respond with degranulation and enhanced oxidative activity. The response to piliated bacteria, however, is delayed as compared to bacteria opsonized with serum, which may account for the reduced bactericidal activity associated with pili-mediated phagocytosis. A number of factors appear to influence the significance of pili-mediated phagocytosis in vivo. These include natural selective pressures in the host tissue, the ability of the organism to undergo pili phase transition and the presence of serum or other host opsonic factors. Antipili antibody does not enhance leukocyte killing of MS + Escherichia coli, but does stimulate leukocyte metabolic activity. Antipili antibody may, therefore, have an adverse effect on the infectious process by promoting the extracellular release of inflammatory material from the granulocyte.},
author = {Silverblatt, F J and Ofek, I},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Silverblatt, Ofek - Interaction of bacterial pili and leukocytes. - 1983.pdf:pdf},
issn = {0300-8126},
journal = {Infection},
keywords = {Animals,Antibodies, Bacterial,Antibodies, Bacterial: physiology,Escherichia coli,Escherichia coli: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: immunology,Fimbriae, Bacterial: metabolism,Humans,Leukocytes,Leukocytes: metabolism,Leukocytes: microbiology,Leukocytes: ultrastructure,Phagocytosis,Proteus mirabilis,Proteus mirabilis: metabolism,Proteus mirabilis: ultrastructure,Pyelonephritis,Pyelonephritis: blood,Pyelonephritis: microbiology,Rats,Receptors, Fc},
number = {4},
pages = {235--8},
pmid = {6137459},
title = {{Interaction of bacterial pili and leukocytes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/6137459},
volume = {11},
year = {1983}
}
@article{Bjarnsholt2013,
abstract = {Most of the research on bacterial pathogenesis has focused on acute infections, but much less is known about the pathogenesis of infections caused by bacteria that grow as aggregates in biofilms. These infections tend to be chronic as they resist innate and adaptive immune defence mechanisms as well as antibiotics, and the treatment of biofilm infections presents a considerable unmet clinical need. To date, there are no drugs that specifically target bacteria in biofilms; however, several approaches are in early-stage development. Here, we review current insights into biofilm physiology and pathology, and discuss how a deep insight into the physical and biological characteristics of biofilms can inform therapeutic strategies and molecular targets for the development of anti-biofilm drugs.},
author = {Bjarnsholt, Thomas and Ciofu, Oana and Molin, S{\o}ren and Givskov, Michael and H{\o}iby, Niels},
doi = {10.1038/nrd4000},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bjarnsholt et al. - Applying insights from biofilm biology to drug development - can a new approach be developed - 2013.pdf:pdf},
isbn = {1474-1784 (Electronic)$\backslash$r1474-1776 (Linking)},
issn = {1474-1784},
journal = {Nature reviews. Drug discovery},
keywords = {Acute Disease,Adaptive Immunity,Animals,Anti-Bacterial Agents,Anti-Bacterial Agents: pharmacology,Bacterial Infections,Bacterial Infections: drug therapy,Bacterial Infections: immunology,Bacterial Infections: microbiology,Biofilms,Biofilms: drug effects,Chronic Disease,Drug Design,Humans,Immunity, Innate,Molecular Targeted Therapy},
number = {10},
pages = {791--808},
pmid = {24080700},
title = {{Applying insights from biofilm biology to drug development - can a new approach be developed?}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24080700},
volume = {12},
year = {2013}
}
@article{Bjornham2009a,
abstract = {A number of biomechanical properties of various types of pili expressed by Escherichia coli, predominantly their force-versus-elongation behavior, have previously been assessed in detail on a single pilus level. In vivo, however, bacteria bind in general to host cells by a multitude of pili, which presumably provides them with adhesion properties that differs from those of single pili. Based upon the previously assessed biomechanical properties of individual pili, this work presents a theoretical analysis of the adhesion properties of multipili-attaching bacteria expressing helixlike pili exposed to an external force. Expressions for the adhesion lifetime of dual- and multipili-attaching bacteria are derived and their validity is verified by Monte Carlo simulations. It is demonstrated that the adhesion lifetime of a multipili-binding bacterium depends to a large degree on the cooperativity of the attaching pili, which, in turn, depends strongly on their internal biomechanical properties, in particular their helixlike structure and its ability to elongate, which, in turn, depends on the intrinsic properties of the bonds, e.g., their lengths and activation energies. It is shown, for example, that a decrease in the length of a layer-to-layer bond in the rod of P pili, expressed by E. coli, by 50{\%} leads to a decrease in the adhesion lifetime of a bacterium attaching by ten pili and exposed to a force of 500 pN by three orders of magnitude. The results indicate moreover that the intrinsic properties of the rod for this particular type of pili are optimized for multipili attachment under a broad range of external forces and presumably also to its in vivo environment. For example, P pili seems to be optimized to withstand a force exposure during approximately 3 s, which correspond to the time it takes for a bolus to pass a bacterium attached to the ureteral wall. Even though the results presented in this work apply quantitatively to one type of pilus, they are assumed to apply qualitatively to all helixlike pili systems expressing slip bonds.},
author = {Bj{\"{o}}rnham, Oscar and Axner, Ove},
doi = {10.1063/1.3148027},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bj{\"{o}}rnham, Axner - Multipili attachment of bacteria with helixlike pili exposed to stress. - 2009.pdf:pdf},
issn = {1089-7690},
journal = {The Journal of chemical physics},
keywords = {Bacterial Adhesion,Bacterial Adhesion: physiology,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Fimbriae, Bacterial: metabolism,Monte Carlo Method,Stress, Mechanical},
month = {jun},
number = {23},
pages = {235102},
pmid = {19548763},
title = {{Multipili attachment of bacteria with helixlike pili exposed to stress.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19548763},
volume = {130},
year = {2009}
}
@article{Sullan2014,
abstract = {Although bacterial pili are known to mediate cell adhesion to a variety of substrates, the molecular interactions behind this process are poorly understood. We report the direct measurement of the forces guiding pili-mediated adhesion, focusing on the medically important probiotic bacterium Lactobacillus rhamnosus GG (LGG). Using non-invasive single-cell force spectroscopy (SCFS), we quantify the adhesion forces between individual bacteria and biotic (mucin, intestinal cells) or abiotic (hydrophobic monolayers) surfaces. On hydrophobic surfaces, bacterial pili strengthen adhesion through remarkable nanospring properties, which - presumably - enable the bacteria to resist high shear forces under physiological conditions. On mucin, nanosprings are more frequent and adhesion forces larger, reflecting the influence of specific pili-mucin bonds. Interestingly, these mechanical responses are no longer observed on human intestinal Caco-2 cells. Rather, force curves exhibit constant force plateaus with extended ruptures reflecting the extraction of membrane nanotethers. These single-cell analyses provide novel insights into the molecular mechanisms by which piliated bacteria colonize surfaces (nanosprings, nanotethers), and offer exciting avenues in nanomedicine for understanding and controlling the adhesion of microbial cells (probiotics, pathogens).},
author = {Sullan, Ruby May a and Beaussart, Audrey and Tripathi, Prachi and Derclaye, Sylvie and El-Kirat-Chatel, Sofiane and Li, James K and Schneider, Yves-Jacques and Vanderleyden, Jos and Lebeer, Sarah and Dufr{\^{e}}ne, Yves F},
doi = {10.1039/c3nr05462d},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sullan et al. - Single-cell force spectroscopy of pili-mediated adhesion. - 2014.pdf:pdf},
issn = {2040-3372},
journal = {Nanoscale},
keywords = {Bacterial Adhesion,Caco-2 Cells,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Humans,Hydrophobic and Hydrophilic Interactions,Lactobacillus rhamnosus,Lactobacillus rhamnosus: physiology,Microscopy, Atomic Force,Mucins,Mucins: chemistry,Mucins: metabolism,Nanomedicine,Surface Properties},
month = {jan},
number = {2},
pages = {1134--43},
pmid = {24296882},
title = {{Single-cell force spectroscopy of pili-mediated adhesion.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24296882},
volume = {6},
year = {2014}
}
@article{Wang2012,
author = {Wang, Shouyu and Xue, Liang and Lai, Jiancheng and Li, Zhenhua},
doi = {10.1088/2040-8978/14/6/065301},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wang et al. - Three-dimensional refractive index reconstruction of red blood cells with one-dimensional moving based on local plane wave.pdf:pdf},
issn = {2040-8978},
journal = {Journal of Optics},
keywords = {1,an important technique to,in colour only in,interferometric microscopy,introduction and background,obtain,optical phase microscopy is,red blood cells,refractive index reconstruction,some figures may appear,the online journal},
month = {jun},
number = {6},
pages = {065301},
title = {{Three-dimensional refractive index reconstruction of red blood cells with one-dimensional moving based on local plane wave approximation}},
url = {http://stacks.iop.org/2040-8986/14/i=6/a=065301?key=crossref.0deac6684e1ff88b114cd05ab37b4451},
volume = {14},
year = {2012}
}
@book{Pope2000,
abstract = {This is a graduate text on turbulent flows, an important topic in fluid dynamics. It is up-to-date, comprehensive, designed for teaching, and is based on a course taught by the author at Cornell University for a number of years. The book consists of two parts followed by a number of appendices. Part I provides a general introduction to turbulent flows, how they behave, how they can be described quantitatively, and the fundamental physical processes involved. Part II is concerned with different approaches for modelling or simulating turbulent flows. The necessary mathematical techniques are presented in the appendices. This book is primarily intended as a graduate level text in turbulent flows for engineering students, but it may also be valuable to students in applied mathematics, physics, oceanography and atmospheric sciences, as well as researchers and practising engineers.},
author = {Pope, Stephen Baily},
booktitle = {Book},
doi = {10.1088/1468-5248/1/1/702},
isbn = {0521598869},
issn = {14685248},
pages = {771},
publisher = {Cambridge University Press},
title = {{Turbulent Flows}},
volume = {1},
year = {2000}
}
@article{Fallman2004,
author = {F{\"{a}}llman, Erik and Schedin, Staffan and Jass, Jana and Andersson, Magnus and Uhlin, Bernt Eric and Axner, Ove},
doi = {dx.doi.org/10.1016/j.bios.2003.12.029},
file = {:E$\backslash$:/Mina Dokument/Mendeley/F{\"{a}}llman et al. - Optical tweezers based force measurement system for quantitating binding interactions system design and application for.pdf:pdf},
journal = {Biosensors and Bioelectronics},
number = {11},
pages = {1429--1437},
title = {{Optical tweezers based force measurement system for quantitating binding interactions: system design and application for the study of bacterial adhesion}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0956566303004615},
volume = {19},
year = {2004}
}
@article{Brenner1961a,
author = {Brenner, Howard},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Brenner - The slow motion of a sphere through a viscous a plane surface - 1961.pdf:pdf},
journal = {Chemical Engineering Science},
pages = {242--251},
title = {{The slow motion of a sphere through a viscous a plane surface}},
volume = {16},
year = {1961}
}
@article{Wakiya1964a,
author = {Wakiya, Shoichi},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wakiya - Effect of a plane wall on the impulsive motion of a sphere in a viscous fluid - 1964.pdf:pdf},
journal = {Journal of the Physical Society of Japan},
number = {8},
pages = {1401--1408},
title = {{Effect of a plane wall on the impulsive motion of a sphere in a viscous fluid}},
volume = {19},
year = {1964}
}
@article{Galkin2013,
abstract = {Enterotoxigenic Escherichia coli (ETEC) is a bacterial pathogen that causes diarrhea in children and travelers in developing countries. ETEC adheres to host epithelial cells in the small intestine via a variety of different pili. The CS1 pilus is a prototype for a family of related pili, including the CFA/I pili, present on ETEC and other Gram-negative bacterial pathogens. These pili are assembled by an outer membrane usher protein that catalyzes subunit polymerization via donor strand complementation, in which the N terminus of each incoming pilin subunit fits into a hydrophobic groove in the terminal subunit, completing a $\beta$-sheet in the Ig fold. Here we determined a crystal structure of the CS1 major pilin subunit, CooA, to a 1.6-{\AA} resolution. CooA is a globular protein with an Ig fold and is similar in structure to the CFA/I major pilin CfaB. We determined three distinct negative-stain electron microscopic reconstructions of the CS1 pilus and generated pseudoatomic-resolution pilus structures using the CooA crystal structure. CS1 pili adopt multiple structural states with differences in subunit orientations and packing. We propose that the structural perturbations are accommodated by flexibility in the N-terminal donor strand of CooA and by plasticity in interactions between exposed flexible loops on adjacent subunits. Our results suggest that CS1 and other pili of this class are extensible filaments that can be stretched in response to mechanical stress encountered during colonization.},
author = {Galkin, Vitold E and Kolappan, Subramaniapillai and Ng, Dixon and Zong, ZuSheng and Li, Juliana and Yu, Xiong and Egelman, Edward H and Craig, Lisa},
doi = {10.1128/JB.01989-12},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Galkin et al. - The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism. - 2013.pdf:pdf},
issn = {1098-5530},
journal = {Journal of bacteriology},
keywords = {Amino Acid Sequence,Bacterial,Bacterial: chemistry,Bacterial: ultrastructure,Crystallography,Electron,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: chemistry,Enterotoxigenic Escherichia coli: ultrastructure,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: chemistry,Microscopy,Models,Molecular,Molecular Sequence Data,X-Ray},
month = {apr},
number = {7},
pages = {1360--70},
pmid = {23175654},
title = {{The structure of the CS1 pilus of enterotoxigenic Escherichia coli reveals structural polymorphism.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23175654},
volume = {195},
year = {2013}
}
@article{Bustanji2003,
abstract = {Fibronectin (Fn) is an important mediator of bacterial invasions and of persistent infections like that of Staphylococcus epidermis. Similar to many other types of cell-protein adhesion, the binding between Fn and S. epidermidis takes place under physiological shear rates. We investigated the dynamics of the interaction between individual living S. epidermidis cells and single Fn molecules under mechanical force by using the scanning force microscope. The mechanical strength of this interaction and the binding site in the Fn molecule were determined. The energy landscape of the binding/unbinding process was mapped, and the force spectrum and the association and dissociation rate constants of the binding pair were measured. The interaction between S. epidermidis cells and Fn molecules is compared with those of two other protein/ligand pairs known to mediate different dynamic states of adhesion of cells under a hydrodynamic flow: the firm adhesion mediated by biotin/avidin interactions, and the rolling adhesion, mediated by L-selectin/P-selectin glycoprotein ligand-1 interactions. The inner barrier in the energy landscape of the Fn case characterizes a high-energy binding mode that can sustain larger deformations and for significantly longer times than the correspondent high-strength L-selectin/P-selectin glycoprotein ligand-1 binding mode. The association kinetics of the former interaction is much slower to settle than the latter. On this basis, the observations made at the macroscopic scale by other authors of a strong lability of the bacterial adhesions mediated by Fn under high turbulent flow are rationalized at the molecular level.},
author = {Bustanji, Yasser and Arciola, Carla Renata and Conti, Matteo and Mandello, Enrico and Montanaro, Lucio and Samor{\'{\i}}, Bruno},
doi = {10.1073/pnas.1735343100},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bustanji et al. - Dynamics of the interaction between a fibronectin molecule and a living bacterium under mechanical force. - 2003.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Avidin,Avidin: chemistry,Bacterial Adhesion,Biophysical Phenomena,Biophysics,Biotin,Biotin: chemistry,Cell Adhesion,Fibronectins,Fibronectins: chemistry,Humans,Kinetics,Microscopy, Atomic Force,Protein Binding,Staphylococcus aureus,Staphylococcus aureus: metabolism,Staphylococcus epidermidis,Staphylococcus epidermidis: metabolism,Time Factors,Water},
month = {nov},
number = {23},
pages = {13292--7},
pmid = {14573699},
title = {{Dynamics of the interaction between a fibronectin molecule and a living bacterium under mechanical force.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=263788{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {100},
year = {2003}
}
@article{Thankavel1997,
abstract = {The FimH subunit of type 1-fimbriated Escherichia coli has been implicated as an important determinant of bacterial adherence and colonization of the urinary tract. Here, we sought to localize the functionally important domain(s) within the FimH molecule and to determine if antibodies against this domain would block adherence of type 1-fimbriated E. coli to the bladder mucosa in situ and in vivo in an established mouse model of cystitis. We generated translational fusion proteins of disparate regions of the FimH molecule with an affinity tag MalE, and tested each of the fusion products in vitro for functional activity. The minimum region responsible for binding mouse bladder epithelial cells and a soluble mannoprotein, horseradish peroxidase, was contained within residues 1-100 of the FimH molecule. We validated and extended these findings by demonstrating that antibodies directed at the putative binding region of FimH or at synthetic peptides corresponding to epitopes within the binding domain could specifically block type 1 fimbriae-mediated bacterial adherence to bladder epithelial cells in situ and yeast cells in vitro. Next, we compared the ability of mice passively immunized intraperitoneally with antisera raised against residues 1-25 and 253-264 of FimH or 1-13 of FimA to resist bladder colonization in vivo after intravesicular challenge with type 1-fimbriated E. coli. Only the antibody directed at the putative binding region of FimH (anti- s-FimH1-25) significantly reduced E. coli bladder infections in the experimental mouse model of urinary tract infections. Similar results were obtained when the mice were actively immunized with synthetic peptides corresponding to residues 1-25 and 253-264 of FimH or 1-13 of FimA. The mechanism of protection was attributed, at least in part, to inhibition of bacterial adherence to the bladder surface by s-FimH1-25-specific antibody molecules that had filtered through the kidneys into the urine. The level of FimH antibodies entering the bladder from the circulatory system of the immunized mice was found to be markedly enhanced upon bacterial challenge. The potential broad spectrum activity of the protective FimH antibody was indicated from its serologic cross-reactivity with various urinary tract bacterial isolates bearing type 1 fimbriae. These findings could be relevant in the design of an efficacious and broadly reactive FimH vaccine against urinary tract infections.},
author = {Thankavel, K and Madison, B and Ikeda, T and Malaviya, R and Shah, a H and Arumugam, P M and Abraham, S N},
doi = {10.1172/JCI119623},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Thankavel et al. - Localization of a domain in the FimH adhesin of Escherichia coli type 1 fimbriae capable of receptor recognition and.pdf:pdf},
isbn = {3143629045},
issn = {0021-9738},
journal = {The Journal of clinical investigation},
keywords = {ATP-Binding Cassette Transporters,Adhesins, Bacterial,Adhesins, Bacterial: immunology,Adhesins, Escherichia coli,Animals,Antibodies, Bacterial,Antibodies, Bacterial: immunology,Bacterial Adhesion,Carrier Proteins,Carrier Proteins: metabolism,Cells, Cultured,Cross Reactions,Escherichia coli,Escherichia coli Proteins,Escherichia coli: immunology,Female,Fimbriae Proteins,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Immunization, Passive,Maltose-Binding Proteins,Mice,Mice, Inbred ICR,Monosaccharide Transport Proteins,Periplasmic Binding Proteins,Urinary Bladder,Urinary Bladder: microbiology,Urinary Tract Infections,Urinary Tract Infections: prevention {\&} control},
month = {sep},
number = {5},
pages = {1123--36},
pmid = {9276729},
title = {{Localization of a domain in the FimH adhesin of Escherichia coli type 1 fimbriae capable of receptor recognition and use of a domain-specific antibody to confer protection against experimental urinary tract infection.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=508287{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {100},
year = {1997}
}
@article{Thomas2004,
abstract = {It is generally assumed that bacteria are washed off surfaces as fluid flow increases because they adhere through 'slip-bonds' that weaken under mechanical force. However, we show here that the opposite is true for Escherichia coli attachment to monomannose-coated surfaces via the type 1 fimbrial adhesive subunit, FimH. Raising the shear stress (within the physiologically relevant range) increased accumulation of type 1 fimbriated bacteria on monomannose surfaces by up to two orders of magnitude, and reducing the shear stress caused them to detach. In contrast, bacterial binding to anti-FimH antibody-coated surfaces showed essentially the opposite behaviour, detaching when the shear stress was increased. These results can be explained if FimH is force-activated; that is, that FimH mediates 'catch-bonds' with mannose that are strengthened by tensile mechanical force. As a result, on monomannose-coated surfaces, bacteria displayed a complex 'stick-and-roll' adhesion in which they tended to roll over the surface at low shear but increasingly halted to stick firmly as the shear was increased. Mutations in FimH that were predicted earlier to increase or decrease force-induced conformational changes in FimH were furthermore shown here to increase or decrease the probability that bacteria exhibited the stationary versus the rolling mode of adhesion. This 'stick-and-roll' adhesion could allow type 1 fimbriated bacteria to move along mannosylated surfaces under relatively low flow conditions and to accumulate preferentially in high shear regions.},
annote = {        From Duplicate 2 (                   Shear-dependent 'stick-and-roll' adhesion of type 1 fimbriated Escherichia coli.                 - Thomas, Wendy E; Nilsson, Lina M; Forero, Manu; Sokurenko, Evgeni V; Vogel, Viola )
                
        
        
      },
author = {Thomas, Wendy E and Nilsson, Lina M and Forero, Manu and Sokurenko, Evgeni V and Vogel, Viola},
doi = {10.1111/j.1365-2958.2004.04226.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Thomas et al. - Shear-dependent 'stick-and-roll' adhesion of type 1 fimbriated Escherichia coli. - 2004.pdf:pdf},
issn = {0950-382X},
journal = {Molecular microbiology},
keywords = {Adhesins,Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: metabolism,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: cytology,Escherichia coli: genetics,Escherichia coli: metabolism,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: genetics,Fimbriae Proteins: metabolism,Mannose,Mannose: metabolism,Mechanical,Models,Molecular,Stress,Surface Properties},
month = {sep},
number = {5},
pages = {1545--57},
pmid = {15387828},
title = {{Shear-dependent 'stick-and-roll' adhesion of type 1 fimbriated Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15387828},
volume = {53},
year = {2004}
}
@article{Otto2008,
abstract = {Staphylococcus epidermidis and Staphylococcus aureus are the most frequent causes of nosocomial infections and infections on indwelling medical devices, which characteristically involve biofilms. Recent advances in staphylococcal molecular biology have provided more detailed insight into the basis of biofilm formation in these opportunistic pathogens. A series of surface proteins mediate initial attachment to host matrix proteins, which is followed by the expression of a cationic glucosamine-based exopolysaccharide that aggregates the bacterial cells. In some cases, proteins may function as alternative aggregating substances. Furthermore, surfactant peptides have now been recognized as key factors involved in generating the three-dimensional structure of a staphylococcal biofilm by cell-cell disruptive forces, which eventually may lead to the detachment of entire cell clusters. Transcriptional profiling experiments have defined the specific physiology of staphylococcal biofilms and demonstrated that biofilm resistance to antimicrobials is due to gene-regulated processes. Finally, novel animal models of staphylococcal biofilm-associated infection have given us important information on which factors define biofilm formation in vivo. These recent advances constitute an important basis for the development of anti-staphylococcal drugs and vaccines.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Otto, M.},
doi = {10.1007/978-3-540-75418-3{\_}10},
eprint = {NIHMS150003},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Otto - Staphylococcal biofilms - 2008.pdf:pdf},
isbn = {9783540754176},
issn = {0070217X},
journal = {Current Topics in Microbiology and Immunology},
pages = {207--228},
pmid = {18453278},
title = {{Staphylococcal biofilms}},
volume = {322},
year = {2008}
}
@article{Hough1962,
abstract = {The purpose of this study was to examine whether an over-stimulation of the vestibular system, induced by thousands of time saccadic head stimulations, affects the vestibular sensitivity, and consequently if such a phenomenon could contribute to the deterioration of postural stability observed after a long distance running exercise. Eighteen athletic subjects performed a 20.5 km over ground race with an average speed of 15 km x h(-1), corresponding roughly to 7,500 strides shocks with associated saccadic accelerations transmitted to the head. A preliminary validation of the exercise protocol was realized to confirm the effect of the sustained exercise on body balance by recording standard postural parameters. A visually perceived eye level (VPEL) task was used to indirectly assess otolithic sensitivity motionless or undergoing low centrifugation conditions, before and after exercise. Results obtained from body balance analysis confirmed a decreased postural stability illustrated by increased postural oscillations after the 20.5 km run. Under low centrifugation conditions, results showed a lowering of the VPEL with the increase of the gravito-inertial acceleration in accordance with the literature. However, no significant change in the VPEL after a sustained running exercise was observed. In conclusion, the vestibular sensitivity at the otolithic level does not seem to be altered by an intensive running exercise and then failed to play a key role in the post-exercise deterioration of postural stability.},
author = {Hough, PVC V C},
doi = {10.1007/s10811-008-9353-1},
isbn = {1081100893531},
issn = {09218971},
journal = {US Patent 3,069,654},
pages = {225--231},
pmid = {12867671},
title = {{Method and means for recognizing complex patterns}},
volume = {21},
year = {1962}
}
@article{Ramstedt2007a,
author = {Ramstedt, Madeleine and Cheng, Nan and Azzaroni, Omar and Mathieu, Hans Jrg and Huck, Wilhelm T S and Mossialos, Dimitris},
doi = {10.1021/la062670},
journal = {Synthesis},
number = {6},
pages = {3314--3321},
title = {{Synthesis and Characterization of Poly ( 3-Sulfopropylmethacrylate ) Brushes for Potential Antibacterial Applications}},
volume = {23},
year = {2007}
}
@article{Rangel2013,
author = {Rangel, Dilia E. and Mar{\'{\i}}n-Medina, Nathaly and Castro, Jaime E. and Gonz{\'{a}}lez-Mancera, Andr{\'{e}}s and Forero-Shelton, Manu},
doi = {10.1371/journal.pone.0065563},
editor = {Heimesaat, Markus M.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rangel et al. - Observation of Bacterial Type I Pili Extension and Contraction under Fluid Flow - 2013.pdf:pdf},
issn = {1932-6203},
journal = {PLoS ONE},
month = {jun},
number = {6},
pages = {e65563},
title = {{Observation of Bacterial Type I Pili Extension and Contraction under Fluid Flow}},
url = {http://dx.plos.org/10.1371/journal.pone.0065563},
volume = {8},
year = {2013}
}
@article{Eliasson2007a,
abstract = {We demonstrate the use of spatially offset Raman spectroscopy (SORS) in the identification of counterfeit pharmaceutical tablets and capsules through different types of packaging. The technique offers a substantially higher sensitivity than that available from conventional backscattering Raman spectroscopy. The approach is particularly beneficial in situations where the conventional Raman backscattering method is hampered or fails because of excessive surface Raman or fluorescence signals emanating from the packaging, capsule shell, or tablet coating contaminating the much weaker subsurface Raman signals of the active pharmaceutical ingredients and excipients held in the product. It is demonstrated that such interfering signals can be effectively suppressed by SORS.},
author = {Eliasson, Charlotte and Matousek, Pavel},
doi = {10.1021/ac062223z},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Eliasson, Matousek - Noninvasive authentication of pharmaceutical products through packaging using spatially offset Raman spectroscopy..pdf:pdf},
issn = {0003-2700},
journal = {Analytical chemistry},
keywords = {Capsules,Capsules: analysis,Pharmaceutical Preparations,Pharmaceutical Preparations: analysis,Sensitivity and Specificity,Spectrum Analysis, Raman,Spectrum Analysis, Raman: methods,Tablets,Tablets: analysis},
month = {feb},
number = {4},
pages = {1696--701},
pmid = {17297975},
title = {{Noninvasive authentication of pharmaceutical products through packaging using spatially offset Raman spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17297975},
volume = {79},
year = {2007}
}
@article{Chattopadhyay2012,
abstract = {Class 5 fimbriae of enterotoxigenic Escherichia coli (ETEC) comprise eight serologically discrete colonization factors that mediate small intestinal adhesion. Their differentiation has been attributed to the pressure imposed by host adaptive immunity. We sequenced the major pilin and minor adhesin subunit genes of a geographically diverse population of ETEC elaborating CFA/I (n = 31), CS17 (n = 20), and CS2 (n = 18) and elucidated the functional effect of microevolutionary processes. Between the fimbrial types, the pairwise nucleotide diversity for the pilin or adhesin genes ranged from 35-43{\%}. Within each fimbrial type, there were 17 non-synonymous and 1 synonymous point mutations among all pilin or adhesin gene copies, implying that each fimbrial type was acquired by ETEC strains very recently, consistent with a recent origin of this E. coli pathotype. The 17 non-synonymous allelic differences occurred in the CFA/I pilin gene cfaB (two changes) and adhesin gene cfaE (three changes), and CS17 adhesin gene csbD (12 changes). All but one amino acid change in the adhesins clustered around the predicted ligand-binding pocket. Functionally, these changes conferred an increase in cell adhesion in a flow chamber assay. In contrast, the two mutations in the non-adhesive CfaB subunit localized to the intersubunit interface and significantly reduced fimbrial adhesion in this assay. In conclusion, naturally occurring mutations in the ETEC adhesive and non-adhesive subunits altered function, were acquired under positive selection, and are predicted to impact bacteria-host interactions.},
author = {Chattopadhyay, Sujay and Tchesnokova, Veronika and McVeigh, Annette and Kisiela, Dagmara I. and Dori, Kathleen and Navarro, Armando and Sokurenko, Evgeni V. and Savarino, Stephen J},
doi = {10.1074/jbc.M111.303735},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chattopadhyay et al. - Adaptive evolution of class 5 fimbrial genes in enterotoxigenic Escherichia coli and its functional consequences.pdf:pdf},
isbn = {1083-351X (Electronic)$\backslash$r0021-9258 (Linking)},
issn = {00219258},
journal = {Journal of Biological Chemistry},
pages = {6150--6158},
pmid = {22215679},
title = {{Adaptive evolution of class 5 fimbrial genes in enterotoxigenic Escherichia coli and its functional consequences}},
volume = {287},
year = {2012}
}
@article{Tchesnokova2011,
abstract = {Escherichia coli causes about 90{\%} of urinary tract infections (UTI), and more than 95{\%} of all UTI-causing E. coli express type 1 fimbriae. The fimbrial tip-positioned adhesive protein FimH utilizes a shear force-enhanced, so-called catch-bond mechanism of interaction with its receptor, mannose, where the lectin domain of FimH shifts from a low- to a high-affinity conformation upon separation from the anchoring pilin domain. Here, we show that immunization with the lectin domain induces antibodies that exclusively or predominantly recognize only the high-affinity conformation. In the lectin domain, we identified four high-affinity-specific epitopes, all positioned away from the mannose-binding pocket, which are recognized by 20 separate clones of monoclonal antibody. None of the monoclonal or polyclonal antibodies against the lectin domain inhibited the adhesive function. On the contrary, the antibodies enhanced FimH-mediated binding to mannosylated ligands and increased by severalfold bacterial adhesion to urothelial cells. Furthermore, by natural conversion from the high- to the low-affinity state, FimH adhesin was able to shed the antibodies bound to it. When whole fimbriae were used, the antifimbrial immune serum that contained a significant amount of antibodies against the lectin domain of FimH was also able to enhance FimH-mediated binding. Thus, bacterial adhesins (or other surface antigens) with the ability to switch between alternative conformations have the potential to induce a conformation-specific immune response that has a function-enhancing rather than -inhibiting impact on the protein. These observations have implications for the development of adhesin-specific vaccines and may serve as a paradigm for antibody-mediated enhancement of pathogen binding.},
author = {Tchesnokova, Veronika and Aprikian, Pavel and Kisiela, Dagmara and Gowey, Sarah and Korotkova, Natalia and Thomas, Wendy E and Sokurenko, Evgeni V},
doi = {10.1128/IAI.05169-11},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tchesnokova et al. - Type 1 fimbrial adhesin FimH elicits an immune response that enhances cell adhesion of Escherichia coli. - 2011.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Tchesnokova et al. - Type 1 fimbrial adhesin FimH elicits an immune response that enhances cell adhesion of Escherichia coli. - 2011(2).pdf:pdf},
issn = {1098-5522},
journal = {Infection and immunity},
keywords = {Adhesins,Animals,Antibodies,Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: immunology,Bacterial: metabolism,Cell Line,Epithelial Cells,Epithelial Cells: microbiology,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: genetics,Escherichia coli: immunology,Escherichia coli: metabolism,Escherichia coli: pathogenicity,Escherichia coli: physiology,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: genetics,Fimbriae Proteins: immunology,Fimbriae Proteins: metabolism,Host-Pathogen Interactions,Humans,Mannose-Binding Lectin,Mannose-Binding Lectin: metabolism,Mice,Models,Molecular,Monoclonal,Monoclonal: immunology,Monoclonal: metabolism,Mutagenesis,Protein Binding,Protein Conformation,Protein Structure,Rabbits,Site-Directed,Tertiary,Urinary Bladder,Urinary Bladder: cytology,Urinary Bladder: microbiology},
month = {oct},
number = {10},
pages = {3895--904},
pmid = {21768279},
title = {{Type 1 fimbrial adhesin FimH elicits an immune response that enhances cell adhesion of Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3187269{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {79},
year = {2011}
}
@article{Schmid2010a,
author = {Schmid, Thomas and Sebesta, Aleksandar and Stadler, Johannes and Opilik, Lothar and Balabin, Roman M. and Zenobi, Renato},
doi = {10.1117/12.845471},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schmid et al. - Tip-enhanced Raman spectroscopy and related techniques in studies of biological materials - 2010.pdf:pdf},
journal = {Synthesis},
keywords = {afm,atomic force microscopy,biofilms,biopolymers,lipids,nanoscale chemical analysis,scanning tunneling microscopy,stm,ters,tip-enhanced raman spectroscopy},
number = {May},
pages = {758603--758603--13},
title = {{Tip-enhanced Raman spectroscopy and related techniques in studies of biological materials}},
url = {http://link.aip.org/link/PSISDG/v7586/i1/p758603/s1{\&}Agg=doi},
volume = {7586},
year = {2010}
}
@article{Chen2007,
author = {Chen, Haodong and Ge, Kuikui and Li, Yinmei and Wu, Jianguang and Gu, Yongqiang and Wei, Haiming},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chen et al. - Application of Optical Tweezers in the Research of Molecular Interaction between Lymphocyte Function Associated Antigen-1.pdf:pdf},
number = {3},
pages = {221--225},
title = {{Application of Optical Tweezers in the Research of Molecular Interaction between Lymphocyte Function Associated Antigen-1 and Its Monoclonal Antibody}},
volume = {1},
year = {2007}
}
@article{Frost2008,
annote = {        From Duplicate 1 (                   Structural Basis of Membrane Invagination by F-BAR Domains                 - Frost, a; Perera, R; Roux, a; Spasov, K; Destaing, O; Egelman, E; Decamilli, P; Unger, V )
                
        
        
      },
author = {Frost, a and Perera, R and Roux, a and Spasov, K and Destaing, O and Egelman, E and Decamilli, P and Unger, V},
doi = {10.1016/j.cell.2007.12.041},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Frost et al. - Structural Basis of Membrane Invagination by F-BAR Domains - 2008.pdf:pdf},
issn = {00928674},
journal = {Cell},
month = {mar},
number = {5},
pages = {807--817},
title = {{Structural Basis of Membrane Invagination by F-BAR Domains}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0092867408001311},
volume = {132},
year = {2008}
}
@article{Uluc2009,
abstract = {The operating microscope is a fixture of modern surgical facilities, and it is a critically important factor in the success of many of the most complex and difficult surgical interventions used in medicine today. The rise of this key surgical tool reflects advances in understanding the principles of optics and vision that have occurred over centuries. The development of reading spectacles in the late 13th century led to the construction of early compound microscopes in the 16th and 17th centuries by Lippershey, Janssen, Galileo, Hooke, and others. Perhaps surprisingly, Leeuwenhoek's simple microscopes of this era offered improved performance over his contemporaries' designs. The intervening years saw improvements that reduced the spherical and chromatic aberrations present in compound microscopes. By the late 19th century, Carl Zeiss and Ernst Abbe ushered the compound microscope into the beginnings of the modern era of commercial design and production. The introduction of the microscope into the operating room by Nyl{\'{e}}n in 1921 initiated a revolution in surgical practice that gained momentum throughout the 1950s with multiple refinements, the introduction of the Zeiss OPMI series, and Kurze's application of the microscope to neurosurgery in 1957. Many of the refinements of the last 50 years have greatly improved the handling and practical operation of the surgical microscope, considerations which are equally important to its optical performance. Today's sophisticated operating microscopes allow for advanced real-time angiographic and tumor imaging. In this paper the authors discuss what might be found in the operating rooms of tomorrow.},
author = {Ulu{\c{c}}, Kutluay and Kujoth, Gregory C and Başkaya, Mustafa K},
doi = {10.3171/2009.6.FOCUS09120},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ulu{\c{c}}, Kujoth, Başkaya - Operating microscopes past, present, and future. - 2009.pdf:pdf},
issn = {1092-0684},
journal = {Neurosurgical focus},
number = {3},
pages = {E4},
pmid = {19722819},
title = {{Operating microscopes: past, present, and future.}},
volume = {27},
year = {2009}
}
@article{Pontes,
author = {Pontes, Bruno and Viana, Nathan B and Salgado, Leonardo T and Farina, Marcos and Neto, Vivaldo Moura and Nussenzveig, Herch Moys{\'{e}}s},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Pontes et al. - Supporting Material Cell Cytoskeleton and Tether Extraction - Unknown.pdf:pdf},
journal = {Transform},
pages = {1--7},
title = {{Supporting Material Cell Cytoskeleton and Tether Extraction}}
}
@article{Thomas2008,
abstract = {One of the most exciting discoveries in biological adhesion is the recent and counter-intuitive observation that the lifetimes of some biological adhesive bonds, called catch bonds, are enhanced by tensile mechanical force. At least two types of adhesive proteins have been shown to form catch bonds—blood proteins called selectins and a bacterial protein called FimH. Both mediate shear-enhanced adhesion, in which cells bind more strongly at high shear than at low shear. Single-molecule experiments and cell-free assays have now clearly demonstrated that catch bonds exist and mediate shear-enhanced adhesion. However, the mechanics of cellular organelles also contribute to shear-enhanced adhesion by modulating the force applied to catch bonds. This review examines how individual catch bond behavior contributes to shear-enhanced cellular adhesion for the two best-understood examples. The lessons from these systems offer design principles for understanding other types of shear-enhanced adhesion and for engineering nanostructured force-dependent adhesives out of catch bonds.},
author = {Thomas, Wendy E},
doi = {10.1146/annurev.bioeng.10.061807.160427},
file = {:C$\backslash$:/Users/LASER/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Thomas - 2008 - Catch Bonds in Adhesion.pdf:pdf},
journal = {Annu. Rev. Biomed. Eng.},
keywords = {molecular biomechanics,multiscale,nanotechnology,selectin leukocytes},
pages = {39--57},
title = {{Catch Bonds in Adhesion}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.bioeng.10.061807.160427},
volume = {10},
year = {2008}
}
@article{Lindberg2008,
abstract = {Uropathogenic Escherichia coli strain J96 carries multiple determinants for fimbrial adhesins. The regulatory protein PapB of P fimbriae has previously been implicated in potential coregulatory events. The focB gene of the F1C fimbria determinant is highly homologous to papB; the translated sequences share 81{\%} identity. In this study we investigated the role of PapB and FocB in regulation of the F1C fimbriae. By using gel mobility shift assays, we showed that FocB binds to sequences in both the pap and foc operons in a somewhat different manner than PapB. The results of both in vitro cross-linking and in vivo oligomerization tests indicated that FocB could function in an oligomeric fashion. Furthermore, our results suggest that PapB and FocB can form heterodimers and that these complexes can repress expression of the foc operon. The effect of FocB on expression of type 1 fimbriae was also tested. Taken together, the results that we present expand our knowledge about a regulatory network for different adhesin gene systems in uropathogenic E. coli and suggest a hierarchy for expression of the fimbrial adhesins.},
author = {Lindberg, Stina and Xia, Yan and Sond{\'{e}}n, Berit and G{\"{o}}ransson, Mikael and Hacker, J{\"{o}}rg and Uhlin, Bernt Eric},
doi = {10.1128/IAI.01010-07},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lindberg et al. - Regulatory Interactions among adhesin gene systems of uropathogenic Escherichia coli. - 2008.pdf:pdf},
isbn = {4690772630},
issn = {1098-5522},
journal = {Infection and immunity},
keywords = {Adhesins, Bacterial,Adhesins, Bacterial: biosynthesis,Adhesins, Bacterial: genetics,DNA, Bacterial,DNA, Bacterial: chemistry,DNA, Bacterial: metabolism,DNA-Binding Proteins,DNA-Binding Proteins: genetics,DNA-Binding Proteins: metabolism,Dimerization,Electrophoretic Mobility Shift Assay,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: metabolism,Escherichia coli: genetics,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: biosynthesis,Fimbriae Proteins: genetics,Gene Expression Regulation, Bacterial,Membrane Proteins,Membrane Proteins: metabolism,Molecular Sequence Data,Promoter Regions, Genetic,Protein Binding,Sequence Analysis, DNA,Transcription Factors,Transcription Factors: metabolism},
month = {feb},
number = {2},
pages = {771--80},
pmid = {18039830},
title = {{Regulatory Interactions among adhesin gene systems of uropathogenic Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2223471{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {76},
year = {2008}
}
@article{Mcdonnell1999,
abstract = {Antiseptics and disinfectants are extensively used in hospitals and other health care settings for a variety of topical and hard-surface applications. A wide variety of active chemical agents (biocides) are found in these products, many of which have been used for hundreds of years, including alcohols, phenols, iodine, and chlorine. Most of these active agents demonstrate broad-spectrum antimicrobial activity; however, little is known about the mode of action of these agents in comparison to antibiotics. This review considers what is known about the mode of action and spectrum of activity of antiseptics and disinfectants. The widespread use of these products has prompted some speculation on the development of microbial resistance, in particular whether antibiotic resistance is induced by antiseptics or disinfectants. Known mechanisms of microbial resistance (both intrinsic and acquired) to biocides are reviewed, with emphasis on the clinical implications of these reports.},
author = {Mcdonnell, Gerald and Russell, a. Denver},
doi = {0893-8512/99/{\$}04.001},
isbn = {0893-8512 (Print)$\backslash$n0893-8512 (Linking)},
issn = {08938512},
journal = {Clinical Microbiology Reviews},
number = {1},
pages = {147--179},
pmid = {9880479},
title = {{Antiseptics and disinfectants: Activity, action, and resistance}},
volume = {12},
year = {1999}
}
@article{Marszalek2002,
abstract = {Under a stretching force, the sugar ring of polysaccharide molecules switches from the chair to the boat-like or inverted chair conformation. This conformational change can be observed by stretching single polysaccharide molecules with an atomic force microscope. In those early experiments, the molecules were stretched at a constant rate while the resulting force changed over wide ranges. However, because the rings undergo force-dependent transitions, an experimental arrangement where the force is the free variable introduces an undesirable level of complexity in the results. Here we demonstrate the use of force-ramp atomic force microscopy to capture the conformational changes in single polysaccharide molecules. Force-ramp atomic force microscopy readily captures the ring transitions under conditions where the entropic elasticity of the molecule is separated from its conformational transitions, enabling a quantitative analysis of the data with a simple two-state model. This analysis directly provides the physico-chemical characteristics of the ring transitions such as the width of the energy barrier, the relative energy of the conformers, and their enthalpic elasticity. Our experiments enhance the ability of single-molecule force spectroscopy to make high-resolution measurements of the conformations of single polysaccharide molecules under a stretching force, making an important addition to polysaccharide spectroscopy.},
author = {Marszalek, Piotr E and Li, Hongbin and Oberhauser, Andres F and Fernandez, Julio M},
doi = {10.1073/pnas.072435699},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Marszalek et al. - Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM. - 2002.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Elasticity,Microscopy, Atomic Force,Molecular Conformation,Polysaccharides,Polysaccharides: chemistry,Thermodynamics},
month = {apr},
number = {7},
pages = {4278--83},
pmid = {11917130},
title = {{Chair-boat transitions in single polysaccharide molecules observed with force-ramp AFM.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=123639{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {99},
year = {2002}
}
@misc{Yip1992,
abstract = {The Hough transform is a robust technique which is useful in detecting straight lines in an edge-enhanced picture. However, the extension of the conventional Hough transform to recover circles and ellipses has been limited by slow speed and excessive memory. This paper presents techniques aimed at improving the efficiency and reducing the memory size of the accumulator array. Based on these techniques, only a 2-dimensional array is needed for the detection of circles and ellipses. The approach centres on the use of parallel edge points and a method on reducing the dimension of the accumulator array.},
author = {Yip, Raymond K.K. and Tam, Peter K.S. and Leung, Dennis N.K.},
booktitle = {Pattern Recognition},
doi = {10.1016/0031-3203(92)90064-P},
issn = {00313203},
pages = {1007--1022},
title = {{Modification of hough transform for circles and ellipses detection using a 2-dimensional array}},
volume = {25},
year = {1992}
}
@article{Righini2008a,
author = {Righini, Maurizio and Volpe, Giovanni and Girard, Christian and Petrov, Dmitri and Quidant, Romain},
doi = {10.1103/PhysRevLett.100.186804},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Righini et al. - Surface Plasmon Optical Tweezers Tunable Optical Manipulation in the Femtonewton Range - 2008.pdf:pdf},
issn = {0031-9007},
journal = {Physical Review Letters},
month = {may},
number = {18},
pages = {8--11},
title = {{Surface Plasmon Optical Tweezers: Tunable Optical Manipulation in the Femtonewton Range}},
url = {http://link.aps.org/doi/10.1103/PhysRevLett.100.186804},
volume = {100},
year = {2008}
}
@article{Bryce2005,
abstract = {BACKGROUND: Child survival efforts can be effective only if they are based on accurate information about causes of deaths. Here, we report on a 4-year effort by WHO to improve the accuracy of this information.

METHODS: WHO established the external Child Health Epidemiology Reference Group (CHERG) in 2001 to develop estimates of the proportion of deaths in children younger than age 5 years attributable to pneumonia, diarrhoea, malaria, measles, and the major causes of death in the first 28 days of life. Various methods, including single-cause and multi-cause proportionate mortality models, were used. The role of undernutrition as an underlying cause of death was estimated in collaboration with CHERG.

FINDINGS: In 2000-03, six causes accounted for 73{\%} of the 10.6 million yearly deaths in children younger than age 5 years: pneumonia (19{\%}), diarrhoea (18{\%}), malaria (8{\%}), neonatal pneumonia or sepsis (10{\%}), preterm delivery (10{\%}), and asphyxia at birth (8{\%}). The four communicable disease categories account for more than half (54{\%}) of all child deaths. The greatest communicable disease killers are similar in all WHO regions with the exception of malaria; 94{\%} of global deaths attributable to this disease occur in the Africa region. Undernutrition is an underlying cause of 53{\%} of all deaths in children younger than age 5 years.

INTERPRETATION: Achievement of the millennium development goal of reducing child mortality by two-thirds from the 1990 rate will depend on renewed efforts to prevent and control pneumonia, diarrhoea, and undernutrition in all WHO regions, and malaria in the Africa region. In all regions, deaths in the neonatal period, primarily due to preterm delivery, sepsis or pneumonia, and birth asphyxia should also be addressed. These estimates of the causes of child deaths should be used to guide public-health policies and programmes.},
author = {Bryce, Jennifer and Boschi-Pinto, Cynthia and Shibuya, Kenji and Black, Robert E},
doi = {10.1016/S0140-6736(05)71877-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bryce et al. - WHO estimates of the causes of death in children. - 2005.pdf:pdf},
issn = {1474-547X},
journal = {Lancet},
keywords = {Cause of Death,Child,Child Mortality,Child, Preschool,Humans,World Health Organization},
number = {9465},
pages = {1147--52},
pmid = {15794969},
title = {{WHO estimates of the causes of death in children.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15794969},
volume = {365},
year = {2005}
}
@article{Niu2007,
author = {Niu, Yang-Yao and Chang, Ding-Yu},
doi = {10.1142/S1016237207000173},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Niu, Chang - Cfd Simulation of Shear Stress and Secondary Flows in Urethra - 2007.pdf:pdf},
issn = {1016-2372},
journal = {Biomedical Engineering: Applications, Basis and Communications},
keywords = {cfd,lower urinary system,paper3,shear stress,urethra,urine flow},
mendeley-tags = {paper3},
number = {02},
pages = {117},
title = {{Cfd Simulation of Shear Stress and Secondary Flows in Urethra}},
url = {http://www.worldscinet.com/bme/19/1902/S1016237207000173.html},
volume = {19},
year = {2007}
}
@article{Schaffer2007b,
abstract = {Optical tweezers are widely used to measure molecular forces in biology. Such measurements are often influenced by a nearby surface that can perturb both the calibration of the tweezers as well as the hydrodynamic forces acting on microspheres to which the biomolecules are attached. In this study, we have used a very stable optical tweezers setup employing a recently developed calibration method (Toli{\'{c}}-N{\o}rrelykke, S. F.; Sch{\"{a}}ffer, E.; Howard, J.; Pavone, F. S.; J{\"{u}}licher, F.; Flyvbjerg, H. Rev. Sci. Instrum. 2006, 77 (10), 103101) to determine how the calibration of the tweezers and the forces on the microspheres depend on the height above the surface. We show that the displacement sensitivity of the tweezers is modulated by a standing light wave between the microsphere and the surface. We measured the dependence of the drag coefficient on height and compared it to exact and closed-form solutions to the Navier-Stokes equations. Also, we measured the surface force gradients in different salt solutions and for different surface blocking methods. For a given blocking method, our data suggest that microspheres can experience attractive and/or repulsive forces close to surfaces. For example, a Teflon layer reduces attractive interactions, and the presence of casein can lead to long-range repulsive interactions. These measurements are a prerequisite for the accurate measurement of normal forces with respect to an interface that occur in biological molecules held between surfaces.},
author = {Sch{\"{a}}ffer, Erik and N{\o}rrelykke, Simon F and Howard, Jonathon},
doi = {10.1021/la0622368},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Sch{\"{a}}ffer, N{\o}rrelykke, Howard - Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers..pdf:pdf},
issn = {0743-7463},
journal = {Langmuir},
keywords = {Calibration,Microspheres,Optical Tweezers,Salts,Salts: chemistry},
month = {mar},
number = {7},
pages = {3654--65},
pmid = {17326669},
title = {{Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17326669},
volume = {23},
year = {2007}
}
@article{Valvatne1996a,
abstract = {An enterotoxigenic Escherichia coli (ETEC) strain producing a previously undescribed putative colonization factor was isolated from a child with diarrhea in India. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of bacterial heat extracts revealed a polypeptide band of 20.8 kDa when the bacteria were grown at 37 degrees C which was absent after growth at 22 degrees C. A specific rabbit antiserum raised against the purified 20.8-kDa protein bound specifically to the fimbriae, as shown by immunoelectron microscopy, and inhibited bacterial adhesion to tissue-cultured Caco-2 cells. Transformation with a recombinant plasmid harboring the cfaD gene, which encodes a positive regulator for several ETEC fimbriae, induced hyperexpression of the 20.8-kDa fimbrial subunit and a substantial increase in the proportion of bacterial cells that were fimbriated. The N-terminal amino acid sequence of the polypeptide showed 65 and 60{\%} identity to the PCFO20 and 987P fimbriae of human and porcine ETEC, respectively. We propose the term CS20 for this new putative colonization factor of human ETEC.},
annote = {        From Duplicate 1 (                   Identification and characterization of CS20, a new putative colonization factor of enterotoxigenic Escherichia coli.                 - Valvatne, H; Sommerfelt, H; Gaastra, W; Bhan, M K; Grewal, H M )
                
        
        
      },
author = {Valvatne, H and Sommerfelt, H and Gaastra, W and Bhan, M K and Grewal, H M},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Valvatne et al. - Identification and characterization of CS20, a new putative colonization factor of enterotoxigenic Escherichia coli. -.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Valvatne et al. - Identification and characterization of CS20, a new putative colonization factor of enterotoxigenic Escherichia coli. -.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
keywords = {Adhesins,Amino Acid,Amino Acid Sequence,Animals,Antibodies,Bacterial,Bacterial Proteins,Bacterial Proteins: genetics,Bacterial Proteins: immunology,Bacterial Proteins: isolation {\&} purification,Bacterial: genetics,Bacterial: immunology,Bacterial: isolation {\&} purification,Electron,Enterotoxins,Enterotoxins: biosynthesis,Escherichia coli,Escherichia coli: genetics,Escherichia coli: metabolism,Escherichia coli: pathogenicity,Genes,Genetic,Humans,Microscopy,Molecular Sequence Data,Molecular Weight,Plasmids,Plasmids: genetics,Rabbits,Regulator,Sequence Homology,Swine,Transformation},
month = {jul},
number = {7},
pages = {2635--42},
pmid = {8698489},
title = {{Identification and characterization of CS20, a new putative colonization factor of enterotoxigenic Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=174120{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {64},
year = {1996}
}
@article{Lee2007b,
abstract = {Holographic optical trapping uses forces exerted by computer-generated holograms to organize microscopic materials into three-dimensional structures. In a complementary manner, holographic video microscopy uses real-time recordings of in-line holograms to create time-resolved volumetric images of three-dimensional microstructures. The combination is exceptionally effective for organizing, inspecting and analyzing soft-matter systems.},
author = {Lee, Sang-Hyuk and Grier, David G},
doi = {10.1364/OE.15.001505},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lee, Grier - Holographic microscopy of holographically trapped three-dimensional structures. - 2007.pdf:pdf},
issn = {1094-4087},
journal = {Optics express},
number = {4},
pages = {1505--1512},
pmid = {19532383},
title = {{Holographic microscopy of holographically trapped three-dimensional structures.}},
volume = {15},
year = {2007}
}
@article{Salit1988,
abstract = {Urinary tract infections caused by Escherichia coli are associated with a local and systemic antibody response. We have studied the serum and urine antibody responses to Escherichia coli in men and women with pyelonephritis, cystitis, and asymptomatic bacteriuria. Protein immunoblots consistently demonstrated serum antibody response to lipopolysaccharide (LPS). Anti-LPS antibody titres rose significantly and progressively when comparing acute with convalescent sera in those who have had their first urinary infection. For those with repeated infections, high titre LPS antibodies were present and did not change significantly between acute and convalescent sera. Antibody responses to the major outer membrane proteins were present but did not differ significantly when compared with normal human serum. A specific anti-P pilus antibody response was demonstrated by immunoblotting. Anti-P pilus antibody was quantitated using ELISA and the titres were found to be very low. Three other techniques were also used to demonstrate the presence of serum antibody. Antibody was detectable by immunofluorescence, but the antigenic specificity of the antibody was more difficult to ascertain. Immunoprecipitation was more specific for determining the nature of the antibody response. Lastly, immunoelectron microscopy was valuable in demonstrating antipilus and antiflagellar antibodies. Immunoelectron microscopy and immunoblotting provided evidence that human antiserum to P pili was modestly cross-reactive and could bind heterologous P pili. These studies indicated that the major antibody response in humans occurs after pyelonephritis and is directed against LPS. An anti-P pilus response is frequently present and is cross-reactive to some extent with other P pili.},
author = {Salit, I E and Hanley, J and Clubb, L and Fanning, S},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Salit et al. - The human antibody response to uropathogenic Escherichia coli a review. - 1988.html:html},
issn = {0008-4166},
journal = {Canadian journal of microbiology},
keywords = {Animals,Antibodies, Bacterial,Antibodies, Bacterial: biosynthesis,Antibodies, Bacterial: urine,Antigens, Bacterial,Antigens, Bacterial: immunology,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli: immunology,Humans,IgG,Urinary Tract Infections,Urinary Tract Infections: immunology,antibodies},
mendeley-tags = {IgG,antibodies},
month = {mar},
number = {3},
pages = {312--8},
pmid = {3046723},
title = {{The human antibody response to uropathogenic Escherichia coli: a review.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/3046723},
volume = {34},
year = {1988}
}
@article{Iovino2001,
abstract = {The results of 520 ps molecular dynamics simulation of histatin-5, a small peptide present in human saliva and possessing antimicrobial activity, dissolved in water and in 2,2,2-trifluoroethanol, are reported. The simulations indicate that histatin-5 is destabilized in water and begins to unfold after 250 ps, while in organic solvent it maintains a regular secondary structure throughout the trajectory. Analysis of the peptide-solvent hydrogen bonds indicates that 2,2,2-trifluoroethanol is a poorer proton acceptor than water. The fluorine atom of the alcohol is almost never engaged in a hydrogen bond and the organic solvent interacts mainly with the peptide through its hydroxyl group. For some residues analysis of the solvent residence time indicated longer values for 2,2,2-trifluoroethanol than for water. The most striking difference is related to the number of times the solvent enters and leaves the first coordination shell of the peptide. This value was more than one order of magnitude higher for water than for the alcohol, suggesting that this may be the main cause of alpha-helix destabilization perpetrated by water.},
author = {Iovino, M and Falconi, M and Marcellini, a and Desideri, a},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Iovino et al. - Molecular dynamics simulation of the antimicrobial salivary peptide histatin-5 in water and in trifluoroethanol a micros.pdf:pdf},
issn = {1397-002X},
journal = {The journal of peptide research : official journal of the American Peptide Society},
keywords = {Amino Acid Sequence,Antifungal Agents,Antifungal Agents: chemistry,Antifungal Agents: metabolism,Circular Dichroism,Computer Simulation,Histatins,Hydrogen Bonding,Models, Molecular,Molecular Sequence Data,Protein Conformation,Salivary Proteins and Peptides,Salivary Proteins and Peptides: chemistry,Salivary Proteins and Peptides: metabolism,Solvents,Solvents: chemistry,Trifluoroethanol,Trifluoroethanol: chemistry,Water,Water: chemistry},
month = {jul},
number = {1},
pages = {45--55},
pmid = {11454169},
title = {{Molecular dynamics simulation of the antimicrobial salivary peptide histatin-5 in water and in trifluoroethanol: a microscopic description of the water destructuring effect.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11454169},
volume = {58},
year = {2001}
}
@article{Valiaev2007a,
abstract = {Elastin-like polypeptides (ELPs) are stimulus-responsive polymers that contain repeats of five amino acids, Val-Pro-Gly-Xaa-Gly (VPGXG), where Xaa is a guest residue that can be any amino acid with the exception of proline. While studying the conformational mechanics of ELPs over a range of solvent conditions by single-molecule force spectroscopy, we noticed that some force-extension curves showed temperature-independent, extensional transitions that could not be fitted with a freely jointed chain or worm-like chain model. Here we show that the observed molecular elongation results from the force-induced peptidyl-prolyl cis-trans isomerization in prolines, which are repeated every fifth residue in the main chain of ELPs. Control experiments with poly(L-proline) demonstrate the similarity of the conformational transition between poly(L-proline) and ELPs. In contrast, the force-extension behavior of poly(L-lysine) showed no deviation in the relevant force range. Force-extension curves in hysteresis experiments showed an elongational difference between extension and relaxation pathways that suggests that the cis conformational state of the prolines could be exhausted on the time scale of the experiment. We present further computational evidence for this mechanism by Monte Carlo simulation of the force-extension behavior using an elastically coupled, two-state model. We believe ours is the first demonstration of force-induced prolyl cis-trans isomerization in proline-containing polypeptides. Our results suggest that single-molecule force spectroscopy could provide an alternate means to assay this important conformational transition in polypeptides.},
annote = {        From Duplicate 1 (                           Force-induced prolyl cis-trans isomerization in elastin-like polypeptides.                         - Valiaev, Alexei; Lim, Dong Woo; Oas, Terrence G.; Chilkoti, Ashutosh; Zauscher, Stefan )
                
        From Duplicate 2 (                           Force-induced prolyl cis-trans isomerization in elastin-like polypeptides.                         - Valiaev, Alexei; Lim, Dong Woo; Oas, Terrence G; Chilkoti, Ashutosh; Zauscher, Stefan )
                
        
        
        
        
      },
author = {Valiaev, Alexei and Lim, Dong Woo and Oas, Terrence G. and Chilkoti, Ashutosh and Zauscher, Stefan},
doi = {10.1021/ja070147r},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Valiaev et al. - Force-induced prolyl cis-trans isomerization in elastin-like polypeptides - 2007(2).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Valiaev et al. - Force-induced prolyl cis-trans isomerization in elastin-like polypeptides - 2007.pdf:pdf},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
keywords = {Elastin,Elastin: chemistry,Isoleucine,Isoleucine: chemistry,Isomerism,Kinetics,Mechanical,Models,Molecular,Molecular Conformation,Oligopeptides,Oligopeptides: chemical synthesis,Oligopeptides: chemistry,Proline,Proline: chemistry,Spectrum Analysis,Stress},
month = {may},
number = {20},
pages = {6491--7},
pmid = {17469821},
title = {{Force-induced prolyl cis-trans isomerization in elastin-like polypeptides}},
url = {http://pubs.acs.org/doi/abs/10.1021/ja070147r http://www.ncbi.nlm.nih.gov/pubmed/17469821},
volume = {129},
year = {2007}
}
@article{Evans1999,
abstract = {Bond dissociation under steadily rising force occurs most frequently at a time governed by the rate of loading (Evans and Ritchie, 1997 Biophys. J. 72:1541-1555). Multiplied by the loading rate, the breakage time specifies the force for most frequent failure (called bond strength) that obeys the same dependence on loading rate. The spectrum of bond strength versus log(loading rate) provides an image of the energy landscape traversed in the course of unbonding. However, when a weak bond is connected to very compliant elements like long polymers, the load applied to the bond does not rise steadily under constant pulling speed. Because of nonsteady loading, the most frequent breakage force can differ significantly from that of a bond loaded at constant rate through stiff linkages. Using generic models for wormlike and freely jointed chains, we have analyzed the kinetic process of failure for a bond loaded by pulling the polymer linkages at constant speed. We find that when linked by either type of polymer chain, a bond is likely to fail at lower force under steady separation than through stiff linkages. Quite unexpectedly, a discontinuous jump can occur in bond strength at slow separation speed in the case of long polymer linkages. We demonstrate that the predictions of strength versus log(loading rate) can rationalize conflicting results obtained recently for unfolding Ig domains along muscle titin with different force techniques.},
author = {Evans, Evan and Ritchie, K},
doi = {10.1016/S0006-3495(99)77399-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans, Ritchie - Strength of a weak bond connecting flexible polymer chains. - 1999.pdf:pdf},
isbn = {0006-3495 (Print)},
issn = {00063495},
journal = {Biophysical journal},
number = {5},
pages = {2439--2447},
pmid = {10233061},
publisher = {Elsevier},
title = {{Strength of a weak bond connecting flexible polymer chains.}},
url = {http://dx.doi.org/10.1016/S0006-3495(99)77399-6},
volume = {76},
year = {1999}
}
@article{Rasmussen2008,
abstract = {We investigated the degree of physiological damage to bacterial cells caused by optical trapping using a 1,064-nm laser. The physiological condition of the cells was determined by their ability to maintain a pH gradient across the cell wall; healthy cells are able to maintain a pH gradient over the cell wall, whereas compromised cells are less efficient, thus giving rise to a diminished pH gradient. The pH gradient was measured by fluorescence ratio imaging microscopy by incorporating a pH-sensitive fluorescent probe, green fluorescent protein or 5(6)-carboxyfluorescein diacetate succinimidyl ester, inside the bacterial cells. We used the gram-negative species Escherichia coli and three gram-positive species, Listeria monocytogenes, Listeria innocua, and Bacillus subtilis. All cells exhibited some degree of physiological damage, but optically trapped E. coli and L. innocua cells and a subpopulation of L. monocytogenes cells, all grown with shaking, showed only a small decrease in pH gradient across the cell wall when trapped by 6 mW of laser power for 60 min. However, another subpopulation of Listeria monocytogenes cells exhibited signs of physiological damage even while trapped at 6 mW, as did B. subtilis cells. Increasing the laser power to 18 mW caused the pH gradient of both Listeria and E. coli cells to decrease within minutes. Moreover, both species of Listeria exhibited more-pronounced physiological damage when grown without shaking than was seen in cells grown with shaking, and the degree of damage is therefore also dependent on the growth conditions.},
author = {Rasmussen, Mette B. and Oddershede, Lene B. and Siegumfeldt, H},
doi = {10.1128/AEM.02265-07},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rasmussen, Oddershede, Siegumfeldt - Optical tweezers cause physiological damage to Escherichia coli and Listeria bacteria. - 2008.pdf:pdf},
issn = {1098-5336},
journal = {Applied and environmental microbiology},
keywords = {Bacillus subtilis,Bacillus subtilis: radiation effects,Cell Membrane,Cell Membrane: metabolism,Escherichia coli,Escherichia coli: radiation effects,Fluorescence,Fluorescence: methods,Lasers,Listeria,Listeria: radiation effects,Microscopy,Optical Tweezers,Proton-Motive Force},
month = {apr},
number = {8},
pages = {2441--6},
pmid = {18310432},
title = {{Optical tweezers cause physiological damage to Escherichia coli and Listeria bacteria.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2293131{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {74},
year = {2008}
}
@article{Chen2011b,
abstract = {This study investigated the structural and mechanical properties of Klebsiella pneumoniae type 3 fimbriae, which constitute a known virulence factor for the bacterium. Transmission electron microscopy and optical tweezers were used to understand the ability of the bacterium to survive flushes. An individual K. pneumoniae type 3 fimbria exhibited a helix-like structure with a pitch of 4.1 nm and a three-phase force-extension curve. The fimbria was first nonlinearly stretched with increasing force. Then, it started to uncoil and extended several micrometers at a fixed force of 66 ± 4 pN (n = 22). Finally, the extension of the fimbria shifted to the third phase with a characteristic force of 102 ± 9 pN (n = 14) at the inflection point. Compared with the P fimbriae and type 1 fimbriae of uropathogenic Escherichia coli, K. pneumoniae type 3 fimbriae have a larger pitch in the helix-like structure and stronger uncoiling and characteristic forces.},
annote = {From Duplicate 1 ( Structural and Mechanical Properties of Klebsiella pneumoniae Type 3 Fimbriae. - Chen, Feng-Jung; Chan, Chia-Han; Huang, Ying-Jung; Liu, Kuo-Liang; Peng, Hwei-Ling; Chang, Hwan-You; Liou, Gunn-Guang; Yew, Tri-Rung; Liu, Cheng-Hsien; Hsu, Ken Y; Hsu, Long )
},
author = {Chen, Feng-Jung and Chan, Chia-Han and Huang, Ying-Jung and Liu, Kuo-Liang and Peng, Hwei-Ling and Chang, Hwan-You and Liou, Gunn-Guang and Yew, Tri-Rung and Liu, Cheng-Hsien and Hsu, Ken Y and Hsu, Long},
doi = {10.1128/JB.01395-10},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chen et al. - Structural and Mechanical Properties of Klebsiella pneumoniae Type 3 Fimbriae. - 2011.pdf:pdf},
issn = {1098-5530},
journal = {Journal of bacteriology},
month = {jan},
number = {7},
pages = {1718--1725},
pmid = {21239584},
title = {{Structural and Mechanical Properties of Klebsiella pneumoniae Type 3 Fimbriae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21239584},
volume = {193},
year = {2011}
}
@article{Czerwinski2009a,
abstract = {Much effort is put into minimizing noise in optical tweezers experiments because noise and drift can mask fundamental behaviours of, e. g., single molecule assays. Various initiatives have been taken to reduce or eliminate noise but it has been difficult to quantify their effect. We propose to use Allan variance as a simple and efficient method to quantify noise in optical tweezers setups. We apply the method to determine the optimal measurement time, frequency, and detection scheme, and quantify the effect of acoustic noise in the lab. The method can also be used on-the-fly for determining optimal parameters of running experiments. (C) 2009 Optical Society of America},
author = {Czerwinski, Fabian and Richardson, Andrew C and Oddershede, Lene B.},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Czerwinski, Richardson, Oddershede - Quantifying Noise in Optical Tweezers by Allan Variance - 2009.pdf:pdf},
journal = {Opt Express},
keywords = {Allan variance,Force,Nanoparticles,optical tweezers},
mendeley-tags = {Allan variance,optical tweezers},
number = {15},
pages = {13255--13269},
title = {{Quantifying Noise in Optical Tweezers by Allan Variance}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=000268399500108 http://apps.isiknowledge.com/InboundService.do?product=WOS{\&}action=retrieve{\&}SrcApp=Papers{\&}UT=000268399500108{\&}SID=N1DPOHoa73oGl3biB3@{\&}SrcAuth=me},
volume = {17},
year = {2009}
}
@article{Cao2011,
author = {Cao, Binrui and Xu, Hong and Mao, Chuanbin},
doi = {10.1002/anie.201102052},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Cao, Xu, Mao - Controlled self-assembly of rodlike bacterial pili particles into ordered lattices. - 2011.pdf:pdf},
issn = {1521-3773},
journal = {Angewandte Chemie (International ed. in English)},
month = {jul},
number = {28},
pages = {6264--8},
pmid = {21626633},
title = {{Controlled self-assembly of rodlike bacterial pili particles into ordered lattices.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3128682{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {50},
year = {2011}
}
@article{Ahmed2008,
author = {Ahmed, Niyaz and Dobrindt, Ulrich and Hacker, J{\"{o}}rg and Hasnain, Seyed E},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ahmed et al. - epidemiology and intervention - 2008.pdf:pdf},
number = {may},
pages = {387--394},
title = {epidemiology and intervention},
volume = {6},
year = {2008}
}
@article{Kim2013a,
abstract = {Precision measurement is a hallmark of physics but the small length scale (∼nanometer) of elementary biological components and thermal fluctuations surrounding them challenge our ability to visualize their action. Here, we highlight the recent developments in single-molecule nanometry where the position of a single fluorescent molecule can be determined with nanometer precision, reaching the limit imposed by the shot noise, and the relative motion between two molecules can be determined with ∼0.3 nm precision at ∼1 ms time resolution, as well as how these new tools are providing fundamental insights into how motor proteins move on cellular highways. We will also discuss how interactions between three and four fluorescent molecules can be used to measure three and six coordinates, respectively, allowing us to correlate the movements of multiple components. Finally, we will discuss recent progress in combining angstrom-precision optical tweezers with single-molecule fluorescent detection, opening new windows for multi-dimensional single-molecule nanometry for biological physics.},
archivePrefix = {arXiv},
arxivId = {NIHMS150003},
author = {Kim, Hajin and Ha, Taekjip},
doi = {10.1088/0034-4885/76/1/016601},
eprint = {NIHMS150003},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kim, Ha - Single-molecule nanometry for biological physics. - 2013.pdf:pdf},
isbn = {2122633255},
issn = {1361-6633},
journal = {Reports on progress in physics. Physical Society (Great Britain)},
keywords = {Fluorescence,Fluorescence: trends,Materials Testing,Materials Testing: methods,Molecular Imaging,Molecular Imaging: trends,Nanoparticles,Nanoparticles: chemistry,Nanoparticles: ultrastructure,Nanotechnology,Nanotechnology: trends,Optical Tweezers,Spectrometry},
number = {1},
pages = {016601},
pmid = {23249673},
title = {{Single-molecule nanometry for biological physics.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3549428{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {76},
year = {2013}
}
@article{Deng2007,
author = {Deng, Yi and Bechhoefer, John and Forde, Nancy R},
doi = {10.1088/1464-4258/9/8/S20},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Deng, Bechhoefer, Forde - Brownian motion in a modulated optical trap - 2007.pdf:pdf},
issn = {1464-4258},
journal = {Journal of Optics A: Pure and Applied Optics},
keywords = {article are in colour,brownian motion,only in the electronic,optical tweezers,some figures in this,time-sharing tweezers,trap modulation,variance,version},
month = {aug},
number = {8},
pages = {S256--S263},
title = {{Brownian motion in a modulated optical trap}},
url = {http://stacks.iop.org/1464-4258/9/i=8/a=S20?key=crossref.71abb1a69e558d0de3feff3f34500241},
volume = {9},
year = {2007}
}
@article{Palacci2015,
author = {Palacci, J{\'{e}}r{\'{e}}mie and Sacanna, Stefano and Abramian, Ana{\"{\i}}s and Barral, J{\'{e}}r{\'{e}}mie and Hanson, Kasey and Grosberg, Alexander Y and Pine, David J and Chaikin, Paul M},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Palacci et al. - Artificial rheotaxis - 2015.pdf:pdf},
number = {May},
pages = {1--6},
title = {{Artificial rheotaxis}},
year = {2015}
}
@misc{Griffiths1987,
abstract = {The dynamics of pyeloureteral flow is described when there is no peristalsis and for peristalsis of high and intermediate frequencies, on the assumption that the ureter is uniform except in the mid-ureter and at the outlet. The possibility of upstream transmission of bladder pressure variations to the renal pelvis is considered. The overall behaviour depends on three principal variables, the maximum tube pressure in the contraction waves, the intrinsic peristaltic carrying capacity and the peristaltic frequency f, expressed in the form fT where T is the time for a peristaltic contraction wave to sweep through the ureter. At intermediate peristaltic frequencies (fT less than but comparable with one) oscillatory flow patterns can occur, in which periods of peristaltically driven flow alternate with extraperistaltic periods of flow through the open ureter. The kidney is better isolated from bladder pressure variations when the peristaltic frequency is high, but high peristaltic frequency can by itself lead to elevated renal pelvic pressure if the flow rate is high. Experimental observations in pigs are presented to support these conclusions.},
annote = {From Duplicate 1 ( Dynamics of the upper urinary tract: II. The effect of variations of peristaltic frequency and bladder pressure on pyeloureteral pressure/flow relations. - Griffiths, D J; Constantinou, C E; Mortensen, J; Djurhuus, J C )
},
author = {Griffiths, Derek J. and Constantinou, C E and Mortensen, J and Djurhuus, J C},
booktitle = {Physics in medicine and biology},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Griffiths et al. - Dynamics of the upper urinary tract II. The effect of variations of peristaltic frequency and bladder pressure on pye.pdf:pdf},
issn = {0031-9155},
keywords = {Animals,Biological,Models,Muscle,Muscle Contraction,Smooth,Smooth: physiology,Ureter,Ureter: physiology,Urinary Bladder,Urinary Bladder: physiology},
month = {jul},
number = {7},
pages = {823--33},
pmid = {3615581},
title = {{Dynamics of the upper urinary tract: II. The effect of variations of peristaltic frequency and bladder pressure on pyeloureteral pressure/flow relations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/3615581},
volume = {32},
year = {1987}
}
@article{Sussman1999,
abstract = {Cystitis is caused by a relatively small number of bacterial species. To colonize and grow in the urinary tract, these organisms have developed and acquired special properties (virulence factors) that allow them to overcome the defences of the urinary tract, particularly clearance by urine flow. These virulence factors are unlikely to be required during transmission from host to host, and sometimes their constitutive expression may actually be disadvantageous. Such factors are therefore regulated by the environment and in a coordinate manner to ensure their most appropriate expression for the conditions encountered. This review focuses on the biology of the urinary tract and the bacterial properties necessary to cause cystitis. The regulation of virulence factors at the different stages of the infection is considered, and a general model for the pathogenesis of urinary tract infection is proposed.},
author = {Sussman, M and Gally, D L},
doi = {10.1146/annurev.med.50.1.149},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sussman, Gally - The biology of cystitis host and bacterial factors. - 1999.pdf:pdf},
issn = {0066-4219},
journal = {Annual review of medicine},
keywords = {Bacteria,Bacteria: growth {\&} development,Bacteria: pathogenicity,Bacterial Physiological Phenomena,Bacterial Proteins,Bacterial Proteins: genetics,Bacterial Proteins: physiology,Biology,Cystitis,Cystitis: microbiology,Cystitis: physiopathology,DNA, Bacterial,DNA, Bacterial: genetics,Female,Gene Expression Regulation, Bacterial,Humans,Male,Urinary Tract,Urinary Tract: microbiology,Urinary Tract: physiopathology,Urination,Urination: physiology,Virulence,Virulence: genetics},
month = {jan},
pages = {149--58},
pmid = {10073269},
title = {{The biology of cystitis: host and bacterial factors.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10073269},
volume = {50},
year = {1999}
}
@article{Percival2014,
abstract = {The presence of viable Helicobacter pylori (H. pylori) in the environment is considered to contribute to the levels of H. pylori found in the human population, which also aids to increase its genetic variability and its environmental adaptability and persistence. H. pylori form biofilms both within the in vitro and in vivo environment. This represents an important attribute that assists the survival of this bacterium within environments that are both hostile and adverse to proliferation. It is the aim of this paper to review the ability of H. pylori to form biofilms in vivo and in vitro and to address the inherent mechanisms considered to significantly enhance its persistence within the host and in external environments. Furthermore, the dissemination of H. pylori in the external environment and within the human body and its impact upon infection control will be discussed.},
author = {Percival, Steven L and Suleman, Louise},
doi = {10.4291/wjgp.v5.i3.122},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Percival, Suleman - Biofilms and Helicobacter pylori Dissemination and persistence within the environment and host. - 2014.pdf:pdf},
issn = {2150-5330},
journal = {World journal of gastrointestinal pathophysiology},
keywords = {biofilm,coccoid forms,helicobacter pylori},
number = {3},
pages = {122--32},
pmid = {25133015},
title = {{Biofilms and Helicobacter pylori: Dissemination and persistence within the environment and host.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4133512{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {5},
year = {2014}
}
@article{Boyle2007,
abstract = {The effect of flowrate and Reynolds Number, Re, on the spatial distribution of individual Pseudomonas aeruginosa cells during their initial attachment to glass flowcells was observed in a series of time-lapse images obtained over a 56-h period. It was shown that flow affected the distribution at Re > 245. Under laminar flow conditions, Re = 96, the distribution of bacterial cells in 200 sub-areas was accurately predicted by using the Poisson distribution and was not dependent on the orientation or shape of the sub-areas. Under turbulent flow conditions, Re = 2220, cells initially attached in streaks along the line of flow. As bacterial cells accumulated on the surface, the streaks broadened and the distribution became more uniform. Analyses showed that, initially, flow had an effect on cell distribution in the flowcell with Re = 245, with significantly greater effects at higher Re. As the cell surface densities increased, the effect of flow direction on cell distribution decreased. It is concluded that the visco-elastic properties of the extracellular polymeric substances (EPS) in which the cells are embedded, significantly affect the distribution of attaching cells.},
author = {Boyle, John D and Lappin-Scott, Hilary},
doi = {10.1080/08927010701218051},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Boyle, Lappin-Scott - The effect of flow direction and magnitude on the initial distribution of Pseudomonas aeruginosa cells attached to.pdf:pdf},
issn = {0892-7014},
journal = {Biofouling},
keywords = {Bacterial Adhesion,Glass,Pseudomonas aeruginosa,Pseudomonas aeruginosa: cytology,Surface Properties},
month = {jan},
number = {3-4},
pages = {139--50},
pmid = {17653925},
title = {{The effect of flow direction and magnitude on the initial distribution of Pseudomonas aeruginosa cells attached to glass.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17653925},
volume = {23},
year = {2007}
}
@article{Felderhof2005,
abstract = {Brownian motion of a particle situated near a wall bounding the fluid in which it is immersed is affected by the wall. Specifically, it is assumed that an incompressible viscous fluid fills a half-space bounded by a plane wall and that the fluid flow satisfies stick boundary conditions at the wall. The fluctuation-dissipation theorem shows that the velocity autocorrelation function of the Brownian particle can be calculated from the frequency-dependent admittance valid locally. It is shown that the t(-3/2) long-time tail of the velocity relaxation function, valid in bulk fluid, is obliterated and replaced by a t(-5/2) long-time tail of positive amplitude for motions parallel to the wall and by a t(-5/2) long-time tail of negative amplitude for motions perpendicular to the wall. The latter finding is at variance with an earlier calculation by Gotoh and Kaneda.},
author = {Felderhof, B. U.},
doi = {10.1021/jp051335b},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Felderhof - Effect of the wall on the velocity autocorrelation function and long-time tail of Brownian motion - 2005.pdf:pdf},
issn = {15206106},
journal = {Journal of Physical Chemistry B},
number = {45},
pages = {21406--21412},
pmid = {16853777},
title = {{Effect of the wall on the velocity autocorrelation function and long-time tail of Brownian motion}},
volume = {109},
year = {2005}
}
@article{Polenz2015,
abstract = {Interfacial polymerization techniques offer a versatile route for microcapsule synthesis. We designed a microfluidic process to synthesize monodisperse polyurea microcapsules (PUMCs); the microcapsules are formed by an interfacial polymerization of isocyanate dissolved in the oil and an amine dissolved in water. We measure the mechanical properties of the capsule as well as transport properties through the membrane using two microfluidic methods. We show that the elasticity and the permeability of the shell are controlled by surfactant additives, added during the synthesis. The control of the nanostructure of the shell by surfactants provides new means to design encapsulation systems with tailored mechanical and physicochemical properties.},
author = {Polenz, Ingmar and Weitz, David a and Baret, Jean-Christophe},
doi = {10.1021/la5040189},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Polenz, Weitz, Baret - Polyurea microcapsules in microfluidics surfactant control of soft membranes. - 2015.pdf:pdf},
issn = {1520-5827},
journal = {Langmuir : the ACS journal of surfaces and colloids},
number = {3},
pages = {1127--34},
pmid = {25531127},
title = {{Polyurea microcapsules in microfluidics: surfactant control of soft membranes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25531127},
volume = {31},
year = {2015}
}
@article{Goransson1989,
annote = {From Duplicate 2 ( Regulatory genes in the thermoregulation of Escherichia coli pili gene transcription. - Goransson, M; Forsman, K; Uhlin, B E )
},
author = {Goransson, M and Forsman, K and Uhlin, Bernt Eric},
doi = {10.1101/gad.3.1.123},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Goransson, Forsman, Uhlin - Regulatory genes in the thermoregulation of Escherichia coli pili gene transcription. - 1989.pdf:pdf},
issn = {0890-9369},
journal = {Genes {\&} Development},
keywords = {1988,31,activationl regulatory networks,adhesion genesl environmental regulationl,microorganisms presumably multiply as,rapidly as envi-,received august 8,revised version accepted october,thermoregulated mrna synthesisl transcription},
month = {jan},
number = {1},
pages = {123--130},
title = {{Regulatory genes in the thermoregulation of Escherichia coli pili gene transcription.}},
url = {http://www.genesdev.org/cgi/doi/10.1101/gad.3.1.123},
volume = {3},
year = {1989}
}
@article{Harris2006,
abstract = {Duplex DNA must remain stable when not in use to protect the genetic material. However, the two strands must be separated whenever genes are copied or expressed to expose the coding strand for synthesis of complementary RNA or DNA bases. Therefore, the double stranded structure must be relatively easy to take apart when required. These conflicting biological requirements have important implications for the mechanical properties of duplex DNA. Considerable insight into the forces required to denature DNA has been provided by nanomanipulation experiments, which measure the mechanical properties of single molecules in the laboratory. This paper describes recent computer simulation methods that have been developed to mimic nanomanipulation experiments and which, quite literally, 'destruction test' duplex DNA in silico. The method is verified by comparison with single molecule stretching experiments that measure the force required to unbind the two DNA strands. The model is then extended to investigate the thermodynamics of DNA bending and twisting. This is of biological importance as the DNA must be very tightly packaged to fit within the nucleus, and is therefore usually found in a highly twisted or supercoiled state (in bacteria) or wrapped tightly around histone proteins into a densely compacted structure (in animals). In particular, these simulations highlight the importance of thermal fluctuations and entropy in determining the biomechanical properties of DNA. This has implications for the action of DNA processing molecular motors, and also for nanotechnology. Biological machines are able to manipulate single molecules reliably on an energy scale comparable to that of thermal noise. The hope is that understanding the statistical mechanisms that a cell uses to achieve this will be invaluable for the future design of 'nanoengines' engineered to perform new technological functions at the nanoscale.},
author = {Harris, Sarah Anne},
doi = {10.1098/rsta.2006.1906},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Harris - Modelling the biomechanical properties of DNA using computer simulation. - 2006.pdf:pdf},
issn = {1364-503X},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
keywords = {Biomechanics,Computational Biology,Computer Simulation,DNA,DNA: chemistry,Models, Molecular,Nucleic Acid Conformation,Thermodynamics},
month = {dec},
number = {1849},
pages = {3319--34},
pmid = {17090462},
title = {{Modelling the biomechanical properties of DNA using computer simulation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17090462},
volume = {364},
year = {2006}
}
@article{Journal2012,
author = {Journal, Brazilian},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Journal - 1,2 , - 2012.pdf:pdf},
keywords = {asialo-gm 1,biofilm formation,cfa,cs2,elisa assays,etec,i,ii,r181-cotd},
pages = {969--980},
title = {1,2* ,},
year = {2012}
}
@misc{TheMendeleySupportTeam2011c,
abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.},
address = {London},
author = {{The Mendeley Support Team}},
booktitle = {Mendeley Desktop},
file = {:E$\backslash$:/Mina Dokument/Mendeley//The Mendeley Support Team - Getting Started with Mendeley - 2011.pdf:pdf},
keywords = {Mendeley,how-to,user manual},
pages = {1--16},
publisher = {Mendeley Ltd.},
title = {{Getting Started with Mendeley}},
url = {http://www.mendeley.com},
year = {2011}
}
@article{Thomas2003,
annote = {        From Duplicate 2 (                   The fimh adhesion protein as a nanoscale mechanical switch                 - Thomas, Wendy E; Sokurenko, Evgeni V; Vogel, Viola )
                
        
        
      },
author = {Thomas, Wendy E and Sokurenko, Evgeni V and Vogel, Viola},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Thomas, Sokurenko, Vogel - The fimh adhesion protein as a nanoscale mechanical switch - 2003.pdf:pdf},
journal = {Bioengineering},
number = {1},
title = {{The fimh adhesion protein as a nanoscale mechanical switch}},
year = {2003}
}
@article{Norregaard2014,
author = {Norregaard, Kamilla and Andersson, Magnus and Sneppen, Kim and Nielsen, Peter Eigil and Brown, Stanley and Oddershede, Lene B.},
doi = {10.4161/bact.27517},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Norregaard et al. - Effect of supercoiling on the $\lambda$ switch - 2014.pdf:pdf},
journal = {Bacteriophage},
keywords = {08,11,2013,ci,cooperativity,epigenetics,pna,protein,submitted,supercoiling,tethered particle motion,$\lambda$ switch},
number = {1},
pages = {e27517},
title = {{Effect of supercoiling on the $\lambda$ switch}},
volume = {4},
year = {2014}
}
@article{Zakrisson2015,
author = {Zakrisson, Johan and Wiklund, Krister and Axner, Ove and Andersson, Magnus},
doi = {10.1088/1478-3975/12/5/056006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zakrisson et al. - Tethered cells in fluid flows—beyond the Stokes’ drag force approach - 2015.pdf:pdf},
issn = {1478-3975},
journal = {Physical Biology},
keywords = {Basset force,article is available online,bacterial adhesion,basset force,fi mbriae,fimbriae,fl uid simulations,fluid simulations,lift force,pili,supplementary material for this,surface corrections},
number = {5},
pages = {056006},
publisher = {IOP Publishing},
title = {{Tethered cells in fluid flows—beyond the Stokes’ drag force approach}},
url = {http://stacks.iop.org/1478-3975/12/i=5/a=056006?key=crossref.d3e3d413c740e31daed9818ac974ab0f},
volume = {12},
year = {2015}
}
@article{Contact,
author = {Contact, Sexual and Treatment, Incontinence},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Contact, Treatment - What Are the Causes of Male Urinary Tract Infection - Unknown.pdf:pdf},
title = {{What Are the Causes of Male Urinary Tract Infection ?}}
}
@article{Oddershede2009,
author = {Oddershede, Lene B.},
keywords = {optical tweezers},
mendeley-tags = {optical tweezers},
pages = {24},
title = {{Optical Tweezers Techniques}},
volume = {1. ed},
year = {2009}
}
@article{Choudhury1999,
author = {Choudhury, D.},
doi = {10.1126/science.285.5430.1061},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Choudhury - X-ray Structure of the FimC-FimH Chaperone-Adhesin Complex from Uropathogenic Escherichia coli - 1999.pdf:pdf},
issn = {00368075},
journal = {Science},
month = {aug},
number = {5430},
pages = {1061--1066},
title = {{X-ray Structure of the FimC-FimH Chaperone-Adhesin Complex from Uropathogenic Escherichia coli}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.285.5430.1061},
volume = {285},
year = {1999}
}
@article{Farabella2014,
abstract = {PapC ushers are outer-membrane proteins enabling assembly and secretion of P pili in uropathogenic E. coli. Their translocation domain is a large $\beta$-barrel occluded by a plug domain, which is displaced to allow the translocation of pilus subunits across the membrane. Previous studies suggested that this gating mechanism is controlled by a $\beta$-hairpin and an $\alpha$-helix. To investigate the role of these elements in allosteric signal communication, we developed a method combining evolutionary and molecular dynamics studies of the native translocation domain and mutants lacking the $\beta$-hairpin and/or the $\alpha$-helix. Analysis of a hybrid residue interaction network suggests distinct regions (residue 'communities') within the translocation domain (especially around $\beta$12-$\beta$14) linking these elements, thereby modulating PapC gating. Antibiotic sensitivity and electrophysiology experiments on a set of alanine-substitution mutants confirmed functional roles for four of these communities. This study illuminates the gating mechanism of PapC ushers and its importance in maintaining outer-membrane permeability.},
author = {Farabella, Irene and Pham, Thieng and Henderson, Nadine S and Geibel, Sebastian and Phan, Gilles and Thanassi, David G and Delcour, Anne H and Waksman, Gabriel and Topf, Maya},
doi = {10.7554/eLife.03532},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Farabella et al. - Allosteric signalling in the outer membrane translocation domain of PapC usher. - 2014.pdf:pdf},
issn = {2050-084X},
journal = {eLife},
keywords = {Alanine,Alanine: chemistry,Alanine: metabolism,Allosteric Regulation,Amino Acid Motifs,Amino Acid Substitution,Anti-Bacterial Agents,Anti-Bacterial Agents: pharmacology,Bacterial,Bacterial: chemistry,Bacterial: drug effects,Bacterial: genetics,Bacterial: metabolism,Cell Membrane Permeability,Erythromycin,Erythromycin: pharmacology,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Escherichia coli Proteins: metabolism,Fimbriae,Gene Expression,Membrane Potentials,Molecular Dynamics Simulation,Molecular Sequence Data,Mutation,Porins,Porins: chemistry,Porins: genetics,Porins: metabolism,Protein Structure,Protein Subunits,Protein Subunits: chemistry,Protein Subunits: genetics,Protein Subunits: metabolism,Protein Transport,Secondary,Signal Transduction,Tertiary,Uropathogenic Escherichia coli,Uropathogenic Escherichia coli: chemistry,Uropathogenic Escherichia coli: drug effects,Uropathogenic Escherichia coli: genetics,Uropathogenic Escherichia coli: metabolism,Vancomycin,Vancomycin: pharmacology},
pages = {1--19},
pmid = {25271373},
title = {{Allosteric signalling in the outer membrane translocation domain of PapC usher.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4356140{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {3},
year = {2014}
}
@article{Dudko2003,
abstract = {Dynamic force spectroscopy of single molecules is described by a model that predicts a distribution of rupture forces, the corresponding mean rupture force, and variance, which are all amenable to experimental tests. The distribution has a pronounced asymmetry, which has recently been observed experimentally. The mean rupture force follows a (lnV)2/3 dependence on the pulling velocity, V, and differs from earlier predictions. Interestingly, at low pulling velocities, a rebinding process is obtained whose signature is an intermittent behavior of the spring force, which delays the rupture. An extension to include conformational changes of the adhesion complex is proposed, which leads to the possibility of bimodal distributions of rupture forces.},
author = {Dudko, O K and Filippov, a E and Klafter, J and Urbakh, M},
doi = {10.1073/pnas.1534554100},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dudko et al. - Beyond the conventional description of dynamic force spectroscopy of adhesion bonds. - 2003.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Spectrum Analysis,Spectrum Analysis: methods,Temperature},
month = {sep},
number = {20},
pages = {11378--81},
pmid = {13679588},
title = {{Beyond the conventional description of dynamic force spectroscopy of adhesion bonds.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=208765{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {100},
year = {2003}
}
@article{Vermeulen2006,
abstract = {Optical traps are commonly constructed with high-numerical-aperture objectives. Oil-immersion objectives suffer from spherical aberrations when used for imaging in aqueous solutions. The effect of spherical aberrations on trapping strength has been modeled by approximation, and only a few experimental results are available in the case of micrometer-sized particles. We present an experimental study of the dependence of lateral and axial optical-trap stiffness on focusing depth for polystyrene and silica beads of 2 microm diameter by using oil- and water-immersion objectives. We demonstrate a strong depth dependence of trap stiffness with the oil-immersion objective, whereas no depth dependence was observed with the water-immersion objective.},
author = {Vermeulen, Karen C and Wuite, Gijs J L and Stienen, Ger J M and Schmidt, Christoph F},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Vermeulen et al. - Optical trap stiffness in the presence and absence of spherical aberrations. - 2006.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
month = {mar},
number = {8},
pages = {1812--9},
pmid = {16572698},
title = {{Optical trap stiffness in the presence and absence of spherical aberrations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16572698},
volume = {45},
year = {2006}
}
@article{Hilleringmann2008,
abstract = {Pili have been identified on the cell surface of Streptococcus pneumoniae, a major cause of morbidity and mortality worldwide. In contrast to Gram-negative bacteria, little is known about the structure of native pili in Gram-positive species and their role in pathogenicity. Triple immunoelectron microscopy of the elongated structure showed that purified pili contained RrgB as the major compound, followed by clustered RrgA and individual RrgC molecules on the pilus surface. The arrangement of gold particles displayed a uniform distribution of anti-RrgB antibodies along the whole pilus, forming a backbone structure. Antibodies against RrgA were found along the filament as particulate aggregates of 2-3 units, often co-localised with single RrgC subunits. Structural analysis using cryo electron microscopy and data obtained from freeze drying/metal shadowing technique showed that pili are oligomeric appendages formed by at least two protofilaments arranged in a coiled-coil, compact superstructure of various diameters. Using extracellular matrix proteins in an enzyme-linked immunosorbent assay, ancillary RrgA was identified as the major adhesin of the pilus. Combining the structural and functional data, a model emerges where the pilus RrgB backbone serves as a carrier for surface located adhesive clusters of RrgA that facilitates the interaction with the host.},
author = {Hilleringmann, Markus and Giusti, Fabiola and Baudner, Barbara C. and Masignani, Vega and Covacci, Antonello and Rappuoli, Rino and Barocchi, Mich{\`{e}}le a. and Ferlenghi, Ilaria},
doi = {10.1371/journal.ppat.1000026},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hilleringmann et al. - Pneumococcal pili are composed of protofilaments exposing adhesive clusters of Rrg A - 2008.pdf:pdf},
isbn = {1553-7374 (Electronic)},
issn = {15537366},
journal = {PLoS Pathogens},
number = {3},
pmid = {18369475},
title = {{Pneumococcal pili are composed of protofilaments exposing adhesive clusters of Rrg A}},
volume = {4},
year = {2008}
}
@article{Oh2012,
author = {Oh, Yoo Jin and Cui, Yidan and Kim, Hyunseok and Li, Yinhua and Hinterdorfer, Peter and Park, Sungsu},
doi = {10.1016/j.bpj.2012.09.004},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Oh et al. - Characterization of Curli A Production on Living Bacterial Surfaces by Scanning Probe Microscopy - 2012.pdf:pdf},
issn = {00063495},
journal = {Biophysical Journal},
month = {oct},
number = {8},
pages = {1666--1671},
publisher = {Biophysical Society},
title = {{Characterization of Curli A Production on Living Bacterial Surfaces by Scanning Probe Microscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0006349512010168},
volume = {103},
year = {2012}
}
@article{Lenaers2012,
abstract = {Rare negative streamwise velocities and extreme wall-normal velocity fluctuations near the wall are investigated for turbulent channel flow at a series of Reynolds numbers based on friction velocity up to Re-tau = 1000. Probability density functions of the wall-shear stress and velocity components are presented as well as joint probability density functions of the velocity components and the pressure. Backflow occurs more often (0.06{\%} at the wall at Re-tau = 1000) and further away (up to y(+) = 8.5) from the wall for increasing Reynolds number. The regions of backflow are circular with an average diameter, based on ensemble averages, of approximately 20 viscous units independent of Reynolds number. A strong oblique vortex outside the viscous sublayer is found to cause this backflow. Extreme wall-normal velocity events occur also more often for increasing Reynolds number. These extreme fluctuations cause high flatness values near the wall (F(v) = 43 at Re-tau = 1000). Positive and negative velocity spikes appear in pairs, located on the two edges of a strong streamwise vortex as documented by Xu et al. [Phys. Fluids 8, 1938 (1996)] for Re-tau = 180. The spikes are elliptical and orientated in streamwise direction with a typical length of 25 and a typical width of 7.5 viscous units at y(+) approximate to 1. The negative spike occurs in a high-speed streak indicating a sweeping motion, while the positive spike is located in between a high and low-speed streak. The joint probability density functions of negative streamwise and extreme wall-normal velocity events show that these events are largely uncorrelated. The majority of both type of events can be found lying underneath a large-scale structure in the outer region with positive sign, which can be understood by considering the more intense velocity fluctuations due to amplitude modulation of the inner layer by the outer layer. Simulations performed at different resolutions give only minor differences. Results from experiments and recent turbulent boundary layer simulations show similar results indicating that these rare events are universal for wall-bounded flows. In order to detect these rare events in experiments, measurement techniques have to be specifically tuned. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3696304]},
annote = {Lenaers, Peter Li, Qiang Brethouwer, Geert Schlatter, Philipp Orlu, Ramis},
author = {Lenaers, P and Li, Q and Brethouwer, G and Schlatter, P and Orlu, R},
doi = {035110 10.1063/1.3696304},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Lenaers et al. - Rare backflow and extreme wall-normal velocity fluctuations in near-wall turbulence - 2012.pdf:pdf},
isbn = {1070-6631},
journal = {Physics of Fluids},
number = {3},
pages = {035110},
title = {{Rare backflow and extreme wall-normal velocity fluctuations in near-wall turbulence}},
url = {<Go to ISI>://WOS:000302224600037},
volume = {24},
year = {2012}
}
@article{Rakshit2014,
abstract = {Cell adhesion proteins play critical roles in positioning cells during development, segregating cells into distinct tissue compartments and in maintaining tissue integrity. The principle function of these proteins is to bind cells together and resist mechanical force. Adhesive proteins also enable migrating cells to adhere and roll on surfaces even in the presence of shear forces exerted by fluid flow. Recently, several experimental and theoretical studies have provided quantitative insights into the physical mechanisms by which adhesion proteins modulate their unbinding kinetics in response to tensile force. This perspective reviews these biophysical investigations. We focus on single molecule studies of cadherins, selectins, integrins, the von Willebrand factor and FimH adhesion proteins; the effect of mechanical force on the lifetime of these interactions has been extensively characterized. We review both theoretical models and experimental investigations and discuss future directions in this exciting area of research.},
author = {Rakshit, Sabyasachi and Sivasankar, Sanjeevi},
doi = {10.1039/c3cp53963f},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rakshit, Sivasankar - Biomechanics of cell adhesion how force regulates the lifetime of adhesive bonds at the single molecule level. - 2.pdf:pdf},
issn = {1463-9084},
journal = {Physical chemistry chemical physics : PCCP},
keywords = {Adhesins, Escherichia coli,Adhesins, Escherichia coli: metabolism,Animals,Bacterial Adhesion,Biomechanical Phenomena,Cell Adhesion,Cell Adhesion Molecules,Cell Adhesion Molecules: metabolism,Computer Simulation,Escherichia coli,Escherichia coli: cytology,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: metabolism,Humans,Models, Biological,Models, Molecular,Stress, Mechanical,von Willebrand Factor,von Willebrand Factor: metabolism},
month = {feb},
number = {6},
pages = {2211--23},
pmid = {24419646},
title = {{Biomechanics of cell adhesion: how force regulates the lifetime of adhesive bonds at the single molecule level.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24419646},
volume = {16},
year = {2014}
}
@article{McEver2002,
abstract = {Interactions of selectins with cell-surface glycoconjugates mediate tethering and rolling adhesion of leukocytes and platelets on vascular surfaces. Recent studies have helped elucidate the molecular details of selectin-ligand interactions, the biosynthetic pathways for constructing selectin ligands, and the biophysical and cell biological features that modulate selectin-dependent rolling under flow.},
author = {McEver, Rodger P},
file = {:E$\backslash$:/Mina Dokument/Mendeley/McEver - Selectins lectins that initiate cell adhesion under flow. - 2002.pdf:pdf},
issn = {0955-0674},
journal = {Current opinion in cell biology},
keywords = {Amino Acid Motifs,Animals,Cell Adhesion,Humans,Leukocytes,Leukocytes: metabolism,Ligands,Models, Biological,Protein Binding,Selectins,Selectins: metabolism,Selectins: physiology},
month = {oct},
number = {5},
pages = {581--6},
pmid = {12231353},
title = {{Selectins: lectins that initiate cell adhesion under flow.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12231353},
volume = {14},
year = {2002}
}
@article{Ishoey2008,
abstract = {Recently developed techniques allow genomic DNA sequencing from single microbial cells [Lasken RS: Single-cell genomic sequencing using multiple displacement amplification. Curr Opin Microbiol 2007, 10:510-516]. Here, we focus on research strategies for putting these methods into practice in the laboratory setting. An immediate consequence of single-cell sequencing is that it provides an alternative to culturing organisms as a prerequisite for genomic sequencing. The microgram amounts of DNA required as template are amplified from a single bacterium by a method called multiple displacement amplification (MDA) avoiding the need to grow cells. The ability to sequence DNA from individual cells will likely have an immense impact on microbiology considering the vast numbers of novel organisms, which have been inaccessible unless culture-independent methods could be used. However, special approaches have been necessary to work with amplified DNA. MDA may not recover the entire genome from the single copy present in most bacteria. Also, some sequence rearrangements can occur during the DNA amplification reaction. Over the past two years many research groups have begun to use MDA, and some practical approaches to single-cell sequencing have been developed. We review the consensus that is emerging on optimum methods, reliability of amplified template, and the proper interpretation of 'composite' genomes which result from the necessity of combining data from several single-cell MDA reactions in order to complete the assembly. Preferred laboratory methods are considered on the basis of experience at several large sequencing centers where >70{\%} of genomes are now often recovered from single cells. Methods are reviewed for preparation of bacterial fractions from environmental samples, single-cell isolation, DNA amplification by MDA, and DNA sequencing.},
author = {Ishoey, Thomas and Woyke, Tanja and Stepanauskas, Ramunas and Novotny, Mark and Lasken, Roger S},
doi = {10.1016/j.mib.2008.05.006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ishoey et al. - Genomic sequencing of single microbial cells from environmental samples. - 2008.pdf:pdf},
issn = {1369-5274},
journal = {Current opinion in microbiology},
keywords = {Bacteria,Bacteria: classification,Bacteria: cytology,Bacteria: genetics,Bacteria: isolation {\&} purification,Genomics,Genomics: methods,Nucleic Acid Amplification Techniques,Nucleic Acid Amplification Techniques: methods,Sequence Analysis, DNA,Sequence Analysis, DNA: methods,Soil Microbiology},
month = {jun},
number = {3},
pages = {198--204},
pmid = {18550420},
title = {{Genomic sequencing of single microbial cells from environmental samples.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18550420},
volume = {11},
year = {2008}
}
@article{Aprikian2011a,
abstract = {There is increasing evidence that the catch bond mechanism, where binding becomes stronger under tensile force, is a common property among non-covalent interactions between biological molecules that are exposed to mechanical force in vivo. Here, by using the multi-protein tip complex of the mannose-binding type 1 fimbriae of Escherichia coli, we show how the entire quaternary structure of the adhesive organella is adapted to facilitate binding under mechanically dynamic conditions induced by flow. The fimbrial tip mediates shear-dependent adhesion of bacteria to uroepithelial cells and demonstrates force-enhanced interaction with mannose in single molecule force spectroscopy experiments. The mannose-binding, lectin domain of the apex-positioned adhesive protein FimH is docked to the anchoring pilin domain in a distinct hooked manner. The hooked conformation is highly stable in molecular dynamics simulations under no force conditions but permits an easy separation of the domains upon application of an external tensile force, allowing the lectin domain to switch from a low- to a high-affinity state. The conformation between the FimH pilin domain and the following FimG subunit of the tip is open and stable even when tensile force is applied, providing an extended lever arm for the hook unhinging under shear. Finally, the conformation between FimG and FimF subunits is highly flexible even in the absence of tensile force, conferring to the FimH adhesin an exploratory function and high binding rates. The fimbrial tip of type 1 Escherichia coli is optimized to have a dual functionality: flexible exploration and force sensing. Comparison to other structures suggests that this property is common in unrelated bacterial and eukaryotic adhesive complexes that must function in dynamic conditions.},
author = {Aprikian, Pavel and Interlandi, Gianluca and Kidd, Brian a and {Le Trong}, Isolde and Tchesnokova, Veronika and Yakovenko, Olga and Whitfield, Matthew J and Bullitt, Esther and Stenkamp, Ronald E and Thomas, Wendy E and Sokurenko, Evgeni V},
doi = {10.1371/journal.pbio.1000617},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Aprikian et al. - The bacterial fimbrial tip acts as a mechanical force sensor. - 2011.pdf:pdf},
issn = {1545-7885},
journal = {PLoS biology},
month = {may},
number = {5},
pages = {e1000617},
pmid = {21572990},
title = {{The bacterial fimbrial tip acts as a mechanical force sensor.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21572990},
volume = {9},
year = {2011}
}
@article{Hamasha,
author = {Hamasha, Khozima and Results, More M},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hamasha, Results - Raman Spectroscopy for the Biochemical Characterization of Bacteria - Unknown.pdf:pdf},
journal = {Immunology},
title = {{Raman Spectroscopy for the Biochemical Characterization of Bacteria}}
}
@article{Wagner2011,
author = {Wagner, Carolin and Stangner, Tim and Gutsche, Christof and Uebersch{\"{a}}r, Olaf and Kremer, Friedrich},
doi = {10.1088/2040-8978/13/11/115302},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wagner et al. - Optical tweezers setup with optical height detection and active height regulation under white light illumination - 2011.pdf:pdf},
issn = {2040-8978},
journal = {Journal of Optics},
month = {nov},
number = {11},
pages = {115302},
title = {{Optical tweezers setup with optical height detection and active height regulation under white light illumination}},
url = {http://stacks.iop.org/2040-8986/13/i=11/a=115302?key=crossref.ae33cef931c143aec5a5faf0e740ace8},
volume = {13},
year = {2011}
}
@article{Azzaroni2005,
abstract = {We have studied the changes in phys. and chem. properties of cationic poly(2-(methacryloyloxy)ethyltrimethylammonium chloride) brushes after collapse driven by ion-pairing interactions in the presence of ClO4- anions.  Results derived from the quartz crystal microbalance technique, at. force microscopy, Fourier transform IR spectroscopy, and contact angle goniometry indicate that ion-paired collapsed polyelectrolyte brushes suffer a dramatic loss of water accompanied by conformational changes leading to markedly different mech. properties.  This scenario is completely different from polyelectrolyte brushes whose collapse is simply driven by pure Coulombic screening, for example, in the presence of Cl- anions.  In addn., wetting measurements indicated that ion-pairing interactions can be used to switch surface characteristics from hydrophilic to hydrophobic in a reversible manner.  The immediate implications of these exptl. results are related to the promising use of polyelectrolyte brushes as biolubricants and the design of "smart" surfaces exhibiting ion-sensitive reversible changes in interfacial properties. [on SciFinder(R)]},
author = {Azzaroni, Omar and Moya, Sergio and Farhan, Tamer and Brown, Andrew a. and Huck, Wilhelm T S},
doi = {10.1021/ma051549r},
isbn = {0024-9297$\backslash$n1520-5835},
issn = {00249297},
journal = {Macromolecules},
number = {24},
pages = {10192--10199},
title = {{Switching the properties of polyelectrolyte brushes via "hydrophobic collapse"}},
volume = {38},
year = {2005}
}
@article{Matousek2009a,
abstract = {This article reviews emerging Raman techniques for deep, non-invasive characterisation of biological tissues. As generic analytical tools, the new methods pave the way for a host of new applications including non-invasive bone disease diagnosis, chemical characterisation of 'stone-like' materials in urology and cancer detection in a number of organs.},
author = {Matousek, Pavel and Stone, Nicholas},
doi = {10.1039/b821100k},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Matousek, Stone - Emerging concepts in deep Raman spectroscopy of biological tissue. - 2009.pdf:pdf},
issn = {1364-5528},
journal = {The Analyst},
keywords = {Animals,Diagnostic Imaging,Diagnostic Imaging: methods,Humans,Signal Processing, Computer-Assisted,Spectrum Analysis, Raman,Spectrum Analysis, Raman: methods,Time Factors,Tomography},
month = {jun},
number = {6},
pages = {1058--66},
pmid = {19475130},
title = {{Emerging concepts in deep Raman spectroscopy of biological tissue.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19475130},
volume = {134},
year = {2009}
}
@article{Mu2002,
author = {Mu, X-Q and Egelman, E.H. and Bullitt, Esther},
doi = {10.1128/JB.184.17.4868},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Mu, Egelman, Bullitt - Structure and function of Hib pili from Haemophilus influenzae type b - 2002.pdf:pdf},
issn = {0021-9193},
journal = {Journal of bacteriology},
number = {17},
pages = {4868},
publisher = {Am Soc Microbiol},
title = {{Structure and function of Hib pili from Haemophilus influenzae type b}},
url = {http://jb.asm.org/cgi/content/abstract/184/17/4868},
volume = {184},
year = {2002}
}
@article{Clements2012a,
author = {Clements, Abigail and Young, Joanna C and Constantinou, Nicholas and Frankel, Gad},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Clements et al. - Infection strategies of enteric pathogenic Escherichia coli © 2012 Landes Bioscience . Do not distribute . © 2012 Land.pdf:pdf},
keywords = {and important pathogens causing,are both natural flora,coli,coli have been,e,enteric e,enteric escherichia coli,gut microbes,host-pathogen interactions,molecular mechanisms of pathogenesis,mortality worldwide,of humans,significant morbidity and,t3ss,traditionally enteric e},
number = {April},
pages = {71--87},
title = {{Infection strategies of enteric pathogenic Escherichia coli © 2012 Landes Bioscience . Do not distribute . © 2012 Landes Bioscience .}},
year = {2012}
}
@article{Camilli2005,
annote = {        From Duplicate 2 (                   [ 48 ] Expression and Properties of Sorting Nexin 9 in Dynamin ‐ Mediated Endocytosis                 - Camilli, De )
                
        
        
      },
author = {Camilli, De and Lundmark, R and Carlsson, S},
doi = {10.1016/S0076-6879(05)04048-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Camilli, Lundmark, Carlsson - Expression and Properties of Sorting Nexin 9 in Dynamin Mediated Endocytosis - 2005.pdf:pdf},
issn = {00766879},
journal = {Methods in Enzymology},
number = {2004},
pages = {545--556},
title = {{Expression and Properties of Sorting Nexin 9 in Dynamin Mediated Endocytosis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0076687905040486},
volume = {404},
year = {2005}
}
@article{Guicheteau1997,
author = {Guicheteau, J and Christesen, S and Emge, D and Hyre, A and Argue, L},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Guicheteau et al. - Bacteria Classification via Surface Enhanced Raman Spectroscopy and Principal Component Analysis - 1997.pdf:pdf},
journal = {Instrumentation},
title = {{Bacteria Classification via Surface Enhanced Raman Spectroscopy and Principal Component Analysis}},
year = {1997}
}
@article{Schmidt2009,
abstract = {The interaction of proteins at cellular interfaces is critical for many biological processes, from intercellular signaling to cell adhesion. For example, the selectin family of adhesion receptors plays a critical role in trafficking during inflammation and immunosurveillance. Quantitative measurements of binding rates between surface-constrained proteins elicit insight into how molecular structural details and post-translational modifications contribute to function. However, nano-scale transport effects can obfuscate measurements in experimental assays. We constructed a biophysical simulation of the motion of a rigid microsphere coated with biomolecular adhesion receptors in shearing flow undergoing thermal motion. The simulation enabled in silico investigation of the effects of kinetic force dependence, molecular deformation, grouping adhesion receptors into clusters, surface-constrained bond formation, and nano-scale vertical transport on outputs that directly map to observable motions. Simulations recreated the jerky, discrete stop-and-go motions observed in P-selectin/PSGL-1 microbead assays with physiologic ligand densities. Motion statistics tied detailed simulated motion data to experimentally reported quantities. New deductions about biomolecular function for P-selectin/PSGL-1 interactions were made. Distributing adhesive forces among P-selectin/PSGL-1 molecules closely grouped in clusters was necessary to achieve bond lifetimes observed in microbead assays. Initial, capturing bond formation effectively occurred across the entire molecular contour length. However, subsequent rebinding events were enhanced by the reduced separation distance following the initial capture. The result demonstrates that vertical transport can contribute to an enhancement in the apparent bond formation rate. A detailed analysis of in silico motions prompted the proposition of wobble autocorrelation as an indicator of two-dimensional function. Insight into two-dimensional bond formation gained from flow cell assays might therefore be important to understand processes involving extended cellular interactions, such as immunological synapse formation. A biologically informative in silico system was created with minimal, high-confidence inputs. Incorporating random effects in surface separation through thermal motion enabled new deductions of the effects of surface-constrained biomolecular function. Important molecular information is embedded in the patterns and statistics of motion.},
author = {Schmidt, Brian J and Papin, Jason a and Lawrence, Michael B},
doi = {10.1371/journal.pcbi.1000612},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Schmidt, Papin, Lawrence - Nano-motion dynamics are determined by surface-tethered selectin mechanokinetics and bond formation. - 2009.pdf:pdf},
issn = {1553-7358},
journal = {PLoS computational biology},
keywords = {Biological,Biomechanics,Computational Biology,Computational Biology: methods,Computer Simulation,Flow,Microspheres,Models, Biological,Motion,Nanotechnology,Protein Binding,Reproducibility of Results,Selectins,Selectins: metabolism,Selectins: physiology,Simulation,Surface Properties},
mendeley-tags = {Flow,Simulation},
month = {dec},
number = {12},
pages = {e1000612},
pmid = {20019797},
title = {{Nano-motion dynamics are determined by surface-tethered selectin mechanokinetics and bond formation.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2787012{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {5},
year = {2009}
}
@article{Kaur2011,
abstract = {Force spectroscopy and recognition imaging are important techniques for characterizing and mapping molecular interactions. In both cases, an antibody is pulled away from its target in times that are much less than the normal residence time of the antibody on its target. The distribution of pulling lengths in force spectroscopy shows the development of additional peaks at high loading rates, indicating that part of the antibody frequently unfolds. This propensity to unfold is reversible, indicating that exposure to high loading rates induces a structural transition to a metastable state. Weakened interactions of the antibody in this metastable state could account for reduced specificity in recognition imaging where the loading rates are always high. The much weaker interaction between the partially unfolded antibody and target, while still specific (as shown by control experiments), results in unbinding on millisecond timescales, giving rise to rapid switching noise in the recognition images. At the lower loading rates used in force spectroscopy, we still find discrepancies between the binding kinetics determined by force spectroscopy and those determined by surface plasmon resonance-possibly a consequence of the short tethers used in recognition imaging. Recognition imaging is nonetheless a powerful tool for interpreting complex atomic force microscopy images, so long as specificity is calibrated in situ, and not inferred from equilibrium binding kinetics.},
author = {Kaur, Parminder and Qiang-Fu and Fuhrmann, Alexander and Ros, Robert and Kutner, Linda Obenauer and Schneeweis, Lumelle a and Navoa, Ryman and Steger, Kirby and Xie, Lei and Yonan, Christopher and Abraham, Ralph and Grace, Michael J and Lindsay, Stuart},
doi = {10.1016/j.bpj.2010.11.050},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kaur et al. - Antibody-unfolding and metastable-state binding in force spectroscopy and recognition imaging. - 2011.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
keywords = {Humans,Imaging, Three-Dimensional,Imaging, Three-Dimensional: methods,Immunoglobulin G,Immunoglobulin G: chemistry,Immunoglobulin G: metabolism,Kinetics,Protein Binding,Protein Conformation,Protein Unfolding,Spectrum Analysis,Spectrum Analysis: methods},
month = {jan},
number = {1},
pages = {243--50},
pmid = {21190677},
publisher = {Biophysical Society},
title = {{Antibody-unfolding and metastable-state binding in force spectroscopy and recognition imaging.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3010837{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {100},
year = {2011}
}
@article{Freedman1998a,
abstract = {Enterotoxigenic Escherichia coli (ETEC) is the most commonly isolated pathogen responsible for travelers' diarrhea and the cause of up to 650 million cases of pediatric diarrhea per year in the developing world. As a safe alternative to the prophylactic use of antibiotics, a hyperimmune bovine milk antibody product with specific activity against purified colonization factor antigens (CFAs) was developed and evaluated in a human challenge study. Twenty-five healthy adult volunteers were challenged orally with 10(9) cfu of a virulent CFA/I-bearing ETEC. In the randomized double-blind trial, 7 of 10 volunteers receiving a lactose-free placebo developed clinical diarrhea after challenge, compared with only 1 of 15 cases in volunteers receiving active product (Fisher's exact test, P < .0017). It is concluded that antibodies against CFAs alone are sufficient for protection and that prophylaxis with milk-derived immunoglobulin is a feasible alternative to existing drug interventions.},
annote = {From Duplicate 1 (Milk immunoglobulin with specific activity against purified colonization factor antigens can protect against oral challenge with enterotoxigenic Escherichia coli. - Freedman, D J; Tacket, C O; Delehanty, a; Maneval, D R; Nataro, J; Crabb, J H)

From Duplicate 1 ( Milk immunoglobulin with specific activity against purified colonization factor antigens can protect against oral challenge with enterotoxigenic Escherichia coli. - Freedman, D J; Tacket, C O; Delehanty, A; Maneval, D R; Nataro, J; Crabb, J H )
},
author = {Freedman, D J and Tacket, C O and Delehanty, a and Maneval, D R and Nataro, J and Crabb, J H},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Freedman et al. - Milk immunoglobulin with specific activity against purified colonization factor antigens can protect against oral c(2).pdf:pdf},
issn = {0022-1899},
journal = {The Journal of infectious diseases},
keywords = {Administration,Adult,Animals,Antibodies,Bacterial,Bacterial Proteins,Bacterial Proteins: immunology,Bacterial Vaccines,Bacterial Vaccines: therapeutic use,Bacterial: blood,Bacterial: therapeutic use,Cattle,Diarrhea,Diarrhea: diagnosis,ETEC,Escherichia coli Infections,Escherichia coli Infections: prevention {\&} control,Feces,Feces: microbiology,Fimbriae Proteins,Humans,IgG,Immunization,Milk Proteins,Milk Proteins: immunology,Oral,Passive},
mendeley-tags = {ETEC,IgG},
month = {mar},
number = {3},
pages = {662--7},
pmid = {9498445},
title = {{Milk immunoglobulin with specific activity against purified colonization factor antigens can protect against oral challenge with enterotoxigenic Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9498445},
volume = {177},
year = {1998}
}
@article{OHanley1985,
abstract = {Most human pyelonephritis Escherichia coli isolates express both mannose (MS)- and globoside (Gal-Gal)-binding pili. An ascending E. coli urinary tract infection model was established in the 16-wk-old female BALB/c mouse to compare the pathogenic significance of MS and Gal-Gal pili and their efficacy as vaccines for the prevention of pyelonephritis. The distribution and density of pilus receptor compounds in urogenital tissues and as soluble compounds in urine were determined with antibodies to the synthetic receptor analogues, alpha D-Gal(1----4) beta D-Gal and alpha D-Man(1----2) alpha D-Man. Both carbohydrates were detected in vagina, bladder, ureter, and renal pelvis epithelium and in collecting duct and tubular cells. A pilus receptor compound also was detected in urine. It competitively inhibited the binding capacity of MS pili and was found to be physically, chemically, and immunologically related to Tamm-Horsfall uromucoid. Infectivity and invasiveness were quantitatively and histologically characterized for four E. coli strains: J96, a human pyelonephritis strain that expresses both MS and Gal-Gal pili; two recombinant strains prepared from J96 chromosomal DNA encoding MS pili or Gal-Gal pili; and the nonpiliated K12 recipient. Intravesicular administration of J96 (10(6) colony-forming units [CFU]) resulted in renal colonization and invasion in each of nine mice. The Gal-Gal clone (10(6) CFU) colonized the kidneys in each of 10 mice but did not invade. In contrast, the MS clone (10(6) CFU) did not colonize renal epithelium or invade. This effect was superceded when larger doses (greater than or equal to 10(10) CFU) of the MS clone were administered in volumes that cause acute vesicoureteric reflux. The efficacy was determined of vaccines composed of pure MS or Gal-Gal pili or the lipopolysaccharide containing O somatic antigen of the challenge strain, J96. The Gal-Gal pilus vaccine blocked renal colonization in 19 of 22 mice and renal invasion in 10 of 11 mice. Gal-Gal pili may be useful immunogens for the prevention of pyelonephritis in anatomically normal urinary tracts.},
author = {O'Hanley, P and Lark, David and Falkow, Stanley and Schoolnik, Gary},
doi = {10.1172/JCI111707},
file = {:E$\backslash$:/Mina Dokument/Mendeley/O'Hanley et al. - Molecular basis of Escherichia coli colonization of the upper urinary tract in BALBc mice. Gal-Gal pili immunization p.pdf:pdf},
issn = {0021-9738},
journal = {The Journal of clinical investigation},
keywords = {Animal,Animals,Bacterial,Bacterial: immunology,Bacterial: physiology,Disease Models,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: etiology,Escherichia coli Infections: prevention {\&} control,Escherichia coli: physiology,Female,Fimbriae,Globosides,Globosides: metabolism,Humans,Immunization,Inbred BALB C,Mannose,Mannose: metabolism,Mice,Pyelonephritis,Pyelonephritis: etiology,Pyelonephritis: prevention {\&} control},
month = {feb},
number = {2},
pages = {347--60},
pmid = {2857730},
title = {{Molecular basis of Escherichia coli colonization of the upper urinary tract in BALB/c mice. Gal-Gal pili immunization prevents Escherichia coli pyelonephritis in the BALB/c mouse model of human pyelonephritis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=423490{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {75},
year = {1985}
}
@article{Sievers2011,
abstract = {Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.},
author = {Sievers, Fabian and Wilm, Andreas and Dineen, David and Gibson, Toby J and Karplus, Kevin and Li, Weizhong and Lopez, Rodrigo and McWilliam, Hamish and Remmert, Michael and S{\"{o}}ding, Johannes and Thompson, Julie D and Higgins, Desmond G},
doi = {10.1038/msb.2011.75},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sievers et al. - Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega - 2011.pdf:pdf},
isbn = {1744-4292 (Electronic)$\backslash$r1744-4292 (Linking)},
issn = {1744-4292},
journal = {Molecular Systems Biology},
keywords = {bioinformatics,hidden markov models,multiple sequence alignment},
number = {539},
pmid = {21988835},
title = {{Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega}},
volume = {7},
year = {2011}
}
@article{Chaoui2003,
author = {Chaoui, M. and Feuillebois, F},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chaoui, Feuillebois - Creeping flow around a sphere in a shear flow - 2003.pdf:pdf},
journal = {Q. Jl Mech. Appl. Math.},
number = {3},
pages = {381--410},
title = {{Creeping flow around a sphere in a shear flow}},
volume = {56},
year = {2003}
}
@article{Gibson2008a,
abstract = {We assess the performance of a CMOS camera for the measurement of particle position within optical tweezers and the associated autocorrelation function and power spectrum. Measurement of the displacement of the particle from the trap center can also be related to the applied force. By considering the Allan variance of these measurements, we show that such cameras are capable of reaching the thermal limits of nanometer and femtonewton accuracies, and hence are suitable for many of the applications that traditionally use quadrant photodiodes. As an example of a multi-particle measurement we show the hydrodynamic coupling between two particles. (C) 2008 Optical Society of America.},
author = {Gibson, Graham M and Leach, Jonathan and Keen, Stephen and Wright, Amanda J and Padgett, Miles J},
journal = {Opt Express},
keywords = {Trap,camera,optical tweezers},
mendeley-tags = {camera,optical tweezers},
number = {19},
pages = {14561--14570},
title = {{Measuring the accuracy of particle position and force in optical tweezers using high-speed video microscopy}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=000259271900026},
volume = {16},
year = {2008}
}
@article{Wilson2012,
author = {Wilson, Laurence and Zhang, Rongjing},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wilson, Zhang - 3D Localization of weak scatterers in Rayleigh-Sommerfeld back-propagation - 2012.pdf:pdf},
journal = {Optics express},
number = {15},
pages = {1177--1179},
title = {{3D Localization of weak scatterers in Rayleigh-Sommerfeld back-propagation}},
volume = {20},
year = {2012}
}
@article{Dholakia2011,
abstract = {Optical forces can be used to manipulate biological and colloidal material in a non-contact manner. This forms the foundation of a wealth of exciting science, particularly in the fields of physics, biology and soft condensed matter. Although the standard Gaussian single-beam trap remains a very powerful tool, shaping the phase and amplitude of a light field provides unusual light patterns that add a major new dimension to research into particle manipulation. This Review summarizes the impact and emerging applications of shaped light in the field of optical manipulation.},
author = {Dholakia, K and {\v{C}}i{\v{z}}m{\'{a}}r, T},
doi = {10.1038/nphoton.2011.80},
isbn = {1749-4885$\backslash$r1749-4893},
issn = {1749-4885},
journal = {Nature Photonics},
number = {6},
pages = {335--342},
publisher = {Nature Publishing Group},
title = {{Shaping the future of manipulation}},
volume = {5},
year = {2011}
}
@article{Guyer1981,
author = {Guyer, M.S. and Reed, R.E. and Steitz, T. and Low, K.B.},
journal = {Cold Spring Harb Symp Quant Biol},
pages = {135--140},
title = {{Identification of a sex-factor-affinity site in E. coli as gamma delta}},
volume = {45},
year = {1981}
}
@article{Mulvey1998,
author = {Mulvey, M. a.},
doi = {10.1126/science.282.5393.1494},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mulvey - Induction and Evasion of Host Defenses by Type 1-Piliated Uropathogenic Escherichia coli - 1998.pdf:pdf},
journal = {Science},
month = {nov},
number = {5393},
pages = {1494--1497},
title = {{Induction and Evasion of Host Defenses by Type 1-Piliated Uropathogenic Escherichia coli}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.282.5393.1494},
volume = {282},
year = {1998}
}
@article{Hall-Stoodley2004,
abstract = {Biofilms--matrix-enclosed microbial accretions that adhere to biological or non-biological surfaces--represent a significant and incompletely understood mode of growth for bacteria. Biofilm formation appears early in the fossil record (approximately 3.25 billion years ago) and is common throughout a diverse range of organisms in both the Archaea and Bacteria lineages, including the 'living fossils' in the most deeply dividing branches of the phylogenetic tree. It is evident that biofilm formation is an ancient and integral component of the prokaryotic life cycle, and is a key factor for survival in diverse environments. Recent advances show that biofilms are structurally complex, dynamic systems with attributes of both primordial multicellular organisms and multifaceted ecosystems. Biofilm formation represents a protected mode of growth that allows cells to survive in hostile environments and also disperse to colonize new niches. The implications of these survival and propagative mechanisms in the context of both the natural environment and infectious diseases are discussed in this review.},
author = {Hall-Stoodley, L and Costerton, J and Stoodley, P},
doi = {10.1038/nrmicro821},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hall-Stoodley, Costerton, Stoodley - Bacterial biofilms from the natural environment to infectious diseases. - 2004.pdf:pdf},
isbn = {1740-1526 (Print)$\backslash$r1740-1526 (Linking)},
issn = {1740-1526},
journal = {Nature Reviews. Microbiology},
keywords = {Biofilm},
mendeley-tags = {Biofilm},
number = {February},
pages = {95--108},
pmid = {15040259},
title = {{Bacterial biofilms: from the natural environment to infectious diseases.}},
volume = {2},
year = {2004}
}
@article{Seeger1991,
abstract = {Optical tweezers, based on a compact diode pumped Nd:YAG laser providing 350 mW at 1,064 nm coupled into a Zeiss IM 35 microscope, were used to sort CD4+ T cells into a capillary for further mechanical handling and to establish contact between single human natural killer (NK) cells and human erythroleukemia cells (K562) as targets. After contact and a lag phase of a few tens of seconds, the target cell starts to change its morphology and membrane blebbing occurs. The kinetics of the attack of the NK cell on K562 cells is not straightforward but governed by temporal oscillations in the shape of the target cell (zeosis). In a second application, the optical tweezers are combined with a UV laser microbeam based on a pulsed UV laser and with flow cytometry and sorting. With the pulsed laser, segments of sorted chromosome 1 of the chinese hamster karyotype (CHV 79) can be easily micro-dissected and subsequently collected using the optical tweezers. This allows preparation of a few hundred chromosome segments per day without mechanical contact and in an absolutely sterile way and thus may provide an interesting basic technique in any type of genome sequencing project.},
author = {Seeger, S and Monajembashi, S and Hutter, K J and Futterman, G and Wolfrum, J and Greulich, K O},
doi = {10.1002/cyto.990120606},
issn = {0196-4763},
journal = {Cytometry},
number = {6},
pages = {497--504},
pmid = {1684929},
title = {{Application of laser optical tweezers in immunology and molecular genetics.}},
volume = {12},
year = {1991}
}
@article{Franosch2009,
abstract = {We have investigated the motion of a single optically trapped colloidal particle close to a limiting wall at time scales where the inertia of the surrounding fluid plays a significant role. The velocity autocorrelation function exhibits a complex interplay due to the momentum relaxation of the particle, the vortex diffusion in the fluid, the obstruction of flow close to the interface, and the harmonic restoring forces due to the optical trap. We show that already a weak trapping force has a significant impact on the velocity autocorrelation function C(t)=v(t)v(0) at times where the hydrodynamic memory leads to an algebraic decay. The long-time behavior for the motion parallel and perpendicular to the wall is derived analytically and compared to numerical results. Then, we discuss the power spectral densities of the displacement and provide simple interpolation formulas. The theoretical predictions are finally compared to recent experimental observations.},
archivePrefix = {arXiv},
arxivId = {1004.3663},
author = {Franosch, Thomas and Jeney, Sylvia},
doi = {10.1103/PhysRevE.79.031402},
eprint = {1004.3663},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Franosch, Jeney - Persistent correlation of constrained colloidal motion - 2009.pdf:pdf},
issn = {15393755},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
number = {3},
pages = {1--11},
pmid = {19391939},
title = {{Persistent correlation of constrained colloidal motion}},
volume = {79},
year = {2009}
}
@article{Jass2004,
abstract = {The mechanical behavior of individual P pili of uropathogenic Escherichia coli has been investigated using optical tweezers. P pili, whose main part constitutes the PapA rod, composed of approximately 10(3) PapA subunits in a helical arrangement, are distributed over the bacterial surface and mediate adhesion to host cells. They are particularly important in the pathogenesis of E. coli colonizing the upper urinary tract and kidneys. A biological model system has been established for in situ measurements of the forces that occur during mechanical stretching of pili. A mathematical model of the force-versus-elongation behavior of an individual pilus has been developed. Three elongation regions of pili were identified. In region I, P pili stretch elastically, up to a relative elongation of 16 +/- 3{\%}. The product of elasticity modulus and area of a P pilus, EA, was assessed to 154 +/- 20 pN (n=6). In region II, the quaternary structure of the PapA rod unfolds under a constant force of 27 +/- 2 pN (n approximately 100) by a sequential breaking of the interactions between adjacent layers of PapA subunits. This unfolding can elongate the pilus up to 7 +/- 2 times. In region III, pili elongate in a nonlinear manner as a result of stretching until the bond ruptures.},
author = {Jass, Jana and Schedin, Staffan and F{\"{a}}llman, Erik and Ohlsson, J{\"{o}}rgen and Nilsson, Ulf J and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1529/biophysj.104.044867},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jass et al. - Physical properties of Escherichia coli P pili measured by optical tweezers. - 2004.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: physiology,Bacterial: ultrastructure,Biological,Cell Culture Techniques,Cell Culture Techniques: methods,Computer Simulation,Elasticity,Escherichia coli,Escherichia coli: cytology,Escherichia coli: physiology,Fimbriae,Lasers,Micromanipulation,Micromanipulation: methods,Models,Physical Stimulation,Physical Stimulation: methods,Tensile Strength},
month = {dec},
number = {6},
pages = {4271--83},
pmid = {15377509},
title = {{Physical properties of Escherichia coli P pili measured by optical tweezers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1304935{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {87},
year = {2004}
}
@article{Floyd2015,
author = {Floyd, Kyle a. and Moore, Jessica L. and Eberly, Allison R. and Good, James a. D. and Shaffer, Carrie L. and Zaver, Himesh and Almqvist, Fredrik and Skaar, Eric P. and Caprioli, Richard M. and Hadjifrangiskou, Maria},
doi = {10.1371/journal.ppat.1004697},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Floyd et al. - Adhesive Fiber Stratification in Uropathogenic Escherichia coli Biofilms Unveils Oxygen-Mediated Control of Type 1 Pili -.pdf:pdf},
issn = {1553-7374},
journal = {PLOS Pathogens},
number = {3},
pages = {e1004697},
title = {{Adhesive Fiber Stratification in Uropathogenic Escherichia coli Biofilms Unveils Oxygen-Mediated Control of Type 1 Pili}},
url = {http://dx.plos.org/10.1371/journal.ppat.1004697},
volume = {11},
year = {2015}
}
@article{Szeliski2010,
abstract = {As humans, we perceive the three-dimensional structure of the world around us with apparent ease. However, despite all of the recent advances in computer vision research, the dream of having a computer interpret an image at the same level as a two-year old remains elusive. Why is computer vision such a challenging problem, and what is the current state of the art?Computer Vision: Algorithms and Applications explores the variety of techniques commonly used to analyze and interpret images. It also describes challenging real-world applications where vision is being successfully used, both for specialized applications such as medical imaging and fun consumer-level tasks such as image editing and stitching, which students can apply to their own personal photos and videos.More than just a source of "recipes", this text/reference also takes a scientific approach to basic vision problems, formulating physical models of the imaging process before inverting this process to produce the best possible descriptions of a scene. Exercises are presented throughout the book, with a heavy emphasis on testing algorithms.Suitable for either an undergraduate or a graduate-level course in computer vision, this textbook focuses on basic techniques that work under real-world conditions and encourages students to push their creative boundaries.Dr. Richard Szeliski has over twenty years' experience in computer vision research, most notably at Digital Equipment Corporation and Microsoft.},
author = {Szeliski, Richard},
doi = {10.1007/978-1-84882-935-0},
isbn = {1848829345},
issn = {10636919},
journal = {Computer},
pages = {832},
pmid = {16259003},
title = {{Computer Vision : Algorithms and Applications}},
volume = {5},
year = {2010}
}
@article{DeSmet2005,
abstract = {Antimicrobial peptides, which have been isolated from many bacteria, fungi, plants, invertebrates and vertebrates, are an important component of the natural defenses of most living organisms. The isolated peptides are very heterogeneous in length, sequence and structure, but most of them are small, cationic and amphipathic. These peptides exhibit broad-spectrum activity against Gram-positive and Gram-negative bacteria, yeasts, fungi and enveloped viruses. A wide variety of human proteins and peptides also have antimicrobial activity and play important roles in innate immunity. In this review we discuss three important groups of human antimicrobial peptides. The defensins are cationic non-glycosylated peptides containing six cysteine residues that form three intramolecular disulfide bridges, resulting in a triple-stranded beta-sheet structure. In humans, two classes of defensins can be found: alpha-defensins and beta-defensins. The defensin-related HE2 isoforms will also be discussed. The second group is the family of histatins, which are small, cationic, histidine-rich peptides present in human saliva. Histatins adopt a random coil conformation in aqueous solvents and form alpha-helices in non-aqueous solvents. The third group comprises only one antimicrobial peptide, the cathelicidin LL-37. This peptide is derived proteolytically from the C-terminal end of the human CAP18 protein. Just like the histatins, it adopts a largely random coil conformation in a hydrophilic environment, and forms an alpha-helical structure in a hydrophobic environment.},
author = {{De Smet}, Kris and Contreras, Roland},
doi = {10.1007/s10529-005-0936-5},
file = {:E$\backslash$:/Mina Dokument/Mendeley/De Smet, Contreras - Human antimicrobial peptides defensins, cathelicidins and histatins. - 2005.pdf:pdf},
issn = {0141-5492},
journal = {Biotechnology letters},
keywords = {Amino Acid Sequence,Anti-Infective Agents,Anti-Infective Agents: chemistry,Anti-Infective Agents: pharmacology,Antimicrobial Cationic Peptides,Antimicrobial Cationic Peptides: chemistry,Antimicrobial Cationic Peptides: genetics,Antimicrobial Cationic Peptides: pharmacology,Bacteria,Bacteria: drug effects,Bacteria: growth {\&} development,Defensins,Defensins: chemistry,Defensins: genetics,Defensins: pharmacology,Fungi,Fungi: drug effects,Fungi: growth {\&} development,Humans,Microbial Sensitivity Tests,Models, Molecular,Molecular Sequence Data,Protein Structure, Secondary,Proteins,Proteins: chemistry,Proteins: genetics,Proteins: pharmacology},
month = {sep},
number = {18},
pages = {1337--47},
pmid = {16215847},
title = {{Human antimicrobial peptides: defensins, cathelicidins and histatins.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16215847},
volume = {27},
year = {2005}
}
@article{Bjornham2008,
abstract = {P pili are fimbrial adhesion organelles expressed by uropathogenic Escherichia coli in the upper urinary tract. They constitute a stiff helix-like polymer consisting of a number of subunits joined by head-to-tail bonds. The elongation and retraction properties of individual P pili exposed to strain have been modeled by Monte Carlo (MC) simulations. The simulation model is based upon a three-state energy landscape that deforms under an applied force. Bond opening and closure are modeled by Bells theory while the elongation of the linearized part of the pilus is described by a worm-like chain model. The simulations are compared with measurements made by force measuring optical tweezers. It was found that the simulations can reproduce pili elongation as well as retraction, under both equilibrium and dynamic conditions, including entropic effects. It is shown that the simulations allow for an assessment of various model parameters, e.g. the unfolding force, energy barrier heights, and various distances in the energy landscape, including their stochastic spread that analytical models are unable to do. The results demonstrate that MC simulations are useful to model elongation and retraction properties of P pili, and therefore presumably also other types of pili, exposed to strain and/or stress. MC simulations are particularly suited for description of helix-like pili since these have an intricate self-regulating mechanical elongation behavior that makes analytical descriptions non-trivial when dynamic processes are studied, or if additional interactions in the rod or the behavior of the adhesion tip needs to be modeled.},
author = {Bj{\"{o}}rnham, Oscar and Axner, Ove and Andersson, Magnus},
doi = {10.1007/s00249-007-0223-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Bj{\"{o}}rnham, Axner, Andersson - Modeling of the elongation and retraction of Escherichia coli P pili under strain by Monte Carlo simulation.pdf:pdf},
issn = {0175-7571},
journal = {European biophysics journal},
keywords = {Atomic Force,Bacterial Adhesion,Bacterial Physiological Phenomena,Biophysics,Biophysics: methods,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: metabolism,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Markov Chains,Mechanical,Microscopy,Monte Carlo Method,Polymers,Polymers: chemistry,Probability,Protein Denaturation,Protein Folding,Stochastic Processes,Stress},
month = {apr},
number = {4},
pages = {381--91},
pmid = {17926029},
title = {{Modeling of the elongation and retraction of Escherichia coli P pili under strain by Monte Carlo simulations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17926029},
volume = {37},
year = {2008}
}
@article{Croxen2010,
abstract = {Escherichia coli is a remarkable and diverse organism. This normally harmless commensal needs only to acquire a combination of mobile genetic elements to become a highly adapted pathogen capable of causing a range of diseases, from gastroenteritis to extraintestinal infections of the urinary tract, bloodstream and central nervous system. The worldwide burden of these diseases is staggering, with hundreds of millions of people affected annually. Eight E. coli pathovars have been well characterized, and each uses a large arsenal of virulence factors to subvert host cellular functions to potentiate its virulence. In this Review, we focus on the recent advances in our understanding of the different pathogenic mechanisms that are used by various E. coli pathovars and how they cause disease in humans.},
author = {Croxen, Matthew a and Finlay, B Brett},
doi = {10.1038/nrmicro2265},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Croxen, Finlay - Molecular mechanisms of Escherichia coli pathogenicity. - 2010.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Croxen, Finlay - Molecular mechanisms of Escherichia coli pathogenicity. - 2010(2).pdf:pdf},
isbn = {1740-1526},
issn = {1740-1534},
journal = {Nature reviews. Microbiology},
keywords = {Biological,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli: genetics,Escherichia coli: pathogenicity,Humans,Models,Virulence,Virulence Factors,Virulence Factors: genetics,Virulence Factors: physiology},
month = {jan},
number = {1},
pages = {26--38},
pmid = {19966814},
title = {{Molecular mechanisms of Escherichia coli pathogenicity.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19966814},
volume = {8},
year = {2010}
}
@article{Ashok2010a,
abstract = {We report a novel fiber probe based Raman detection system on a microfluidic platform where a split Raman probe is directly embedded into a polydimethylsiloxane (PDMS) chip. In contrast to previous Raman detection schemes in microfluidics, probe based detection offers reduced background and portability. Compared to conventional backscattering probe designs, the split fiber probe we used in this system, results in a reduced size and offers flexibility to modify the collection geometry to minimize the background generated by the fibers. Also our microfluidic chip design enables us to obtain an alignment free system. As a proof of concept we demonstrate the sensitivity of the device for urea detection at relevant human physiological levels with a low acquisition time. The development of this system on a microfluidic platform means portable, lab on a chip devices for biological analyte detection and environmental sensing using Raman spectroscopy are now within reach.},
author = {Ashok, P C and Singh, G P and Tan, K M and Dholakia, K},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ashok et al. - Fiber probe based microfluidic raman spectroscopy. - 2010.pdf:pdf},
issn = {1094-4087},
journal = {Optics express},
keywords = {Ethanol,Ethanol: analysis,Limit of Detection,Microfluidics,Microfluidics: instrumentation,Microfluidics: methods,Optical Fibers,Rheology,Spectrum Analysis, Raman,Spectrum Analysis, Raman: instrumentation,Spectrum Analysis, Raman: methods,Time Factors,Urea,Urea: analysis},
month = {apr},
number = {8},
pages = {7642--9},
pmid = {20588604},
title = {{Fiber probe based microfluidic raman spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20588604},
volume = {18},
year = {2010}
}
@article{Donnenberg2000,
abstract = {Enteric bacteria use a limited array of macromolecular systems to implement diverse pathogenic strategies. The cellular targets of several enteric virulence factors have recently been identified. The themes that have emerged from these studies include the exploitation of molecules that regulate the actin cytoskeleton and the activation of apoptotic pathways to serve the pathogen.},
author = {Donnenberg, M S},
doi = {10.1038/35021212},
isbn = {0028-0836 (Print)},
issn = {0028-0836},
journal = {Nature},
number = {6797},
pages = {768--774},
pmid = {10963606},
title = {{Pathogenic strategies of enteric bacteria.}},
volume = {406},
year = {2000}
}
@article{Cuvelier2005a,
author = {Cuvelier, D and Chiaruttini, N and Bassereau, P and Nassoy, P},
doi = {10.1209/epl/i2005-10173-4},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Cuvelier et al. - Pulling long tubes from firmly adhered vesicles - 2005.pdf:pdf},
issn = {0295-5075},
journal = {Europhysics Letters (EPL)},
month = {sep},
number = {6},
pages = {1015--1021},
title = {{Pulling long tubes from firmly adhered vesicles}},
url = {http://stacks.iop.org/0295-5075/71/i=6/a=1015?key=crossref.f906d06373727559f7b1d71bf32213b7},
volume = {71},
year = {2005}
}
@article{Abbondanzieri2005a,
abstract = {During transcription, RNA polymerase (RNAP) moves processively along a DNA template, creating a complementary RNA. Here we present the development of an ultra-stable optical trapping system with angstrom-level resolution, which we used to monitor transcriptional elongation by single molecules of Escherichia coli RNAP. Records showed discrete steps averaging 3.7 +/- 0.6 angstrom, a distance equivalent to the mean rise per base found in B-DNA. By combining our results with quantitative gel analysis, we conclude that RNAP advances along DNA by a single base pair per nucleotide addition to the nascent RNA. We also determined the force-velocity relationship for transcription at both saturating and sub-saturating nucleotide concentrations; fits to these data returned a characteristic distance parameter equivalent to one base pair. Global fits were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release, but consistent with a brownian ratchet model incorporating a secondary NTP binding site.},
author = {Abbondanzieri, E A and Greenleaf, W J and Shaevitz, J W and Landick, R and Block, S M},
doi = {10.1038/nature04268},
journal = {Nature},
keywords = {Backtracking,Dna,Hand-Over-Hand,Kinetics,Mechanism,Optical Force Clamp,Single-Molecule,Structural Basis,Transcription Elongation,Translocation},
pages = {460--465},
title = {{Direct observation of base-pair stepping by RNA polymerase}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=000233458200041},
volume = {438},
year = {2005}
}
@article{Amir2014,
author = {Amir, A. and Babaeipour, F. and McIntosh, D. B. and Nelson, D. R. and Jun, S.},
doi = {10.1073/pnas.1317497111},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Amir et al. - Bending forces plastically deform growing bacterial cell walls - 2014.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {16},
pages = {5778--5783},
title = {{Bending forces plastically deform growing bacterial cell walls}},
url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1317497111},
volume = {111},
year = {2014}
}
@article{Taheri-Araghi2014,
author = {Taheri-Araghi, Sattar and Brown, Steven D. and Sauls, John T. and McIntosh, Dustin B. and Jun, Suckjoon},
doi = {10.1146/annurev-biophys-060414-034236},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Taheri-Araghi et al. - Single-Cell Physiology - 2014.pdf:pdf},
issn = {1936-122X},
journal = {Annual Review of Biophysics},
keywords = {cell cycle,growth,microbiology,microfluidics,quantitative biology,systems biology},
number = {1},
pages = {150306093435004},
title = {{Single-Cell Physiology}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-060414-034236},
volume = {44},
year = {2014}
}
@article{Takemura2003,
author = {Takemura, Fumio and Magnaudet, Jacques},
doi = {10.1017/S0022112003006232},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Takemura, Magnaudet - The transverse force on clean and contaminated bubbles rising near a vertical wall at moderate Reynolds number - 2.pdf:pdf},
issn = {00221120},
journal = {Journal of Fluid Mechanics},
month = {nov},
pages = {235--253},
title = {{The transverse force on clean and contaminated bubbles rising near a vertical wall at moderate Reynolds number}},
url = {http://www.journals.cambridge.org/abstract{\_}S0022112003006232},
volume = {495},
year = {2003}
}
@article{Andersson2006a,
abstract = {A model of the elongation of P pili expressed by uropathogenic Escherichia coli exposed to stress is presented. The model is based upon the sticky chain concept, which is based upon Hooke's law for elongation of the layer-to-layer and head-to-tail bonds between neighboring units in the PapA rod and a kinetic description of the opening and closing of bonds, described by rate equations and an energy landscape model. It provides an accurate description of the elongation behavior of P pili under stress and supports a hypothesis that the PapA rod shows all three basic stereotypes of elongation/unfolding: elongation of bonds in parallel, the zipper mode of unfolding, and elongation and unfolding of bonds in series. The two first elongation regions are dominated by a cooperative bond opening, in which each bond is influenced by its neighbor, whereas the third region can be described by individual bond opening, in which the bonds open and close randomly. A methodology for a swift extraction of model parameters from force-versus-elongation measurements performed under equilibrium conditions is derived. Entities such as the free energy, the stiffness, the elastic elongation, the opening length of the various bonds, and the number of PapA units in the rod are determined.},
annote = {From Duplicate 1 ( A sticky chain model of the elongation and unfolding of Escherichia coli P pili under stress. - Andersson, Magnus; F{\"{a}}llman, Erik; Uhlin, Bernt Eric; Axner, Ove )
},
author = {Andersson, Magnus and F{\"{a}}llman, Erik and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1529/biophysj.105.074674},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - A sticky chain model of the elongation and unfolding of Escherichia coli P pili under stress. - 2006.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Bacterial,Bacterial: physiology,Biological,Cellular,Cellular: physiology,Computer Simulation,Elasticity,Escherichia coli,Escherichia coli: physiology,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: physiology,Mechanical,Mechanotransduction,Micromanipulation,Models,Stress},
number = {5},
pages = {1521--34},
pmid = {16361334},
title = {{A sticky chain model of the elongation and unfolding of Escherichia coli P pili under stress.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16361334},
volume = {90},
year = {2006}
}
@article{Korhonen1985,
abstract = {Sixty-three Escherichia coli strains isolated from neonatal sepsis or meningitis were studied and compared with previous data on fecal or urinary pyelonephritis-associated isolates from children. Characteristics significantly associated with neonatal infection were capsular type K1 (54{\%}), O group 18 (27{\%}), rough-type lipopolysaccharide together with K1 capsule (19{\%}), and S fimbriae (29{\%}). Within the neonatal infection group, the K1 capsule and rough lipopolysaccharide were most common among the youngest infants (0 to 21 days old) and in meningitis. Hemolysin production, P fimbriae, and X adhesions (adhesions not identifiable as type 1, P, or S) were significantly more common in the two materials from infections as compared with the fecal isolates. One large clone of 11 strains (O18:K1:H7, with both type 1 and S fimbriae) and three smaller ones (O7:K1:H1 and O6:K2:H1, both with type 1 and P fimbriae and X adhesions; and R:K1:H33 with no adhesions) were identified among the strains from neonatal infections. Only O6:K2:H1 strains were also common among the strains from pyelonephritis.},
author = {Korhonen, T K and Valtonen, M V and Parkkinen, J and V{\"{a}}is{\"{a}}nen-Rhen, V and Finne, J and Orskov, F and Orskov, I and Svenson, S B and M{\"{a}}kel{\"{a}}, P H},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Korhonen et al. - Serotypes, hemolysin production, and receptor recognition of Escherichia coli strains associated with neonatal sepsis.pdf:pdf},
issn = {0019-9567},
journal = {Infection and immunity},
keywords = {Adhesins, Escherichia coli,Antigens, Bacterial,Antigens, Bacterial: analysis,Antigens, Surface,Antigens, Surface: analysis,Bacterial Proteins,Bacterial Proteins: metabolism,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli: classification,Escherichia coli: immunology,Escherichia coli: pathogenicity,Escherichia coli: ultrastructure,Fimbriae, Bacterial,Hemolysin Proteins,Hemolysin Proteins: biosynthesis,Humans,Infant,Infant, Newborn,Lipopolysaccharides,Lipopolysaccharides: analysis,Meningitis,Meningitis: microbiology,O Antigens,Sepsis,Sepsis: microbiology,Serotyping,Virulence},
month = {may},
number = {2},
pages = {486--91},
pmid = {2580792},
title = {{Serotypes, hemolysin production, and receptor recognition of Escherichia coli strains associated with neonatal sepsis and meningitis.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=261353{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {48},
year = {1985}
}
@article{Bowyer2008,
author = {Bowyer, Kevin W. and Hollingsworth, Karen and Flynn, Patrick J.},
doi = {10.1016/j.cviu.2007.08.005},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bowyer, Hollingsworth, Flynn - Image understanding for iris biometrics A survey - 2008.pdf:pdf},
issn = {10773142},
journal = {Computer Vision and Image Understanding},
month = {may},
number = {2},
pages = {281--307},
title = {{Image understanding for iris biometrics: A survey}},
volume = {110},
year = {2008}
}
@article{Salomo2008,
abstract = {Optical tweezers (OT) are ideally suited to study the interaction of single receptor-ligand bonds. Here we introduce a newly developed assay using OT to investigate the interactions between Protein A from Staphylococcus aureus and Immunoglobulin G from rabbit serum (RIgG). We demonstrate that the rupture forces depend on the loading rate and on the sodium chloride concentration. The measured loading rate effect is well known in the literature and the data we obtained were found to be in good agreement with an already published theoretical model. The dependence of the rupture forces on the salt concentration demonstrates the influence of hydrophobic interactions on the bond strength. Our experimental setup can probe the interaction between a single receptor and its specific ligand under changing conditions and hence offers manifold applications in single molecule biotechnology.},
author = {Salomo, Mathias and Keyser, Ulrich F and Struhalla, Marc and Kremer, Friedrich},
doi = {10.1007/s00249-008-0310-3},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Salomo et al. - Optical tweezers to study single protein Aimmunoglobulin G interactions at varying conditions. - 2008.pdf:pdf},
isbn = {0024900803103},
issn = {0175-7571},
journal = {European biophysics journal : EBJ},
keywords = {Chemical,Computer Simulation,Elasticity,Immunoglobulin G,Immunoglobulin G: chemistry,Mechanical,Models,Molecular,Optical Tweezers,Protein Binding,Staphylococcal Protein A,Staphylococcal Protein A: chemistry,Stress,antibodies},
mendeley-tags = {antibodies},
month = {jul},
number = {6},
pages = {927--34},
pmid = {18379774},
title = {{Optical tweezers to study single protein A/immunoglobulin G interactions at varying conditions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18379774},
volume = {37},
year = {2008}
}
@article{DuPont2009,
abstract = {BACKGROUND: Travellers' diarrhoea is the most common medical complaint among persons venturing into developing areas from industrialized regions.

AIM: To review recent developments dealing with microbiological, clinical, pathophysiological and therapeutic aspects of travellers' diarrhoea.

METHODS: The author's extensive file plus a review of publications listed in PubMed on January 22, 2009 on the topic of travellers' diarrhoea were reviewed.

RESULTS: Travellers' diarrhoea is largely caused by detectable and undetected bacterial enteropathogens, explaining the remarkable effectiveness of antibacterial agents in prophylaxis and therapy of the illness. A number of host genetic polymorphisms have been recently linked with susceptibility to travellers' diarrhoea. Novel antisecretory agents are being developed for treatment considering their physiological effects in acute diarrhoea. All travellers should be armed with one of three antibacterial drugs, ciprofloxacin, rifaximin or azithromycin, before their trips to use in self therapy should diarrhoea occur during travel. Loperamide may treat milder forms of travellers' diarrhoea and can be employed with antibacterial drugs.

CONCLUSIONS: Diarrhoea will continue to plague international travellers to high-risk regions. More studies of the incidence rate, relative important of the various pathogens by geographical region of the world, host risk factors and optimal therapeutic approach are needed.},
author = {DuPont, H L},
doi = {10.1111/j.1365-2036.2009.04028.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/DuPont - Systematic review the epidemiology and clinical features of travellers' diarrhoea. - 2009.pdf:pdf},
issn = {1365-2036},
journal = {Alimentary pharmacology {\&} therapeutics},
keywords = {Anti-Bacterial Agents,Anti-Bacterial Agents: therapeutic use,Antidiarrheals,Antidiarrheals: therapeutic use,Clinical Trials as Topic,Diarrhea,Diarrhea: drug therapy,Diarrhea: epidemiology,Diarrhea: etiology,Disease Susceptibility,Gastroenteritis,Gastroenteritis: drug therapy,Humans,Travel},
month = {aug},
number = {3},
pages = {187--96},
pmid = {19392866},
title = {{Systematic review: the epidemiology and clinical features of travellers' diarrhoea.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19392866},
volume = {30},
year = {2009}
}
@article{Whitfield2011b,
annote = {        From Duplicate 2 (                   A Nanoadhesive Composed of Receptor-Ligand Bonds                 - Whitfield, Matthew; Thomas, Wendy E )
                
        From Duplicate 1 (                           A Nanoadhesive Composed of Receptor-Ligand Bonds                         - Whitfield, Matthew; Thomas, Wendy E )
                
        From Duplicate 1 (                           A Nanoadhesive Composed of Receptor-Ligand Bonds                         - Whitfield, Matthew; Thomas, Wendy E )
                
        
        
        
        
        
        
      },
author = {Whitfield, Matthew and Thomas, Wendy E},
doi = {10.1080/00218464.2011.575311},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Whitfield, Thomas - A Nanoadhesive Composed of Receptor-Ligand Bonds - 2011.pdf:pdf},
issn = {0021-8464},
journal = {The Journal of Adhesion},
month = {may},
number = {5},
pages = {427--446},
title = {{A Nanoadhesive Composed of Receptor-Ligand Bonds}},
url = {http://www.tandfonline.com/doi/abs/10.1080/00218464.2011.575311 http://www.informaworld.com/openurl?genre=article{\&}doi=10.1080/00218464.2011.575311{\&}magic=crossref||D404A21C5BB053405B1A640AFFD44AE3},
volume = {87},
year = {2011}
}
@article{Rheinlaender2012,
abstract = {Many bacteria are characterized by nanoscale ultrastructures, for example S-layers, flagella, fimbriae, or pili. The last two are especially important for attachment to different abiotic and biotic surfaces and for host-pathogen interactions. In this study, we investigated the geometric and elastic properties of pili of different Corynebacterium diphtheriae strains by atomic force microscopy (AFM). We performed quantitative contour-length analysis of bacterial pili and found that the visible contour length of the pili can be described by a log-normal distribution. Our data revealed significant strain-specific variations in the mean visible contour length of the pili, ranging from 260 to 1,590 nm. To estimate their full contour length, which is not directly accessible from the AFM images, we developed a simple correction model. Using this model, we determined the mean full contour length as 510-2,060 nm. To obtain the persistence length we used two different methods of analysis, one based on the end-to-end distance of the pili and one based on the bending angles of short segments. In comparison, the bending angle analysis proved to be more precise and resulted in persistence lengths in the narrow range of 220-280 nm, with no significant strain-specific variations. This is small compared with some other bacterial polymers, for example type IV pili, F-pili, or flagella.},
author = {Rheinlaender, Johannes and Gr{\"{a}}bner, Anna and Ott, Lisa and Burkovski, Andreas and Sch{\"{a}}ffer, Tilman E},
doi = {10.1007/s00249-012-0818-4},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rheinlaender et al. - Contour and persistence length of Corynebacterium diphtheriae pili by atomic force microscopy. - 2012.pdf:pdf},
issn = {1432-1017},
journal = {European biophysics journal : EBJ},
keywords = {bacteria {\'{a}} afm {\'{a}},contour length {\'{a}} persistence},
month = {may},
pmid = {22588485},
title = {{Contour and persistence length of Corynebacterium diphtheriae pili by atomic force microscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22588485},
year = {2012}
}
@article{Essig2003,
abstract = {Phenotypic alterations resulting from flow-induced mechanical strains is a growing field of research in many cell types such as vascular endothelial and smooth muscle cells, chondrocytes or osteocytes. Although it has been acknowledged for several decades that tubular flow is a main determinant of tubular behavior in terms of vectorial transport of water and solutes, the effect of flow on other characteristics of proximal tubular cell phenotype was ignored until recently. The purpose of the review is to summarize the various effects of shear-stress, recently demonstrated in renal proximal cells.},
author = {Essig, Marie and Friedlander, G{\'{e}}rard},
doi = {10.1097/01.mnh.0000049808.98789.9a},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Essig, Friedlander - Shear-stress-responsive signal transduction mechanisms in renal proximal tubule cells. - 2003.pdf:pdf},
isbn = {0000049808},
issn = {1062-4821},
journal = {Current opinion in nephrology and hypertension},
keywords = {Animals,Cytoskeleton,Cytoskeleton: physiology,Extracellular Matrix,Extracellular Matrix: physiology,Humans,Kidney Tubules, Proximal,Kidney Tubules, Proximal: cytology,Kidney Tubules, Proximal: physiology,Mechanotransduction, Cellular,Mechanotransduction, Cellular: physiology,Stress, Mechanical},
month = {jan},
number = {1},
pages = {31--4},
pmid = {12496663},
title = {{Shear-stress-responsive signal transduction mechanisms in renal proximal tubule cells.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12496663},
volume = {12},
year = {2003}
}
@article{Krishnamoorthy2014,
author = {Krishnamoorthy, Mahentha and Hakobyan, Shoghik and Ramstedt, Madeleine and Gautrot, Julien E},
journal = {Chemical Reviews},
pages = {10976--11026},
title = {{Surface-Initiated Polymer Brushes in the Biomedical Field : Applications in Membrane Science , Biosensing , Cell Culture , Regenerative Medicine and Antibacterial Coatings}},
volume = {114},
year = {2014}
}
@book{Abrams1997a,
address = {London},
author = {Abrams, P},
chapter = {362},
isbn = {3540196781},
publisher = {Springer - Verlag},
title = {{Urodynamics}},
year = {1997}
}
@article{Chen2004,
abstract = {While bio-labeled immunoglobulin (IgG) or antibodies are extensively used in imaging studies and therapeutic modality, there have been no reports describing atomic force microscopy (AFM) micrographs of these labeled IgG molecules. Here, AFM studies of phycoerythrin (PE)-conjugated IgG were undertaken to examine whether PE conjugation induced conformational changes or molecular interaction, and subsequently resulted in an alteration in nano-structures of PE-conjugated IgG complex. Once immobilized on mica, single PE-conjugated IgG molecule exhibited globular shape with approximately 60 microns in diameter and 5 microns in height. PE-conjugated IgG were able to form monomers, spindle-like trimers, and hexamers that developed through an end-end connection of two trimers, after they were continuously immobilized on mica. Interestingly, these multimers could aggregate in different directions to form circular monolayers with a highly dense core of PE-conjugated IgG polymers. The formation of these well-organized polymers and aggregates of PE-conjugated IgG may be attributed to the PE conjugation as well as the air-liquid tension on subtract. These findings may help to understand the nano-structures of bio-labeled IgG or antibodies, and facilitate the potential use of PE-conjugated antibodies as markers or immunosensers for AFM bio-analytics of biomolecules in cells and membranes.},
author = {Chen, Yong and Cai, Jiye and Xu, Qingcai and Chen, Zheng W},
doi = {10.1016/j.molimm.2004.05.012},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chen et al. - Atomic force bio-analytics of polymerization and aggregation of phycoerythrin-conjugated immunoglobulin G molecules. - 200.pdf:pdf},
issn = {0161-5890},
journal = {Molecular immunology},
keywords = {Affinity Labels,Affinity Labels: chemistry,Animals,Dimerization,Immunoglobulin G,Immunoglobulin G: chemistry,Immunoglobulin G: drug effects,Mice,Microscopy, Atomic Force,Molecular Probes,Molecular Probes: chemistry,Phycoerythrin,Phycoerythrin: chemistry,Phycoerythrin: pharmacology,Polymers,Protein Conformation,Protein Conformation: drug effects},
month = {nov},
number = {12},
pages = {1247--52},
pmid = {15482861},
title = {{Atomic force bio-analytics of polymerization and aggregation of phycoerythrin-conjugated immunoglobulin G molecules.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2873175{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {41},
year = {2004}
}
@article{Shen2006,
abstract = {The numerical calculation of the Rayleigh-Sommerfeld diffraction integral is investigated. The implementation of a fast-Fourier-transform (FFT) based direct integration (FFT-DI) method is presented, and Simpson's rule is used to improve the calculation accuracy. The sampling interval, the size of the computation window, and their influence on numerical accuracy and on computational complexity are discussed for the FFT-DI and the FFT-based angular spectrum (FFT-AS) methods. The performance of the FFT-DI method is verified by numerical simulation and compared with that of the FFT-AS method.},
author = {Shen, Fabin and Wang, Anbo},
doi = {10.1364/AO.45.001102},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Shen, Wang - Fast-Fourier-transform based numerical integration method for the Rayleigh-Sommerfeld diffraction formula. - 2006.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
number = {6},
pages = {1102--1110},
pmid = {16523770},
title = {{Fast-Fourier-transform based numerical integration method for the Rayleigh-Sommerfeld diffraction formula.}},
volume = {45},
year = {2006}
}
@article{Moritz2010,
author = {Moritz, Tobias J and Taylor, Douglas S and Krol, Denise M and Fritch, John and W, James},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Moritz et al. - Detection of doxorubicin-induced apoptosis of leukemic T-lymphocytes by laser tweezers Raman spectroscopy - 2010.pdf:pdf},
journal = {Optics Express},
number = {4},
pages = {1138--1147},
title = {{Detection of doxorubicin-induced apoptosis of leukemic T-lymphocytes by laser tweezers Raman spectroscopy}},
volume = {1},
year = {2010}
}
@article{Xu1990,
author = {Xu, L. and Oja, E. and Kultanen, P.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Unknown - ref18 RHT.pdf - Unknown.pdf:pdf},
journal = {Pattern Recogn. Lett.},
title = {{A new curve detection method: Randomized Hough Transform (RHT)}},
volume = {11},
year = {1990}
}
@article{Tuson2013,
abstract = {The interaction of bacteria with surfaces has important implications in a range of areas, including bioenergy, biofouling, biofilm formation, and the infection of plants and animals. Many of the interactions of bacteria with surfaces produce changes in the expression of genes that influence cell morphology and behavior, including genes essential for motility and surface attachment. Despite the attention that these phenotypes have garnered, the bacterial systems used for sensing and responding to surfaces are still not well understood. An understanding of these mechanisms will guide the development of new classes of materials that inhibit and promote cell growth, and complement studies of the physiology of bacteria in contact with surfaces. Recent studies from a range of fields in science and engineering are poised to guide future investigations in this area. This review summarizes recent studies on bacteria-surface interactions, discusses mechanisms of surface sensing and consequences of cell attachment, provides an overview of surfaces that have been used in bacterial studies, and highlights unanswered questions in this field.},
author = {Tuson, Hannah H and Weibel, Douglas B},
doi = {10.1039/C3SM27705D},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tuson, Weibel - Bacteria-surface interactions. - 2013.pdf:pdf},
issn = {1744-683X},
journal = {Soft matter},
month = {may},
number = {18},
pages = {4368--4380},
pmid = {23930134},
title = {{Bacteria-surface interactions.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3733390{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {9},
year = {2013}
}
@article{Neuman2008,
author = {Neuman, Keir C and Nagy, Attila},
doi = {10.1038/NMETH.1218},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Neuman, Nagy - Single-molecule force spectroscopy optical tweezers , magnetic tweezers and atomic force microscopy - 2008.pdf:pdf},
journal = {Nature Methods},
number = {6},
pages = {491--505},
title = {{Single-molecule force spectroscopy : optical tweezers , magnetic tweezers and atomic force microscopy}},
volume = {5},
year = {2008}
}
@article{Chang2000,
abstract = {Leukocyte adhesion under flow in the microvasculature is mediated by binding between cell surface receptors and complementary ligands expressed on the surface of the endothelium. Leukocytes adhere to endothelium in a two-step mechanism: rolling (primarily mediated by selectins) followed by firm adhesion (primarily mediated by integrins). Using a computational method called "Adhesive Dynamics," we have simulated the adhesion of a cell to a surface in flow, and elucidated the relationship between receptor-ligand functional properties and the dynamics of adhesion. We express this relationship in a state diagram, a one-to-one map between the biophysical properties of adhesion molecules and various adhesive behaviors. Behaviors that are observed in simulations include firm adhesion, transient adhesion (rolling), and no adhesion. We varied the dissociative properties, association rate, bond elasticity, and shear rate and found that the unstressed dissociation rate, k(r)(o), and the bond interaction length, gamma, are the most important molecular properties controlling the dynamics of adhesion. Experimental k(r)(o) and gamma values from the literature for molecules that are known to mediate rolling adhesion fall within the rolling region of the state diagram. We explain why L-selectin-mediated rolling, which has faster k(r)(o) than other selectins, is accompanied by a smaller value for gamma. We also show how changes in association rate, shear rate, and bond elasticity alter the dynamics of adhesion. The state diagram (which must be mapped for each receptor-ligand system) presents a concise and comprehensive means of understanding the relationship between bond functional properties and the dynamics of adhesion mediated by receptor-ligand bonds.},
author = {Chang, K C and Tees, D F and Hammer, D a},
doi = {10.1073/pnas.200240897},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chang, Tees, Hammer - The state diagram for cell adhesion under flow leukocyte rolling and firm adhesion. - 2000.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
keywords = {Atomic Force,Cell Adhesion,Leukocytes,Leukocytes: cytology,Microscopy,paper3},
mendeley-tags = {paper3},
month = {oct},
number = {21},
pages = {11262--7},
pmid = {11005837},
title = {{The state diagram for cell adhesion under flow: leukocyte rolling and firm adhesion.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=17188{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {97},
year = {2000}
}
@article{Cuvelier2005b,
abstract = {Tethers are nanocylinders of lipid bilayer membrane, arising in situations ranging from micromanipulation experiments on synthetic vesicles to the formation of dynamic tubular networks in the Golgi apparatus. Relying on the extensive theoretical and experimental works aimed to understand the physics of individual tethers formation, we addressed the problem of the interaction between two nanotubes. By using a combination of micropipette manipulation and optical tweezers, we quantitatively studied the process of coalescence that occurred when the separation distance between both vesicle-tether junctions became smaller than a threshold length. Our experiments, which were supported by an original theoretical analysis, demonstrated that the measurements of the tether force and angle between tethers at coalescence directly yield the bending rigidity, kappa, and the membrane tension, sigma, of the vesicles. Contrary to other methods used to probe the bending rigidity of vesicles, the proposed approach permits a direct measurement of kappa without requiring any control of the membrane tension. Finally, after validation of the method and proposal of possible applications, we experimentally investigated the dynamics of the coalescence process.},
author = {Cuvelier, Damien and Der{\'{e}}nyi, Imre and Bassereau, Patricia and Nassoy, Pierre},
doi = {10.1529/biophysj.104.056473},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Cuvelier et al. - Coalescence of membrane tethers experiments, theory, and applications. - 2005.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Animals,Artificial,Biological,Biophysics,Biophysics: methods,Calibration,Cell Membrane,Cell Membrane: chemistry,Chickens,Cytoskeleton,Cytoskeleton: metabolism,Electrochemistry,Lipid Bilayers,Lipid Bilayers: chemistry,Lipid Bilayers: metabolism,Lipids,Lipids: chemistry,Membrane Fluidity,Membranes,Membranes: chemistry,Microscopy,Models,Phosphatidylcholines,Phosphatidylcholines: chemistry,Statistical,Surface Properties,Theoretical,Time Factors,Video},
month = {apr},
number = {4},
pages = {2714--26},
pmid = {15695629},
title = {{Coalescence of membrane tethers: experiments, theory, and applications.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1305367{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {88},
year = {2005}
}
@article{Hout,
author = {Hout, Michiel Van Den and Krudde, Vincent and Janssen, Xander J A and Nynke, H},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hout et al. - Supplementary Information for Distinguishable Populations Report on Interactions of Single DNA Molecules with Solid ‐ Sta.pdf:pdf},
pages = {3--6},
title = {{Supplementary Information for : Distinguishable Populations Report on Interactions of Single DNA Molecules with Solid ‐ State Nanopores}}
}
@article{Rao2010a,
author = {Rao, Satish and Raj, Saurabh and Balint, Stefan and Fons, Carlota Bardina and Campoy, Susana and Llagostera, Montserrat and Petrov, Dmitri},
doi = {10.1063/1.3431628},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rao et al. - Single DNA molecule detection in an optical trap using surface-enhanced Raman scattering - 2010.pdf:pdf},
issn = {00036951},
journal = {Applied Physics Letters},
number = {21},
pages = {213701},
title = {{Single DNA molecule detection in an optical trap using surface-enhanced Raman scattering}},
url = {http://link.aip.org/link/APPLAB/v96/i21/p213701/s1{\&}Agg=doi},
volume = {96},
year = {2010}
}
@article{Nataro1998,
author = {Nataro, James P and Kaper, James B},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Nataro, Kaper - Diarrheagenic Escherichia coli - 1998.pdf:pdf},
journal = {Microbiology},
number = {1},
pages = {142--201},
title = {{Diarrheagenic Escherichia coli}},
volume = {11},
year = {1998}
}
@article{Son2015,
author = {Son, Kwangmin and Brumley, Douglas R. and Stocker, Roman},
doi = {10.1038/nrmicro3567},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Son, Brumley, Stocker - Live from under the lens exploring microbial motility with dynamic imaging and microfluidics - 2015.pdf:pdf},
issn = {1740-1526},
journal = {Nature Reviews Microbiology},
number = {12},
pages = {761--775},
publisher = {Nature Publishing Group},
title = {{Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics}},
url = {http://www.nature.com/doifinder/10.1038/nrmicro3567},
volume = {13},
year = {2015}
}
@article{Hjelm1979,
abstract = {The relationship between urinary immunoglobulin levels and coating of a panel of bacteria by these immunoglobulins has been investigated. The results indicate that elevated urinary immunoglobulin levels are a distinct hazard in interpreting tests for antibody-coated bacteria as indicating upper or lower urinary tract infections.},
author = {Hjelm, E and Forsum, U and Frodin, L},
doi = {10.1136/jcp.32.12.1206},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hjelm, Forsum, Frodin - Significance of urinary immunoglobulins in tests for antibody-coated bacteria. - 1979.pdf:pdf},
issn = {0021-9746},
journal = {Journal of Clinical Pathology},
keywords = {Antibody-Coated Bacteria Test,Bacteria,Bacteria: immunology,False Positive Reactions,Fluorescent Antibody Technique,Humans,Immunoglobulins,Immunoglobulins: urine,Neoplasm Staging,Urinary,Urinary Bladder Neoplasms,Urinary Bladder Neoplasms: immunology,Urinary Bladder Neoplasms: pathology},
month = {dec},
number = {12},
pages = {1206--1210},
pmid = {395168},
title = {{Significance of urinary immunoglobulins in tests for antibody-coated bacteria.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1145936{\&}tool=pmcentrez{\&}rendertype=abstract http://jcp.bmj.com/cgi/doi/10.1136/jcp.32.12.1206},
volume = {32},
year = {1979}
}
@article{Tan2011,
abstract = {The ability to control the dispersion, aggregation, and assembly of colloidal systems is important for a number of applications, for instance, Pickering emulsions, drug and gene delivery, control of fluid rheology, and the formation of colloidal crystal arrays. We generated a responsive colloidal system based on polymer-brush-grafted silica nanoparticles and demonstrated that such a colloidal system can be used to produce stable oil-in-water Pickering emulsions. Cationic poly(2-(methacryloyloxy)-ethyl-trimethyl-ammonium chloride) (PMETAC) brushes were grown from silica nanoparticles (diameter ∼320 nm) through surface-initiated atom-transfer radical polymerization (ATRP). PMETAC brushes are attractive coatings for controlling the behavior of colloidal systems, owing to their ion-specific collapse resulting in the switching of surface hydrophilicity. Fourier transform infrared (FT-IR) spectroscopy, thermogravimetric analysis (TGA), transmission electron microscopy (TEM), dynamic light scattering (DLS), and zeta-potential measurements indicated the successful grafting of PMETAC brushes on nanoparticles. The resulting colloidal dispersion was shown to be responsive to perchlorate ions (ClO(4)(-)), which triggered particle aggregation and enabled the generation of Pickering emulsions. The onset of aggregation depended on the polymer chain length. Aggregation was not affected by the initiator density and brush conformational changes. Further studies suggested that particle aggregation and the formation of stable Pickering emulsions were not simply due to brush collapse but also were due to a gradual shielding of electrostatic repulsion. Finally, the stability and homogeneity of the resulting Pickering emulsions were studied.},
author = {Tan, Khooi Y. and Gautrot, Julien E. and Huck, Wilhelm T S},
doi = {10.1021/la102904r},
isbn = {1520-5827 (Electronic)$\backslash$r0743-7463 (Linking)},
issn = {07437463},
journal = {Langmuir},
number = {4},
pages = {1251--1259},
pmid = {20839829},
title = {{Formation of Pickering emulsions using ion-specific responsive colloids}},
volume = {27},
year = {2011}
}
@article{Katsikogianni2010a,
abstract = {Staphylococcus epidermidis adhesion onto materials with specific chemical functionalities, under flow, was investigated by using surfaces prepared by self-assembly of alkyl silane monolayers on glass. Terminal methyl (CH(3)) and amino (NH(2)) groups were formed by chemical vapor deposition of silanes, at elevated temperature. Carboxyl (COOH) terminated groups were prepared by further modification of NH(2) groups with succide anhydride and positively charged NH(2) groups by adsorption of poly-L: -lysine hydrobromide. Hydroxyl (OH) terminated glass was used as control. Surface modification was verified by contact angle measurements, atomic force microscopy and X-ray photoelectron spectroscopy. A parallel plate flow chamber was used to evaluate bacterial adhesion at various shear rates. Adhesion was found to be depended on the monolayer's terminal functionality. It was higher on the CH(3) followed by the positively charged NH(2), the non-charged NH(2) groups, the COOH and minimal on the OH-terminated glass. The increase in the material surface free energy significantly reduced the adhesion of a hydrophilic bacterial strain, and this is in accordance with the predictions of the thermodynamic theory. However, the increase in the shear rate restricted the predictability of the theory and revealed macromolecular interactions between bacteria and NH(2)- and COOH-terminated surfaces.},
author = {Katsikogianni, M G and Missirlis, Y F},
doi = {10.1007/s10856-009-3975-y},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Katsikogianni, Missirlis - Bacterial adhesion onto materials with specific surface chemistries under flow conditions. - 2010.pdf:pdf},
issn = {1573-4838},
journal = {Journal of materials science. Materials in medicine},
keywords = {Adsorption,Atomic Force,Atomic Force: methods,Bacterial Adhesion,Bromides,Bromides: chemistry,Cell Culture Techniques,Cell Culture Techniques: instrumentation,Glass,Glycerol,Glycerol: chemistry,Mechanical,Microscopy,Polylysine,Polylysine: chemistry,Silanes,Staphylococcus epidermidis,Staphylococcus epidermidis: metabolism,Stress,Temperature,Thermodynamics,Water,Water: chemistry,Wettability},
month = {mar},
number = {3},
pages = {963--8},
pmid = {20044774},
title = {{Bacterial adhesion onto materials with specific surface chemistries under flow conditions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20044774},
volume = {21},
year = {2010}
}
@article{Nada2011b,
abstract = {Enterotoxigenic Escherichia coli (ETEC) is recognized to be a common cause of acute watery diarrhea in children from developing countries. Colonization factors (CFAs) have been identified predominantly in ETEC isolates secreting heat-stable enterotoxin (ST) or cosecreting ST with a heat-labile toxin (LT). We hypothesized that LT-only-secreting ETEC produces unique colonization factors not previously described in ST and LTST-secreting ETEC. A set of degenerate primers based on nucleotide sequence similarities between the major structural genes of CS20 (csnA), CS18 (fotA), CS12 (cswA), and porcine antigen 987 (fasA) was developed and used to screen a collection of 266 LT-secreting ETEC isolates in which no known CFA was detected. PCR-amplified products of different molecular masses were obtained from 49 (18.4{\%}) isolates. Nucleotide sequence analysis of the PCR amplicons followed by GenBank nucleotide BLASTn analysis revealed five novel DNA sequences; translated amino acid BLASTx analysis confirmed sequence similarity to class 1b major structural proteins encoded by csnA, fotA, and fasA. Strains expressing the novel CFAs were phylotyped and analyzed using multilocus sequence typing (MLST; Achtman scheme), and the types detected were compared to those of a collection of archived global E. coli strains. In conclusion, application of the degenerate primer sets to ETEC isolates from surveillance studies increased the total number of ETEC isolates with detectable CFAs by almost 20{\%}. Additionally, MLST analysis suggests that for many CFAs, there may be a requirement for certain genetic backgrounds to acquire and maintain plasmids carrying genes encoding CFAs.},
annote = {From Duplicate 1 ( Discovery and phylogenetic analysis of novel members of class b enterotoxigenic Escherichia coli adhesive fimbriae. - Nada, Rania a; Shaheen, Hind I; Khalil, Sami B; Mansour, Adel; El-Sayed, Nasr; Touni, Iman; Weiner, Matthew; Armstrong, Adam W; Klena, John D )
},
author = {Nada, Rania A and Shaheen, Hind I and Khalil, Sami B and Mansour, Adel and El-Sayed, Nasr and Touni, Iman and Weiner, Matthew and Armstrong, Adam W and Klena, John D},
doi = {10.1128/JCM.02006-10},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Nada et al. - Discovery and phylogenetic analysis of novel members of class b enterotoxigenic Escherichia coli adhesive fimbriae. - 2011.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Nada et al. - Discovery and phylogenetic analysis of novel members of class b enterotoxigenic Escherichia coli adhesive fimbriae. - 2011.pdf:pdf},
issn = {1098-660X},
journal = {Journal of clinical microbiology},
keywords = {Adhesins,Bacterial,Bacterial Typing Techniques,Bacterial: chemistry,Bacterial: genetics,Child,Cluster Analysis,DNA,DNA Primers,DNA Primers: genetics,ETEC,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: classification,Enterotoxigenic Escherichia coli: genetics,Enterotoxigenic Escherichia coli: isolation {\&} puri,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli Proteins,Escherichia coli Proteins: genetics,Fimbriae,Genotype,Humans,Molecular Sequence Data,Multilocus Sequence Typing,Phylogeny,Polymerase Chain Reaction,Preschool,Sequence Analysis,class,fimbriae},
mendeley-tags = {ETEC,class,fimbriae},
month = {apr},
number = {4},
pages = {1403--10},
pmid = {21289147},
title = {{Discovery and phylogenetic analysis of novel members of class b enterotoxigenic Escherichia coli adhesive fimbriae.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3122862{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {49},
year = {2011}
}
@article{Dubois2007,
abstract = {The pathogenicity of many bacteria colonizing the gastrointestinal tract often depends on their ability to gain access to cells that are normally non-phagocytic. Helicobacter pylori colonizes the stomach of over half the world population and is the main cause of peptic ulcer disease and gastric cancer. It is generally considered to be a non-invasive pathogen present only in the lumen of the stomach and attached to gastric epithelial cells although a number of in vivo and in vitro studies have demonstrated that H. pylori is in fact invasive. In addition, H. pylori can repopulate the extracellular environment after complete elimination of extracellular bacteria with gentamicin, suggesting it may be considered a facultative intracellular bacterium. This review examines the validity of these observations and describes the evidence suggesting that the intracellular presence of H. pylori plays a role in the induction of diseases, in immune evasion, and in life-long persistence of the bacterium in the stomach of a majority of humans.},
author = {Dubois, Andre and Bor{\'{e}}n, Thomas},
doi = {10.1111/j.1462-5822.2007.00921.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dubois, Bor{\'{e}}n - Helicobacter pylori is invasive and it may be a facultative intracellular organism. - 2007.pdf:pdf},
issn = {1462-5814},
journal = {Cellular microbiology},
keywords = {Animals,Cells, Cultured,Epithelial Cells,Epithelial Cells: microbiology,Helicobacter Infections,Helicobacter Infections: microbiology,Helicobacter pylori,Helicobacter pylori: growth {\&} development,Helicobacter pylori: ultrastructure,Humans,Microscopy, Electron,Peptic Ulcer,Peptic Ulcer: microbiology},
month = {may},
number = {5},
pages = {1108--16},
pmid = {17388791},
title = {{Helicobacter pylori is invasive and it may be a facultative intracellular organism.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1913845{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {9},
year = {2007}
}
@article{Ruan2015,
author = {Ruan, Xiaosai and Sack, David a. and Zhang, Weiping},
doi = {10.1371/journal.pone.0121623},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ruan, Sack, Zhang - Genetic Fusions of a CFAIIIIV MEFA (Multiepitope Fusion Antigen) and a Toxoid Fusion of Heat-Stable Toxin (STa) and.pdf:pdf},
issn = {1932-6203},
journal = {Plos One},
number = {3},
pages = {e0121623},
title = {{Genetic Fusions of a CFA/I/II/IV MEFA (Multiepitope Fusion Antigen) and a Toxoid Fusion of Heat-Stable Toxin (STa) and Heat-Labile Toxin (LT) of Enterotoxigenic Escherichia coli (ETEC) Retain Broad Anti-CFA and Antitoxin Antigenicity}},
url = {http://dx.plos.org/10.1371/journal.pone.0121623},
volume = {10},
year = {2015}
}
@article{Mu2005,
abstract = {Pyelonephritic Escherichia coli cause urinary tract infections that involve the kidneys. Initiation of infection is dependent on P-pili expressed on the bacterial surface. In this work, an essential interface for assembly of the helical rod structure of P-pili has been located on the major pilin subunit, PapA. Based on primary sequence alignment, secondary structure analysis, and quaternary structure modeling of the PapA subunit, we predicted the location of a site that is critical for in vivo assembly of the native macromolecular structure of P-pili. A rigid helical rod of PapA subunits comprising most of the pilus length is stabilized by n to n+3 subunit-subunit interactions, and is important for normal function of these pili. Using site-directed mutagenesis, ultrastructural analysis by electron cryomicroscopy, immunocytochemistry, and molecular modeling we show that residues 106-109 (Asn, Gly, Ala, Gly) are essential for assembly of native P-pilus filaments. Mutation of these residues disrupts assembly of the native P-pilus helix. Extended fibrillar structures do still assemble, verifying that n to n+1 subunit-subunit interactions are maintained in the mutant fiber morphology. Observation of this fibrillar morphology in the mutant fiber was predicted by our modeling studies. These mutant P-pili data validate the predictive value of our model for understanding subunit-subunit interactions between PapA monomers. Alteration of the pilus structure from a 7-8 nm helical rod to a 2 nm fibrillar structure may compromise the ability of these bacteria to adhere and remain bound to the host cell, thus providing a possible therapeutic target for antimicrobial drugs.},
author = {Mu, Xiang-Qi and Jiang, Zhenghui G and Bullitt, Esther},
doi = {10.1016/j.jmb.2004.11.037},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Mu, Jiang, Bullitt - Localization of a critical interface for helical rod formation of bacterial adhesion P-pili. - 2005.pdf:pdf},
issn = {0022-2836},
journal = {Journal of molecular biology},
keywords = {Bacterial Adhesion,Binding Sites,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: ultrastructure,Escherichia coli: chemistry,Escherichia coli: cytology,Escherichia coli: genetics,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae, Bacterial,Fimbriae, Bacterial: chemistry,Fimbriae, Bacterial: genetics,Fimbriae, Bacterial: metabolism,Fimbriae, Bacterial: ultrastructure,Microscopy, Electron,Models, Molecular,Mutation,Mutation: genetics,Protein Structure, Tertiary},
month = {feb},
number = {1},
pages = {13--20},
pmid = {15663923},
title = {{Localization of a critical interface for helical rod formation of bacterial adhesion P-pili.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15663923},
volume = {346},
year = {2005}
}
@article{Berry2011a,
annote = {        From Duplicate 1 (                           Flow dynamics of a tethered elastic capsule                         - Berry, J. D.; Carberry, J.; Thompson, M. C. )
                
        From Duplicate 1 (                           Flow dynamics of a tethered elastic capsule                         - Berry, J. D.; Carberry, J.; Thompson, M. C. )
                
        From Duplicate 1 (                           Flow dynamics of a tethered elastic capsule                         - Berry, J. D.; Carberry, J.; Thompson, M. C. )
                
        
        
        
        
        
        
      },
author = {Berry, J. D. and Carberry, J. and Thompson, M. C.},
doi = {10.1063/1.3553225},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Berry, Carberry, Thompson - Flow dynamics of a tethered elastic capsule - 2011.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Berry, Carberry, Thompson - Flow dynamics of a tethered elastic capsule - 2011(2).pdf:pdf},
issn = {10706631},
journal = {Physics of Fluids},
keywords = {flow,shear force,stokes},
mendeley-tags = {flow,shear force,stokes},
number = {2},
pages = {021901},
title = {{Flow dynamics of a tethered elastic capsule}},
url = {http://link.aip.org/link/PHFLE6/v23/i2/p021901/s1{\&}Agg=doi},
volume = {23},
year = {2011}
}
@article{Guo2009,
author = {Guo, Siyu and Pridmore, Tony and Kong, Yaguang and Zhang, Xufang},
doi = {10.1016/j.patrec.2009.05.003},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Guo et al. - An improved Hough transform voting scheme utilizing surround suppression - 2009.pdf:pdf},
issn = {01678655},
journal = {Pattern Recognition Letters},
month = {oct},
number = {13},
pages = {1241--1252},
publisher = {Elsevier B.V.},
title = {{An improved Hough transform voting scheme utilizing surround suppression}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0167865509001032},
volume = {30},
year = {2009}
}
@article{Neal1991,
author = {Neal, Durwood E and Kaack, M Bernice and Baskin, Gary and Roberts, James A},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Neal et al. - Attenuation of Antibody Response to Acute Pyelonephritis by Treatment with Antibiotics - 1991.pdf:pdf},
number = {11},
pages = {2340--2344},
title = {{Attenuation of Antibody Response to Acute Pyelonephritis by Treatment with Antibiotics}},
volume = {35},
year = {1991}
}
@article{Evans2001,
author = {Evans, Evan},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Evans - Probing the relation between Force - Lifetime - and Chemistry in single molecular bonds - 2001.pdf:pdf},
journal = {Annu. Rev. Biophys. Biomol. Struct.},
keywords = {a dissociation pathway is,a weak bond along,and,bonds,dynamic force spectroscopy,energy barriers in macromolecular,excitations,fully explored through brownian-thermal,imaging the landscape of,multiple molecular bonds,s abstract on laboratory,strengths of single and,the energy landscape of,time scales},
pages = {105--128},
title = {{Probing the relation between Force - Lifetime - and Chemistry in single molecular bonds}},
volume = {30},
year = {2001}
}
@article{Xu1996d,
annote = {        From Duplicate 1 (                   Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment                 - Xu, C.; Zhang, Z.; den Toonder, J. M. J.; Nieuwstadt, F. T. M. )
                
        From Duplicate 1 (                           Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment                         - Xu, C.; Zhang, Z.; den Toonder, J. M. J.; Nieuwstadt, F. T. M. )
                
        From Duplicate 3 (                           Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment                         - Xu, C.; Zhang, Z.; den Toonder, J. M. J.; Nieuwstadt, F. T. M. )
                
        
        
        
        
        
        
      },
author = {Xu, C. and Zhang, Z. and den Toonder, J. M. J. and Nieuwstadt, F. T. M.},
doi = {10.1063/1.868973},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Xu et al. - Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment - 1996.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Xu et al. - Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment - 1996.pdf:pdf},
issn = {10706631},
journal = {Physics of Fluids},
number = {7},
pages = {1938},
title = {{Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment}},
url = {http://link.aip.org/link/PHFLE6/v8/i7/p1938/s1{\&}Agg=doi},
volume = {8},
year = {1996}
}
@article{Zhang2002,
abstract = {A mathematical model was developed to quantify the efficiency of cell-substrate attachment in the parallel-plate flow chamber. The model decouples the physical features of the system that affect cell-substrate collision rates from the biological features that influence cellular adhesivity. Thus, experimental data on cell rolling and adhesion density are converted into "frequency" parameters that quantify the "efficiency" with which cells in the flow chamber progress from the free stream to rolling, and transition from rolling to firm arrest. The model was partially validated by comparing simulation results with experiments where neutrophils rolled and adhered onto substrates composed of cotransfected cells bearing E-selectin and intercellular adhesion molecule-1 (ICAM-1). Results suggest that: 1) Neutrophils contact the E-selectin substrate on average for 4-8.5s before tethering. This contact duration is insensitive to applied shear stress. 2) At 2 dyn/cm(2), approximately 28{\%} of the collisions between the cells and substrate result in primary capture. Also, approximately 5-7{\%} of collisions between neutrophils in the free stream and previously recruited neutrophils bound on the substrate result in secondary capture. These percentages were higher at lower shears. 3) An adherent cell may influence the flow streams in its vicinity up to a distance of 2.5 cell diameters away. 4) Our estimates of selectin on-rate in cellular systems compare favorably with data from reconstituted systems with immobilized soluble E-selectin. In magnitude, the observed on-rates occur in the order, L-selectin > P-selectin > E-selectin.},
author = {Zhang, Yi and Neelamegham, Sriram},
doi = {10.1016/S0006-3495(02)73956-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Zhang, Neelamegham - Estimating the efficiency of cell capture and arrest in flow chambers study of neutrophil binding via E-selectin an.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Algorithms,Animals,Biophysical Phenomena,Biophysics,Cell Adhesion,Cell Line,E-Selectin,E-Selectin: metabolism,Humans,Intercellular Adhesion Molecule-1,Intercellular Adhesion Molecule-1: metabolism,Kinetics,Ligands,Mice,Models, Theoretical,Neutrophils,Neutrophils: cytology,Neutrophils: metabolism,Protein Binding,Stress, Mechanical,Time Factors,Transfection},
month = {oct},
number = {4},
pages = {1934--52},
pmid = {12324413},
publisher = {Elsevier},
title = {{Estimating the efficiency of cell capture and arrest in flow chambers: study of neutrophil binding via E-selectin and ICAM-1.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302284{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {83},
year = {2002}
}
@article{Carter2009a,
abstract = {The most commonly used optical-trapping assays are coupled to surfaces, yet such assays lack atomic-scale ( approximately 0.1 nm) spatial resolution due to drift between the surface and trap. We used active stabilization techniques to minimize surface motion to 0.1 nm in three dimensions and decrease multiple types of trap laser noise (pointing, intensity, mode, and polarization). As a result, we achieved nearly the thermal limit (<0.05 nm) of bead detection over a broad range of trap stiffness (k(T) = 0.05-0.5 pN/nm) and frequency (Deltaf = 0.03-100 Hz). We next demonstrated sensitivity to one-basepair (0.34-nm) steps along DNA in a surface-coupled assay at moderate force (6 pN). Moreover, basepair stability was achieved immediately after substantial (3.4 pN) changes in force. Active intensity stabilization also led to enhanced force precision ( approximately 0.01{\%}) that resolved 0.1-pN force-induced changes in DNA hairpin unfolding dynamics. This work brings the benefit of atomic-scale resolution, currently limited to dual-beam trapping assays, along with enhanced force precision to the widely used, surface-coupled optical-trapping assay.},
author = {Carter, Ashley R and Seol, Yeonee and Perkins, Thomas T},
doi = {10.1016/j.bpj.2008.12.3933},
journal = {BiophysJ},
keywords = {DNA,optical tweezers},
mendeley-tags = {DNA,optical tweezers},
number = {7},
pages = {2926--2934},
title = {{Precision surface-coupled optical-trapping assay with one-basepair resolution}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=19348774 http://www.sciencedirect.com/science?{\_}ob=ArticleURL{\&}{\_}udi=B94RW-4W04GHV-18{\&}{\_}user=641710{\&}{\_}rdoc=1{\&}{\_}fmt={\&}{\_}orig=search{\&}{\_}sort=d{\&}view=c{\&}{\_}acct=C000034378{\&}{\_}ve},
volume = {96},
year = {2009}
}
@article{Hayasaki2014,
author = {Hayasaki, Yoshio and Sato, Akira},
doi = {10.1016/j.optcom.2014.02.014},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hayasaki, Sato - Holographic three-dimensional motion detection of an optically trapped sub-100nm gold nanoparticle - 2014.pdf:pdf},
issn = {00304018},
journal = {Optics Communications},
keywords = {Digital holography,Nanoparticle,Optical manipulation,Optical tweezers,Three-dimensional target tracking},
month = {jul},
pages = {22--26},
publisher = {Elsevier},
title = {{Holographic three-dimensional motion detection of an optically trapped sub-100nm gold nanoparticle}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0030401814001461},
volume = {322},
year = {2014}
}
@article{Magazzu2015,
author = {Magazz{\'{u}}, a. and Spadaro, D. and Donato, M. G. and Sayed, R. and Messina, E. and D’Andrea, C. and Foti, a. and Fazio, B. and Iat{\'{\i}}, M. a. and Irrera, a. and Saija, R. and Gucciardi, P. G. and Marag{\'{o}}, O. M.},
doi = {10.1007/s12210-015-0395-4},
issn = {2037-4631},
journal = {Rendiconti Lincei},
title = {{Optical tweezers: a non-destructive tool for soft and biomaterial investigations}},
year = {2015}
}
@article{Barsegov2006,
abstract = {We present, to our knowledge, a new theory that takes internal dynamics of proteins into account to describe forced-unfolding and force-quench refolding in single molecule experiments. In the current experimental setup (using either atomic force microscopy or laser optical tweezers) the distribution of unfolding times, P(t), is measured by applying a constant stretching force f(S) from which the apparent f(S)-dependent unfolding rate is obtained. To describe the complexity of the underlying energy landscape requires additional probes that can incorporate the dynamics of tension propagation and relaxation of the polypeptide chain upon force quench. We introduce a theory of force correlation spectroscopy to map the parameters of the energy landscape of proteins. In force correlation spectroscopy, the joint distribution P(T, t) of folding and unfolding times is constructed by repeated application of cycles of stretching at constant f(S) separated by release periods T during which the force is quenched to f(Q) < f(S). During the release period, the protein can collapse to a manifold of compact states or refold. We show that P(T, t) at various f(S) and f(Q) values can be used to resolve the kinetics of unfolding as well as formation of native contacts. We also present methods to extract the parameters of the energy landscape using chain extension as the reaction coordinate and P(T, t). The theory and a wormlike chain model for the unfolded states allows us to obtain the persistence length l(p) and the f(Q)-dependent relaxation time, giving us an estimate of collapse timescale at the single molecular level, in the coil states of the polypeptide chain. Thus, a more complete description of landscape of protein native interactions can be mapped out if unfolding time data are collected at several values of f(S) and f(Q). We illustrate the utility of the proposed formalism by analyzing simulations of unfolding-refolding trajectories of a coarse-grained protein (S1) with beta-sheet architecture for several values of f(S), T, and f(Q) = 0. The simulations of stretch-relax trajectories are used to map many of the parameters that characterize the energy landscape of S1.},
author = {Barsegov, V and Klimov, D K and Thirumalai, D},
doi = {10.1529/biophysj.105.075937},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Barsegov, Klimov, Thirumalai - Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy theory.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Biomechanics,Biophysics,Biophysics: instrumentation,Computer Simulation,Lasers,Microscopy, Atomic Force,Models, Molecular,Peptides,Peptides: chemistry,Protein Binding,Protein Folding,Proteins,Proteins: chemistry},
month = {jun},
number = {11},
pages = {3827--41},
pmid = {16533852},
title = {{Mapping the energy landscape of biomolecules using single molecule force correlation spectroscopy: theory and applications.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1459511{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {90},
year = {2006}
}
@article{Balsalobre2003,
author = {Balsalobre, Carlos and Morschh{\"{a}}user, Joachim and Jass, Jana and Hacker, J{\"{o}}rg and Uhlin, Bernt Eric},
doi = {10.1128/JB.185.2.620},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Balsalobre et al. - Transcriptional Analysis of the sfa Determinant Revealing Multiple mRNA Processing Events in the Biogenesis of S Fim.pdf:pdf},
isbn = {4690772630},
journal = {Journal of bacteriology},
number = {2},
pages = {620--629},
title = {{Transcriptional Analysis of the sfa Determinant Revealing Multiple mRNA Processing Events in the Biogenesis of S Fimbriae in Pathogenic Escherichia coli}},
volume = {185},
year = {2003}
}
@article{Pelletier2012,
abstract = {Replicating bacterial chromosomes continuously demix from each other and segregate within a compact volume inside the cell called the nucleoid. Although many proteins involved in this process have been identified, the nature of the global forces that shape and segregate the chromosomes has remained unclear because of limited knowledge of the micromechanical properties of the chromosome. In this work, we demonstrate experimentally the fundamentally soft nature of the bacterial chromosome and the entropic forces that can compact it in a crowded intracellular environment. We developed a unique "micropiston" and measured the force-compression behavior of single Escherichia coli chromosomes in confinement. Our data show that forces on the order of 100 pN and free energies on the order of 10(5) k(B)T are sufficient to compress the chromosome to its in vivo size. For comparison, the pressure required to hold the chromosome at this size is a thousand-fold smaller than the surrounding turgor pressure inside the cell. Furthermore, by manipulation of molecular crowding conditions (entropic forces), we were able to observe in real time fast (approximately 10 s), abrupt, reversible, and repeatable compaction-decompaction cycles of individual chromosomes in confinement. In contrast, we observed much slower dissociation kinetics of a histone-like protein HU from the whole chromosome during its in vivo to in vitro transition. These results for the first time provide quantitative, experimental support for a physical model in which the bacterial chromosome behaves as a loaded entropic spring in vivo.},
author = {Pelletier, J. and Halvorsen, K. and Ha, B.-Y. and Paparcone, R. and Sandler, S. J. and Woldringh, C. L. and Wong, W. P. and Jun, S.},
doi = {10.1073/pnas.1208689109},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Pelletier et al. - PNAS Plus Physical manipulation of the Escherichia coli chromosome reveals its soft nature - 2012.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {40},
pages = {E2649--E2656},
pmid = {22984156},
title = {{PNAS Plus: Physical manipulation of the Escherichia coli chromosome reveals its soft nature}},
volume = {109},
year = {2012}
}
@article{Rickgauer2006,
author = {Rickgauer, John Peter and Fuller, Derek N and Smith, Douglas E},
doi = {10.1529/biophysj.106.089524},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Rickgauer, Fuller, Smith - DNA as a Metrology Standard for Length and Force Measurements with Optical Tweezers - 2006.pdf:pdf},
journal = {Biophysical Journal},
number = {December},
pages = {20--22},
title = {{DNA as a Metrology Standard for Length and Force Measurements with Optical Tweezers}},
volume = {91},
year = {2006}
}
@article{Dunne2002,
abstract = {The process of surface adhesion and biofilm development is a survival strategy employed by virtually all bacteria and refined over millions of years. This process is designed to anchor microorganisms in a nutritionally advantageous environment and to permit their escape to greener pastures when essential growth factors have been exhausted. Bacterial attachment to a surface can be divided into several distinct phases, including primary and reversible adhesion, secondary and irreversible adhesion, and biofilm formation. Each of these phases is ultimately controlled by the expression of one or more gene products. Ultrastructurally, the mature bacterial biofilm resembles an underwater coral reef containing pyramidal or mushroom-shaped microcolonies of organisms embedded within an extracellular glycocalyx, with channels and cavities to allow the exchange of nutrients and waste. The biofilm protects its inhabitants from predators, dehydration, biocides, and other environmental extremes while regulating population growth and diversity through primitive cell signals. From a physiological standpoint, surface-bound bacteria behave quite differently from their planktonic counterparts. Recognizing that bacteria naturally occur as surface-bound and often polymicrobic communities, the practice of performing antimicrobial susceptibility tests using pure cultures and in a planktonic growth mode should be questioned. That this model does not reflect conditions found in nature might help explain the difficulties encountered in the management and treatment of biomedical implant infections.},
author = {Dunne, W Michael and Dunne, W Michael},
doi = {10.1128/CMR.15.2.155},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dunne, Dunne - Bacterial Adhesion Seen Any Good Bio lms Lately - 2002.pdf:pdf},
isbn = {0893-8512},
issn = {0893-8512, 1098-6618},
journal = {Society},
keywords = {Biofilm},
mendeley-tags = {Biofilm},
number = {2},
pages = {155--166},
title = {{Bacterial Adhesion: Seen Any Good Bio lms Lately?}},
volume = {15},
year = {2002}
}
@article{Tobias2010,
abstract = {Enterotoxigenic Escherichia coli (ETEC) are an important cause of diarrheal morbidity in developing countries, especially in children and also of traveler's diarrhea. Colonization factors (CFs) of ETEC, like CFA/I and CS2 which are genetically and structurally related, play a substantial role in pathogenicity, and since intestinal-mucosal immune responses against CFs appear to be protective, much effort has focused on the development of a CF-based ETEC vaccine. We have constructed hybrid operons in which the major CS2 subunit-encoding cotA gene was inserted into the CFA/I operon, either replacing (hybrid I) or being added to the major CFA/I subunit-encoding cfaB gene (hybrid II). Using specific monoclonal antibodies against the major subunits of CFA/I and CS2, high levels of surface expression of both fimbrial subunits were shown in E. coli carrying the hybrid II operon. Oral immunization of mice with formalin-killed bacteria expressing hybrid II fimbriae induced strong CFA/I- and CS2-specific serum IgG + IgM and fecal IgA antibody responses, which were higher than those achieved by similar immunization with the reference strains. Bacteria expressing hybrid fimbriae are potential candidate strains in an oral-killed CF-ETEC vaccine, and the approach represents an attractive and novel means of producing a broad-spectrum ETEC vaccine.},
author = {Tobias, Joshua and Svennerholm, Ann-Mari and Holmgren, Jan and Lebens, Michael},
doi = {10.1007/s00253-010-2577-4},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tobias et al. - Construction and expression of immunogenic hybrid enterotoxigenic Escherichia coli CFAI and CS2 colonization fimbriae fo.pdf:pdf},
isbn = {0025301025774},
issn = {01757598},
journal = {Applied Microbiology and Biotechnology},
keywords = {CFA/I,CS2,ETEC,Hybrid fimbriae,Vaccine},
pages = {1355--1365},
pmid = {20405124},
title = {{Construction and expression of immunogenic hybrid enterotoxigenic Escherichia coli CFA/I and CS2 colonization fimbriae for use in vaccines}},
volume = {87},
year = {2010}
}
@article{Koster2010,
abstract = {Entangling and twisting of cellular DNA (i.e., supercoiling) are problems inherent to the helical structure of double-stranded DNA. Supercoiling affects transcription, DNA replication, and chromosomal segregation. Consequently the cell must fine-tune supercoiling to optimize these key processes. Here, we summarize how supercoiling is generated and review experimental and theoretical insights into supercoil relaxation. We distinguish between the passive dissipation of supercoils by diffusion and the active removal of supercoils by topoisomerase enzymes. We also review single-molecule studies that elucidate the timescales and mechanisms of supercoil removal.},
author = {Koster, Daniel a and Crut, Aur{\'{e}}lien and Shuman, Stewart and Bjornsti, Mary-Ann and Dekker, Nynke H},
doi = {10.1016/j.cell.2010.08.001},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Koster et al. - Cellular strategies for regulating DNA supercoiling a single-molecule perspective. - 2010.pdf:pdf},
issn = {1097-4172},
journal = {Cell},
keywords = {Animals,Cell Physiological Phenomena,DNA,DNA Topoisomerases, Type I,DNA Topoisomerases, Type I: metabolism,DNA, Superhelical,DNA, Superhelical: chemistry,DNA, Superhelical: metabolism,DNA: chemistry,DNA: metabolism,Humans},
month = {aug},
number = {4},
pages = {519--30},
pmid = {20723754},
title = {{Cellular strategies for regulating DNA supercoiling: a single-molecule perspective.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2997354{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {142},
year = {2010}
}
@article{Helmerson1997,
abstract = {We used optical tweezers (optical trapping technology) to measure the force required to separate antigen-antibody bonds. Under competitive-binding conditions, we used the force determination to detect and measure protein antigen concentrations as small as 1 fmol/L (10(-15) mol/L).},
author = {Helmerson, K and Kishore, R and Phillips, W D and Weetall, H H},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Helmerson et al. - Optical tweezers-based immunosensor detects femtomolar concentrations of antigens. - 1997.pdf:pdf},
issn = {0009-9147},
journal = {Clinical chemistry},
keywords = {Antibodies,Antibodies: metabolism,Antigen-Antibody Complex,Antigen-Antibody Complex: metabolism,Antigens,Antigens: analysis,Immunoassay,Immunoassay: methods,Lasers,Microchemistry,Microspheres,Optics and Photonics,Sensitivity and Specificity,Serum Albumin, Bovine,Serum Albumin, Bovine: immunology},
month = {feb},
number = {2},
pages = {379--83},
pmid = {9023143},
title = {{Optical tweezers-based immunosensor detects femtomolar concentrations of antigens.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9023143},
volume = {43},
year = {1997}
}
@article{Jeney2008,
abstract = {The motion of an optically trapped sphere constrained by the vicinity of a wall is investigated at times where hydrodynamic memory is significant. First, we quantify, in bulk, the influence of confinement arising from the trapping potential on the sphere's velocity autocorrelation function C(t). Next, we study the splitting of C(t) into C{\_}{\{}parallel{\}}(t) and C{\_}{\{}perpendicular{\}}(t), when the sphere is approached towards a surface. Thereby, we monitor the crossover from a slow t{\{}-3/2{\}} long-time tail, away from the wall, to a faster t{\{}-5/2{\}} decay, due to the subtle interplay between hydrodynamic backflow and wall effects. Finally, we discuss the resulting asymmetric time-dependent diffusion coefficients.},
archivePrefix = {arXiv},
arxivId = {0805.3227},
author = {Jeney, Sylvia and Luki{\'{c}}, Branimir and Kraus, Jonas a. and Franosch, Thomas and Forr{\'{o}}, L{\'{a}}szl{\'{o}}},
doi = {10.1103/PhysRevLett.100.240604},
eprint = {0805.3227},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jeney et al. - Anisotropic memory effects in confined colloidal diffusion - 2008.pdf:pdf},
issn = {00319007},
journal = {Physical Review Letters},
number = {24},
pages = {5--8},
pmid = {18643565},
title = {{Anisotropic memory effects in confined colloidal diffusion}},
volume = {100},
year = {2008}
}
@article{Meng1995,
author = {Meng, Hui and Hussain, Fazle},
journal = {Applied Optics},
number = {11},
pages = {1827--1840},
title = {{In-line recording and off-axis viewing technique for holographic particle velocimetry.}},
volume = {34},
year = {1995}
}
@article{Klenin2000,
author = {Klenin, Konstantin and Hammermann, Markus and Langowski, J{\"{o}}rg},
doi = {10.1021/ma9914467},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Klenin, Hammermann, Langowski - Modeling Dynamic Light Scattering of Supercoiled DNA - 2000.pdf:pdf},
issn = {0024-9297},
journal = {Macromolecules},
month = {feb},
number = {4},
pages = {1459--1466},
title = {{Modeling Dynamic Light Scattering of Supercoiled DNA}},
url = {http://pubs.acs.org/doi/abs/10.1021/ma9914467},
volume = {33},
year = {2000}
}
@article{Dienerowitz2012,
author = {Dienerowitz, M and Gibson, G and Dienerowitz, F and Padgett, M},
doi = {10.1088/2040-8978/14/4/045003},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Dienerowitz et al. - Expanding the toolbox for nanoparticle trapping and spectroscopy with holographic optical tweezers - 2012.pdf:pdf},
issn = {2040-8978},
journal = {Journal of Optics},
keywords = {045003,14,available from stacks,darkfield,holographic optical tweezers,imaging,in colour only in,iop,jopt,mmedia,nanoparticle trapping and spectroscopy,org,s online supplementary data,some figures may appear,the online journal,video-based particle tracking},
month = {apr},
number = {4},
pages = {045003},
title = {{Expanding the toolbox for nanoparticle trapping and spectroscopy with holographic optical tweezers}},
url = {http://stacks.iop.org/2040-8986/14/i=4/a=045003?key=crossref.82fb0c0fb97d384755946b652b4fc9df},
volume = {14},
year = {2012}
}
@article{Smith1991,
author = {Smith, C. R. and Walker, J. D. a. and Haidari, a. H. and Sobrun, U.},
doi = {10.1098/rsta.1991.0070},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Smith et al. - On the Dynamics of Near-Wall Turbulence - 1991.pdf:pdf},
issn = {1364-503X},
journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences},
month = {aug},
number = {1641},
pages = {131--175},
title = {{On the Dynamics of Near-Wall Turbulence}},
url = {http://rsta.royalsocietypublishing.org/cgi/doi/10.1098/rsta.1991.0070},
volume = {336},
year = {1991}
}
@article{Rehse2012,
abstract = {The recent progress made in developing laser-induced breakdown spectroscopy (LIBS) has transformed LIBS from an elemental analysis technique to one that can be applied for the reagentless analysis of molecularly complex biological materials or clinical specimens. Rapid advances in the LIBS technology have spawned a growing number of recently published articles in peer-reviewed journals which have consistently demonstrated the capability of LIBS to rapidly detect, biochemically characterize and analyse, and/or accurately identify various biological, biomedical or clinical samples. These analyses are inherently real-time, require no sample preparation, and offer high sensitivity and specificity. This overview of the biomedical applications of LIBS is meant to summarize the research that has been performed to date, as well as to suggest to health care providers several possible specific future applications which, if successfully implemented, would be significantly beneficial to humankind.},
author = {Rehse, S J and Salimnia, H and Miziolek, a W},
doi = {10.3109/03091902.2011.645946},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Rehse, Salimnia, Miziolek - Laser-induced breakdown spectroscopy (LIBS) an overview of recent progress and future potential for biomedic.pdf:pdf},
issn = {1464-522X},
journal = {Journal of medical engineering {\&} technology},
keywords = {diagnostics,laser-induced breakdown spectroscopy,medical,point-of-care,rapid pathogen identification},
month = {feb},
number = {2},
pages = {77--89},
pmid = {22268995},
title = {{Laser-induced breakdown spectroscopy (LIBS): an overview of recent progress and future potential for biomedical applications.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22268995},
volume = {36},
year = {2012}
}
@article{Mazilu2010a,
author = {Mazilu, Michael and {De Luca}, Anna Chiara and Riches, Andrew and Herrington, C. Simon and Dholakia, Kishan},
doi = {10.1364/OE.18.011382},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mazilu et al. - Optimal algorithm for fluorescence suppression of modulated Raman spectroscopy - 2010.pdf:pdf},
issn = {1094-4087},
journal = {Optics Express},
month = {may},
number = {11},
pages = {11382},
title = {{Optimal algorithm for fluorescence suppression of modulated Raman spectroscopy}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=oe-18-11-11382},
volume = {18},
year = {2010}
}
@article{Wakiya1964,
author = {Wakiya, Shoichi},
journal = {Journal of the Physical Society of Japan},
number = {8},
pages = {1401--1408},
title = {{Effect of a Plane Wall on the Impulse Motion of a Sphere in a Viscous Fluid}},
volume = {19},
year = {1964}
}
@article{Min2009,
abstract = {We present a single-cell motility assay, which allows the quantification of bacterial swimming in a well-controlled environment, for durations of up to an hour and with a temporal resolution greater than the flagellar rotation rates of approximately 100 Hz. The assay is based on an instrument combining optical tweezers, light and fluorescence microscopy, and a microfluidic chamber. Using this device we characterized the long-term statistics of the run-tumble time series in individual Escherichia coli cells. We also quantified higher-order features of bacterial swimming, such as changes in velocity and reversals of swimming direction.},
author = {Min, Taejin L and Mears, Patrick J and Chubiz, Lon M and Rao, Christopher V and Golding, Ido and Chemla, Yann R},
doi = {10.1038/nmeth.1380},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Min et al. - High-resolution, long-term characterization of bacterial motility using optical tweezers. - 2009.pdf:pdf},
issn = {1548-7105},
journal = {Nature methods},
keywords = {Escherichia coli,Escherichia coli: physiology,Flagella,Flagella: physiology,Locomotion,Locomotion: physiology,Microfluidic Analytical Techniques,Microscopy, Fluorescence,Microscopy, Fluorescence: instrumentation,Molecular Motor Proteins,Molecular Motor Proteins: physiology,Optical Tweezers,Rotation},
month = {nov},
number = {11},
pages = {831--5},
pmid = {19801991},
publisher = {Nature Publishing Group},
title = {{High-resolution, long-term characterization of bacterial motility using optical tweezers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2784139{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {6},
year = {2009}
}
@article{Wall1999,
author = {Wall, D and Kaiser, D},
journal = {Molecular microbiology},
title = {{Type IV pili and cell motility}},
url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.1999.01339.x/full},
year = {1999}
}
@article{Umeki2000,
author = {Umeki, Tsuneyuki},
doi = {10.2207/qjjws1943.69.7{\_}557},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Umeki - Technical Writing - 2000.pdf:pdf},
issn = {0021-4787},
journal = {Journal of the Japan Welding Society},
number = {7},
pages = {557--558},
title = {{Technical Writing}},
volume = {69},
year = {2000}
}
@article{Leach2009,
author = {Leach, J. and Mushfique, H. and Keen, S. and {Di Leonardo}, R. and Ruocco, G. and Cooper, J. and Padgett, M.},
doi = {10.1103/PhysRevE.79.026301},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Leach et al. - Comparison of Fax{\'{e}}n’s correction for a microsphere translating or rotating near a surface - 2009.pdf:pdf},
issn = {1539-3755},
journal = {Physical Review E},
month = {feb},
number = {2},
pages = {1--4},
title = {{Comparison of Fax{\'{e}}n’s correction for a microsphere translating or rotating near a surface}},
url = {http://link.aps.org/doi/10.1103/PhysRevE.79.026301},
volume = {79},
year = {2009}
}
@article{Tolic-Nørrelykke2004,
author = {Toli{\'{c}}-N{\o}rrelykke, Iva Marija and Berg-S{\o}rensen, Kirstine and Flyvbjerg, Henrik},
doi = {10.1016/j.cpc.2004.02.012},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Toli{\'{c}}-N{\o}rrelykke, Berg-S{\o}rensen, Flyvbjerg - MatLab program for precision calibration of optical tweezers - 2004.pdf:pdf},
issn = {00104655},
journal = {Computer Physics Communications},
month = {jun},
number = {3},
pages = {225--240},
title = {{MatLab program for precision calibration of optical tweezers}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0010465504001043},
volume = {159},
year = {2004}
}
@article{Czerwinski2009b,
abstract = {Much effort is put into minimizing noise in optical tweezers experiments because noise and drift can mask fundamental behaviours of, e.g., single molecule assays. Various initiatives have been taken to reduce or eliminate noise but it has been difficult to quantify their effect. We propose to use Allan variance as a simple and efficient method to quantify noise in optical tweezers setups.We apply the method to determine the optimal measurement time, frequency, and detection scheme, and quantify the effect of acoustic noise in the lab. The method can also be used on-the-fly for determining optimal parameters of running experiments.},
author = {Czerwinski, Fabian and Richardson, Andrew C and Oddershede, Lene B},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Czerwinski, Richardson, Oddershede - Quantifying Noise in Optical Tweezers by Allan Variance - 2009.pdf:pdf},
issn = {1094-4087},
journal = {Optics express},
keywords = {Acoustics,Calibration,Equipment Design,Fourier Analysis,Lasers,Light,Magnetics,Microscopy,Microscopy: methods,Models, Statistical,Monte Carlo Method,Optical Tweezers,Optics and Photonics,Photochemistry,Photochemistry: methods,Probability,Stochastic Processes},
month = {jul},
number = {15},
pages = {13255--69},
pmid = {19654731},
title = {{Quantifying noise in optical tweezers by allan variance.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19654731},
volume = {17},
year = {2009}
}
@article{Letter1998,
author = {Letter, Biophysics},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Letter - Thermal noise limitations on micromechanical experiments - 1998.pdf:pdf},
journal = {European Biophysics Journal},
keywords = {atomic,force microscopy,micromechanics,optical tweezers,single molecules,thermal noise},
pages = {75 -- 81},
title = {{Thermal noise limitations on micromechanical experiments}},
volume = {9876},
year = {1998}
}
@misc{Shedin,
author = {Shedin, Staffan},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Shedin - Anteckningar kalibrering 2.pdf - Unknown.pdf:pdf},
title = {{Anteckningar kalibrering 2.pdf}}
}
@article{Burnham2009,
author = {Burnham, D R and McGloin, D},
doi = {10.1088/1367-2630/11/6/063022},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Burnham, McGloin - Radius measurements of optically trapped aerosols through Brownian motion - 2009.pdf:pdf},
issn = {1367-2630},
journal = {New Journal of Physics},
month = {jun},
number = {6},
pages = {063022},
title = {{Radius measurements of optically trapped aerosols through Brownian motion}},
url = {http://stacks.iop.org/1367-2630/11/i=6/a=063022?key=crossref.974a1f5dda55a2b6ddde4cf6eb3f8549},
volume = {11},
year = {2009}
}
@article{Andreasson2010a,
author = {Andreasson, Johan O L and Greenleaf, William J and Laporta, Arthur and Block, Steven M},
doi = {10.1016/S0076-6879(10)75015-1},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Andreasson et al. - An Optical Apparatus for Rotation and Trapping - 2010.pdf:pdf},
journal = {Methods},
number = {10},
title = {{An Optical Apparatus for Rotation and Trapping}},
volume = {475},
year = {2010}
}
@article{Ha2009,
author = {Ha, Chungil and Ou-Yang, H. Daniel and Pak, Hyuk Kyu},
doi = {10.1117/12.843376},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Ha, Ou-Yang, Pak - Study of a colloidal sphere near flat walls using oscillating optical tweezers - 2009.pdf:pdf},
keywords = {Study of a colloidal sphere near flat walls using,colloidal sphere,faxen,oscillating optical tweezers,s law},
pages = {750702--750702--8},
title = {{Study of a colloidal sphere near flat walls using oscillating optical tweezers}},
url = {http://link.aip.org/link/PSISDG/v7507/i1/p750702/s1{\&}Agg=doi},
volume = {7507},
year = {2009}
}
@article{Tolic-Norrelykke2006a,
author = {Tolić-No̸rrelykke, Simon F. and Schäffer, Erik and Howard, Jonathon and Pavone, Francesco S. and Jülicher, Frank and Flyvbjerg, Henrik},
doi = {10.1063/1.2356852},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tolić-No̸rrelykke et al. - Calibration of optical tweezers with positional detection in the back focal plane - 2006.pdf:pdf},
issn = {00346748},
journal = {Review of Scientific Instruments},
number = {10},
pages = {103101},
title = {{Calibration of optical tweezers with positional detection in the back focal plane}},
url = {http://link.aip.org/link/RSINAK/v77/i10/p103101/s1{\&}Agg=doi},
volume = {77},
year = {2006}
}
@article{Reihani2007,
abstract = {The efficiency of an optical trap is limited by its axial strength. Light focused by oil-immersion objectives provides stronger traps but suffers from spherical aberrations, thus restricting the axial stability and working distance. By changing the refractive index of the immersion media we compensate spherical aberrations and measure axial trapping strengths at least twice as large as previously reported. Moreover, the spherical aberrations can be compensated at any desired depth. The improved trapping efficiency implies significantly less heating of the particles, thus diminishing previously published concerns about using gold nanoparticles as handles for optical manipulation.},
author = {Reihani, S Nader S and Oddershede, Lene B},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Reihani, Oddershede - Optimizing immersion media refractive index improves optical trapping by compensating spherical aberrations. - 200.pdf:pdf},
issn = {0146-9592},
journal = {Optics letters},
month = {jul},
number = {14},
pages = {1998--2000},
pmid = {17632622},
title = {{Optimizing immersion media refractive index improves optical trapping by compensating spherical aberrations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17632622},
volume = {32},
year = {2007}
}
@article{Vermeulen2006a,
abstract = {Optical traps are commonly constructed with high-numerical-aperture objectives. Oil-immersion objectives suffer from spherical aberrations when used for imaging in aqueous solutions. The effect of spherical aberrations on trapping strength has been modeled by approximation, and only a few experimental results are available in the case of micrometer-sized particles. We present an experimental study of the dependence of lateral and axial optical-trap stiffness on focusing depth for polystyrene and silica beads of 2 microm diameter by using oil- and water-immersion objectives. We demonstrate a strong depth dependence of trap stiffness with the oil-immersion objective, whereas no depth dependence was observed with the water-immersion objective.},
author = {Vermeulen, Karen C and Wuite, Gijs J L and Stienen, Ger J M and Schmidt, Christoph F},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Vermeulen et al. - Optical trap stiffness in the presence and absence of spherical aberrations. - 2006.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
month = {mar},
number = {8},
pages = {1812--9},
pmid = {16572698},
title = {{Optical trap stiffness in the presence and absence of spherical aberrations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16572698},
volume = {45},
year = {2006}
}
@article{Lee2007c,
abstract = {The application of optical traps has come to the fore in the last three decades. They provide a powerful, sterile and noninvasive tool for the manipulation of cells, single biological macromolecules, colloidal microparticles and nanoparticles. An optically trapped microsphere may act as a force transducer that is used to measure forces in the piconewton regime. By setting up a well-calibrated single-beam optical trap within a fluorescence microscope system, one can measure forces and collect fluorescence signals upon biological systems simultaneously. In this protocol, we aim to provide a clear exposition of the methodology of assembling and operating a single-beam gradient force trap (optical tweezers) on an inverted fluorescence microscope. A step-by-step guide is given for alignment and operation, with discussion of common pitfalls.},
author = {Lee, Woei Ming and Reece, Peter J and Marchington, Robert F and Metzger, Nikolaus K and Dholakia, Kishan},
doi = {10.1038/nprot.2007.446},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lee et al. - Construction and calibration of an optical trap on a fluorescence optical microscope. - 2007.pdf:pdf},
issn = {1750-2799},
journal = {Nature protocols},
keywords = {Micromanipulation,Micromanipulation: instrumentation,Microscopy, Fluorescence,Microscopy, Fluorescence: instrumentation,Microspheres,Optical Tweezers,Optics and Photonics,Optics and Photonics: instrumentation,Particle Size},
month = {jan},
number = {12},
pages = {3226--38},
pmid = {18079723},
title = {{Construction and calibration of an optical trap on a fluorescence optical microscope.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18079723},
volume = {2},
year = {2007}
}
@article{Schaffer2007d,
abstract = {Optical tweezers are widely used to measure molecular forces in biology. Such measurements are often influenced by a nearby surface that can perturb both the calibration of the tweezers as well as the hydrodynamic forces acting on microspheres to which the biomolecules are attached. In this study, we have used a very stable optical tweezers setup employing a recently developed calibration method (Toli{\'{c}}-N{\o}rrelykke, S. F.; Sch{\"{a}}ffer, E.; Howard, J.; Pavone, F. S.; J{\"{u}}licher, F.; Flyvbjerg, H. Rev. Sci. Instrum. 2006, 77 (10), 103101) to determine how the calibration of the tweezers and the forces on the microspheres depend on the height above the surface. We show that the displacement sensitivity of the tweezers is modulated by a standing light wave between the microsphere and the surface. We measured the dependence of the drag coefficient on height and compared it to exact and closed-form solutions to the Navier-Stokes equations. Also, we measured the surface force gradients in different salt solutions and for different surface blocking methods. For a given blocking method, our data suggest that microspheres can experience attractive and/or repulsive forces close to surfaces. For example, a Teflon layer reduces attractive interactions, and the presence of casein can lead to long-range repulsive interactions. These measurements are a prerequisite for the accurate measurement of normal forces with respect to an interface that occur in biological molecules held between surfaces.},
author = {Sch{\"{a}}ffer, Erik and N{\o}rrelykke, Simon F and Howard, Jonathon},
doi = {10.1021/la0622368},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Sch{\"{a}}ffer, N{\o}rrelykke, Howard - Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers..pdf:pdf},
issn = {0743-7463},
journal = {Langmuir : the ACS journal of surfaces and colloids},
keywords = {Calibration,Microspheres,Optical Tweezers,Salts,Salts: chemistry},
month = {mar},
number = {7},
pages = {3654--65},
pmid = {17326669},
title = {{Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17326669},
volume = {23},
year = {2007}
}
@article{Reihani2007b,
abstract = {The efficiency of an optical trap is limited by its axial strength. Light focused by oil-immersion objectives provides stronger traps but suffers from spherical aberrations, thus restricting the axial stability and working distance. By changing the refractive index of the immersion media we compensate spherical aberrations and measure axial trapping strengths at least twice as large as previously reported. Moreover, the spherical aberrations can be compensated at any desired depth. The improved trapping efficiency implies significantly less heating of the particles, thus diminishing previously published concerns about using gold nanoparticles as handles for optical manipulation.},
author = {Reihani, S Nader S and Oddershede, Lene B.},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Reihani, Oddershede - Optimizing immersion media refractive index improves optical trapping by compensating spherical aberrations. - 200.pdf:pdf},
issn = {0146-9592},
journal = {Optics letters},
month = {jul},
number = {14},
pages = {1998--2000},
pmid = {17632622},
title = {{Optimizing immersion media refractive index improves optical trapping by compensating spherical aberrations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17632622},
volume = {32},
year = {2007}
}
@article{Sinclair2004a,
abstract = {We report on the limitations of using a spatial light modulator (SLM) within optical tweezers to produce both lateral and axial displacements. We find that lateral displacements of optical traps are limited by the optical efficiency of the SLM, whereas the axial displacements are limited by the abberations of the objective lens. In addition, we show the SLM can be used for correcting abberations arising from trapping deep within the sample. The maximum possible lateral and axial displacements were 50pm and 40pm, respectively.},
author = {Sinclair, Gavin and Jordan, P and Leach, Jonathan and Padgett, Miles J and Cooper, J.},
doi = {10.1080/095003403},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Sinclair et al. - Defining the trapping limits of holographical optical tweezers - 2004.pdf:pdf},
journal = {Journal of Modern Optics},
number = {October 2011},
pages = {409--414},
title = {{Defining the trapping limits of holographical optical tweezers}},
volume = {61},
year = {2004}
}
@article{Hwang2008a,
author = {Hwang, Sun-Uk and Lee, Yong-Gu},
doi = {10.1364/OE.16.021170},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Hwang, Lee - Simulation of an oil immersion objective lens a simplified ray-optics model considering Abbe’s sine condition - 2008.pdf:pdf},
issn = {1094-4087},
journal = {Optics Express},
month = {dec},
number = {26},
pages = {21170},
title = {{Simulation of an oil immersion objective lens: a simplified ray-optics model considering Abbe’s sine condition}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=oe-16-26-21170},
volume = {16},
year = {2008}
}
@article{Ganic2004a,
abstract = {There has been an interest to understand the trapping performance produced by a laser beam with a complex wavefront structure because the current methods for calculating trapping force ignore the effect of diffraction by a vectorial electromagnetic wave. In this letter, we present a method for determining radiation trapping force on a micro-particle, based on the vectorial diffraction theory and the Maxwell stress tensor approach. This exact method enables one to deal with not only complex apodization, phase, and polarization structures of trapping laser beams but also the effect of spherical aberration present in the trapping system.},
author = {Ganic, Djenan and Gan, Xiaosong and Gu, Min},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Ganic, Gan, Gu - Exact radiation trapping force calculation based on vectorial diffraction theory. - 2004.pdf:pdf},
issn = {1094-4087},
journal = {Optics express},
month = {jun},
number = {12},
pages = {2670--5},
pmid = {19475108},
title = {{Exact radiation trapping force calculation based on vectorial diffraction theory.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19475108},
volume = {12},
year = {2004}
}
@book{Peterman2010a,
abstract = {The technically challenging field of single-molecule biophysics has established itself in the last decade by granting access to detailed information about the fate of individual biomolecules, unattainable in traditional biochemical assays. The appeal of single-molecule methods lies in the directness of the information obtained from individual biomolecules. Technological improvements in single-molecule methods have made it possible to combine optical tweezers, fluorescence microscopy, and microfluidic flow systems. Such a combination of techniques has opened new possibilities to study complex biochemical reactions on the single-molecule level. In this chapter, we provide general considerations for the development of a combined optical trapping, fluorescence microscopy, and microfluidics instrument, along with methods to solve technical issues that are critical for designing successful experiments. Finally, we present several experiments to illustrate the power of this combination of techniques.},
author = {Peterman, Erwin J G and Gross, Peter and Wuite, Gijs J L},
booktitle = {Single Molecule Tools Part BSuperResolution Particle Tracking Multiparameter and Force Based Methods},
doi = {10.1016/S0076-6879(10)75017-5},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Peterman, Gross, Wuite - Combining Optical Tweezers , Single-Molecule Fluorescence Microscopy , and Microfluidics for Studies of DNA – P.pdf:pdf},
issn = {00766879},
number = {10},
pages = {427--453},
pmid = {20627167},
publisher = {Elsevier Inc.},
title = {{Combining Optical Tweezers , Single-Molecule Fluorescence Microscopy , and Microfluidics for Studies of DNA – Protein Interactions}},
url = {http://dx.doi.org/10.1016/S0076-6879(10)75017-5},
volume = {475},
year = {2010}
}
@article{Thomas2008,
abstract = {One of the most exciting discoveries in biological adhesion is the recent and counter-intuitive observation that the lifetimes of some biological adhesive bonds, called catch bonds, are enhanced by tensile mechanical force. At least two types of adhesive proteins have been shown to form catch bonds—blood proteins called selectins and a bacterial protein called FimH. Both mediate shear-enhanced adhesion, in which cells bind more strongly at high shear than at low shear. Single-molecule experiments and cell-free assays have now clearly demonstrated that catch bonds exist and mediate shear-enhanced adhesion. However, the mechanics of cellular organelles also contribute to shear-enhanced adhesion by modulating the force applied to catch bonds. This review examines how individual catch bond behavior contributes to shear-enhanced cellular adhesion for the two best-understood examples. The lessons from these systems offer design principles for understanding other types of shear-enhanced adhesion and for engineering nanostructured force-dependent adhesives out of catch bonds.},
author = {Thomas, Wendy E},
doi = {10.1146/annurev.bioeng.10.061807.160427},
file = {:C$\backslash$:/Users/LASER/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Thomas - 2008 - Catch Bonds in Adhesion.pdf:pdf},
journal = {Annu. Rev. Biomed. Eng.},
keywords = {molecular biomechanics,multiscale,nanotechnology,selectin leukocytes},
pages = {39--57},
title = {{Catch Bonds in Adhesion}},
url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.bioeng.10.061807.160427},
volume = {10},
year = {2008}
}
@article{Zakrisson2012h,
abstract = {Biopolymers are vital structures for many living organisms; for a variety of bacteria, adhesion polymers play a crucial role for the initiation of colonization. Some bacteria express, on their surface, attachment organelles (pili) that comprise subunits formed into stiff helix-like structures that possess unique biomechanical properties. These helix-like structures possess a high degree of flexibility that gives the biopolymers a unique extendibility. This has been considered beneficial for piliated bacteria adhering to host surfaces in the presence of a fluid flow. We show in this work that helix-like pili have the ability to act as efficient dampers of force that can, for a limited time, lower the load on the force-mediating adhesin-receptor bond on the tip of an individual pilus. The model presented is applied to bacteria adhering with a single pilus of either of the two most common types expressed by uropathogenic Escherichia coli, P or type 1 pili, subjected to realistic flows. The results indicate that for moderate flows ({\~{}}25 mm/s) the force experienced by the adhesin-receptor interaction at the tip of the pilus can be reduced by a factor of {\~{}}6 and {\~{}}4, respectively. The uncoiling ability provides a bacterium with a "go with the flow" possibility that acts as a damping. It is surmised that this can be an important factor for the initial part of the adhesion process, in particular in turbulent flows, and thereby be of use for bacteria in their striving to survive a natural defense such as fluid rinsing actions.},
author = {Zakrisson, Johan and Wiklund, Krister and Axner, Ove and Andersson, Magnus},
doi = {10.1007/s00249-012-0814-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Zakrisson et al. - Helix-like biopolymers can act as dampers of force for bacteria in flows. - 2012.pdf:pdf},
issn = {1432-1017},
journal = {European biophysics journal},
keywords = {Bacteria,Bacteria: metabolism,Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial Physiological Phenomena,Bacterial: physiology,Biological,Biomechanics,Biopolymers,Biopolymers: chemistry,Biopolymers: metabolism,Computer Simulation,Fimbriae,Mechanical,Models,Stress},
month = {jun},
number = {6},
pages = {551--60},
pmid = {22562139},
title = {{Helix-like biopolymers can act as dampers of force for bacteria in flows.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22562139},
volume = {41},
year = {2012}
}
@article{Saffman1965c,
annote = {ISI Document Delivery No.: 65713
Times Cited: 1055
Cited Reference Count: 16
Saffman, pg
Cambridge univ press
New york
Part 2},
author = {Saffman, P G},
doi = {10.1017/s0022112065000824},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
language = {English},
pages = {385},
title = {{Lift on a small sphere in a slow shear flow}},
url = {<Go to ISI>://WOS:A19656571300015},
volume = {22},
year = {1965}
}
@article{Andersson2006n,
abstract = {The rapid development of the optical tweezers technique has broadened the applicability of the technique from physics to biology. Although the construction of an optical tweezers system only requires basic skills in optics, the realization of an optical tweezers set LIP is not always as easy as it seems. A number of designs for moveable traps have been presented in the literature. It is not clear to the readers, however, how the movability of the trap affects its quality. We have therefore scrutinized and compared the most commonly used techniques for steering of an optical trap in terms of the aberrations they introduce. The study shows that a moveable trap based on the movement of a lens introduces significantly more aberration than the systems based on fiber optics or the tilting of a mirror.},
annote = {From Duplicate 1 ( Techniques for moveable traps: the influence of aberration in optical tweezers - F{\"{a}}llman, Erik, Andersson, Magnus; Axner, Ove; )
},
author = {Andersson, Magnus and F{\"{a}}llman, Erik and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1117/12.642206},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - Force measuring optical tweezers system for long time measurements of P pili stability - 2006.pdf:pdf},
issn = {0277786X},
journal = {Proceedings of SPIE},
keywords = {BIOLOGICAL APPLICATIONS,CONSTRUCTION,DESIGN,FORCE,LASER,MANIPULATION,MICROMANIPULATION,MICROSCOPE,beam steering,dual trap,force measurement,optical tweezers},
pages = {286--295},
publisher = {SPIE},
title = {{Force measuring optical tweezers system for long time measurements of P pili stability}},
url = {http://apps.isiknowledge.com/full{\_}record.do?product=WOS{\&}search{\_}mode=GeneralSearch{\&}qid=6{\&}SID=S1MHGALlH8ko5hHPpbg{\&}page=1{\&}doc=1},
volume = {6088},
year = {2006}
}
@article{Katsikogianni2004c,
abstract = {This article reviews the mechanisms of bacterial adhesion to biomaterial surfaces, the factors affecting the adhesion, the techniques used in estimating bacteria-material interactions and the models that have been developed in order to predict adhesion. The process of bacterial adhesion includes an initial physicochemical interaction phase and a late molecular and cellular one. It is a complicated process influenced by many factors, including the bacterial properties, the material surface characteristics, the environmental factors, such as the presence of serum proteins and the associated flow conditions. Two categories of techniques used in estimating bacteria-material interactions are described: those that utilize fluid flowing against the adhered bacteria and counting the percentage of bacteria that detach, and those that manipulate single bacteria in various configurations which lend themselves to more specific force application and provide the basis for theoretical analysis of the receptor-ligand interactions. The theories that are reviewed are the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, the thermodynamic approach and the extended DLVO theory. Over the years, significant work has been done to investigate the process of bacterial adhesion to biomaterial surfaces, however a lot of questions still remain unanswered.},
author = {Katsikogianni, M and Missirlis, Y F},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Katsikogianni, Missirlis - Concise review of mechanisms of bacterial adhesion to biomaterials and of techniques used in estimating bacte.pdf:pdf},
issn = {1473-2262},
journal = {European cells {\&} materials},
keywords = {Bacteria,Bacteria: cytology,Bacteria: pathogenicity,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial Physiological Phenomena,Biocompatible Materials,Biocompatible Materials: chemistry,Biocompatible Materials: metabolism,Chemistry, Physical,Chemistry, Physical: methods},
month = {dec},
pages = {37--57},
pmid = {15593018},
title = {{Concise review of mechanisms of bacterial adhesion to biomaterials and of techniques used in estimating bacteria-material interactions.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15593018},
volume = {8},
year = {2004}
}
@article{Siegel1994,
abstract = {Atherosclerosis of the human arterial system produces major clinical symptoms when the plaque advances to create a high-grade stenosis. The hemodynamic shear rates produced in high-grade stenoses are important in the understanding of atheromatous plaque rupture and thrombosis. This study was designed to quantify the physiologic stress levels experienced by endothelial cells and platelets in the region of vascular stenoses. The steady hemodynamic flow field was solved for stenoses with percent area reductions of 50, 75, and 90 percent over a range of physiologic Reynolds numbers (100-400). The maximum wall shear rate in the throat region can be shown to vary by the square root of the Reynolds number. The shear rate results can be generalized to apply to a range of stenosis lengths and flow rates. Using dimensions typical for a human carotid or coronary artery, wall shear rates were found to vary from a maximum of 20,000 s-1 upstream of the throat to a minimum of -630 s-1 in the recirculation zone for a 90 percent stenosis. An example is given which illustrates how these values can be used to understand the relationship between hemodynamic shear and platelet deposition.},
author = {Siegel, J M and Markou, C P and Ku, D N and Hanson, S R},
file = {::},
issn = {0148-0731},
journal = {Journal of biomechanical engineering},
keywords = {Arteriosclerosis,Arteriosclerosis: physiopathology,Blood Platelets,Carotid Stenosis,Carotid Stenosis: physiopathology,Coronary Disease,Coronary Disease: physiopathology,Endothelium, Vascular,Endothelium, Vascular: physiopathology,Hemorheology,Humans,Models, Cardiovascular,Numerical Analysis, Computer-Assisted},
month = {nov},
number = {4},
pages = {446--51},
pmid = {7869720},
title = {{A scaling law for wall shear rate through an arterial stenosis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/7869720},
volume = {116},
year = {1994}
}
@article{Castelain2009h,
abstract = {Bacterial adhesion organelles, known as fimbria or pili, are expressed by gram-positive as well as gram-negative bacteria families. These appendages play a key role in the first steps of the invasion and infection processes, and they therefore provide bacteria with pathogenic abilities. To improve the knowledge of pili-mediated bacterial adhesion to host cells and how these pili behave under the presence of an external force, we first characterize, using force measuring optical tweezers, open coil-like T4 pili expressed by gram-positive Streptococcus pneumoniae with respect to their biomechanical properties. It is shown that their elongation behavior can be well described by the worm-like chain model and that they possess a large degree of flexibility. Their properties are then compared with those of helix-like pili expressed by gram-negative uropathogenic Escherichia coli (UPEC), which have different pili architecture. The differences suggest that these two types of pili have distinctly dissimilar mechanisms to adhere and sustain external forces. Helix-like pili expressed by UPEC bacteria adhere to host cells by single adhesins located at the distal end of the pili while their helix-like structures act as shock absorbers to dampen the irregularly shear forces induced by urine flow and to increase the cooperativity of the pili ensemble, whereas open coil-like pili expressed by S. pneumoniae adhere to cells by a multitude of adhesins distributed along the pili. It is hypothesized that these two types of pili represent different strategies of adhering to host cells in the presence of external forces. When exposed to significant forces, bacteria expressing helix-like pili remain attached by distributing the external force among a multitude of pili, whereas bacteria expressing open coil-like pili sustain large forces primarily by their multitude of binding adhesins which presumably detach sequentially.},
author = {Castelain, Micka{\"{e}}l and Koutris, Efstratios and Andersson, Magnus and Wiklund, Krister and Bj{\"{o}}rnham, Oscar and Schedin, Staffan and Axner, Ove},
doi = {10.1002/cphc.200900195},
issn = {1439-7641},
journal = {ChemPhysChem},
keywords = {Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: chemistry,Bacterial: physiology,Biomechanics,Fimbriae,Optical Tweezers,Streptococcus pneumoniae,Streptococcus pneumoniae: chemistry,Streptococcus pneumoniae: physiology},
month = {jul},
number = {9-10},
pages = {1533--40},
pmid = {19565578},
publisher = {WILEY-V C H VERLAG GMBH},
title = {{Characterization of the biomechanical properties of T4 pili expressed by Streptococcus pneumoniae--a comparison between helix-like and open coil-like pili.}},
url = {http://apps.isiknowledge.com/full{\_}record.do?product=WOS{\&}search{\_}mode=GeneralSearch{\&}qid=1{\&}SID=S1MHGALlH8ko5hHPpbg{\&}page=1{\&}doc=1},
volume = {10},
year = {2009}
}
@article{Brenner1961a,
annote = {Brenner, h},
author = {Brenner, H},
doi = {10.1016/0009-2509(61)80035-3},
isbn = {0009-2509},
journal = {Chemical Engineering Science},
number = {3-4},
pages = {242--251},
title = {{The slow motion of a sphere through a viscous fluid towards a plane surface}},
url = {<Go to ISI>://WOS:A1961XG76500009},
volume = {16},
year = {1961}
}
@article{Zakrisson2012g,
abstract = {Biopolymers are vital structures for many living organisms; for a variety of bacteria, adhesion polymers play a crucial role for the initiation of colonization. Some bacteria express, on their surface, attachment organelles (pili) that comprise subunits formed into stiff helix-like structures that possess unique biomechanical properties. These helix-like structures possess a high degree of flexibility that gives the biopolymers a unique extendibility. This has been considered beneficial for piliated bacteria adhering to host surfaces in the presence of a fluid flow. We show in this work that helix-like pili have the ability to act as efficient dampers of force that can, for a limited time, lower the load on the force-mediating adhesin-receptor bond on the tip of an individual pilus. The model presented is applied to bacteria adhering with a single pilus of either of the two most common types expressed by uropathogenic Escherichia coli, P or type 1 pili, subjected to realistic flows. The results indicate that for moderate flows ({\~{}}25 mm/s) the force experienced by the adhesin-receptor interaction at the tip of the pilus can be reduced by a factor of {\~{}}6 and {\~{}}4, respectively. The uncoiling ability provides a bacterium with a "go with the flow" possibility that acts as a damping. It is surmised that this can be an important factor for the initial part of the adhesion process, in particular in turbulent flows, and thereby be of use for bacteria in their striving to survive a natural defense such as fluid rinsing actions.},
author = {Zakrisson, Johan and Wiklund, Krister and Axner, Ove and Andersson, Magnus},
doi = {10.1007/s00249-012-0814-8},
file = {::},
issn = {1432-1017},
journal = {European biophysics journal : EBJ},
keywords = {Bacteria,Bacteria: metabolism,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial Physiological Phenomena,Biomechanics,Biopolymers,Biopolymers: chemistry,Biopolymers: metabolism,Computer Simulation,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Models, Biological,Stress, Mechanical},
month = {jun},
number = {6},
pages = {551--60},
pmid = {22562139},
title = {{Helix-like biopolymers can act as dampers of force for bacteria in flows.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22562139},
volume = {41},
year = {2012}
}
@article{Whitfield2011f,
author = {Whitfield, Matthew and Thomas, Wendy E},
doi = {10.1080/00218464.2011.575311},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Whitfield, Thomas - A Nanoadhesive Composed of Receptor-Ligand Bonds - 2011.pdf:pdf},
issn = {0021-8464},
journal = {The Journal of Adhesion},
month = {may},
number = {5},
pages = {427--446},
title = {{A Nanoadhesive Composed of Receptor-Ligand Bonds}},
url = {http://www.tandfonline.com/doi/abs/10.1080/00218464.2011.575311},
volume = {87},
year = {2011}
}
@article{Griffiths1983c,
author = {Griffiths, Derek J.},
doi = {10.1002/nau.1930020210},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Griffiths - The mechanics of urine transport in the upper urinary tract 2. The discharge of the bolus into the bladder and dynamics at h.pdf:pdf},
issn = {07332467},
journal = {Neurourology and Urodynamics},
keywords = {bolus discharge,diuresis,pelvic pressure,peristaltic transport,ureterovesical junction},
number = {2},
pages = {167--173},
title = {{The mechanics of urine transport in the upper urinary tract: 2. The discharge of the bolus into the bladder and dynamics at high rates of flow}},
url = {http://doi.wiley.com/10.1002/nau.1930020210},
volume = {2},
year = {1983}
}
@article{Jass2004g,
abstract = {The mechanical behavior of individual P pili of uropathogenic Escherichia coli has been investigated using optical tweezers. P pili, whose main part constitutes the PapA rod, composed of approximately 10(3) PapA subunits in a helical arrangement, are distributed over the bacterial surface and mediate adhesion to host cells. They are particularly important in the pathogenesis of E. coli colonizing the upper urinary tract and kidneys. A biological model system has been established for in situ measurements of the forces that occur during mechanical stretching of pili. A mathematical model of the force-versus-elongation behavior of an individual pilus has been developed. Three elongation regions of pili were identified. In region I, P pili stretch elastically, up to a relative elongation of 16 +/- 3{\%}. The product of elasticity modulus and area of a P pilus, EA, was assessed to 154 +/- 20 pN (n=6). In region II, the quaternary structure of the PapA rod unfolds under a constant force of 27 +/- 2 pN (n approximately 100) by a sequential breaking of the interactions between adjacent layers of PapA subunits. This unfolding can elongate the pilus up to 7 +/- 2 times. In region III, pili elongate in a nonlinear manner as a result of stretching until the bond ruptures.},
author = {Jass, Jana and Schedin, Staffan and F{\"{a}}llman, Erik and Ohlsson, J{\"{o}}rgen and Nilsson, Ulf J and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1529/biophysj.104.044867},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Bacterial Adhesion,Bacterial Adhesion: physiology,Cell Culture Techniques,Cell Culture Techniques: methods,Computer Simulation,Elasticity,Escherichia coli,Escherichia coli: cytology,Escherichia coli: physiology,Fimbriae, Bacterial,Fimbriae, Bacterial: physiology,Fimbriae, Bacterial: ultrastructure,Lasers,Micromanipulation,Micromanipulation: methods,Models, Biological,Physical Stimulation,Physical Stimulation: methods,Tensile Strength},
month = {dec},
number = {6},
pages = {4271--83},
pmid = {15377509},
title = {{Physical properties of Escherichia coli P pili measured by optical tweezers.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1304935{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {87},
year = {2004}
}
@article{Kinn1996c,
abstract = {The development of new surgical techniques for bladder substitution and continent urinary diversion has extended interest in urodynamics of the upper urinary tract. From a subdiscipline attracting mainly scientists and bioengineers, renal pelvic kinetics and ureteral peristalsis have evolved as important factors in routine clinical urology. The observed changes in peristaltic pattern during high diuresis, obstruction and urinary reflux have influenced management of stone disease and neurogenic bladder. The demonstration that high intravesical pressure is reflected to the kidney not only when the ureteric orifice is incompetent, but also during high diuresis, established the necessity for low pressures in neobladders. Much further clarification of urinary transport from the renal tubules to the bladder should be achievable by refined techniques of fluoroscopy, isotopic renography and manometry.},
author = {Kinn, a C},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kinn - Progress in urodynamic research on the upper urinary tract implications for practical urology. - 1996.pdf:pdf},
issn = {0300-5623},
journal = {Urological research},
keywords = {Humans,Hydronephrosis,Hydronephrosis: physiopathology,Kidney Calculi,Kidney Calculi: physiopathology,Research,Ureter,Ureter: physiology,Urinary Diversion,Urinary Tract Physiological Phenomena,Urodynamics,Urology,Urology: trends,Vesico-Ureteral Reflux,Vesico-Ureteral Reflux: physiopathology},
month = {jan},
number = {1},
pages = {1--7},
pmid = {8966835},
title = {{Progress in urodynamic research on the upper urinary tract: implications for practical urology.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/8966835},
volume = {24},
year = {1996}
}
@article{Cherukat1994a,
abstract = {An expression which predicts the inertial lift, to lowest order, on a rigid sphere translating in a linear shear flow field near a flat infinite wall has been derived. This expression may be used when the wall lies within the inner region of the sphere's disturbance flow. It is valid even when the gap is small compared to the radius of the sphere. When the sphere is far from the wall, the lift force predicted by the present analysis converges to the value predicted by earlier analyses which consider the sphere as a point force or a force doublet singularity. The effect of rotation of the sphere on the lift has also been analysed.},
annote = {ISI Document Delivery No.: NG420
Times Cited: 94
Cited Reference Count: 20
Cherukat, p mclaughlin, jb
Cambridge univ press
New york},
author = {Cherukat, P and McLaughlin, J B},
doi = {10.1017/s0022112094004015},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
keywords = {lateral migration,particle,plane},
language = {English},
pages = {1--18},
title = {{The inertial lift on a rigid sphere in a linear shear-flow field near a flat wall}},
url = {<Go to ISI>://WOS:A1994NG42000001},
volume = {263},
year = {1994}
}
@article{Li2009c,
abstract = {Adhesion pili (fimbriae) play a critical role in initiating the events that lead to intestinal colonization and diarrheal disease by enterotoxigenic Escherichia coli (ETEC), an E. coli pathotype that inflicts an enormous global disease burden. We elucidate atomic structures of an ETEC major pilin subunit, CfaB, from colonization factor antigen I (CFA/I) fimbriae. These data are used to construct models for 2 morphological forms of CFA/I fimbriae that are both observed in vivo: the helical filament into which it is typically assembled, and an extended, unwound conformation. Modeling and corroborative mutational data indicate that proline isomerization is involved in the conversion between these helical and extended forms. Our findings affirm the strong structural similarities seen between class 5 fimbriae (from bacteria primarily causing gastrointestinal disease) and class 1 pili (from bacteria that cause urinary, respiratory, and other infections) in the absence of significant primary sequence similarity. They also suggest that morphological and biochemical differences between fimbrial types, regardless of class, provide structural specialization that facilitates survival of each bacterial pathotype in its preferred host microenvironment. Last, we present structural evidence for bacterial use of antigenic variation to evade host immune responses, in that residues occupying the predicted surface-exposed face of CfaB and related class 5 pilins show much higher genetic sequence variability than the remainder of the pilin protein.},
author = {Li, Yong-Fu and Poole, Steven and Nishio, Kazuya and Jang, Ken and Rasulova, Fatima and McVeigh, Annette and Savarino, Stephen J and Xia, Di and Bullitt, Esther},
doi = {10.1073/pnas.0812843106},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Li et al. - Structure of CFAI fimbriae from enterotoxigenic Escherichia coli. - 2009.pdf:pdf},
issn = {1091-6490},
journal = {PNAS},
keywords = {Antigens,Bacterial,Bacterial: chemistry,Bacterial: genetics,Bacterial: immunology,Binding Sites,Crystallography,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: chemistry,Enterotoxigenic Escherichia coli: genetics,Escherichia coli Infections,Escherichia coli Infections: immunology,Escherichia coli Infections: microbiology,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: genetics,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: genetics,Fimbriae Proteins: immunology,Models,Molecular,Mutation,Proline,Proline: chemistry,Proline: genetics,Protein Structure,Protein Subunits,Protein Subunits: chemistry,Protein Subunits: genetics,Secondary,Tertiary,X-Ray},
month = {jun},
number = {26},
pages = {10793--8},
pmid = {19515814},
title = {{Structure of CFA/I fimbriae from enterotoxigenic Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2705562{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {106},
year = {2009}
}
@inproceedings{Diaz2004c,
abstract = {Abstract – Urinary system concerns with the excretion of urine, and the waste products of metabolism. The kidneys separate urea, mineral salts, toxins, and other waste products from the blood, and to conserve water, salts, and electrolytes. At least one kidney must function properly for life to be maintained. Each kidney contains 1.2 million filtering units called nephrons. After filtration, blood leaving the glomerulus flows through the network of capillaries that surrounds each tubule; water and certain salts, are restored to the blood. The purified blood returns to the renal vein. Urine from the kidney pelvis passes into the ureters. Muscles in the walls of the ureters send the urine in small spurts into the bladder, for temporary storage of urine. A full bladder stimulates sensory nerves in the bladder wall that relax the sphincter and allow release of the urine. The released urine enters the urethra, a tube lined with mucus membrane that conveys the urine to the outside. The male urethra terminates at the tip of the penis. The female urethra is less than 5 cm long and opens just in front of the entrance to the vagina. The urinary system disorders are: Congenital malformation, injury, infection, presence of kidney stones, or calculi, other types of obstruction, and tumors, cystitis, nephritis, nephrosis.},
author = {Diaz, Luis De Jesus and Rosado, Yarimar Padua and Gonz{\'{a}}lez, Melissa P{\'{e}}rez},
booktitle = {Engineering},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Diaz, Rosado, Gonz{\'{a}}lez - Biofluid dynamics of the human urinary system 1 - 2004.pdf:pdf},
keywords = {biofluids of human body,body,human,kidneys,newtonian fluids,systems of human,urine},
pages = {1--36},
title = {{Biofluid dynamics of the human urinary system 1}},
year = {2004}
}
@article{Thomas2002e,
abstract = {Surface adhesion of bacteria generally occurs in the presence of shear stress, and the lifetime of receptor bonds is expected to be shortened in the presence of external force. However, by using Escherichia coli expressing the lectin-like adhesin FimH and guinea pig erythrocytes in flow chamber experiments, we show that bacterial attachment to target cells switches from loose to firm upon a 10-fold increase in shear stress applied. Steered molecular dynamics simulations of tertiary structure of the FimH receptor binding domain and subsequent site-directed mutagenesis studies indicate that shear-enhancement of the FimH-receptor interactions involves extension of the interdomain linker chain under mechanical force. The ability of FimH to function as a force sensor provides a molecular mechanism for discrimination between surface-exposed and soluble receptor molecules.},
author = {Thomas, Wendy E and Trintchina, Elena and Forero, Manu and Vogel, Viola and Sokurenko, Evgeni V},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Thomas et al. - Bacterial adhesion to target cells enhanced by shear force. - 2002.pdf:pdf},
issn = {0092-8674},
journal = {Cell},
keywords = {Adhesins, Bacterial,Adhesins, Bacterial: chemistry,Adhesins, Bacterial: genetics,Adhesins, Bacterial: metabolism,Adhesins, Escherichia coli,Animals,Bacterial Adhesion,Biomechanics,Cell Aggregation,Computer Simulation,Erythrocytes,Erythrocytes: cytology,Erythrocytes: microbiology,Escherichia coli,Escherichia coli: genetics,Escherichia coli: physiology,Fimbriae Proteins,Guinea Pigs,Models, Molecular,Mutation,Protein Structure, Tertiary,Structure-Activity Relationship},
month = {jun},
number = {7},
pages = {913--23},
pmid = {12110187},
title = {{Bacterial adhesion to target cells enhanced by shear force.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12110187},
volume = {109},
year = {2002}
}
@article{Marchioli2002c,
abstract = {Particle transfer in the wall region of turbulent boundary layers is dominated by the coherent structures which control the turbulence regeneration cycle. Coherent structures bring particles toward and away from the wall and favour particle segregation in the viscous region, giving rise to non-uniform particle. distribution profiles which peak close to the wall. The object of this work is to understand the reasons for higher particle concentration in the wall region by examining turbulent transfer of heavy particles to and away from the wall in connection with the coherent structures of the boundary layer. We will examine the behaviour of a dilute dispersion of heavy particles - flyashes in air - in a vertical channel flow, using pseudo-spectral direct numerical simulation to calculate the turbulent flow field at a shear Reynolds number Re-tau = 150, and Lagrangian tracking to describe the dynamics of particles. Drag force, gravity and Saffman lift are used in the equation of motion for the particles, which are assumed to have no influence on the flow field. Particle interaction with the wall is fully elastic. As reported in several previous investigations, we found that particles are transferred by sweeps - Q2 type events - in the wall region, where they preferentially accumulate in the low-speed streak environments, whereas ejections - Q4 type events - transfer particles from the wall region to the outer flow. We quantify the efficiency of the instantaneous realizations of the Reynolds stresses events in transferring different size particles to the wall and away from the wall, respectively. Our findings confirm that sweeps and ejections are efficient transfer mechanisms for particles. In particular, we find that only those sweep and ejection events with substantial spatial coherence are effective in transferring particles. However, the efficiency of the transfer mechanisms is conditioned by the presence of particles to be transferred. In the case of ejections, particles are more rarely available since, when in the viscous wall layer, they are concentrated under the low-speed streaks. Even though the low-speed streaks are ejection-like environments, particles remain trapped for a long time. This phenomenon, which causes accumulation of particles in the near-wall region, can be interpreted in terms of overall fluxes toward and away from the wall by the theory of turbophoresis. This theory, proposed initially by Caporaloni et al. (1975) and re-examined later by Reeks (1983), can help to explain the existence of net particle fluxes toward the wall as a manifestation of the skewness in the velocity distribution of the particles (Reeks 1983). To understand the local and instantaneous mechanisms which give rise to the phenomenon of turbophoresis, we focus on the near-wall region of the turbulent boundary layer. We examine the role of the rear-end of a quasistreamwise vortex very near to the wall in preventing particles in the proximity of the wall from being re-entrained by the pumping action of the large, farther from the wall, forward-end of a following quasi-streamwise vortex. We examine several mechanisms for turbulence structures near the wall and we find that the mechanism based on the archetypal quasi-streamwise structures identified by Schoppa {\&} Hussain (1997), the parent-offspring regeneration cycle for near-wall quasi-streamwise vortices discussed by Brooke {\&} Hanratty (1993), and the mechanism based on coherent packets of hairpin vortices, the fundamental super-structure characterized by Adrian, Meinhart {\&} Tomkins (2000), all depict the same characteristic pattern whic},
annote = {Marchioli, C Soldati, A},
author = {Marchioli, C and Soldati, A},
doi = {10.1017/s0022112002001738},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Marchioli, Soldati - Mechanisms for particle transfer and segregation in a turbulent boundary layer - 2002.pdf:pdf},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
pages = {283--315},
title = {{Mechanisms for particle transfer and segregation in a turbulent boundary layer}},
url = {<Go to ISI>://WOS:000178731400011},
volume = {468},
year = {2002}
}
@article{Thomas2004c,
abstract = {It is generally assumed that bacteria are washed off surfaces as fluid flow increases because they adhere through 'slip-bonds' that weaken under mechanical force. However, we show here that the opposite is true for Escherichia coli attachment to monomannose-coated surfaces via the type 1 fimbrial adhesive subunit, FimH. Raising the shear stress (within the physiologically relevant range) increased accumulation of type 1 fimbriated bacteria on monomannose surfaces by up to two orders of magnitude, and reducing the shear stress caused them to detach. In contrast, bacterial binding to anti-FimH antibody-coated surfaces showed essentially the opposite behaviour, detaching when the shear stress was increased. These results can be explained if FimH is force-activated; that is, that FimH mediates 'catch-bonds' with mannose that are strengthened by tensile mechanical force. As a result, on monomannose-coated surfaces, bacteria displayed a complex 'stick-and-roll' adhesion in which they tended to roll over the surface at low shear but increasingly halted to stick firmly as the shear was increased. Mutations in FimH that were predicted earlier to increase or decrease force-induced conformational changes in FimH were furthermore shown here to increase or decrease the probability that bacteria exhibited the stationary versus the rolling mode of adhesion. This 'stick-and-roll' adhesion could allow type 1 fimbriated bacteria to move along mannosylated surfaces under relatively low flow conditions and to accumulate preferentially in high shear regions.},
author = {Thomas, Wendy E and Nilsson, Lina M and Forero, Manu and Sokurenko, Evgeni V and Vogel, Viola},
doi = {10.1111/j.1365-2958.2004.04226.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Thomas et al. - Shear-dependent 'stick-and-roll' adhesion of type 1 fimbriated Escherichia coli. - 2004.pdf:pdf},
issn = {0950-382X},
journal = {Molecular microbiology},
keywords = {Adhesins, Escherichia coli,Adhesins, Escherichia coli: chemistry,Adhesins, Escherichia coli: genetics,Adhesins, Escherichia coli: metabolism,Bacterial Adhesion,Bacterial Adhesion: physiology,Escherichia coli,Escherichia coli: cytology,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: genetics,Fimbriae Proteins: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: metabolism,Mannose,Mannose: metabolism,Models, Molecular,Stress, Mechanical,Surface Properties},
month = {sep},
number = {5},
pages = {1545--57},
pmid = {15387828},
title = {{Shear-dependent 'stick-and-roll' adhesion of type 1 fimbriated Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15387828},
volume = {53},
year = {2004}
}
@article{Andersson2006m,
abstract = {Surface organelles (so-called pili) expressed on the bacterial membrane mediate the adhesion of Escherichia coli causing urinary tract infection. These pili possess some extraordinary elongation properties that are assumed to allow a close bacterium-to-host contact even in the presence of shear forces caused by urine flow. The elongation properties of P pili have therefore been assessed for low elongation speeds (steady-state conditions). This work reports on the behavior of P pili probed by dynamic force spectroscopy. A kinetic model for the unfolding of a helixlike chain structure is derived and verified. It is shown that the unfolding of the quaternary structure of the PapA rod takes place at a constant force that is almost independent of elongation speed for slow elongations (up to approximately 0.4 mum/s), whereas it shows a dynamic response with a logarithmic dependence for fast elongations. The results provide information about the energy landscape and reaction rates. The bond length and thermal bond opening and closure rates for the layer-to-layer bond have been assessed to approximately 0.76 nm, approximately 0.8 Hz, and approximately 8 GHz, respectively. The results also support a previously constructed sticky-chain model for elongation of the PapA rod that until now had been experimentally verified only under steady-state conditions.},
author = {Andersson, Magnus and F{\"{a}}llman, Erik and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1529/biophysj.106.087429},
file = {::},
journal = {Biophysical journal},
number = {7},
pages = {2717--25},
title = {{Dynamic force spectroscopy of E. coli P pili.}},
volume = {91},
year = {2006}
}
@article{Jin2010a,
author = {Jin, Qinghua and Zhang, Xiaojun and Li, Xiaoyang and Wang, Jianliu},
doi = {10.1007/s11465-010-0027-8},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jin et al. - Dynamics analysis of bladder-urethra system based on CFD - 2010.pdf:pdf},
issn = {1673-3479},
journal = {Frontiers of Mechanical Engineering in China},
keywords = {bladder-urethra system,cfd,computational fluid dynamics,stress urinary incon-,sui,tinence},
month = {may},
number = {3},
pages = {336--340},
title = {{Dynamics analysis of bladder-urethra system based on CFD}},
url = {http://www.springerlink.com/index/10.1007/s11465-010-0027-8},
volume = {5},
year = {2010}
}
@article{Mulvey2002b,
author = {Mulvey, Matthew A},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Mulvey - Microreview Adhesion and entry of uropathogenic Escherichia coli - 2002.pdf:pdf},
journal = {Cellular microbiology},
number = {5},
pages = {257--271},
title = {{Microreview Adhesion and entry of uropathogenic Escherichia coli}},
volume = {4},
year = {2002}
}
@book{Abrams1997c,
address = {London},
author = {Abrams, P},
chapter = {362},
isbn = {3540196781},
publisher = {Springer - Verlag},
title = {{Urodynamics}},
year = {1997}
}
@article{LeTrong2010c,
abstract = {The Escherichia coli fimbrial adhesive protein, FimH, mediates shear-dependent binding to mannosylated surfaces via force-enhanced allosteric catch bonds, but the underlying structural mechanism was previously unknown. Here we present the crystal structure of FimH incorporated into the multiprotein fimbrial tip, where the anchoring (pilin) domain of FimH interacts with the mannose-binding (lectin) domain and causes a twist in the beta sandwich fold of the latter. This loosens the mannose-binding pocket on the opposite end of the lectin domain, resulting in an inactive low-affinity state of the adhesin. The autoinhibition effect of the pilin domain is removed by application of tensile force across the bond, which separates the domains and causes the lectin domain to untwist and clamp tightly around the ligand like a finger-trap toy. Thus, beta sandwich domains, which are common in multidomain proteins exposed to tensile force in vivo, can undergo drastic allosteric changes and be subjected to mechanical regulation.},
author = {{Le Trong}, Isolde and Aprikian, Pavel and Kidd, Brian a and Forero-Shelton, Manu and Tchesnokova, Veronika and Rajagopal, Ponni and Rodriguez, Victoria and Interlandi, Gianluca and Klevit, Rachel and Vogel, Viola and Stenkamp, Ronald E and Sokurenko, Evgeni V and Thomas, Wendy E},
doi = {10.1016/j.cell.2010.03.038},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Le Trong et al. - Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like beta sheet twisting. - 2010.pdf:pdf},
issn = {1097-4172},
journal = {Cell},
keywords = {Adhesins, Escherichia coli,Adhesins, Escherichia coli: chemistry,Adhesins, Escherichia coli: metabolism,Allosteric Regulation,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Models, Molecular,Protein Structure, Secondary,Protein Structure, Tertiary},
month = {may},
number = {4},
pages = {645--55},
pmid = {20478255},
publisher = {Elsevier Ltd},
title = {{Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like beta sheet twisting.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2905812{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {141},
year = {2010}
}
@misc{Goldman1967d,
annote = {From Duplicate 1 ( Slow viscous motion of a sphere parallel to a plane wall.pdf - Goldman, A.J; Cox, R.G.; Brenner, H. )
},
author = {Goldman, A.J and Cox, R.G. and Brenner, H.},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Goldman, Cox, Brenner - Slow Viscous Motion of a Sphere Parallel to a Plane Wall - II Couette flow, Chem - 1967.pdf:pdf},
keywords = {Flow,shear force,sphere},
mendeley-tags = {Flow,shear force,sphere},
pages = {653--660},
title = {{Slow viscous motion of a sphere parallel to a plane wall.pdf}},
year = {1967}
}
@article{Chen2011c,
abstract = {This study investigated the structural and mechanical properties of Klebsiella pneumoniae type 3 fimbriae, which constitute a known virulence factor for the bacterium. Transmission electron microscopy and optical tweezers were used to understand the ability of the bacterium to survive flushes. An individual K. pneumoniae type 3 fimbria exhibited a helix-like structure with a pitch of 4.1 nm and a three-phase force-extension curve. The fimbria was first nonlinearly stretched with increasing force. Then, it started to uncoil and extended several micrometers at a fixed force of 66 ± 4 pN (n = 22). Finally, the extension of the fimbria shifted to the third phase with a characteristic force of 102 ± 9 pN (n = 14) at the inflection point. Compared with the P fimbriae and type 1 fimbriae of uropathogenic Escherichia coli, K. pneumoniae type 3 fimbriae have a larger pitch in the helix-like structure and stronger uncoiling and characteristic forces.},
author = {Chen, Feng-Jung and Chan, Chia-Han and Huang, Ying-Jung and Liu, Kuo-Liang and Peng, Hwei-Ling and Chang, Hwan-You and Liou, Gunn-Guang and Yew, Tri-Rung and Liu, Cheng-Hsien and Hsu, Ken Y and Hsu, Long},
doi = {10.1128/JB.01395-10},
issn = {1098-5530},
journal = {Journal of bacteriology},
month = {jan},
number = {7},
pages = {1718--1725},
pmid = {21239584},
title = {{Structural and Mechanical Properties of Klebsiella pneumoniae Type 3 Fimbriae.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21239584},
volume = {193},
year = {2011}
}
@article{Kim1987c,
annote = {Kim, j moin, p moser, r},
author = {Kim, J and Moin, P and Moser, R},
doi = {10.1017/s0022112087000892},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Kim, Moin, Moser - Turbulence statistics in fully-developed channel flow at low reynolds-number - 1987.pdf:pdf},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
pages = {133--166},
title = {{Turbulence statistics in fully-developed channel flow at low reynolds-number}},
url = {<Go to ISI>://WOS:A1987H239500008},
volume = {177},
year = {1987}
}
@article{Jeffrey2003d,
abstract = {The guinea pig ileum responds to distension with characteristic wall movements, luminal pressure gradients, and outflow (the peristaltic reflex). To date, little is known about whether the peristaltic reflex generates flow events other than laminar flow. Here we used a numerical method to solve for the flow generated by moving walls to assess occlusive contractions (case 1), nonocclusive contractions (case 2), and contractions with steep shoulders (case 3) for which visual parameters of wall movements are published. We found that all three contraction cases produced pressure differentials across the coapting segment, downstream and reverse flow, and vortical flow patterns that redistributed particles and mixed liquids. Contractions generated pressures and shear stresses, particularly along the moving section of the wall. The nonocclusive contraction was much less effective than the occlusive contraction with the steep shoulders; the occlusive contraction with flat shoulders had an intermediate effect. Our analysis shows that even peristaltic contractions produce not only laminar flow but also many flow events likely to promote digestion and absorption. The visual patterns of contractions impact the patterns of luminal flow, and precise definition of wall movements is critical to quantify the fluid mechanical consequences of intestinal contractions.},
author = {Jeffrey, Brian and Udaykumar, Holavanahalli S and Schulze, Konrad S},
doi = {10.1152/ajpgi.00062.2003},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Jeffrey, Udaykumar, Schulze - Flow fields generated by peristaltic reflex in isolated guinea pig ileum impact of contraction depth an(2).pdf:pdf},
issn = {0193-1857},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
keywords = {Animals,Biological,Gastrointestinal Motility,Gastrointestinal Motility: physiology,Gastrointestinal Transit,Gastrointestinal Transit: physiology,Guinea Pigs,Ileum,Ileum: physiology,Models,Peristalsis,Peristalsis: physiology,Reflex,Reflex: physiology},
month = {nov},
number = {5},
pages = {907--18},
pmid = {14561588},
title = {{Flow fields generated by peristaltic reflex in isolated guinea pig ileum: impact of contraction depth and shoulders.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14561588},
volume = {285},
year = {2003}
}
@article{Li2013,
author = {Li, Tongcang and Raizen, Mark G.},
doi = {10.1002/andp.201200232},
file = {::},
issn = {00033804},
journal = {Annalen der Physik},
month = {apr},
number = {4},
pages = {281--295},
title = {{Brownian motion at short time scales}},
url = {http://doi.wiley.com/10.1002/andp.201200232},
volume = {525},
year = {2013}
}
@article{Castelain2011c,
abstract = {Uropathogenic Escherichia coli (UPEC) express various kinds of organelles, so-called pili or fimbriae, that mediate adhesion to host tissue in the urinary tract through specific receptor-adhesin interactions. The biomechanical properties of these pili have been considered important for the ability of bacteria to withstand shear forces from rinsing urine flows. Force-measuring optical tweezers have been used to characterize individual organelles of F1C type expressed by UPEC bacteria with respect to such properties. Qualitatively, the force-versus-elongation response was found to be similar to that of other types of helix-like pili expressed by UPEC, i.e., type 1, P, and S, with force-induced elongation in three regions, one of which represents the important uncoiling mechanism of the helix-like quaternary structure. Quantitatively, the steady-state uncoiling force was assessed as 26.4 ±1.4 pN, which is similar to those of other pili (which range from 21 pN for S(I) to 30 pN for type 1). The corner velocity for dynamic response (1,400 nm/s) was found to be larger than those of the other pili (400-700 nm/s for S and P pili, and 6 nm/s for type 1). The kinetics were found to be faster, with a thermal opening rate of 17 Hz, a few times higher than S and P pili, and three orders of magnitude higher than type 1. These data suggest that F1C pili are, like P and S pili, evolutionarily selected to primarily withstand the conditions expressed in the upper urinary tract.},
author = {Castelain, Micka{\"{e}}l and Ehlers, Sarah and Klinth, Jeanna and Lindberg, Stina and Andersson, Magnus and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1007/s00249-010-0648-1},
issn = {1432-1017},
journal = {European biophysics journal},
keywords = {andersson {\'{a}},bacterial adhesion {\'{a}} dynamic,castelain {\'{a}} s,ehlers {\'{a}} j,force,kinetics,klinth {\'{a}} m,m,spectroscopy {\'{a}} pili relaxation,{\'{a}} uncoiling {\'{a}} bond},
month = {mar},
number = {3},
pages = {305--16},
pmid = {21161524},
title = {{Fast uncoiling kinetics of F1C pili expressed by uropathogenic Escherichia coli are revealed on a single pilus level using force-measuring optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21161524},
volume = {40},
year = {2011}
}
@article{Lenaers2012a,
abstract = {Rare negative streamwise velocities and extreme wall-normal velocity fluctuations near the wall are investigated for turbulent channel flow at a series of Reynolds numbers based on friction velocity up to Re-tau = 1000. Probability density functions of the wall-shear stress and velocity components are presented as well as joint probability density functions of the velocity components and the pressure. Backflow occurs more often (0.06{\%} at the wall at Re-tau = 1000) and further away (up to y(+) = 8.5) from the wall for increasing Reynolds number. The regions of backflow are circular with an average diameter, based on ensemble averages, of approximately 20 viscous units independent of Reynolds number. A strong oblique vortex outside the viscous sublayer is found to cause this backflow. Extreme wall-normal velocity events occur also more often for increasing Reynolds number. These extreme fluctuations cause high flatness values near the wall (F(v) = 43 at Re-tau = 1000). Positive and negative velocity spikes appear in pairs, located on the two edges of a strong streamwise vortex as documented by Xu et al. [Phys. Fluids 8, 1938 (1996)] for Re-tau = 180. The spikes are elliptical and orientated in streamwise direction with a typical length of 25 and a typical width of 7.5 viscous units at y(+) approximate to 1. The negative spike occurs in a high-speed streak indicating a sweeping motion, while the positive spike is located in between a high and low-speed streak. The joint probability density functions of negative streamwise and extreme wall-normal velocity events show that these events are largely uncorrelated. The majority of both type of events can be found lying underneath a large-scale structure in the outer region with positive sign, which can be understood by considering the more intense velocity fluctuations due to amplitude modulation of the inner layer by the outer layer. Simulations performed at different resolutions give only minor differences. Results from experiments and recent turbulent boundary layer simulations show similar results indicating that these rare events are universal for wall-bounded flows. In order to detect these rare events in experiments, measurement techniques have to be specifically tuned. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3696304]},
annote = {Lenaers, Peter Li, Qiang Brethouwer, Geert Schlatter, Philipp Orlu, Ramis},
author = {Lenaers, P and Li, Q and Brethouwer, G and Schlatter, P and Orlu, R},
doi = {035110 10.1063/1.3696304},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Lenaers et al. - Rare backflow and extreme wall-normal velocity fluctuations in near-wall turbulence - 2012.pdf:pdf},
isbn = {1070-6631},
journal = {Physics of Fluids},
number = {3},
title = {{Rare backflow and extreme wall-normal velocity fluctuations in near-wall turbulence}},
url = {<Go to ISI>://WOS:000302224600037},
volume = {24},
year = {2012}
}
@article{Gyrya2010c,
abstract = {Recently, there has been a number of experimental studies convincingly demonstrating that a suspension of self-propelled bacteria (microswimmers in general) may have an effective viscosity significantly smaller than the viscosity of the ambient fluid. This is in sharp contrast with suspensions of hard passive inclusions, whose presence always increases the viscosity. Here we present a 2D model for a suspension of microswimmers in a fluid and analyze it analytically in the dilute regime (no swimmer-swimmer interactions) and numerically using a Mimetic Finite Difference discretization. Our analysis shows that in the dilute regime (in the absence of rotational diffusion) the effective shear viscosity is not affected by self-propulsion. But at the moderate concentrations (due to swimmer-swimmer interactions) the effective viscosity decreases linearly as a function of the propulsion strength of the swimmers. These findings prove that (i) a physically observable decrease of viscosity for a suspension of self-propelled microswimmers can be explained purely by hydrodynamic interactions and (ii) self-propulsion and interaction of swimmers are both essential to the reduction of the effective shear viscosity. We also performed a number of numerical experiments analyzing the dynamics of swimmers resulting from pairwise interactions. The numerical results agree with the physically observed phenomena (e.g., attraction of swimmer to swimmer and swimmer to the wall). This is viewed as an additional validation of the model and the numerical scheme.},
author = {Gyrya, V and Lipnikov, K and Aranson, I S and Berlyand, L},
doi = {10.1007/s00285-010-0351-y},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gyrya et al. - Effective shear viscosity and dynamics of suspensions of micro-swimmers from small to moderate concentrations. - 2010.pdf:pdf},
issn = {1432-1416},
journal = {Journal of mathematical biology},
month = {jun},
pmid = {20563812},
title = {{Effective shear viscosity and dynamics of suspensions of micro-swimmers from small to moderate concentrations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20563812},
year = {2010}
}
@article{Bullitt1998d,
abstract = {P-pili on uropathogenic bacteria are 68-A-diameter rods typically 1 microm in length. These structures project from the outer membrane of Escherichia coli, and contain on their distal tip a thin fibrillum, 25 A in diameter and 150 A long, displaying an adhesin protein responsible for the binding of the bacterium to the surface of epithelial cells lining the urinary tract. Operationally, it is possible to identify three morphologically distinct states of the 68-A-diameter P-pili rods, based on the degree of curvature each can adopt. These states are designated "straight," "curved," and "highly curved." The rods can also be unwound to form thin "threads" that are very similar to the tip fibrillae. Electron microscope data are used to distinguish among these four morphological states and to define limits on the shapes of the pilus proteins. The mechanical properties of the PapA polymers are assessed, and implications of rod polymorphism for pilus function are discussed. A wide variety of data are considered in light of the possibility that all pilins are similar in molecular architecture, with specific differences designed to optimize their specialized functions in the pilus assembly.},
author = {Bullitt, Esther and Makowski, L},
doi = {10.1016/S0006-3495(98)77821-X},
file = {::},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Amino Acid,Amino Acid Sequence,Bacterial,Bacterial Outer Membrane Proteins,Bacterial Outer Membrane Proteins: biosynthesis,Bacterial Outer Membrane Proteins: chemistry,Bacterial Outer Membrane Proteins: ultrastructure,Codon,Conserved Sequence,Electron,Escherichia coli,Escherichia coli: metabolism,Escherichia coli: pathogenicity,Escherichia coli: ultrastructure,Fimbriae Proteins,Gene Expression Regulation,Macromolecular Substances,Microscopy,Models,Molecular,Molecular Sequence Data,Pili,Sequence Alignment,Sequence Homology,Sex,Sex: chemistry,Sex: ultrastructure},
month = {jan},
number = {1},
pages = {623--32},
pmid = {9449363},
title = {{Bacterial adhesion pili are heterologous assemblies of similar subunits.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1299415{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {74},
year = {1998}
}
@article{Pel2007c,
abstract = {A novel, non-invasive method to diagnose bladder outlet obstruction involves the recording of noise with a contact microphone pressed against the perineum (between anus and scrotum). This noise results from flow-generated vortices caused by prostatic obstruction. We developed a computational fluid dynamic (CFD) urethral model including urethral geometry to study the relation between generated noise and the degree of obstruction. This model comprised a bladder, bladder neck, prostate and urethra. Calculations were carried out at four bladder pressures, five degrees of obstruction and three obstruction shapes. For each of the sixty simulations, the velocity and pressure distributions along the urethra were calculated including wall shear stresses to localize flow transition from disturbed to normal. Negative pressures at the obstruction outlet induced recirculation of flow. The location of transition was independent of the applied bladder pressure, but it depended primarily on the degree and secondarily on the shape of the obstruction. Based on the presented results, we hypothesize that the location of the maximum amplitude of perineal noise mainly depends on the degree and shape of the prostatic obstruction. Our future aim is to test our hypothesis in male patients and to extend the presented model to 3D with a viscoelastic urethral wall to calculate the fluid-wall interaction.},
author = {Pel, Johan J M and van Mastrigt, Ron},
doi = {10.1088/0967-3334/28/1/002},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Pel, van Mastrigt - Development of a CFD urethral model to study flow-generated vortices under different conditions of prostatic obstruc.pdf:pdf},
issn = {0967-3334},
journal = {Physiological measurement},
keywords = {Humans,Male,Models, Biological,Prostatic Diseases,Prostatic Diseases: pathology,Prostatic Diseases: physiopathology,Shear Strength,Urethra,Urethra: physiology,Urinary Bladder,Urinary Bladder: physiology},
month = {jan},
number = {1},
pages = {13--23},
pmid = {17151416},
title = {{Development of a CFD urethral model to study flow-generated vortices under different conditions of prostatic obstruction.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17151416},
volume = {28},
year = {2007}
}
@article{Fry2011c,
author = {Fry, C H and Sadananda, P and Wood, D N and Thiruchelvam, N and Jabr, R I and Clayton, R},
doi = {10.1002/nau},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Fry et al. - Modeling the Urinary Tract — Computational , Physical , and Biological Methods - 2011.pdf:pdf},
journal = {Neurourology and Urodynamics},
keywords = {encrustation,lower urinary tract,mathematical modeling,neurological models,tissue engineering},
number = {January},
pages = {692--699},
title = {{Modeling the Urinary Tract — Computational , Physical , and Biological Methods}},
volume = {699},
year = {2011}
}
@article{Castelain2009g,
abstract = {S pili are members of the chaperone-usher-pathway-assembled pili family that are predominantly associated with neonatal meningitis (S(II)) and believed to play a role in ascending urinary tract infections (S(I)). We used force-measuring optical tweezers to characterize the intrinsic biomechanical properties and kinetics of S(II) and S(I) pili. Under steady-state conditions, a sequential unfolding of the layers in the helix-like rod occurred at somewhat different forces, 26 pN for S(II) pili and 21 pN for S(I) pili, and there was an apparent difference in the kinetics, 1.3 and 8.8 Hz. Tests with bacteria defective in a newly recognized sfa gene (sfaX (II)) indicated that absence of the sfaX (II) gene weakens the interactions of the fimbrium slightly and decreases the kinetics. Data of S(I) are compared with those of previously assessed pili primary associated with urinary tract infections, the P and type 1 pili. S pili have weaker layer-to-layer bonds than both P and type 1 pili, 21, 28 and 30 pN, respectively. In addition, the S pili kinetics are {\~{}}10 times faster than the kinetics of P pili and {\~{}}550 times faster than the kinetics of type 1 pili. Our results also show that the biomechanical properties of pili expressed ectopically from a plasmid in a laboratory strain (HB101) and pili expressed from the chromosome of a clinical isolate (IHE3034) are identical. Moreover, we demonstrate that it is possible to distinguish, by analyzing force-extension data, the different types of pili expressed by an individual cell of a clinical bacterial isolate.},
author = {Castelain, Micka{\"{e}}l and Sj{\"{o}}str{\"{o}}m, Annika E and F{\"{a}}llman, Erik and Uhlin, Bernt Eric and Andersson, Magnus},
doi = {10.1007/s00249-009-0552-8},
issn = {1432-1017},
journal = {European biophysics journal},
keywords = {bond breaking {\'{a}} unfolding,coli {\'{a}},fimbriae {\'{a}} uropathogenic escherichia,{\'{a}} optical tweezers},
pages = {1105--1115},
pmid = {19885656},
title = {{Unfolding and refolding properties of S pili on extraintestinal pathogenic Escherichia coli.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19885656},
volume = {39},
year = {2009}
}
@article{Johnson1991d,
abstract = {Uropathogenic strains of Escherichia coli are characterized by the expression of distinctive bacterial properties, products, or structures referred to as virulence factors because they help the organism overcome host defenses and colonize or invade the urinary tract. Virulence factors of recognized importance in the pathogenesis of urinary tract infection (UTI) include adhesins (P fimbriae, certain other mannose-resistant adhesins, and type 1 fimbriae), the aerobactin system, hemolysin, K capsule, and resistance to serum killing. This review summarizes the virtual explosion of information regarding the epidemiology, biochemistry, mechanisms of action, and genetic basis of these urovirulence factors that has occurred in the past decade and identifies areas in need of further study. Virulence factor expression is more common among certain genetically related groups of E. coli which constitute virulent clones within the larger E. coli population. In general, the more virulence factors a strain expresses, the more severe an infection it is able to cause. Certain virulence factors specifically favor the development of pyelonephritis, others favor cystitis, and others favor asymptomatic bacteriuria. The currently defined virulence factors clearly contribute to the virulence of wild-type strains but are usually insufficient in themselves to transform an avirulent organism into a pathogen, demonstrating that other as-yet-undefined virulence properties await discovery. Virulence factor testing is a useful epidemiological and research tool but as yet has no defined clinical role. Immunological and biochemical anti-virulence factor interventions are effective in animal models of UTI and hold promise for the prevention of UTI in humans.},
author = {Johnson, J R},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Johnson - Virulence factors in Escherichia coli urinary tract infection. - 1991.pdf:pdf},
issn = {0893-8512},
journal = {Clinical microbiology reviews},
keywords = {Adhesins,Animals,Antigens,Bacterial,Bacterial Adhesion,Bacterial Outer Membrane Proteins,Blood Bactericidal Activity,Escherichia coli,Escherichia coli Infections,Escherichia coli Infections: microbiology,Escherichia coli: immunology,Escherichia coli: pathogenicity,Fimbriae,Hemolysin Proteins,Humans,Hydroxamic Acids,Surface,Virulence},
month = {jan},
number = {1},
pages = {80--128},
pmid = {1672263},
title = {{Virulence factors in Escherichia coli urinary tract infection.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=358180{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {4},
year = {1991}
}
@article{Vogel2004c,
author = {Vogel, Alexandre and Elmabsout, Badaoui and Gintz, Daniel},
doi = {10.1016/j.crme.2004.03.017},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Vogel, Elmabsout, Gintz - Mod{\'{e}}lisation du champ des vitesses de l'urine dans un bolus ur{\'{e}}t{\'{e}}ral - 2004.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Vogel, Elmabsout, Gintz - Mod{\'{e}}lisation du champ des vitesses de l'urine dans un bolus ur{\'{e}}t{\'{e}}ral - 2004.doc:doc},
issn = {16310721},
journal = {Comptes Rendus M{\'{e}}canique},
keywords = {0,03 m s,1,2,abridged english version,and gintz et al,between the bladder and,biomechanics,bolus,by isolated pockets,called bolus,gintz,it,modelling,on the work of,speed v 0,the kidney,this study is based,through the,ureter,ureter at a constant,urine flow,urine transport is made},
month = {sep},
number = {9},
pages = {737--742},
title = {{Mod{\'{e}}lisation du champ des vitesses de l'urine dans un bolus ur{\'{e}}t{\'{e}}ral}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1631072104001184},
volume = {332},
year = {2004}
}
@article{Saffman1968a,
annote = {ISI Document Delivery No.: A7106
Times Cited: 318
Cited Reference Count: 1
Saffman, pg
Cambridge univ press
New york
Part 3},
author = {Saffman, P G},
isbn = {0022-1120},
journal = {Journal of Fluid Mechanics},
language = {English},
pages = {624},
title = {{Correction}},
url = {<Go to ISI>://WOS:A1968A710600014},
volume = {31},
year = {1968}
}
@article{Yakovenko2008e,
abstract = {The bacterial adhesive protein, FimH, is the most common adhesin of Escherichia coli and mediates weak adhesion at low flow but strong adhesion at high flow. There is evidence that this occurs because FimH forms catch bonds, defined as bonds that are strengthened by tensile mechanical force. Here, we applied force to single isolated FimH bonds with an atomic force microscope in order to test this directly. If force was loaded slowly, most of the bonds broke up at low force (<60 piconewtons of rupture force). However, when force was loaded rapidly, all bonds survived until much higher force (140-180 piconewtons of rupture force), behavior that indicates a catch bond. Structural mutations or pretreatment with a monoclonal antibody, both of which allosterically stabilize a high affinity conformation of FimH, cause all bonds to survive until high forces regardless of the rate at which force is applied. Pretreatment of FimH bonds with intermediate force has the same strengthening effect on the bonds. This demonstrates that FimH forms catch bonds and that tensile force induces an allosteric switch to the high affinity, strong binding conformation of the adhesin. The catch bond behavior of FimH, the amount of force needed to regulate FimH, and the allosteric mechanism all provide insight into how bacteria bind and form biofilms in fluid flow. Additionally, these observations may provide a means for designing antiadhesive mechanisms.},
author = {Yakovenko, Olga and Sharma, Shivani and Forero, Manu and Tchesnokova, Veronika and Aprikian, Pavel and Kidd, Brian and Mach, Albert and Vogel, Viola and Sokurenko, Evgeni and Thomas, Wendy E},
doi = {10.1074/jbc.M707815200},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Yakovenko et al. - FimH forms catch bonds that are enhanced by mechanical force due to allosteric regulation. - 2008(2).pdf:pdf},
issn = {0021-9258},
journal = {The Journal of biological chemistry},
keywords = {Adhesins, Bacterial,Adhesins, Bacterial: chemistry,Adhesins, Escherichia coli,Adhesins, Escherichia coli: chemistry,Adhesins, Escherichia coli: physiology,Allosteric Regulation,Allosteric Site,Bacterial Adhesion,Escherichia coli,Escherichia coli: metabolism,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: physiology,Gene Expression Regulation, Bacterial,Kinetics,Microscopy, Atomic Force,Models, Biological,Models, Chemical,Molecular Conformation,Protein Conformation,Stress, Mechanical},
month = {apr},
number = {17},
pages = {11596--605},
pmid = {18292092},
title = {{FimH forms catch bonds that are enhanced by mechanical force due to allosteric regulation.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18292092},
volume = {283},
year = {2008}
}
@article{Schaffer2007e,
abstract = {Optical tweezers are widely used to measure molecular forces in biology. Such measurements are often influenced by a nearby surface that can perturb both the calibration of the tweezers as well as the hydrodynamic forces acting on microspheres to which the biomolecules are attached. In this study, we have used a very stable optical tweezers setup employing a recently developed calibration method (Toli{\'{c}}-N{\o}rrelykke, S. F.; Sch{\"{a}}ffer, E.; Howard, J.; Pavone, F. S.; J{\"{u}}licher, F.; Flyvbjerg, H. Rev. Sci. Instrum. 2006, 77 (10), 103101) to determine how the calibration of the tweezers and the forces on the microspheres depend on the height above the surface. We show that the displacement sensitivity of the tweezers is modulated by a standing light wave between the microsphere and the surface. We measured the dependence of the drag coefficient on height and compared it to exact and closed-form solutions to the Navier-Stokes equations. Also, we measured the surface force gradients in different salt solutions and for different surface blocking methods. For a given blocking method, our data suggest that microspheres can experience attractive and/or repulsive forces close to surfaces. For example, a Teflon layer reduces attractive interactions, and the presence of casein can lead to long-range repulsive interactions. These measurements are a prerequisite for the accurate measurement of normal forces with respect to an interface that occur in biological molecules held between surfaces.},
author = {Sch{\"{a}}ffer, Erik and N{\o}rrelykke, Simon F and Howard, Jonathon},
doi = {10.1021/la0622368},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Sch{\"{a}}ffer, N{\o}rrelykke, Howard - Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers..pdf:pdf},
issn = {0743-7463},
journal = {Langmuir},
keywords = {Calibration,Microspheres,Optical Tweezers,Salts,Salts: chemistry},
month = {mar},
number = {7},
pages = {3654--65},
pmid = {17326669},
title = {{Surface forces and drag coefficients of microspheres near a plane surface measured with optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17326669},
volume = {23},
year = {2007}
}
@book{Happel1983c,
address = {Dordrecht},
author = {Happel, J and Brenner, H},
isbn = {9789024728770},
pages = {572},
publisher = {Kluwer Academic Publishers},
title = {{Low Reynolds Number Hydrodynamics}},
year = {1983}
}
@article{Wu2010c,
abstract = {We present an optical tweezer sensor for shear stress mapping in microfluidic systems of different internal geometries. The sensor is able to measure the shear stress acting on microspheres of different sizes that model cell based biological operations. Without the need for a spatial modulator or a holographic disk, the sensor allows for direct shear stress detection at arbitrary positions in straight and curved microfluidic devices. Analytical calculations are carried out and compared with the experimental results. It is observed that a decrease in the microsphere size results in an increase in the shear stress the particle experiences.},
author = {Wu, Jing and Day, Daniel and Gu, Min},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Wu, Day, Gu - Shear stress mapping in microfluidic devices by optical tweezers. - 2010.pdf:pdf},
issn = {1094-4087},
journal = {Optics express},
month = {apr},
number = {8},
pages = {7611--6},
pmid = {20588600},
title = {{Shear stress mapping in microfluidic devices by optical tweezers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20588600},
volume = {18},
year = {2010}
}
@article{Andersson2008d,
abstract = {Bacterial adhesion to surfaces mediated by specific adhesion organelles that promote infections, as exemplified by the pili of uropathogenic E. coli, is studied mostly at the level of cell-cell interactions and thereby reflects the averaged behavior of multiple pili. The role of pilus rod structure has therefore only been estimated from the outcome of experiments involving large numbers of organelles at the same time. It has, however, lately become clear that the biomechanical behavior of the pilus shafts play an important, albeit hitherto rather unrecognized, role in the adhesion process. For example, it has been observed that shafts from two different strains, even though they are similar in structure, result in large differences in the ability of the bacteria to adhere to their host tissue. However, in order to identify all properties of pilus structures that are of importance in the adhesion process, the biomechanical properties of pili must be assessed at the single-molecule level. Due to the low range of forces of these structures, until recently it was not possible to obtain such information. However, with the development of force-measuring optical tweezers (FMOT) with force resolution in the low piconewton range, it has lately become possible to assess forces mediated by individual pili on single living bacteria in real time. FMOT allows for a more or less detailed mapping of the biomechanical properties of individual pilus shafts, in particular those that are associated with their elongation and contraction under stress. This Mi- nireview presents the FMOT technique, the biological model system, and results from assessment of the biomechanical properties of bacterial pili. The information retrieved is also compared with that obtained by atomic force microscopy.},
author = {Andersson, Magnus and Axner, Ove and Almqvist, Fredrik and Uhlin, Bernt Eric and F{\"{a}}llman, Erik},
doi = {10.1002/cphc.200700389},
issn = {1439-7641},
journal = {ChemPhysChem},
keywords = {Bacterial,Bacterial Adhesion,Bacterial Adhesion: physiology,Bacterial: chemistry,Bacterial: genetics,Biological,Biopolymers,Biopolymers: chemistry,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: pathogenicity,Escherichia coli: physiology,Fimbriae,Hydrogen-Ion Concentration,Mechanical,Models,Optical Tweezers,Protein Folding,Stress,Surface Properties},
month = {feb},
number = {2},
pages = {221--35},
pmid = {18181116},
title = {{Physical properties of biopolymers assessed by optical tweezers: analysis of folding and refolding of bacterial pili.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18181116},
volume = {9},
year = {2008}
}
@article{Whitfield2010f,
abstract = {Escherichia coli exhibit both shear-stabilized rolling and a transition to stationary adhesion while adhering in fluid flow. Understanding the mechanism by which this shear-enhanced adhesion occurs is an important step in understanding bacterial pathogenesis. In this work, simulations are used to investigate the relative contributions of fimbrial deformation and bond transitions to the rolling and stationary adhesion of E. coli. Each E. coli body is surrounded by many long, thin fimbriae terminating in a single FimH receptor that is capable of forming a catch bond with mannose. As simulated cells progress along a mannosylated surface under flow, the fimbriae bend and buckle as they interact with the surface, and FimH-mannose bonds form and break according to a two-state, allosteric catch-bond model. In simulations, shear-stabilized rolling resulted from an increase in the low-affinity bond number due to increased fimbrial deformation with shear. Catch-bond formation did not occur during cell rolling, but instead led to the transition to stationary adhesion. In contrast, in leukocyte and platelet systems, catch bonds appear to be involved in the stabilization of rolling, and integrin activation is required for stationary adhesion.},
annote = {
        From Duplicate 1 ( 
        
        
          Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations.
        
        
         - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )

        
        

        From Duplicate 2 ( 
        
        
          Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations.
        
        
         - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )

        
        

        From Duplicate 2 ( 
        
        
          Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations.
        
        
         - Whitfield, Matthew; Ghose, Tia; Thomas, Wendy E )

        
        

        

        

        

        

        

        

      },
author = {Whitfield, Matthew and Ghose, Tia and Thomas, Wendy E},
doi = {10.1016/j.bpj.2010.08.045},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Whitfield, Ghose, Thomas - Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - 2010.pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley/Whitfield, Ghose, Thomas - Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - 2010(3).pdf:pdf;:E$\backslash$:/Mina Dokument/Mendeley//Whitfield, Ghose, Thomas - Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations. - 2010.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
month = {oct},
number = {8},
pages = {2470--8},
pmid = {20959087},
publisher = {Biophysical Society},
title = {{Shear-Stabilized Rolling Behavior of E. coli Examined with Simulations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20959087},
volume = {99},
year = {2010}
}
@article{Forero2006c,
abstract = {We determined whether the molecular structures through which force is applied to receptor-ligand pairs are tuned to optimize cell adhesion under flow. The adhesive tethers of our model system, Escherichia coli, are type I fimbriae, which are anchored to the outer membrane of most E. coli strains. They consist of a fimbrial rod (0.3-1.5 microm in length) built from a helically coiled structural subunit, FimA, and an adhesive subunit, FimH, incorporated at the fimbrial tip. Previously reported data suggest that FimH binds to mannosylated ligands on the surfaces of host cells via catch bonds that are enhanced by the shear-originated tensile force. To understand whether the mechanical properties of the fimbrial rod regulate the stability of the FimH-mannose bond, we pulled the fimbriae via a mannosylated tip of an atomic force microscope. Individual fimbriae rapidly elongate for up to 10 microm at forces above 60 pN and rapidly contract again at forces below 25 pN. At intermediate forces, fimbriae change length more slowly, and discrete 5.0 +/- 0.3-nm changes in length can be observed, consistent with uncoiling and coiling of the helical quaternary structure of one FimA subunit at a time. The force range at which fimbriae are relatively stable in length is the same as the optimal force range at which FimH-mannose bonds are longest lived. Higher or lower forces, which cause shorter bond lifetimes, cause rapid length changes in the fimbria that help maintain force at the optimal range for sustaining the FimH-mannose interaction. The modulation of force and the rate at which it is transmitted from the bacterial cell to the adhesive catch bond present a novel physiological role for the fimbrial rod in bacterial host cell adhesion. This suggests that the mechanical properties of the fimbrial shaft have codeveloped to optimize the stability of the terminal adhesive under flow.},
author = {Forero, Manu and Yakovenko, Olga and Sokurenko, Evgeni V and Thomas, Wendy E and Vogel, Viola},
doi = {10.1371/journal.pbio.0040298},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Forero et al. - Uncoiling mechanics of Escherichia coli type I fimbriae are optimized for catch bonds. - 2006.pdf:pdf},
issn = {1545-7885},
journal = {PLoS biology},
keywords = {Adhesins,Atomic Force,Atomic Force: methods,Bacterial,Bacterial Adhesion,Bacterial: metabolism,Bacterial: physiology,Biological,Compressive Strength,Escherichia coli,Escherichia coli: metabolism,Escherichia coli: physiology,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: metabolism,Fimbriae Proteins: physiology,Ligands,Mannose,Mannose-Binding Lectin,Mannose-Binding Lectin: metabolism,Mannose: metabolism,Mechanical,Microscopy,Models,Protein Structure,Quaternary,Stress},
month = {sep},
number = {9},
pages = {e298},
pmid = {16933977},
title = {{Uncoiling mechanics of Escherichia coli type I fimbriae are optimized for catch bonds.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16933977},
volume = {4},
year = {2006}
}
@article{Aprikian2011d,
abstract = {There is increasing evidence that the catch bond mechanism, where binding becomes stronger under tensile force, is a common property among non-covalent interactions between biological molecules that are exposed to mechanical force in vivo. Here, by using the multi-protein tip complex of the mannose-binding type 1 fimbriae of Escherichia coli, we show how the entire quaternary structure of the adhesive organella is adapted to facilitate binding under mechanically dynamic conditions induced by flow. The fimbrial tip mediates shear-dependent adhesion of bacteria to uroepithelial cells and demonstrates force-enhanced interaction with mannose in single molecule force spectroscopy experiments. The mannose-binding, lectin domain of the apex-positioned adhesive protein FimH is docked to the anchoring pilin domain in a distinct hooked manner. The hooked conformation is highly stable in molecular dynamics simulations under no force conditions but permits an easy separation of the domains upon application of an external tensile force, allowing the lectin domain to switch from a low- to a high-affinity state. The conformation between the FimH pilin domain and the following FimG subunit of the tip is open and stable even when tensile force is applied, providing an extended lever arm for the hook unhinging under shear. Finally, the conformation between FimG and FimF subunits is highly flexible even in the absence of tensile force, conferring to the FimH adhesin an exploratory function and high binding rates. The fimbrial tip of type 1 Escherichia coli is optimized to have a dual functionality: flexible exploration and force sensing. Comparison to other structures suggests that this property is common in unrelated bacterial and eukaryotic adhesive complexes that must function in dynamic conditions.},
author = {Aprikian, Pavel and Interlandi, Gianluca and Kidd, Brian a and {Le Trong}, Isolde and Tchesnokova, Veronika and Yakovenko, Olga and Whitfield, Matt J and Bullitt, Esther and Stenkamp, Ronald E and Thomas, Wendy E and Sokurenko, Evgeni V},
doi = {10.1371/journal.pbio.1000617},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Aprikian et al. - The bacterial fimbrial tip acts as a mechanical force sensor. - 2011.pdf:pdf},
issn = {1545-7885},
journal = {PLoS biology},
month = {may},
number = {5},
pages = {e1000617},
pmid = {21572990},
title = {{The bacterial fimbrial tip acts as a mechanical force sensor.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21572990},
volume = {9},
year = {2011}
}
@article{Xu1996g,
author = {Xu, C. and Zhang, Z. and den Toonder, J. M. J. and Nieuwstadt, F. T. M.},
doi = {10.1063/1.868973},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Xu et al. - Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment - 1996.pdf:pdf},
issn = {10706631},
journal = {Physics of Fluids},
number = {7},
pages = {1938},
title = {{Origin of high kurtosis levels in the viscous sublayer. Direct numerical simulation and experiment}},
url = {http://link.aip.org/link/PHFLE6/v8/i7/p1938/s1{\&}Agg=doi},
volume = {8},
year = {1996}
}
@misc{Griffiths1987g,
abstract = {The dynamics of pyeloureteral flow is described when there is no peristalsis and for peristalsis of high and intermediate frequencies, on the assumption that the ureter is uniform except in the mid-ureter and at the outlet. The possibility of upstream transmission of bladder pressure variations to the renal pelvis is considered. The overall behaviour depends on three principal variables, the maximum tube pressure in the contraction waves, the intrinsic peristaltic carrying capacity and the peristaltic frequency f, expressed in the form fT where T is the time for a peristaltic contraction wave to sweep through the ureter. At intermediate peristaltic frequencies (fT less than but comparable with one) oscillatory flow patterns can occur, in which periods of peristaltically driven flow alternate with extraperistaltic periods of flow through the open ureter. The kidney is better isolated from bladder pressure variations when the peristaltic frequency is high, but high peristaltic frequency can by itself lead to elevated renal pelvic pressure if the flow rate is high. Experimental observations in pigs are presented to support these conclusions.},
author = {Griffiths, D J and Constantinou, C E and Mortensen, J and Djurhuus, J C},
booktitle = {Physics in medicine and biology},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Griffiths et al. - Dynamics of the upper urinary tract II. The effect of variations of peristaltic frequency and bladder pressure on pye.pdf:pdf},
issn = {0031-9155},
keywords = {Animals,Models, Biological,Muscle Contraction,Muscle, Smooth,Muscle, Smooth: physiology,Ureter,Ureter: physiology,Urinary Bladder,Urinary Bladder: physiology},
month = {jul},
number = {7},
pages = {823--33},
pmid = {3615581},
title = {{Dynamics of the upper urinary tract: II. The effect of variations of peristaltic frequency and bladder pressure on pyeloureteral pressure/flow relations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/3615581},
volume = {32},
year = {1987}
}
@article{Thomas2007c,
author = {Thomas, Wendy E},
doi = {10.2174/157341307779940544},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Thomas - Understanding the Counterintuitive Phenomenon of Catch Bonds - 2007.pdf:pdf},
issn = {15734137},
journal = {Current Nanoscience},
month = {feb},
number = {1},
pages = {63--77},
title = {{Understanding the Counterintuitive Phenomenon of Catch Bonds}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=1573-4137{\&}volume=3{\&}issue=1{\&}spage=63},
volume = {3},
year = {2007}
}
@article{Tchesnokova2010c,
abstract = {In the intestine, enterotoxigenic Escherichia coli works against peristaltic forces, adhering to the epithelium via the colonization factor antigen I (CFA/I) fimbrial adhesin CfaE. The CfaE adhesin is similar in localization and tertiary (but not primary) structure to FimH, the type 1 fimbrial adhesin of uropathogenic E. coli, which shows shear-dependent binding to epithelial receptors by an allosteric catch-bond mechanism. Thus, we speculated that CfaE is also capable of shear-enhanced binding. Indeed, bovine erythrocytes coursing over immobilized CFA/I fimbriae in flow chambers exhibited low accumulation levels and fast rolling at low shear, but an 80-fold increase in accumulation and threefold decrease in rolling velocity at elevated shear. This effect was reversible and abolished by pre-incubation of fimbriae with anti-CfaE antibody. Erythrocytes bound to whole CfaE in the same shear-enhanced manner, but to CfaE adhesin domain in a shear-inhibitable fashion. Residue replacements designed to disrupt CfaE interdomain interaction decreased the shear dependency of adhesion and increased binding under static conditions to human intestinal epithelial cells. These findings indicate that close interaction between adhesive and anchoring pilin domains of CfaE keeps the former in a low-affinity state that toggles into a high-affinity state upon separation of two domains, all consistent with an allosteric catch-bond mechanism of CfaE binding.},
author = {Tchesnokova, Veronika and McVeigh, Annette L and Kidd, Brian and Yakovenko, Olga and Thomas, Wendy E and Sokurenko, Evgeni V and Savarino, Stephen J},
doi = {10.1111/j.1365-2958.2010.07116.x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Tchesnokova et al. - Shear-enhanced binding of intestinal colonization factor antigen I of enterotoxigenic Escherichia coli. - 2010.pdf:pdf},
issn = {1365-2958},
journal = {Molecular microbiology},
keywords = {Animals,Binding Sites,Cattle,Enterotoxigenic Escherichia coli,Enterotoxigenic Escherichia coli: pathogenicity,Erythrocytes,Erythrocytes: metabolism,Escherichia coli Proteins,Escherichia coli Proteins: metabolism,Fimbriae Proteins,Fimbriae Proteins: metabolism,Models, Molecular,Protein Binding,Protein Structure, Tertiary,Virulence Factors,Virulence Factors: metabolism},
month = {apr},
number = {2},
pages = {489--502},
pmid = {20345656},
title = {{Shear-enhanced binding of intestinal colonization factor antigen I of enterotoxigenic Escherichia coli.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2929265{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {76},
year = {2010}
}
@article{Bell1978c,
author = {Bell, George},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Bell - Models for the Specific adhesion of cells to cells - 1978.pdf:pdf},
journal = {Science},
keywords = {Dynamic force spectroscopy,cell},
pages = {618--627},
title = {{Models for the Specific adhesion of cells to cells}},
volume = {200},
year = {1978}
}
@article{Griffiths1987f,
author = {Griffiths, Derek J.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Griffiths - Dynamics of the upper urinary tract I. Peristaltic flow through a distensible tube of limited length - 1987.pdf:pdf},
journal = {Physics in medicine and biology},
number = {7},
pages = {813--822},
title = {{Dynamics of the upper urinary tract: I. Peristaltic flow through a distensible tube of limited length}},
volume = {32},
year = {1987}
}
@article{Andersson2012e,
abstract = {Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrheal disease worldwide. Adhesion pili (or fimbriae), such as the CFA/I (colonization factor antigen I) organelles that enable ETEC to attach efficiently to the host intestinal tract epithelium, are critical virulence factors for initiation of infection. We characterized the intrinsic biomechanical properties and kinetics of individual CFA/I pili at the single-organelle level, demonstrating that weak external forces (7.5 pN) are sufficient to unwind the intact helical filament of this prototypical ETEC pilus and that it quickly regains its original structure when the force is removed. While the general relationship between exertion of force and an increase in the filament length for CFA/I pili associated with diarrheal disease is analogous to that of P pili and type 1 pili, associated with urinary tract and other infections, the biomechanical properties of these different pili differ in key quantitative details. Unique features of CFA/I pili, including the significantly lower force required for unwinding, the higher extension speed at which the pili enter a dynamic range of unwinding, and the appearance of sudden force drops during unwinding, can be attributed to morphological features of CFA/I pili including weak layer-to-layer interactions between subunits on adjacent turns of the helix and the approximately horizontal orientation of pilin subunits with respect to the filament axis. Our results indicate that ETEC CFA/I pili are flexible organelles optimized to withstand harsh motion without breaking, resulting in continued attachment to the intestinal epithelium by the pathogenic bacteria that express these pili.},
annote = {From Duplicate 1 ( A structural basis for sustained bacterial adhesion: biomechanical properties of CFA/I pili. - Andersson, Magnus; Bj{\"{o}}rnham, Oscar; Svantesson, Mats; Badahdah, Arwa; Uhlin, Bernt Eric; Bullitt, Esther )

From Duplicate 3 ( A Structural Basis for Sustained Bacterial Adhesion: Biomechanical Properties of CFA/I Pili. - Andersson, Magnus; Bj{\"{o}}rnham, Oscar; Svantesson, Mats; Badahdah, Arwa; Uhlin, Bernt Eric; Bullitt, Esther )
},
author = {Andersson, Magnus and Bj{\"{o}}rnham, Oscar and Svantesson, Mats and Badahdah, Arwa and Uhlin, Bernt Eric and Bullitt, Esther},
doi = {10.1016/j.jmb.2011.12.006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Andersson et al. - A structural basis for sustained bacterial adhesion biomechanical properties of CFAI pili. - 2012(2).pdf:pdf},
issn = {1089-8638},
journal = {Journal of molecular biology},
keywords = {Adhesins,Bacterial,Bacterial Adhesion,Bacterial: physiology,Bacterial: ultrastructure,Biomechanics,Escherichia coli,Escherichia coli: physiology,Escherichia coli: ultrastructure,Fimbriae Proteins,Fimbriae Proteins: physiology,Fimbriae Proteins: ultrastructure,Protein Structure,Secondary,enterotoxigenic Escherichia coli,enterotoxigenic escherichia,fimbriae,force spectroscopy,optical tweezers,unwinding},
month = {feb},
number = {5},
pages = {918--28},
pmid = {22178477},
publisher = {Elsevier B.V.},
title = {{A structural basis for sustained bacterial adhesion: biomechanical properties of CFA/I pili.}},
url = {http://dx.doi.org/10.1016/j.jmb.2011.12.006 http://www.ncbi.nlm.nih.gov/pubmed/22178477},
volume = {415},
year = {2012}
}
@article{Thomas2006f,
abstract = {High shear enhances the adhesion of Escherichia coli bacteria binding to mannose coated surfaces via the adhesin FimH, raising the question as to whether FimH forms catch bonds that are stronger under tensile mechanical force. Here, we study the length of time that E. coli pause on mannosylated surfaces and report a double exponential decay in the duration of the pauses. This double exponential decay is unlike previous single molecule or whole cell data for other catch bonds, and indicates the existence of two distinct conformational states. We present a mathematical model, derived from the common notion of chemical allostery, which describes the lifetime of a catch bond in which mechanical force regulates the transitions between two conformational states that have different unbinding rates. The model explains these characteristics of the data: a double exponential decay, an increase in both the likelihood and lifetime of the high-binding state with shear stress, and a biphasic effect of force on detachment rates. The model parameters estimated from the data are consistent with the force-induced structural changes shown earlier in FimH. This strongly suggests that FimH forms allosteric catch bonds. The model advances our understanding of both catch bonds and the role of allostery in regulating protein activity.},
author = {Thomas, Wendy E and Forero, Manu and Yakovenko, Olga and Nilsson, Lina M and Vicini, Paolo and Sokurenko, Evgeni and Vogel, Viola},
doi = {10.1529/biophysj.105.066548},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Thomas et al. - Catch-bond model derived from allostery explains force-activated bacterial adhesion. - 2006.pdf:pdf},
issn = {0006-3495},
journal = {Biophysical journal},
keywords = {Adhesins,Allosteric Site,Bacterial,Bacterial Adhesion,Bacterial: chemistry,Biological,Biophysics,Biophysics: methods,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: metabolism,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: chemistry,Ligands,Mannose,Mannose: chemistry,Mechanical,Microscopy,Models,Protein Binding,Protein Conformation,Statistical,Stress,Temperature,Theoretical,Time Factors,Video},
month = {feb},
number = {3},
pages = {753--64},
pmid = {16272438},
title = {{Catch-bond model derived from allostery explains force-activated bacterial adhesion.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1367101{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {90},
year = {2006}
}
@article{Vahidi2011c,
abstract = {Ureteral peristaltic mechanism facilitates urine transport from the kidney to the bladder. Numerical analysis of the peristaltic flow in the ureter aims to further our understanding of the reflux phenomenon and other ureteral abnormalities. Fluid-structure interaction (FSI) plays an important role in accuracy of this approach and the arbitrary Lagrangian-Eulerian (ALE) formulation is a strong method to analyze the coupled fluid-structure interaction between the compliant wall and the surrounding fluid. This formulation, however, was not used in previous studies of peristalsis in living organisms. In the present investigation, a numerical simulation is introduced and solved through ALE formulation to perform the ureteral flow and stress analysis. The incompressible Navier-Stokes equations are used as the governing equations for the fluid, and a linear elastic model is utilized for the compliant wall. The wall stimulation is modeled by nonlinear contact analysis using a rigid contact surface since an appropriate model for simulation of ureteral peristalsis needs to contain cell-to-cell wall stimulation. In contrast to previous studies, the wall displacements are not predetermined in the presented model of this finite-length compliant tube, neither the peristalsis needs to be periodic. Moreover, the temporal changes of ureteral wall intraluminal shear stress during peristalsis are included in our study. Iterative computing of two-way coupling is used to solve the governing equations. Two phases of nonperistaltic and peristaltic transport of urine in the ureter are discussed. Results are obtained following an analysis of the effects of the ureteral wall compliance, the pressure difference between the ureteral inlet and outlet, the maximum height of the contraction wave, the contraction wave velocity, and the number of contraction waves on the ureteral outlet flow. The results indicate that the proximal part of the ureter is prone to a higher shear stress during peristalsis compared with its middle and distal parts. It is also shown that the peristalsis is more efficient as the maximum height of the contraction wave increases. Finally, it is concluded that improper function of ureteropelvic junction results in the passage of part of urine back flow even in the case of slow start-up of the peristaltic contraction wave.},
author = {Vahidi, Bahman and Fatouraee, Nasser and Imanparast, Ali and Moghadam, Abbas Nasiraei},
doi = {10.1115/1.4003316},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Vahidi et al. - A mathematical simulation of the ureter effects of the model parameters on ureteral pressureflow relations. - 2011.pdf:pdf},
issn = {1528-8951},
journal = {Journal of biomechanical engineering},
keywords = {Biological,Computer Simulation,Humans,Hydrodynamics,Linear Models,Mechanical,Models,Peristalsis,Peristalsis: physiology,Pressure,Shear Strength,Shear Strength: physiology,Stress,Ureter,Ureter: physiology,Urination,Urination: physiology,Urine,Urine: physiology},
month = {mar},
number = {3},
pages = {031004--1},
pmid = {21303180},
title = {{A mathematical simulation of the ureter: effects of the model parameters on ureteral pressure/flow relations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21303180},
volume = {133},
year = {2011}
}
@article{Zakrisson2013c,
abstract = {Type 1 fimbriae mediate adhesion of uropathogenic Escherichia coli to host cells. It has been hypothesized that due to their ability to uncoil under exposure to force, fimbriae can reduce fluid shear stress on the adhesin-receptor interaction by which the bacterium adheres to the surface. In this work, we develop a model that describes how the force on the adhesin-receptor interaction of a type 1 fimbria varies as a bacterium is affected by a time-dependent fluid flow mimicking in vivo conditions. The model combines in vivo hydrodynamic conditions with previously assessed biomechanical properties of the fimbriae. Numerical methods are used to solve for the motion and adhesion force under the presence of time-dependent fluid profiles. It is found that a bacterium tethered with a type 1 pilus will experience significantly reduced shear stress for moderate to high flow velocities and that the maximum stress the adhesin will experience is limited to ∼120 pN, which is sufficient to activate the conformational change of the FimH adhesin into its stronger state but also lower than the force required for breaking it under rapid loading. Our model thus supports the assumption that the type 1 fimbria shaft and the FimH adhesin-receptor interaction are optimized to each other, and that they give piliated bacteria significant advantages in rapidly changing fluidic environments.},
author = {Zakrisson, Johan and Wiklund, Krister and Axner, Ove and Andersson, Magnus},
doi = {10.1016/j.bpj.2013.03.059},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Zakrisson et al. - The shaft of the type 1 fimbriae regulates an externalforce to match the FimH catch bond - 2013.pdf:pdf},
issn = {1542-0086},
journal = {Biophysical journal},
month = {may},
number = {10},
pages = {2137--48},
pmid = {23708354},
publisher = {Biophysical Society},
title = {{The shaft of the type 1 fimbriae regulates an external force to match the FimH catch bond.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23708354},
volume = {104},
year = {2013}
}
@article{Lecuyer2011c,
abstract = {Although ubiquitous, the processes by which bacteria colonize surfaces remain poorly understood. Here we report results for the influence of the wall shear stress on the early-stage adhesion of Pseudomonas aeruginosa PA14 on glass and polydimethylsiloxane surfaces. We use image analysis to measure the residence time of each adhering bacterium under flow. Our main finding is that, on either surface, the characteristic residence time of bacteria increases approximately linearly as the shear stress increases (0-3.5 Pa). To investigate this phenomenon, we used mutant strains defective in surface organelles (type I pili, type IV pili, or the flagellum) or extracellular matrix production. Our results show that, although these bacterial surface features influence the frequency of adhesion events and the early-stage detachment probability, none of them is responsible for the trend in the shear-enhanced adhesion time. These observations bring what we believe are new insights into the mechanism of bacterial attachment in shear flows, and suggest a role for other intrinsic features of the cell surface, or a dynamic cell response to shear stress.},
author = {Lecuyer, Sigolene and Rusconi, Roberto and Shen, Yi and Forsyth, Alison and Vlamakis, Hera and Kolter, Roberto and Stone, Howard A},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lecuyer et al. - Shear stress increases the residence time of adhesion of Pseudomonas aeruginosa. - 2011.pdf:pdf},
institution = {Harvard University, Cambridge, Massachusetts, USA.},
journal = {Biophysical Journal},
number = {2},
pages = {341--350},
pmid = {21244830},
publisher = {Biophysical Society},
title = {{Shear stress increases the residence time of adhesion of Pseudomonas aeruginosa.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21244830},
volume = {100},
year = {2011}
}
@article{Melican2011c,
abstract = {The progression of a natural bacterial infection is a dynamic process influenced by the physiological characteristics of the target organ. Recent developments in live animal imaging allow for the study of the dynamic microbe-host interplay in real-time as the infection progresses within an organ of a live host. Here we used multiphoton microscopy-based live animal imaging, combined with advanced surgical procedures, to investigate the role of uropathogenic Escherichia coli (UPEC) attachment organelles P and Type 1 fimbriae in renal bacterial infection. A GFP+ expressing variant of UPEC strain CFT073 and genetically well-defined isogenic mutants were microinfused into rat glomerulus or proximal tubules. Within 2 h bacteria colonized along the flat squamous epithelium of the Bowman's capsule despite being exposed to the primary filtrate. When facing the challenge of the filtrate flow in the proximal tubule, the P and Type 1 fimbriae appeared to act in synergy to promote colonization. P fimbriae enhanced early colonization of the tubular epithelium, while Type 1 fimbriae mediated colonization of the center of the tubule via a mechanism believed to involve inter-bacterial binding and biofilm formation. The heterogeneous bacterial community within the tubule subsequently affected renal filtration leading to total obstruction of the nephron within 8 h. Our results reveal the importance of physiological factors such as filtration in determining bacterial colonization patterns, and demonstrate that the spatial resolution of an infectious niche can be as small as the center, or periphery, of a tubule lumen. Furthermore, our data show how secondary physiological injuries such as obstruction contribute to the full pathophysiology of pyelonephritis.},
author = {Melican, Keira and Sandoval, Ruben M and Kader, Abdul and Josefsson, Lina and Tanner, George a and Molitoris, Bruce a and Richter-Dahlfors, Agneta},
doi = {10.1371/journal.ppat.1001298},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Melican et al. - Uropathogenic Escherichia coli P and Type 1 fimbriae act in synergy in a living host to facilitate renal colonization l.pdf:pdf},
issn = {1553-7374},
journal = {PLoS pathogens},
keywords = {Animals,Bacterial,Bacterial Adhesion,Bacterial: physiology,Escherichia coli Infections,Escherichia coli Infections: microbiology,Female,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: metabolism,Kidney,Kidney: microbiology,Kidney: physiopathology,Nephrons,Nephrons: microbiology,Nephrons: physiopathology,Rats,Sprague-Dawley,Ureteral Obstruction,Ureteral Obstruction: pathology,Uropathogenic Escherichia coli,Uropathogenic Escherichia coli: physiology},
month = {feb},
number = {2},
pages = {e1001298},
pmid = {21383970},
title = {{Uropathogenic Escherichia coli P and Type 1 fimbriae act in synergy in a living host to facilitate renal colonization leading to nephron obstruction.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3044688{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {7},
year = {2011}
}
@article{Lentle2008c,
abstract = {The physical properties of digesta may influence mixing, efficiency of digestion, and absorption within the lumen of the intestine. We review how the physical properties of digesta change during transit through the various segments of the intestine, and how their influence on flow and mixing may be modulated by peristaltic activity. We examine how, in more fluid digesta, the solid and liquid phases interact to influence flow and mixing. Similarly, how in viscid digesta, shear strength, plasticity and elasticity of contained particulate material may influence the permeation of the fluid phase and secretions into and out of the digesta bolus. The manner in which the solid and liquid phases of digesta interact in a partly gaseous environment, such as the lower bowel, to influence bolus cohesion is also examined. Those mechanisms that promote the formation of a less viscous layer at the mucosal interface to promote plug flow are reviewed, and their effect on the efficiency of mixing and digestion discussed. It is recommended that in any future work investigating the character of mixing in the intestine, a wider range of appropriate digesta properties be measured and that, in investigations of intestinal movement, perfusates with similar characteristics to digesta be used.},
author = {Lentle, R G and Janssen, P W M},
doi = {10.1007/s00360-008-0264-x},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Lentle, Janssen - Physical characteristics of digesta and their influence on flow and mixing in the mammalian intestine a review. - 2008.pdf:pdf},
issn = {0174-1578},
journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology},
keywords = {Animals,Digestion,Digestion: physiology,Elasticity,Food,Gastrointestinal Contents,Gastrointestinal Contents: chemistry,Gastrointestinal Motility,Gastrointestinal Transit,Intestinal Absorption,Intestines,Intestines: physiology,Models, Animal,Models, Biological,Particle Size,Peristalsis,Permeability,Rheology,Shear Strength,Viscosity},
month = {aug},
number = {6},
pages = {673--90},
pmid = {18401586},
title = {{Physical characteristics of digesta and their influence on flow and mixing in the mammalian intestine: a review.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18401586},
volume = {178},
year = {2008}
}
@article{Fallman2005c,
abstract = {P pili are protein filaments expressed by uropathogenic Escherichia coli that mediate binding to glycolipids on epithelial cell surfaces, which is a prerequisite for bacterial infection. When a bacterium, attached to a cell surface, is exposed to external forces, the pili, which are composed of approximately 10(3) PapA protein subunits arranged in a helical conformation, can elongate by unfolding to a linear conformation. This property is considered important for the ability of a bacterium to withstand shear forces caused by urine flow. It has hitherto been assumed that this elongation is plastic, thus constituting a permanent conformational deformation. We demonstrate, using optical tweezers, that this is not the case; the unfolding of the helical structure to a linear conformation is fully reversible. It is surmised that this reversibility helps the bacteria regain close contact to the host cells after exposure to significant shear forces, which is believed to facilitate their colonization.},
author = {F{\"{a}}llman, Erik and Schedin, Staffan and Jass, Jana and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1038/sj.embor.7400310},
file = {:E$\backslash$:/Mina Dokument/Mendeley/F{\"{a}}llman et al. - The unfolding of the P pili quaternary structure by stretching is reversible, not plastic. - 2005.pdf:pdf},
issn = {1469-221X},
journal = {EMBO reports},
keywords = {Bacterial,Bacterial: chemistry,Bacterial: metabolism,Escherichia coli,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: metabolism,Escherichia coli: chemistry,Fimbriae,Fimbriae Proteins,Fimbriae Proteins: chemistry,Fimbriae Proteins: metabolism,Protein Denaturation,Protein Folding,Protein Structure,Quaternary},
month = {jan},
number = {1},
pages = {52--6},
pmid = {15592451},
title = {{The unfolding of the P pili quaternary structure by stretching is reversible, not plastic.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1299220{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {6},
year = {2005}
}
@article{Smith1991c,
author = {Smith, C. R. and Walker, J. D. a. and Haidari, a. H. and Sobrun, U.},
doi = {10.1098/rsta.1991.0070},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Smith et al. - On the Dynamics of Near-Wall Turbulence - 1991.pdf:pdf},
issn = {1364-503X},
journal = {Philosophical Transactions of the Royal Society A},
month = {aug},
number = {1641},
pages = {131--175},
title = {{On the Dynamics of Near-Wall Turbulence}},
url = {http://rsta.royalsocietypublishing.org/cgi/doi/10.1098/rsta.1991.0070},
volume = {336},
year = {1991}
}
@article{Hermansson1999c,
author = {Hermansson, Malte},
doi = {10.1016/S0927-7765(99)00029-6},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hermansson - The DLVO theory in microbial adhesion - 1999.pdf:pdf},
issn = {09277765},
journal = {Colloids and Surfaces B: Biointerfaces},
keywords = {adhesion,bacteria,colloid stability,dlvo theory},
month = {aug},
number = {1-4},
pages = {105--119},
title = {{The DLVO theory in microbial adhesion}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0927776599000296},
volume = {14},
year = {1999}
}
@article{Klinth2012d,
abstract = {Gram-negative bacteria often initiate their colonization by use of extended attachment organelles, so called pili. When exposed to force, the rod of helix-like pili has been found to be highly extendable, mainly attributed to uncoiling and recoiling of its quaternary structure. This provides the bacteria with the ability to redistribute an external force among a multitude of pili, which enables them to withstand strong rinsing flows, which, in turn, facilitates adherence and colonization processes critical to virulence. Thus, pili fibers are possible targets for novel antibacterial agents. By use of a substance that compromises compliance of the pili, the ability of bacteria to redistribute external forces can be impaired, so they will no longer be able to resist strong urine flow and thus be removed from the host. It is possible such a substance can serve as an alternative to existing antibiotics in the future or be a part of a multi-drug. In this work we investigated whether it is possible to achieve this by targeting the recoiling process. The test substance was purified PapD. The effect of PapD on the compliance of P pili was assessed at the single organelle level by use of force-measuring optical tweezers. We showed that the recoiling process, and thus the biomechanical compliance, in particular the recoiling process, can be impaired by the presence of PapD. This leads to a new concept in the search for novel drug candidates combating uropathogenic bacterial infections--"coilicides", targeting the subunits of which the pilus rod is composed.},
author = {Klinth, Jeanna E and Pinkner, Jerome S and Hultgren, Scott J and Almqvist, Fredrik and Uhlin, Bernt Eric and Axner, Ove},
doi = {10.1007/s00249-011-0784-2},
isbn = {0024901107842},
issn = {1432-1017},
journal = {European biophysics journal : EBJ},
keywords = {Anti-Bacterial Agents,Anti-Bacterial Agents: pharmacology,Anti-Bacterial Agents: therapeutic use,Biomechanics,Escherichia coli Infections,Escherichia coli Infections: drug therapy,Escherichia coli Infections: microbiology,Escherichia coli Proteins,Escherichia coli Proteins: chemistry,Escherichia coli Proteins: metabolism,Fimbriae, Bacterial,Fimbriae, Bacterial: drug effects,Fimbriae, Bacterial: metabolism,Mechanical Processes,Models, Molecular,Optical Tweezers,Protein Conformation,Urinary Tract Infections,Urinary Tract Infections: drug therapy,Urinary Tract Infections: microbiology,Uropathogenic Escherichia coli,Uropathogenic Escherichia coli: cytology,Uropathogenic Escherichia coli: drug effects,Uropathogenic Escherichia coli: metabolism},
month = {mar},
number = {3},
pages = {285--95},
pmid = {22237603},
title = {{Impairment of the biomechanical compliance of P pili: a novel means of inhibiting uropathogenic bacterial infections?}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3281203{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {41},
year = {2012}
}
@article{Stipe2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was carried out on twenty-three low to high alloy steel samples to quantify their concentrations of chromium, nickel, and manganese. LIBS spectral data were correlated to known concentrations of the samples and three calibration methods were compared. A standard LIBS calibration technique using peak area integration normalized by an internal standard was compared to peak area integration normalized by total light and the multivariate statistical technique of partial least squares. For the partial least squares analysis, the PLS-1 algorithm was used, where a predictive model is generated for each element separately. Partial least squares regression coefficients show that the algorithm correctly identifies the atomic emission peaks of interest for each of the elements. Predictive capabilities of each calibration approach were quantified by calculating the standard and relative errors of prediction. The performance of partial least squares is on par with using iron as an internal standard but has the key advantage that it can be applied to samples where the concentrations of all elements are unknown.},
author = {Stipe, Christopher B and Hensley, Brian D and Boersema, Jeffrey L and Buckley, Steven G},
institution = {Seattle University, Mechanical Engineering Department, Seattle, Washington 98122, USA. stipec@seattleu.edu},
journal = {Applied Spectroscopy},
number = {2},
pages = {154--160},
pmid = {20149276},
title = {{Laser-induced breakdown spectroscopy of steel: a comparison of univariate and multivariate calibration methods.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20149276},
volume = {64},
year = {2010}
}
@article{Induced2006,
author = {Induced, Laser and Spectroscopy, Breakdown and Spectroscopy, Raman and Setup, Experimental and Co, Torr and Libs, The and Nd, Surelite Continuum and Hr, Ocean Optics and Raman, The and Nd, Big Sky and Spectrometer, Raman Holospec and Instruments, Princeton},
journal = {Spectrochimica Acta},
pages = {1--2},
title = {{Lunar and Planetary Science XXXVII (2006) 2069.pdf}},
volume = {10964},
year = {2006}
}
@article{Sakka2009,
abstract = {Emission spectra of the laser ablation plume formed by the irradiation of Cu65/Zn35 binary alloy in water at the room temperature with 150-ns pulsed laser were measured. The spectra were analyzed by comparing with the theoretical calculation based on the assumption that self-absorption effect is negligible and that the same temperature can be applied to Cu atoms and Zn atoms in the plume. The calculation reproduced the spectra very well and gave reasonable temperature as a best-fit parameter. However, the best-fit value of the Cu atomic density relative to Zn is significantly low compared with the target composition. Care should be taken to perform in situ LIBS in liquid due to the complicated plume formation mechanism and dynamics of material intake into the plume.},
author = {Sakka, Tetsuo and Yamagata, Hajimu and Oguchi, Hisayuki and Fukami, Kazuhiro and Ogata, Yukio H},
doi = {10.1016/j.apsusc.2009.04.086},
issn = {01694332},
journal = {Applied Surface Science},
keywords = {laser induced breakdown spectroscopy,liquid phase laser ablation},
number = {24},
pages = {9576--9580},
title = {{Emission spectroscopy of laser ablation plume: Composition analysis of a target in water}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169433209004309},
volume = {255},
year = {2009}
}
@article{Feoli-Fonseca2001,
abstract = {Human papillomaviruses (HPV) are etiological agents of cervical cancer. In order to address clinical demand for HPV detection and sequence typing, mostly in pre-cancerous cervical lesions, we applied our two-tier PCR-direct sequencing (PCR-DS) approach based on the use of both MY09/MY11 and GP5 + /GP6 + sets of primers. We tested 691 pathological specimens, all of which were biopsies, 75{\%} of which were diagnosed histologically as cervical intraepithelial neoplasia (CIN) grades I-III. In total, 484 samples (70{\%}) tested HPV-positive, yielding 531 HPV sequences from 47 HPV types, including two novel types. Four most frequently found HPV types accounted for 52.9{\%} of all isolates: HPV6, 16, 11, and 31 (21.5{\%}, 20.0{\%}, 7.0{\%}, and 4.5{\%}, respectively). Some interesting results are the following: all currently known high-risk HPV (14 types) and low-risk HPV (6 types) were detected; HPV18 was not the 1st or 2nd but rather the 4th-5th most frequent high-risk HPV type; the highest detection rate for HPV (86{\%}) among samples suspected to be HPV-infected was found in the youngest age group (0-10 years old), including 70{\%} (44/63) "genital" HPV types; HPV types of undetermined cervical cancer risk represented 19{\%} and of the total HPV isolates but were strongly increased in co-infections (36.5{\%} of all isolates). To our knowledge, this is the largest sequencing-based study of HPV. The HPV types of unknown cancer risk, representing the majority of the known HPV types, 27 of the 47 types detected in this study, are not likely to play a major role in cervical cancer because their prevalence in CIN-I, II, and III declines from 16{\%} to 8{\%} to 2.5{\%}. The two-tier PCR-DS method provides greater sensitivity than cycle sequencing using only one pair of primers. It could be used in a simple laboratory setting for quick and reliable typing of known and novel HPV from clinical specimens with fine sequence precision. It could also be applied to anti-cancer vaccine development.},
author = {Feoli-Fonseca, J C and Oligny, L L and Brochu, P and Simard, P and Falconi, S and Yotov, W V},
institution = {Department of Pathology, Ste-Justine Hospital, Women and Children University Hospital Center, University of Montreal, Montreal, Quebec, Canada.},
journal = {Journal of Medical Virology},
number = {4},
pages = {284--292},
pmid = {11241459},
title = {{Human papillomavirus (HPV) study of 691 pathological specimens from Quebec by PCR-direct sequencing approach.}},
volume = {63},
year = {2001}
}
@article{Caneve2005,
abstract = {Laser-induced breakdown spectroscopy was applied to test the possibility of detecting and identifying asbestos in different samples in view of the perspective at field operation without sample preparation which is peculiar to this technique. Several like-resin materials were first investigated by laser-induced breakdown spectroscopy, in order to find an asbestos container assuring safe laboratory operation during the material characterization aimed to identify indicators suitable for a quick identification on field. Successively, spectra of asbestos samples of both in serpentine and amphibole forms were measured and the variability in elemental composition was calculated from the emission spectra. Ratios of intensities of characteristic elements were tested as indicators for asbestos recognition. Laser-induced breakdown spectroscopy results were compared with those obtained by analyzing the same asbestos samples with a scanning electron microscopy equipped with an energy dispersive X-ray spectroscopy, a good correlation was found for Mg/Si and Fe/Si, thus showing the capability of laser-induced breakdown spectroscopy as a diagnostic tool for this category of materials. In particular, it was demonstrated that the method based on two indicators derived from laser-induced breakdown spectroscopy intensity ratios allows to discriminate between asbestos and cements in single shot measurements suitable to field operation.},
author = {Caneve, L and Colao, F and Fabbri, F and Fantoni, R and Spizzichino, V and Striber, J},
doi = {10.1016/j.sab.2005.05.014},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {asbestos,intensity ratios,libs},
number = {7-8},
pages = {1115--1120},
title = {{Laser-induced breakdown spectroscopy analysis of asbestos}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854705001461},
volume = {60},
year = {2005}
}
@article{Alvey2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is an analytical technique real-time geochemical analysis that is being developed for portable use outside of the laboratory. In this study, statistical signal processing and classification techniques were applied to single-shot, broadband LIBS spectra, comprising measured plasma light intensities between 200 and 960 nm, for a suite of 157 garnets of different composition from 92 locations worldwide. Partial least squares discriminant analysis was applied to sets of 25 LIBS spectra for each garnet sample and used to classify the garnet samples based on composition and geographic origin. Careful consideration was given to the cross-validation procedure to ensure that the classification algorithm is robust to unseen data. The results indicate that broadband LIBS analysis can be used to discriminate garnets of different composition and has the potential to discern geographic origin.},
author = {Alvey, Daniel C and Morton, Kenneth and Harmon, Russell S and Gottfried, Jennifer L and Remus, Jeremiah J and Collins, Leslie M and Wise, Michael A},
doi = {10.1364/AO.49.00C168},
journal = {Applied Optics},
number = {13},
pages = {C168----C180},
title = {{Laser-induced breakdown spectroscopy-based geochemical fingerprinting for the rapid analysis and discrimination of minerals: the example of garnet}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-49-13-C168},
volume = {49},
year = {2010}
}
@article{Dumitrescu2007,
abstract = {This article reports what are to the authors' knowledge the first gas-phase laser-induced breakdown spectroscopy (LIBS) measurements using a fiber-optically delivered spark. A silver- and polymer-coated hollow fiber delivered high-energy nanosecond 1064 nm Nd:YAG laser pulses, which were focused to generate high-energy-density plasmas in ultra-lean methane-air mixtures. Emissions from these plasmas were collected and spectroscopically analyzed to quantify relative fuel-to-air ratio. These measurements were compared with others made using traditional LIBS techniques without the fiber-optically delivered spark. Similar results were obtained, but with larger shot-to-shot variability, for the case of the fiber-optically delivered spark.},
author = {Dumitrescu, Cosmin and Puzinauskas, Paulius and Olcmen, Semih and Buckley, Steven G and Joshi, Sachin and Yalin, Azer P},
institution = {Department of Mechanical Engineering, University of Alabama, Tuscaloosa, Alabama 35487-0286, USA.},
journal = {Applied Spectroscopy},
number = {12},
pages = {1338--1343},
pmid = {18198026},
title = {{Fiber-optic spark delivery for gas-phase laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18198026},
volume = {61},
year = {2007}
}
@article{Tran2000,
abstract = {The feasibility of laser induced breakdown spectroscopy (LIBS) as an online tool for trace metal analysis in terephthalic acid (TA) was evaluated. Millions of metric tonnes of TA are produced each year as a raw material for various kinds of polyesters used to make many consumer and industrial products. The conventional techniques used for trace metal analysis in TA are electrothermal atomization atomic absorption spectrometry (ETA-AAS) and inductively coupled plasma optical emission spectroscopy (ICP-OES). However, these techniques require digestion of the sample and dissolution and so are very time consuming and are not suitable for online analysis. LIBS, if it meets the sensitivity and accuracy requirements, will be a very effective tool for online analysis of the production of terephthalic acid and other organic particles. In this work, the main elements of interest, including Mn, Co, Fe, and Na, were studied. The strongest emission line of each element was chosen to obtain the best detection limit. The experimental parameters, including delay time, gate time, sample stage moving speed, and laser repetition rate, were optimized to maximize the signal-to-noise and signal-to-background ratios. Two sampling methods were studied: compressed pellet and loose powder on sticky tape. The preliminary results indicated that there was no difference between these two sampling methods in term of sensitivity and precision. Therefore, the loose powder on sticky tape was preferred for making online analysis of loose powders possible. One unknown and two certified samples were used to determine the accuracy of the method, and the results were compared to those obtained by ICP-OES.},
author = {Tran, Michael and Sun, Qing and Smith, Benjamin and Winefordner, James D},
doi = {10.1016/S0003-2670(00)00990-9},
issn = {00032670},
journal = {Analytica Chimica Acta},
keywords = {libs,loose powders,online analysis,terephthalic acid,trace elements},
number = {2},
pages = {153--158},
title = {{Direct determination of trace elements in terephthalic acid by laser induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0003267000009909},
volume = {419},
year = {2000}
}
@article{Doucet2007,
abstract = {In the present work, quantitative analysis of major and minor elements in aluminum alloys is investigated using chemometrics and laser-induced plasma spectroscopy with a commercially available laser-induced breakdown (LIBS) spectrometer. Multivariate calibrations use the entire signal matrix for all elements in a single multivariate regression model. This enables accounting for the correlation between variables often referred to as matrix effects in conventional univariate modeling. Modeling the entire signal matrix improves robustness over traditional univariate calibration since it can compensate for matrix effects. Several nonlinear data pretreatment methods have been used to correct for nonlinear behaviors of the analytical signals prior to performing the multivariate calibration. The use of multivariate calibration in combination with cubic implicit nonlinear data pretreatment showed the most accurate results. The accuracy reported with the developed multivariate calibration is better than 5{\%} for the major alloying elements. Based on the results obtained, the use of chemometrics and laser-induced plasma spectroscopy have been successfully applied to the quantitative analysis of major and minor alloying elements in aluminum.},
author = {Doucet, Fran{\c{c}}ois R and Belliveau, Thomas F and Fortier, Jean-Luc and Hubert, Joseph},
institution = {Universit{\'{e}} de Montr{\'{e}}al, Facult{\'{e}} des arts et des sciences, D{\'{e}}partement de chimie, P.O. BOX: 6128 station A, Montr{\'{e}}al, Qu{\'{e}}bec, Canada H3C 3J7.},
journal = {Applied Spectroscopy},
number = {3},
pages = {327--332},
pmid = {17389074},
title = {{Use of chemometrics and laser-induced breakdown spectroscopy for quantitative analysis of major and minor elements in aluminum alloys.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17389074},
volume = {61},
year = {2007}
}
@article{Pedarnig2008,
abstract = {Multi-component oxide ceramics and epitaxial oxide thin films are analyzed by laser-induced breakdown spectroscopy (LIBS). Furthermore, pulsed-laser deposition (PLD) of thin films is investigated by long-term monitoring of the optical plasma emission. Both nano-composite high-temperature superconductors (HTS) consisting of YBa2Cu3O7 - delta bulk and Y2Ba4MCuOx (M-2411, M = Ag, Nb) nano-particles, and semiconducting ZnO doped with Aluminum and Lithium are ablated by nano-second laser pulses. The plasma emission is recorded using grating spectrometers with intensified gated detectors. The LIBS signals of nano-particles correlate with the nominal content of the M-2411 phase (0-15 mol{\%}) and reveal a strong signal of Ytterbium impurity (3-35 ppm). In situ monitoring of the PLD process shows element signals that are stable for more than 10,000 laser pulses for both HTS and ZnO ceramics. The relative concentration of elements in thin films and ceramics as determined by LIBS is almost the same.},
author = {Pedarnig, J D and Heitz, J and Stehrer, T and Praher, B and Viskup, R and Siraj, K and Moser, A and Vlad, A and Bodea, M A and B{\"{a}}uerle, D and Babu, N Hari and Cardwell, D A},
doi = {10.1016/j.sab.2008.06.012},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1117--1121},
publisher = {Elsevier B.V.},
title = {{Characterization of nano-composite oxide ceramics and monitoring of oxide thin film growth by laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854708002127},
volume = {63},
year = {2008}
}
@article{D'Angelo2008,
abstract = {In this work, laser-induced breakdown spectroscopy (LIBS) has been applied to the characterization of a plasma generated on a ternary Co-Cr-Mo alloy commonly used on hip prosthesis in air at atmospheric pressure. A method to achieve analytical results without employing any reference sample was implemented within a two-region plasma picture of a hot dense core surrounded by a colder periphery, where both self-absorption and inhomogeneity effects were taken into account. High resolution spectra of three strong Co I-II lines from different regions of the plasma plume were recorded and the analysis was carried out by means of a least-squares calibration-free algorithm. In this approach, theoretical spectra were matched to the experimental line profiles. Thus, the plasma parameters (temperature, atom, ion and electron densities) and the line widths were obtained, demonstrating the feasibility of the method to characterize the physical state of a laser-induced plasma.},
author = {D'Angelo, Cristian A and {D{\'{\i}}az Pace}, Diego M and Bertuccelli, Graciela and Bertuccelli, Daniela},
doi = {10.1016/j.sab.2007.10.049},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {analytic spectroscopy,laser,plasma},
number = {3},
pages = {367--374},
title = {{Laser induced breakdown spectroscopy on metallic alloys: Solving inhomogeneous optically thick plasmas}},
url = {http://www.sciencedirect.com/science/article/B6THN-4R8H1R5-1/2/e9eae9836504cd7c0605ff88b46d6b15},
volume = {63},
year = {2008}
}
@article{Hariri2006,
abstract = {BACKGROUND AND OBJECTIVES: The diagnostic feasibility of optical coherence tomography (OCT) and laser-induced fluorescence (LIF) have been evaluated for human colorectal cancer. This study applies these technologies to a murine model of colorectal adenoma. STUDY DESIGN/MATERIALS AND METHODS: The lower colon of 10 Apc(Min) and two C57BL/6J mice was surveyed over five 4-week intervals using a prototype 2.0 mm diameter OCT-LIF endoscope-based system. Four categories were histologically classified: control C57BL/6J, adenomatous, non-diseased regions of adenomatous, and non-diseased Apc(Min). OCT images were compared to histology. Spectra from the four categories were compared via the Student's t-test. RESULTS: Three Apc(Min) and two control mice completed the study. One adenoma was histologically identified; OCT visualized mucosal thickening/abnormal mass development over the imaging timepoints. LIF spectral comparisons revealed decreased 405 nm intensity and the presence of a peak at 680 nm in the adenomatous Apc(Min). CONCLUSIONS: These preliminary data indicate endoscopic OCT-LIF has the potential to identify colorectal adenomas in murine models.},
author = {Hariri, Lida P and Tumlinson, Alexandre R and Besselsen, David G and Utzinger, Urs and Gerner, Eugene W and Barton, Jennifer K},
institution = {Division of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA.},
journal = {Lasers in Surgery and Medicine},
keywords = {adenoma,adenoma pathology,animal,animals,colorectal neoplasms,colorectal neoplasms pathology,disease models,endoscopy,fluorescence,inbred c57bl,lasers,lasers diagnostic use,mice,optical coherence,pilot projects,spectrometry,tomography},
number = {4},
pages = {305--313},
pmid = {16596657},
title = {{Endoscopic optical coherence tomography and laser-induced fluorescence spectroscopy in a murine colon cancer model.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16596657},
volume = {38},
year = {2006}
}
@article{Gondal2007b,
abstract = {Laser-Induced Breakdown Spectroscopy (LIBS) was applied for the identification of various kinds of plastics for management and recycling of plastic waste. In order to fingerprint these plastics, a laser-produced plasma emission was recorded for spectral analysis of various kinds of plastics. The plasma was generated by focusing a Nd:YAG laser radiation at wavelength = 1064 nm having laser energy = 40 mJ. The 6 main family of plastics tested are: Low Density Polyethylene (LDPE), High Density Polyethylene (HDPE), Polypropylenes (PP), Polystyrene (PS), Polyethylene Terephthalate (PET) and Polyvinyl chloride (PVC). The capability of this technique is demonstrated by the analysis of the major constituents carbon and hydrogen present in polymer matrices. The LIBS signal intensity measured for carbon and hydrogen was detrimental for the fingerprinting of various kinds of plastics. The C/H line intensity ratio was 1.68, 1.51, 1.42, 1.16, 1.01 and 0.91 for HDPE, LDPE, PS, PP, PET and PVC respectively. The detection limits of carbon and hydrogen were found to be approximately 6 micro g/g by applying 20 laser shots. The unique features of LIBS are: it is a simple, rapid, remote, real-time analysis without sampling requirements. The study demonstrated that LIBS could be applied as a best tool for sorting out different kinds plastics on a fast scale for waste management. The health hazards of different kinds of plastics are also described.},
author = {Gondal, Mohammed A and Siddiqui, Mohammad N},
institution = {Laser Research Laboratory, Physics Department, King Fahd University of Petroleum {\&} Minerals, Dhahran, Saudi Arabia. magondal@kfupm.edu.sa},
journal = {Journal of environmental science and health Part A Toxichazardous substances environmental engineering},
number = {13},
pages = {1989--1997},
pmid = {17990161},
title = {{Identification of different kinds of plastics using laser-induced breakdown spectroscopy for waste management.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17990161},
volume = {42},
year = {2007}
}
@article{Mansour2009,
abstract = {One of the most recently applied laser-based techniques in combustion environment is the laser-induced breakdown spectroscopy (LIBS). The technique has been extensively and successfully applied to elemental concentration measurements in solids and liquids. The LIBS signal is much weaker in gases and hence more work is required for quantitative measurements in flames. In the present work we used two orthogonal Nd:YAG lasers that operate at the fundamental wavelength with laser pulse energy of about 100 mJ/pulse. A Princeton-Instruments IMAX ICCD camera attached to a PI-Echelle spectrometer was used for signal detection. The lasers are focused using two 5-cm lenses. Several calibration points have been collected in well defined and homogeneous mixtures of air and fuel in order to be used as references for the measurements in turbulent partially premixed flames. This work shows that the application of the LIBS technique in a turbulent combustion environment is feasible and signal is enhanced by applying an orthogonal dual-pulse arrangement for air-fuel.},
author = {Mansour, Mohy S and Imam, Hisham and Elsayed, Khaled A and Abbass, Wafaa},
doi = {10.1016/j.sab.2009.07.022},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1079--1084},
title = {{Local equivalence ratio measurements in turbulent partially premixed flames using laser-induced breakdown spectroscopy}},
url = {http://www.sciencedirect.com/science/article/B6THN-4WXHBTD-3/2/e897b933548e9f2f27cbeb8f29e01888},
volume = {64},
year = {2009}
}
@article{Yao2010a,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been applied for the multi-elemental analysis of fertilizer. With a set of 11 fertilizer samples containing different levels of phosphorus and potassium, it was identified that the line intensity of the analyte does not follow a straightforward correlation with the element concentration with the presence of matrix effects. Instead, the line intensity of a given analyte element is not only related to that analyte, but also to other elements present in the samples. Further analysis reveals the correlations among the line intensities of the main components. Based on the correlation analysis, a set of calibration models were generated for phosphorus and potassium with the method of partial least squares (PLS) analysis, which is known as a multivariate calibration method. The prediction accuracy and reproducibility of these PLS models were then validated using independent LIBS measurements. The results show that the predicted concentrations with these models provided by LIBS measurements are in good agreement with the reference concentrations, which confirms that the LIBS technique has good potential for the in situ rapid determination of the main elements present in fertilizer.},
author = {Yao, Shunchun and Lu, Jidong and Li, Junyan and Chen, Kai and Li, Jun and Dong, Meirong},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {11},
pages = {1733--1738},
publisher = {The Royal Society of Chemistry},
title = {{Multi-elemental analysis of fertilizer using laser-induced breakdown spectroscopy coupled with partial least squares regression}},
url = {http://dx.doi.org/10.1039/C0JA00027B},
volume = {25},
year = {2010}
}
@article{Wang2010,
abstract = {This paper presents a new approach of applying partial least squares method combined with a physical principle based dominant factor. The characteristic line intensity of the specific element was taken to build up the dominant factor to reflect the major elemental concentration and partial least squares (PLS) approach was then applied to further improve the model accuracy. The deviation evolution of characteristic line intensity from the ideal condition was depicted and according to the deviation understanding, efforts were taken to model the non-linear self-absorption and inter-element interference effects to improve the accuracy of dominant factor model. With a dominant factor to carry the main quantitative information, the novel multivariate model combines advantages of both the conventional univariate and PLS models and partially avoids the overuse of the unrelated noise in the spectrum for PLS application. The dominant factor makes the combination model more robust over a wide concentration range and PLS application improves the model accuracy for samples with matrices within the calibration sample set. Results show that RMSEP of the final dominant factor based PLS model decreased to 2.33{\%} from 5.25{\%} when using the conventional PLS approach with full spectral information. Furthermore, with the development in understanding the physics of the laser-induced plasma, there is potential to easily improve the accuracy of the dominant factor model as well as the proposed novel multivariate model.},
author = {Wang, Zhe and Feng, Jie and Li, Lizhi and Ni, Weidou and Li, Zheng},
journal = {Journal Of Analytical Atomic Spectrometry},
pages = {17},
title = {{A Novel Multivariate Model Based on Dominant Factor for Laser-induced Breakdown Spectroscopy Measurements}},
url = {http://arxiv.org/abs/1012.2735},
year = {2010}
}
@article{Feng2011,
abstract = {Thirty-three bituminous coal samples were utilized to test the application of laser-induced breakdown spectroscopy technique for coal elemental concentration measurement in the air. The heterogeneity of the samples and the pyrolysis or combustion of coal during the laser-sample interaction processes were analyzed to be the main reason for large fluctuation of detected spectra and low calibration quality. Compared with the generally applied normalization with the whole spectral area, normalization with segmental spectral area was found to largely improve the measurement precision and accuracy. The concentrations of major element C in coal were determined by a novel partial least squares (PLS) model based on dominant factor. Dominant C concentration information was taken from the carbon characteristic line intensity since it contains the most-related information, even if not accurately. This dominant factor model was further improved by inducting non-linear relation by partially modeling the inter-element interference effect. The residuals were further corrected by PLS with the full spectrum information. With the physical-principle-based dominant factor to calculate the main quantitative information and to partially explicitly include the non-linear relation, the proposed PLS model avoids the overuse of unrelated noise to some extent and becomes more robust over a wider C concentration range. Results show that RMSEP in the proposed PLS model decreased to 4.47{\%} from 5.52{\%} for the conventional PLS with full spectrum input, while R(2) remained as high as 0.999, and RMSEC{\&}P was reduced from 3.60{\%} to 2.92{\%}, showing the overall improvement of the proposed PLS model.},
author = {Feng, Jie and Wang, Zhe and West, Logan and Li, Zheng and Ni, Weidou},
institution = {State Key Laboratory of Power Systems, Department of Thermal Engineering, Tsinghua-BP Clean Energy Center, Tsinghua University, Beijing, China.},
journal = {Analytical and Bioanalytical Chemistry},
keywords = {bituminous coal,dominant factor,laser induced breakdown spectroscopy,partial least squares},
number = {10},
pages = {3261--3271},
pmid = {21416399},
title = {{A PLS model based on dominant factor for coal analysis using laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21416399},
volume = {400},
year = {2011}
}
@article{Aguilera2009b,
abstract = {Optical emission of laser-induced plasma on the surface of fresh vegetables provides sensitive analysis of trace elements for in situ or online detection of these materials. This emergent technique promises applications with expected outcomes in food security or nutrition quality, as well as environment pollution detection. Characterization of the plasma induced on such soft and humid materials represents the first step towards quantitative measurement using this technique. In this paper, we present the experimental setup and protocol that optimize the plasma generation on fresh vegetables, potatoes for instance. The temporal evolution of the plasma properties are investigated using time-resolved laser-induced breakdown spectroscopy (LIBS). In particular, the electron density and the temperatures of the plasma are reported as functions of its decay time. The temperatures are evaluated from the well known Boltzmann and Saha-Boltzmann plot methods. These temperatures are further compared to that of the typical molecular species, CN, for laser-induced plasma from plant materials. This comparison validates the local thermodynamic equilibrium (LTE) in the specific case of fresh vegetables ablated in the typical LIBS conditions. A study of the temporal evolution of the signal to noise ratio also provides practical indications for an optimized detection of trace elements. We demonstrate finally that, under certain conditions, the calibration-free LIBS procedure can be applied to determine the concentrations of trace elements in fresh vegetables.},
author = {Aguilera, J A and Arag{\'{o}}n, C and Cristoforetti, G and Tognoni, E},
doi = {10.1016/j.sab.2009.06.002},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {7},
pages = {685--689},
publisher = {Elsevier B.V.},
title = {{Application of calibration-free laser-induced breakdown spectroscopy to radially resolved spectra from a copper-based alloy laser-induced plasma}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709001414},
volume = {64},
year = {2009}
}
@article{Hahn2003,
author = {Hahn, David W and Miziolek, Andrzej W and Palleschi, Vincenzo},
issn = {0003-6935},
journal = {Applied optics},
month = {oct},
number = {30},
pages = {5937},
pmid = {14594049},
title = {{Laser-induced breakdown spectroscopy: an introduction to the feature issue.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594049},
volume = {42},
year = {2003}
}
@article{Cremers2009,
author = {Cremers, David A and Chinni, Rosemarie C},
doi = {10.1080/05704920903058755},
issn = {05704928},
journal = {Applied Spectroscopy Reviews},
number = {6},
pages = {457--506},
title = {{Laser-Induced Breakdown Spectroscopy—Capabilities and Limitations}},
url = {http://www.tandfonline.com/doi/abs/10.1080/05704920903058755},
volume = {44},
year = {2009}
}
@article{Windom2011,
abstract = {Molybdenum disulfide (MoS2) and molybdenum trioxide are investigated using Raman spectroscopy with emphasis on the application to tribological systems. The Raman vibrational modes were investigated for excitation wavelengths at 632.8 and 488 nm using both micro-crystalline MoS2 powder and natural MoS2 crystals. Differences are noted in the Raman spectra for these two different wavelengths, which are attributed to resonance effects due to overlap of the 632.8 nm source with electronic absorption bands. In addition, significant laser intensity effects are found that result in laser-induced transformation of MoS2 to MoO3. Finally, the transformation to molybdenum trioxide is explored as a function of temperature and atmosphere, revealing an apparent transformation at 375 K in the presence of oxygen. Overall, Raman spectroscopy is an useful tool for tribological study of MoS2 coatings, including the role of molybdenum trioxide transformations, although careful attention must be given to the laser excitation parameters (both wavelength and intensity) when interpreting Raman spectra.},
author = {Windom, Bret C. and Sawyer, W. G. and Hahn, David W.},
file = {::},
issn = {1023-8883},
journal = {Tribology Letters},
keywords = {molybdenum disulfide {\'{a}} raman,spectroscopy,{\'{a}} oxidation resistance},
month = {mar},
number = {3},
pages = {301--310},
title = {{A Raman Spectroscopic Study of MoS2 and MoO3: Applications to Tribological Systems}},
url = {http://www.springerlink.com/index/10.1007/s11249-011-9774-x},
volume = {42},
year = {2011}
}
@article{Cowpe2011,
abstract = {Laser-Induced Breakdown Spectroscopy (LIBS) was applied to the analysis of bio-ceramic samples. The relationship between sample hardness and LIBS plasma properties was investigated, with comparison to conventional Vickers hardness measurements. The plasma excitation temperature Te was determined using the line-to-continuum ratio for the Si (I) 288.16 nm emission line; we have demonstrated a linear relationship between sample surface hardness and plasma temperature. Results indicate that hardness determination based on measurements of Te offers greater reproducibility than Vickers hardness measurements, under the conditions considered here. The validity of spectroscopic diagnostics based on LTE was confirmed.},
author = {Cowpe, JS and Moorehead, RD and Moser, D and Astin, JS and Karthikeyan, S and Kilcoyne, SH and Crofts, G and Pilkington, RD},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {energy},
number = {3-4},
pages = {290--294},
publisher = {Elsevier},
title = {{Hardness determination of bio-ceramics using laser-induced breakdown spectroscopy}},
url = {http://dx.doi.org/10.1016/j.sab.2011.03.007},
volume = {66},
year = {2011}
}
@article{Asgill2010a,
abstract = {We explore the use of a combination of double-pulse and single-pulse laser-induced breakdown spectroscopy (LIBS) methodologies as a means of differentiating between solid-phase and gaseous-phase analytes (namely, carbon) in an aerosol stream. A range of spectral data was recorded for double-pulse and singlepulse configurations, including both ns and fs prepulse widths, while varying the gas-phase mass percentage of the carbon from about 10{\%} to 90{\%} for various fixed carbon concentrations. The carbon emission response, as measured by the peak-to-continuum ratio, was greater for the double-pulse configuration as compared with the single-pulse response and was also enhanced as the percentage of solid-phase carbon was increased. Using a combination of the double-pulse and single-pulse emission signals, a monotonically increasing response function was found to correlate with the percentage of gas-phase analyte. However, individual data points at the measured gas-phase percentages reveal considerable scatter from the predicted trend. Furthermore, the double-pulse to single-pulse ratio was only pronounced with the ns–ns configuration as compared with the fs–ns scheme. Overall, the LIBS methodology has been demonstrated as a potential means to discriminate between gas-phase and particulatephase fractions of the same elemental species in an aerosol, although future optimization of the temporal parameters should be explored to improve the precision and accuracy of this approach. © 2010 Optical Society of America},
author = {Asgill, Michael E and Brown, Michael S and Frische, Kyle and Roquemore, William M and Hahn, David W},
doi = {300.6365, 300.6210.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Asgill et al. - breakdown spectroscopy for distinguishing between gaseous and particulate phase analytes - 2010.pdf:pdf},
journal = {Applied Optics},
number = {13},
title = {breakdown spectroscopy for distinguishing between gaseous and particulate phase analytes},
volume = {49},
year = {2010}
}
@article{Tognoni2007,
abstract = {Calibration-Free Laser-Induced Breakdown Spectroscopy (CF-LIBS) has been proposed several years ago as an approach for quantitative analysis of Laser-Induced Breakdown Spectroscopy spectra. Recently developed refinement of the spectral processing method is described in the present work. Accurate quantitative results have been demonstrated for several metallic alloys. However, the degree of accuracy that can be achieved with Calibration-Free Laser-Induced Breakdown Spectroscopy analysis of generic samples still needs to be thoroughly investigated. The authors have undertaken a systematic study of errors and biasing factors affecting the calculation in the Calibration-Free Laser-Induced Breakdown Spectroscopy spectra processing. These factors may be classified in three main groups: 1) experimental aberrations (intensity fluctuations and inaccuracy in the correction for spectral efficiency of a detection system), 2) inaccuracy in theoretical parameters used for calculations (Stark broadening coefficients and partition functions) and 3) plasma non-ideality (departure from thermal equilibrium, spatial and temporal inhomogeneities, optical thickness, etc.). In this study, the effects of experimental aberrations and accuracy of spectral data were investigated, assuming that the analytical plasma is ideal. Departure of the plasma conditions from ideality will be the object of future work. The current study was based on numerical simulation. Two kinds of metallic alloys, iron-based and aluminum-based, were studied. The relative weight of the error contributions was found to depend on the sample composition. For the here-investigated samples, the experimental aberrations contribute to the overall uncertainty on the quantitative results more than theoretical parameters. The described simulation method can be applied to the Calibration-Free Laser-Induced Breakdown Spectroscopy analysis of any other kind of sample.},
author = {Tognoni, E and Cristoforetti, G and Legnaioli, S and Palleschi, V and Salvetti, A and Mueller, M and Panne, U and Gornushkin, I},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {accuracy,libs,precision,quantitative analysis,standard less analysis},
number = {12},
pages = {1287--1302},
title = {{A numerical study of expected accuracy and precision in Calibration-Free Laser-Induced Breakdown Spectroscopy in the assumption of ideal analytical plasma}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707003187},
volume = {62},
year = {2007}
}
@article{Yun2002a,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is presented for the on-line multielement analysis of molten radioactive glass at a simulated vitrification process of high level liquid waste (HLLW). A plasma plume is produced by focusing the third harmonic of a Nd: YAG laser ($\lambda$ = 355 nm) onto the glass melt surface at 1200 C, and the plasma emission is guided via optical fiber and is characterized by an echelle spectrometer for the spectral range from 200 to 780 nm with a resolution of 0.01 nm. Compared to a Czerny-Turner spectrometer, the echelle spectrometer appears distinctively superior for its broad operational spectral range and high resolution. The laser-induced plasma is found as optically thin and locally in thermodynamic equilibrium (LTE) as characterized by measuring the electron density and plasma temperature. The matrix temperature effect on the spectral emission is observed as significant, increasing the emission line intensities with increasing temperature, but differently from element to element. The applicability of LIBS is demonstrated on a laboratory scale with an inactive simulated HLLW glass melt for various analytical characteristics concerned.},
author = {Yun, Jong-Il and Klenze, Reinhardt and Kim, Jae-Il},
doi = {10.1366/0003702021955097},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {4},
pages = {437--448},
title = {{Laser-Induced Breakdown Spectroscopy for the On-Line Multielement Analysis of Highly Radioactive Glass Melt. Part I: Characterization and Evaluation of the Method}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=56{\&}issue=4{\&}spage=437},
volume = {56},
year = {2002}
}
@article{Yamamoto2005,
abstract = {Laser-induced breakdown spectroscopy (LIBS) measurements are typically carried out using pulses (50 mJ) from a flashlamp-pumped electro-optically Q-switched Nd:YAG laser (EO-laser) or excimer laser. Here we report LIBS analyses of solids using an acousto-optically Q-switched Nd:YAG laser (AO-laser) producing 150 ns pulses of lower energy (10 mJ) at repetition rates up to 6 kHz. The high repetition rate allows increased spatial or depth sampling over a given time period compared to the EO-laser. Results of AO-laser based LIBS analysis of (1) steels, (2) soils, and (3) surface stains and dusts are described. Detection limits for Cr, Cu, Mn, Ni, and Si in steel ranged from 0.11 to 0.24{\%} using a commercial polychromator-based detection system with limits 4-30 times lower achieved using a laboratory-based detection system. The minimum detectable masses of Ba, Cr, Mn, and Sr on a metal surface were estimated with 1.2 pg/shot achieved for Sr. Detection limits for Ba and Sr in soil were 296 and 52 ppm, respectively. The temperatures, spectra, and emission decay curves from plasmas generated by the AO- and EO-lasers are compared and some characteristics of particles ablated by the AO-laser are described.},
author = {Yamamoto, Karen Y and Cremers, David A and Foster, Leeann E and Davies, Mathew P and Harris, Ronny D},
institution = {Group C-ADI, MS J565, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.},
journal = {Applied Spectroscopy},
keywords = {environmental monitoring,environmental monitoring methods,lasers,metals,metals analysis,soil,soil analysis,spectrum analysis,spectrum analysis instrumentation,spectrum analysis methods},
number = {9},
pages = {1082--1097},
pmid = {16197630},
title = {{Laser-induced breakdown spectroscopy analysis of solids using a long-pulse (150 ns) Q-switched Nd:YAG laser.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16197630},
volume = {59},
year = {2005}
}
@article{Hrdlicka2010,
abstract = {The development of a remote laser-induced breakdown spectroscopy (LIBS) setup with an off-axis Newtonian collection optics, Galilean-based focusing telescope, and a 532 nm flattop laser beam source is presented. The device was tested at a 6 m distance on a slice of bone to simulate its possible use in the field, e.g., during archaeological excavations. It is shown that this setup is sufficiently sensitive to both major (P, Mg) and minor elements (Na, Zn, Sr). The measured quantities of Mg, Zn, and Sr correspond to the values obtained by reference laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) measurements within an approximately 20{\%} range of uncertainty. A single point calibration was performed by use of a bone meal standard . The radial element distribution is almost invariable by use of LA-ICP-MS, whereas the LIBS measurement showed a strong dependence on the sample porosity. Based on these results, this remote LIBS setup with a relatively large (350 mm) collecting mirror is capable of semiquantitative analysis at the level of units of mg kg1.},
author = {Hrdli{\v{c}}ka, Ale{\v{s}} and Proke{\v{s}}, Lubom{\'{\i}}r and Staňkov{\'{a}}, Alice and Novotn{\'{y}}, Karel and Vite{\v{s}}n{\'{\i}}kov{\'{a}}, Anna and Kanick{\'{y}}, Viktor and Otruba, V{\'{\i}}t{\v{e}}zslav and Kaiser, Jozef and Novotn{\'{y}}, Jan and Malina, Radom{\'{\i}}r and P{\'{a}}len{\'{\i}}kov{\'{a}}, Kateřina},
doi = {10.1364/AO.49.000C16},
issn = {00036935},
journal = {Applied Optics},
number = {13},
pages = {C16},
publisher = {OSA},
title = {{Development of a remote laser-induced breakdown spectroscopy system for investigation of calcified tissue samples}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=ao-49-13-C16},
volume = {49},
year = {2010}
}
@article{Suominen2003,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been applied to the analysis of three chromium-doped soils. Two chemometric techniques, principal components analysis (PCA) and neural networks analysis (NNA), were used to discriminate the soils on the basis of their LIBS spectra. An excellent rate of correct classification was achieved and a better ability of neural networks to cope with real-world, noisy spectra was demonstrated. Neural networks were then used for measuring chromium concentration in one of the soils. We performed a detailed optimization of the inputs of the network so as to improve its predictive performances and we studied the effect of the presence of matrix-specific information in the inputs examined. Finally the inputs of the network-the spectral intensities-were replaced by the line areas. This provided the best results with a prediction accuracy and precision of about 5{\%} in the determination of chromium concentration and a significant reduction of the data, too.},
author = {Suominen, K},
chapter = {292},
doi = {10.1046/j.1365-2389.2003.00524.x},
issn = {16182642},
journal = {European Journal of Soil Science},
number = {2},
pages = {1194--293},
publisher = {Academic Press},
title = {{Pinus sylvestris}},
volume = {61,},
year = {2003}
}
@article{Windom2009,
abstract = {Laser-ablation laser-induced breakdown spectroscopy (LA-LIBS) is proposed as a novel analytical scheme with goals of improved analyte response, minimization of sample matrix effects, and use of non-matrix matched standards. A direct comparison of the LA-LIBS approach and a traditional direct LIBS analysis was made for a set of seven reference materials, ranging from nearly pure iron to copper-nickel and aluminum alloys. The precision of each approach was assessed using calibration curves, and the LA-LIBS configuration was demonstrated to consistently produce a superior analytical response, as assessed by the linear least-squares fit correlation coefficient and y-intercept values. Significantly, the normalized (by Fe) response of the four targeted analyte species (Al, Mn, Mg and Cu) was successfully reduced to a single calibration curve with the LA-LIBS approach. In addition, particle size measurements of the laser-ablation plume were recorded along with SEM and white-light interferometry analysis of ablation craters for assessment of the analytical sample as presented to the analytical LIBS plasma. Finally, the effect of carrier gas is explored by substitution of nitrogen with helium.},
author = {Windom, Bret C. and Hahn, David W.},
doi = {10.1039/b913495f},
file = {::},
issn = {0267-9477},
journal = {Journal of Analytical Atomic Spectrometry},
number = {12},
pages = {1665},
title = {{Laser ablation—laser induced breakdown spectroscopy (LA-LIBS): A means for overcoming matrix effects leading to improved analyte response}},
url = {http://xlink.rsc.org/?DOI=b913495f},
volume = {24},
year = {2009}
}
@article{Burgio2000,
abstract = {The combined application of two laser-based analytical techniques-laser-induced breakdown spectroscopy (LIBS) and Raman microscopy-for pigment identification on painted artworks is demonstrated. Detailed spectral data are presented from analyses performed on a 19th century Byzantine icon, which was examined in order to identify the pigments used in the original painted structure, as well as in interventions carried out subsequently for restorative purposes. LIBS measurements yielded elemental analytical data which suggest the presence of certain pigments and, in addition, provide information on the stratigraphy of the paint layers. Identification of most pigments and of the materials used in the preparation layer was performed by Raman microscopy. Index Headings: Laser-induced breakdown spectroscopy; LIBS; Raman microscopy; Artwork analysis; Pigment identification.},
author = {Burgio, Lucia and Clark, Robin J H and Stratoudaki, Theodosia and Doulgeridis, Michael and Anglos, Demetrios},
journal = {Applied Spectroscopy},
number = {4},
pages = {463--469},
publisher = {OSA},
title = {{Optics InfoBase - Pigment Identification in Painted Artworks: A Dual Analytical Approach Employing Laser-Induced Breakdown Spectroscopy and Raman Microscopy}},
url = {http://as.osa.org/abstract.cfm?URI=as-54-4-463},
volume = {54},
year = {2000}
}
@article{DeGiacomo2005,
abstract = {In this work the laser induced plasma obtained in air at atmospheric pressure by the interaction of a fs (femtosecond) or a ns (nanosecond) laser pulse with a metallic titanium target has been investigated by optical emission spectroscopy. The temporal evolution of plasma parameters such as electron number density and excitation temperature has been determined in order to highlight the processes involved when the emission spectra are acquired at short time delays from the ablating laser pulse. A survey of elementary processes implicated during plasma formation and expansion of ns- and fs-Laser Induced Plasma has been performed. Departures from equilibrium conditions are even discussed. The dynamic aspects corresponding to ns- and fs-LIP have been investigated by optical time of flight (TOF) and by fast emission imaging. The overall results have been used for clarifying the basic mechanisms occurring during plasma expansion due to either ns or fs laser source when experimental conditions usually used for laser-induced breakdown spectroscopy (LIBS) applications are employed.},
author = {{De Giacomo}, A and Dell'Aglio, M and Santagata, A and Teghil, R},
doi = {10.1016/j.sab.2005.05.026},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {elementary processes,fs laser induced plasma,libs,titanium},
number = {7-8},
pages = {935--947},
title = {{Early stage emission spectroscopy study of metallic titanium plasma induced in air by femtosecond- and nanosecond-laser pulses}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854705001588},
volume = {60},
year = {2005}
}
@article{Oh2007,
abstract = {The experimental conditions associated with slurry measurements to achieve good precision by using laser-induced breakdown spectroscopy (LIBS) are examined. LIBS analysis was applied to a special waste slurry sample that contains 85.4{\%} water, 2.5{\%} ferric oxide Fe(2)O(3), 1.7{\%} alumina Al(2)O(3), and small quantities of oxides of boron and chromium. While liquids add challenge to LIBS measurements, the analysis was successfully performed on iron and aluminum. Two slurry circulation systems were devised to overcome the major technical problems associated with LIBS measurements of slurry samples, namely, sedimentation and change in the lens-to-sample distance during measurement. LIBS slurry measurements using both circulation systems are compared. The results show that the experimental configuration plays a crucial role for online slurry analysis.},
author = {Oh, Seong Yong and Miller, Tracy and Yueh, Fang Yu and Singh, Jagdish P},
institution = {Institute for Clean Energy Technology, Mississippi State University, Starkville, Mississippi 39759-7704, USA.},
journal = {Applied Optics},
number = {19},
pages = {4020--4025},
pmid = {17571141},
title = {{Comparative study of laser-induced breakdown spectroscopy measurement using two slurry circulation systems.}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-46-19-4020},
volume = {46},
year = {2007}
}
@article{Corsi2006,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is a promising technique for in situ environmental analysis. The potential of this technique for accurate quantitative analysis could be greatly improved using an innovative experimental setup - based on the use of two laser pulses suitably retarded - and analyzing the results with a standard-less procedure which overcomes the problems related to matrix effects. A new mobile instrument for soil analysis, developed at the Applied Laser Spectroscopy Laboratory in Pisa, is presented, and some experimental results are given.},
author = {Corsi, M and Cristoforetti, G and Hidalgo, M and Legnaioli, S and Palleschi, V and Salvetti, A and Tognoni, E and Vallebona, C},
doi = {10.1016/j.apgeochem.2006.02.004},
issn = {08832927},
journal = {Applied Geochemistry},
number = {5},
pages = {748--755},
title = {{Double pulse, calibration-free laser-induced breakdown spectroscopy: A new technique for in situ standard-less analysis of polluted soils}},
url = {http://www.sciencedirect.com/science/article/B6VDG-4JHMY04-4/2/d0ec9c40c99251bed33ac72250da1173},
volume = {21},
year = {2006}
}
@article{DeGiacomo2006,
abstract = {Double-pulse laser-induced plasma spectroscopy (DP-LIPS) is applied to submerged targets to investigate its feasibility for elemental analysis. The role of experimental parameters, such as inter-pulse delay and detection time, has been discussed in terms of the dynamics of the laser-induced bubble produced by the first pulse and its confinement effect on the plasma produced by the second laser pulse. The analytical performance of this technique applied to targets in a water environment are discussed. The elemental analysis of submerged copper alloys by DP-LIPS has been compared with conventional (single-pulse) LIBS in air. Theoretical investigation of the plasma dynamics in water bubbles and open air has been performed.},
author = {{De Giacomo}, A and Dell'Aglio, M and Casavola, A and Colonna, G and {De Pascale}, O and Capitelli, M},
institution = {Chemistry Department, University of Bari, Via Orabona 4, 70126, Bari, Italy. alessandro.degiacomo@ba.imip.cnr.it},
journal = {Analytical and Bioanalytical Chemistry},
number = {2},
pages = {303--311},
pmid = {16544131},
title = {{Elemental chemical analysis of submerged targets by double-pulse laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16544131},
volume = {385},
year = {2006}
}
@article{Lewis2011,
abstract = {Soil bacteria are sensitive to ecological change and can be assessed to gauge anthropogenic influences and ecosystem health. In recent years, there has been a significant increase in the focus on new technologies that can be applied to the evaluation of soil quality. Laser-induced breakdown spectroscopy (LIBS) is a promising technique that has been used for the investigation and characterization of explosives, solids, liquids, gases, biological and environmental samples. In this study, bacteria from un-mined and a chronosequence of reclaimed bauxite soils were isolated on Luria-Bertani agar media. Polymerase chain reaction amplification of the bacterial 16S rDNA, sequencing, and phylogenetic analysis were applied to each isolated soil bacteria from the sample sites resulting in the identification and classification of the organisms. Femtosecond LIBS performed on the isolated bacteria showed atomic and ionic emission lines in the spectrum containing inorganic elements such as sodium (Na), magnesium (Mg), potassium (K), zinc (Zn), and calcium (Ca). Principal component analysis and partial least squares regression analysis were performed on the acquired bacterial spectra demonstrating that LIBS has the potential to differentiate and discriminate among bacteria in the un-mined and reclaimed chronosequence of bauxite soils.},
author = {Lewis, Dawn E and Martinez, Jorge and Akpovo, Charlemagne a and Johnson, Lewis and Chauhan, Ashvini and Edington, Maurice D},
doi = {10.1007/s00216-011-5274-y},
file = {::},
issn = {1618-2650},
journal = {Analytical and bioanalytical chemistry},
keywords = {Aluminum Oxide,Aluminum Oxide: chemistry,Bacteria,Bacteria: classification,Bacteria: isolation {\&} purification,Bacteria: metabolism,DNA, Ribosomal,DNA, Ribosomal: genetics,Environmental Monitoring,Lasers,Metals, Heavy,Metals, Heavy: analysis,Metals, Heavy: chemistry,Phylogeny,Polymerase Chain Reaction,Soil,Soil Pollutants,Soil Pollutants: analysis,Soil: analysis,Spectrum Analysis},
month = {oct},
number = {7},
pages = {2225--36},
pmid = {21826458},
title = {{Discrimination of bacteria from Jamaican bauxite soils using laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21826458},
volume = {401},
year = {2011}
}
@article{Asimellis2006a,
abstract = {We report development and application of an in-situ applicable method to determine phosphate ore rock quality based on Laser-Induced Breakdown Spectroscopy (LIBS). This is an economically viable method for real-time evaluation of ore phosphate rocks in order to separate high-silica pebbles prior to deep beneficiation. This is achieved by monitoring relative emission line intensities from key probe elements via single laser ablation shots: the ratio of the phosphorous to silica line intensities (P/Si ratio) provides a simple and reliable indicator of ore rock quality. This is a unique LIBS application where no other current analytical spectroscopic method (ICP or XRF) can be applied. Method development is discussed, and results with actual ore samples are presented.},
author = {Asimellis, G and Giannoudakos, A and Kompitsas, M},
doi = {10.1016/j.sab.2006.10.011},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {laser induced breakdown spectroscopy,phosphate mine beneficiation,phosphorus detection},
number = {12},
pages = {1253--1259},
title = {{Phosphate ore beneficiation via determination of phosphorus-to-silica ratios by Laser Induced Breakdown Spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854706002928},
volume = {61},
year = {2006}
}
@article{Ruiz2010,
abstract = {The application of laser-induced breakdown spectroscopy (LIBS) for online analysis of novel Zn based alloy coatings during continuous production of galvannealed steel has been demonstrated. Field trials were carried out at the ThyssenKrupp Steel (TKS) pilot plant in Dortmund, Germany. For this purpose, a portable LIBS demonstrator was constructed and evaluated, based on a dual-pulse Q-switched Nd:YAG laser, operated at 1064 nm. This system was used to generate plasmas on the moving sample surface after the annealing process, in order to control on-line the thickness of Mg on electrolytically galvanized steel. For variable Mg thicknesses (depending on strip speed of the pilot line, 100-1200 nm), and for steel sheets with a predetermined and constant Zn thickness (of 2 or 9 $\mu$m), a satisfactory agreement between plant LIBS measurements and data from laboratory chemical analysis (dissolution of the metallic coating and subsequent inductively coupled plasma-optical emission spectroscopy (ICP-OES) analysis) of Mg coating thicknesses has been obtained. The effects of environmental conditions on field measurements (strip temperature, mechanical vibrations, moisture on surface, etc.) have been demonstrated to be negligible, whereas minimal damage (crater diameters less than 150 $\mu$m) to the sample surface was caused.},
author = {Ruiz, Javier and Gonz{\'{a}}lez, Alina and Cabal{\'{\i}}n, Luisa Mar{\'{\i}}a and Laserna, Jos{\'{e}} Javier},
institution = {Department of Applied Physics I, Faculty of Sciences, University of M{\'{a}}laga, E-29071 M{\'{a}}laga, Spain.},
journal = {Applied Spectroscopy},
number = {12},
pages = {1342--1349},
pmid = {21144151},
title = {{On-line laser-induced breakdown spectroscopy determination of magnesium coating thickness on electrolytically galvanized steel in motion.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21144151},
volume = {64},
year = {2010}
}
@article{Gautier2004,
abstract = {Single- and double-pulse laser-induced breakdown spectroscopy (LIBS) was applied on aluminum samples at atmospheric pressure in air. In the case of the double-pulse scheme, experiments were carried out with an ablation laser emitting at 532 nm and a reheating laser emitting at 1064 nm in an orthogonal beam geometry. With the use of a 1-m focal length monochromator and an echelle spectrometer both equipped with an intensified charge coupled device (ICCD), the studies on the effect of the delay between the two laser pulses displayed optimum enhancements of line emissions only at 200 ns in the reheating scheme developed here. The experimental parameters, like the signal acquisition delay, were largely studied. The line intensity enhancements were also investigated in dependence on physical parameters, such as the excitation energy levels of the lines observed. Moreover, the relative importance of ionic and neutral lines in the emission spectra was precisely characterized. From the different investigations, the behaviors of the line emissions towards the double-pulse technique were related to their excitation energy levels. A correlation between the increases in intensity and the excitation energy levels of the line emissions was highlighted. As a result, the reheating scheme showed improvements of sensitivity for elements emitting ionic lines compared with the corresponding single-pulse experiments.},
author = {Gautier, C{\'{e}}line and Fichet, Pascal and Menut, Denis and Lacour, Jean-Luc and L'Hermite, Daniel and Dubessy, Jean},
doi = {10.1016/j.sab.2004.05.002},
isbn = {3316908773},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {aluminum,double pulse,echelle spectrometer,laser induced breakdown spectroscopy,libs},
number = {7},
pages = {975--986},
title = {{Study of the double-pulse setup with an orthogonal beam geometry for laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854704001193},
volume = {59},
year = {2004}
}
@article{Moon2009,
abstract = {This paper illustrates the application of the well-known approach of duplicating the emission from a plasma by placing a spherical mirror behind it in order to characterize the degree of self-absorption of atomic transitions. It is shown that this simple expedient provides a quick check for the existence of optically thick plasma conditions, and allows one to follow the temporal evolution of the plasma optical depth from the early decay of the continuum emission to the end of the plasma lifetime. The method is applied to a plasma induced at atmospheric pressure by focusing an Nd:YAG laser on different Al-alloy targets. Moreover, if the resolution of the monochromator allows one to obtain the true physical profiles of the lines investigated, a self-absorption correction factor can be calculated, following a methodology described in the plasma diagnostic literature. It is shown that this correction can be used to improve the linearity of calibration curves and to identify outliers in the Saha-Boltzmann plot for temperature evaluation. The data obtained are still the result of line-of-sight measurements, and therefore can only be interpreted in terms of some space-averaged values of the parameters evaluated. Despite this limitation, it is argued that the simple addition of a mirror to a laser induced plasma emission experiment has many advantageous features and should find a more widespread use when performing laser induced breakdown spectroscopy experiments.},
author = {Moon, Heh-Young and Herrera, Kathleen K and Omenetto, Nicol{\'{o}} and Smith, Benjamin W and Winefordner, J D},
doi = {10.1016/j.sab.2009.06.011},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {7},
pages = {702--713},
publisher = {Elsevier B.V.},
title = {{On the usefulness of a duplicating mirror to evaluate self-absorption effects in laser induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709001694},
volume = {64},
year = {2009}
}
@book{Bachor2004,
abstract = {Laser induced breakdown spectroscopy (LIBS) has been evaluated for the determination of micronutrients (B, Cu, Fe, Mn and Zn) in pellets of plant materials, using NIST, BCR and GBW biological certified reference materials for analytical calibration. Pellets of approximately 2 mm thick and 15 mm diameter were prepared by transferring 0.5 g of powdered material to a 15 mm die set and applying 8.0 tons cm- 2. An experimental setup was designed by using a Nd:YAG laser operating at 1064 nm (200 mJ per pulse, 10 Hz) and an Echelle spectrometer with ICCD detector. Repeatability precision varied from 4 to 30{\%} from measurements obtained in 10 different positions (8 laser shots per test portion) in the same sample pellet. Limits of detection were appropriate for routine analysis of plant materials and were 2.2 mg kg- 1 B, 3.0 mg kg- 1 Cu, 3.6 mg kg- 1 Fe, 1.8 mg kg- 1 Mn and 1.2 mg kg- 1 Zn. Analysis of different plant samples were carried out by LIBS and results were compared with those obtained by ICP OES after wet acid decomposition.},
author = {Bachor, Hans-A and Ralph, Timothy C},
booktitle = {WileyVCH},
editor = {Textbook, Physics},
institution = {University of Minnesota},
issn = {05848547},
number = {5},
pages = {434},
publisher = {Wiley-VCH},
title = {{A Guide to Experiments in Quantum Optics}},
url = {http://www.amazon.com/Guide-Experiments-Quantum-Optics/dp/3527403930},
volume = {64},
year = {2004}
}
@article{Lazic2001,
abstract = {Application of laser induced breakdown spectroscopy (LIBS) in the quantitative analysis of elemental composition of soils with different origins and Antarctic marine sediments has been considered. The analytical method followed includes the usual plasma modeling at local thermal equilibrium (LTE) based on average temperature and electron density values, as well as spectra normalization, introduced in order to reduce the effects related both to the substrate optical and thermal properties and to the influence of laser parameters on quantitative data. The computational algorithm takes into account only atomic species and their first ionization states, which is sufficient at the plasma temperature measured in the experiments. Calibration curves are finally generated for each element of interest measured on certified samples with different provenience and matrix composition. In this paper a model is developed which takes into account the effects responsible for non-linearities in the relationship between line intensity and elemental concentration. The model properly includes line re-absorption and contributions from space regions with different plasma densities. Its application permits us to obtain the correlation coefficients between the LIBS measured and certified concentration of each element analyzed. These coefficients, specific for a given experimental layout and atomic lines data base, are successively applied in analytical LIBS measurements allowing for the direct determination of a single element concentration in any sample, regardless of its unknown matrix composition. The LIBS method presented here was tested on a priori unknown samples, and gave uncertainties in concentration varying from 15 to 40{\%} over a large concentration range covering several orders of magnitude. The measuring error depends on element type, on the concentration value and also on the number of certified samples used for the initial calibration. The present results are already significant for some field application, such as on-board marine sediment analysis where a significant matrix variation with layer depth is common.},
author = {Lazic, V and Barbini, R and Colao, F and Fantoni, R and Palucci, A},
doi = {10.1016/S0584-8547(01)00211-7},
isbn = {3906940055},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {concentration,libs,self absorption,soil},
number = {6},
pages = {807--820},
publisher = {Elsevier Science},
title = {{Self-absorption model in quantitative laser induced breakdown spectroscopy measurements on soils and sediments}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701002117},
volume = {56},
year = {2001}
}
@article{Shehada2000,
abstract = {The development of a new laser-induced fluorescence (LIF) spectroscopy technique for the measurement of the attenuation spectrum of tissue is described. The technique, termed laser induced fluorescence attenuation spectroscopy (LIFAS), has been applied to study the effects of hypoxia on the in vivo optical properties of renal and myocardial tissue in the 350-600-nm band. Excimer laser (Xe-Cl) is used to excite a small volume of the tissue (rabbit model, N=20) and induce autofluorescence. The emitted LIF is monitored fiber optically at two locations that are unevenly displaced about the fluorescing volume. The optical attenuation of the tissue is calculated from the dual LIF measurements by assuming an exponential decay of the fluorescence with distance. The results indicate that hypoxia modulates the attenuation spectrum leading to characteristic changes in its shape. Primarily, the spectral profile becomes more concave between 455 nm and 505 nm and two spectral peaks at about 540 and 580 nm disappear leaving in their place a single peak at about 555 nm. The attenuation spectra of normoxic and hypoxic tissue are used to train partial least squares multivariate model for spectral classification. The model detected acute renal and myocardial hypoxia with an accuracy greater than 90{\%} (range: 90{\%}-96{\%}) and 74{\%} (range: 74{\%}-90{\%}), respectively.},
author = {Shehada, R E N and Marmarelis, V Z and Mansour, H N and Grundfest, W S},
doi = {10.1109/10.827290},
file = {::},
institution = {Department of Biomedical Engineering, University of Southern California, Los Angeles, USA. shehada@usc.edu},
issn = {00189294},
journal = {IEEE Transactions on Biomedical Engineering},
keywords = {animals,anoxia,anoxia diagnosis,cell hypoxia,female,fluorescence,fluorescence methods,hyperoxia,hyperoxia diagnosis,kidney,kidney chemistry,kidney metabolism,lasers,lasers diagnostic use,male,myocardial ischemia,myocardial ischemia diagnosis,myocardium,myocardium chemistry,myocardium metabolism,optics photonics,oxygen,oxygen metabolism,predictive value tests,rabbits,spectrometry},
number = {3},
pages = {301--312},
pmid = {10743771},
title = {{Laser induced fluorescence attenuation spectroscopy: detection of hypoxia.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10743771},
volume = {47},
year = {2000}
}
@article{Harmon2006,
abstract = {Laser induced breakdown spectroscopy (LIBS) is a simple spark spectrochemical sensor technology in which a laser beam is directed at a sample surface to create a high-temperature microplasma and a detector used to collect the spectrum of light emission and record its intensity at specific wavelengths. LIBS is an emerging chemical sensor technology undergoing rapid advancement in instrumentation capability and in areas of application. Attributes of a LIBS sensor system include: (i) small size and weight; (ii) technologically mature, inherently rugged, and affordable components; (iii) real-time response; (iv) in situ analysis with no sample preparation required; (v) a high sensitivity to low atomic weight elements which are difficult to determine by other field-portable sensor techniques, and (vi) point sensing or standoff detection. Recent developments in broadband LIBS provide the capability for detection at very high resolution (0.1 nm) of all elements in any unknown target material because all chemical elements emit in the 200-980 nm spectral region. This progress portends a unique potential for the development of a rugged and reliable field-portable chemical sensor that has the potential to be utilized in variety of geochemical, mineralogical, and environmental applications.},
author = {Harmon, R and Delucia, F and Mcmanus, C and Mcmillan, N and Jenkins, T and Walsh, M and Miziolek, A},
doi = {10.1016/j.apgeochem.2006.02.003},
issn = {08832927},
journal = {Applied Geochemistry},
number = {5},
pages = {730--747},
title = {{Laser-induced breakdown spectroscopy – An emerging chemical sensor technology for real-time field-portable, geochemical, mineralogical, and environmental applications}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0883292706000424},
volume = {21},
year = {2006}
}
@article{Gronlund2005,
abstract = {We report, for what we believe to be the first time, on remote imaging laser-induced breakdown spectroscopy (LIBS). Measurements have been performed by using a tripled Nd:YAG laser working at 355 nm with 170 mJ pulse energy, with an expanded beam that is focused onto a target at 60 m distance. The LIBS signal is detected by using an on-axis Newtonian telescope and an optical multichannel analyzer. The imaging is performed by scanning the laser beam on the target. The same setup is also used in demonstrations of remote laser ablation for cleaning of contaminated objects with applications toward cultural heritage.},
author = {Gr{\"{o}}nlund, Rasmus and Lundqvist, Mats and Svanberg, Sune},
institution = {Atomic Physics Division, Lund Institute of Technology, P.O. Box 118, S-221 00 Lund, Sweden.},
journal = {Optics Letters},
number = {21},
pages = {2882--2884},
pmid = {16279457},
title = {{Remote imaging laser-induced breakdown spectroscopy and remote cultural heritage ablative cleaning.}},
volume = {30},
year = {2005}
}
@article{Silva2000,
abstract = {Two laser-based analytical techniques, Laser Induced Breakdown Spectroscopy (LIBS) and Raman microscopy, have been used for the identification of pigments on a polychrome from the Rococo period. Detailed spectral data are presented from analyses performed on a fragment of a gilded altarpiece from the church of Escatro´n, Zaragoza, Spain. LIBS measurements yielded elemental analytical data which suggest the presence of certain pigments and, in addition, provide information on the stratigraphy of the paint layers. Identification of most pigments and of the materials used in the preparation layer was performed by Raman microscopy. q2000 Elsevier Science B.V. All rights reserved.},
author = {Silva, D and Stratoudaki, T and Anglos, D and Burgio, L},
journal = {Journal of Molecular Structure},
keywords = {laser induced breakdown spectroscopy,pigments,polychromes on wood,raman microscopy,spanish cultural heritage},
pages = {191--198},
title = {{Analysis of pigments in polychromes by use of laser induced breakdown spectroscopy and Raman microscopy ଝ}},
volume = {551},
year = {2000}
}
@article{Aydin2008a,
abstract = {The aim of this work is to provide a procedure to determine time-resolved electron temperatures with minimized relative errors by the Boltzmann plot method. The applied procedure consists of two parts, a systematic theoretical spectral line selection and an iterative Boltzmann plot algorithm. After a pre-selection of an appropriate non-disturbed or overlapped set of spectral lines of a particular atomic or ionic species Boltzmann plots are generated using experimentally recorded data for every time window and laser pulse energy of interest. Spectral lines with the highest average deviations from the regression function are assumed as being not representative for the considered ensemble of spectral lines and are therefore discarded gradually until a threshold value for the coefficient of determination is exceeded. Laser-induced breakdown spectroscopy (LIBS) is applied for time-resolved and spatially integrated investigations of plasmas on 1.1750 C75 steel alloy samples with laser pulse energies ranging between 200 $\mu$J and 2 mJ. For the specific chemical composition ofthese samples a selection of atomic and ionic Fe spectral lines has been carried out. In spite of the fact that onlylaser pulse energies in the low millijoule regime are applied the final sets of spectral lines comprise in total 61Fe I and 12 Fe II emission lines. By applying this method electron temperatures can be determined withaveraged relative errors of down to 1.8{\%} for Fe I and 4.4{\%} for Fe II emission lines.},
author = {Aydin, {\"{U}}mit and Roth, Peter and Gehlen, Christoph Dominic and Noll, Reinhard},
chapter = {1060},
doi = {10.1016/j.sab.2008.08.003},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1060--1065},
publisher = {Elsevier B.V.},
title = {{Spectral line selection for time-resolved investigations of laser-induced plasmas by an iterative Boltzmann plot method}},
url = {http://www.sciencedirect.com/science/article/B6THN-4T8SM0P-1/2/44f49ac3e856df67f14460ba6ae2667b},
volume = {63},
year = {2008}
}
@article{Yueh2009,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is an on-line, real-time technology that can produce immediate information about the elemental contents of tissue samples. We have previously shown that LIBS may be used to distinguish cancerous from non-cancerous tissue. In this work, we study LIBS spectra produced from chicken brain, lung, spleen, liver, kidney and skeletal muscle. Different data processing techniques were used to study if the information contained in these LIBS spectra is able to differentiate between different types of tissue samples and then identify unknown tissues. We have demonstrated a clear distinguishing between each of the known tissue types with only 21 selected analyte lines from each observed LIBS spectrum. We found that in order to produce an analytical model to work well with new sample we need to have representative training data to cover a wide range of spectral variation due to experimental or environmental changes.},
author = {Yueh, Fang-Yu and Zheng, Hongbo and Singh, Jagdish P and Burgess, Shane},
doi = {10.1016/j.sab.2009.07.025},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1059--1067},
publisher = {Elsevier B.V.},
title = {{Preliminary evaluation of laser-induced breakdown spectroscopy for tissue classification}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709002237},
volume = {64},
year = {2009}
}
@article{Rai2001,
abstract = {In the present work we demonstrate a fiber-optic laser-induced breakdown spectroscopy (FO LIBS) system for delivering laser energy to a sample surface to produce a spark as well as to collect the resulting radiation from the laser-induced spark. In order to improve the signal/background (S/B) ratio, various experimental parameters, such as laser energy, gate delay and width, detector gain, lenses of different focal lengths and sample surface, were tested. In order to provide high reliability and repeatability in the analysis, we also measured plasma parameters, such as electron density and plasma temperature, and determined their influence on the measurement results. The performance of FO LIBS was also compared with that of a LIBS system that does not use a fiber to transmit the laser beam. LIBS spectra with a good S/B were recorded at 2-mus gate delay and width. LIBS spectra of six different Al alloy samples were recorded to obtain calibration data. We were able to obtain linear calibration data for numerous elements (Cr, Zn, Fe, Ni, Mn, Mg and Cu). A linear calibration curve for LIBS intensity ratio vs. concentration ratio reduces the effect of physical variables (i.e. shot-to-shot power fluctuation, sample-to-surface distance, and physical properties of the samples). Our results reveal that this system may be useful in designing a high-temperature LIBS probe for measuring the elemental composition of Al melt.},
author = {Rai, A},
doi = {10.1016/S0584-8547(01)00299-3},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {aluminum alloys,calibration,fiber optic,laser induced breakdown spectroscopy},
number = {12},
pages = {2371--2383},
publisher = {Elsevier B.V.},
title = {{Parametric study of a fiber-optic laser-induced breakdown spectroscopy probe for analysis of aluminum alloys}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701002993},
volume = {56},
year = {2001}
}
@article{Senesi2009,
abstract = {Soil is unanimously considered as one of the most important sink of heavy metals released by human activities. Heavy metal analysis of natural and polluted soils is generally conducted by the use of atomic absorption spectroscopy (AAS) or inductively coupled plasma optical emission spectroscopy (ICP-OES) on adequately obtained soil extracts. Although in recent years the emergent technique of laser-induced breakdown spectroscopy (LIBS) has been applied widely and with increasing success for the qualitative and quantitative analyses of a number of heavy metals in soil matrices with relevant simplification of the conventional methodologies, the technique still requires further confirmation before it can be applied fully successfully in soil analyses. The main objective of this work was to demonstrate that new developments in LIBS technique are able to provide reliable qualitative and quantitative analytical evaluation of several heavy metals in soils, with special focus on the element chromium (Cr), and with reference to the concentrations measured by conventional ICP spectroscopy. The preliminary qualitative LIBS analysis of five soil samples and one sewage sludge sample has allowed the detection of a number of elements including Al, Ca, Cr, Cu, Fe, Mg, Mn, Pb, Si, Ti, V and Zn. Of these, a quantitative analysis was also possible for the elements Cr, Cu, Pb, V and Zn based on the obtained linearity of the calibration curves constructed for each heavy metal, i.e., the proportionality between the intensity of the LIBS emission peaks and the concentration of each heavy metal in the sample measured by ICP. In particular, a triplet of emission lines for Cr could be used for its quantitative measurement. The consistency of experiments made on various samples was supported by the same characteristics of the laser-induced plasma (LIP), i.e., the typical linear distribution confirming the existence of local thermodynamic equilibrium (LTE) condition, and similar excitation temperatures and comparable electron number density measured for all samples. An index of the anthropogenic contribution of Cr in polluted soils was calculated in comparison to a non-polluted reference soil. Thus, the intensity ratios of the emission lines of heavy metal can be used to detect in few minutes the polluted areas for which a more detailed sampling and analysis can be useful.},
author = {Senesi, G S and Dell'Aglio, M and Gaudiuso, R and {De Giacomo}, A and Zaccone, C and {De Pascale}, O and Miano, T M and Capitelli, M},
institution = {IMIP-CNR-Bari, Via Amendola 122/D, Bari 70126, Italy. giorgio.senesi@ba.imip.cnr.it},
journal = {Environmental Research},
number = {4},
pages = {413--420},
pmid = {19272593},
publisher = {Elsevier B. V.},
title = {{Heavy metal concentrations in soils as determined by laser-induced breakdown spectroscopy (LIBS), with special emphasis on chromium.}},
url = {http://www.sciencedirect.com/science/article/B6WDS-4VT17V0-3/2/87631f0ca1725bd8b8f4fed7372dece5},
volume = {109},
year = {2009}
}
@article{Bukin2009,
abstract = {Abstract Optical breakdown spectra on seawater and distilled water faces excited by Ti-sapphire laser pulses with durations of 50 fs and 650 fs were studied experimentally in normal atmosphere. The time dependence of the intensity of the Na I (588.9 nm) and Mg II (279.5 nm) emission lines was studied, and the limit of detection of Na in an aqueous NaCl solution was established at 106 g/l.},
author = {Bukin, O A and Golik, S S and Il’in, A A and Kul’chin, Yu N and Sokolova, E B and Baulo, E N},
doi = {10.1134/S1024856009020122},
issn = {10248560},
journal = {Atmospheric and Oceanic Optics},
number = {2},
pages = {209--213},
title = {{Laser-induced breakdown spectroscopy of liquid media with femtosecond laser excitation}},
url = {http://dx.doi.org/10.1134/S1024856009020122},
volume = {22},
year = {2009}
}
@article{Gomez2006,
abstract = {The present article focuses on a comparison between cleaning process of graffitis on urban buildings by using laser radiation at 308爊m (XeCl excimer laser) and 1064爊m (Nd:YAG laser). Laser-induced breakdown spectroscopy (LIBS) elemental analysis was applied as real-time diagnostic technique, safeguarding against possible damage of the substrate during ablation rate studies. The morphological analysis of the etched surfaces by optical microscopy and environmental scanning electron microscopy reveals remarkable features of interest to understand the wavelength dependence of the ablation efficiency. The ablation threshold fluences of different paints sprayed on several substrates were determined applying a photoacoustic technique. To remove graffitis from urban buildings the laser radiation at 1064爊m was observed to be the most efficient wavelength, supporting the best result.},
author = {Gomez, C and Costela, A and Garciamoreno, I and Sastre, R},
doi = {10.1016/j.apsusc.2005.04.051},
issn = {01694332},
journal = {Applied Surface Science},
keywords = {excimer,graffitis,laser cleaning,laser induced breakdown spectroscopy,nd,photoacoustic technique,yag},
number = {8},
pages = {2782--2793},
title = {{Comparative study between IR and UV laser radiation applied to the removal of graffitis on urban buildings}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169433205008172},
volume = {252},
year = {2006}
}
@article{Garcia2000,
abstract = {The combination of angle-resolved laser ablation with the use of a collimated beam is presented as a new approach to increase the depth-resolved capabilities of laser-induced breakdown spectrometry (LIBS). The effect of beam conditioning and the reduction of the effective sampling depth due to the angular dependence of laser ablation allow ablation rates lower than 2 nm/pulse for coated materials (Sn-coated steels and Cr-coated samples). Spectral information is obtained on a single-laser-shot basis. The effect of incidence angle has been examined from differentiated emission profiles, demonstrating the beneficial effect of working at incidence different from normal. A compromise between depth resolution and emission signal must be found at large angles due to the lower irradiance resulting from the increase in beam size at the interface for large angles of incidence. A comparison of the proposed approach with the analysis provided by a commercial glow-discharge device glow discharge optical emission spectroscopy (GD-OES) demonstrated quite satisfactory results.},
author = {Garc{\'{\i}}a, C C and Corral, M and Vadillo, J M and Laserna, J J},
doi = {10.1366/0003702001950526},
journal = {Applied Spectroscopy},
pages = {1027--1031},
title = {{Angle-Resolved Laser-Induced Breakdown Spectrometry for Depth Profiling of Coated Materials}},
url = {http://www.ingentaconnect.com/content/sas/sas/2000/00000054/00000007/art00016},
volume = {54},
year = {2000}
}
@article{Mielke2003,
abstract = {Knowledge of the three-dimensional structure of proteins is integral to understanding their functions, and a necessity in the era of proteomics. A wide range of computational methods is employed to estimate the secondary, tertiary, and quaternary structures of proteins. Comprehensive experimental methods, on the other hand, are limited to nuclear magnetic resonance (NMR) and X-ray crystallography. The full characterization of individual structures, using either of these techniques, is extremely time intensive. The demands of high throughput proteomics necessitate the development of new, faster experimental methods for providing structural information. As a first step toward such a method, we explore the possibility of determining the structural classes of proteins directly from their NMR spectra, prior to resonance assignment, using averaged chemical shifts. This is achieved by correlating NMR-based information with empirical structure-based information available in widely used electronic databases. The results are analyzed statistically for their significance. The robustness of the method as a structure predictor is probed by applying it to a set of proteins of unknown structure. Our results show that this NMR-based method can be used as a low-resolution tool for protein structural class identification.},
author = {Mielke, S P and Krishnan, V V},
institution = {Biophysics Graduate Group, University of California, Davis, CA 95616, USA.},
journal = {Bioinformatics},
number = {16},
pages = {2054--2064},
pmid = {14594710},
title = {{Protein structural class identification directly from NMR spectra using averaged chemical shifts.}},
url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/16/2054},
volume = {19},
year = {2003}
}
@article{Yaroshchyk2004a,
abstract = {Optimal conditions are determined for laser-induced breakdown spectroscopy in liquid jets by investigating laser de-focusing and laser energy variation in aqueous liquid jets containing dilute levels of calcium chloride. It has been found that the atomic emission shows a strong correlation with both laser pulse energy and focal position. The data cannot be rationalized on the basis of electron density or ionization temperature changes alone, but rather it requires the additional consideration of the volume of the liquid sample interacting with the laser and that portion of the volume which is above the threshold energy for plasma formation. A moving breakdown model has been applied to the plasma formation in the jet to calculate the amount of sample ablated with sufficient energy for plasma formation, which models well the observed results and allows prediction of optimal focusing conditions for a given laser energy.},
author = {Yaroshchyk, Pavel and Morrison, Richard J S and Body, Doug and Chadwick, Bruce L},
doi = {10.1366/0003702042475592},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {11},
pages = {1353--1359},
pmid = {18070410},
publisher = {OSA},
title = {{Theoretical Modeling of Optimal Focusing Conditions Using Laser-Induced Breakdown Spectroscopy in Liquid Jets}},
url = {http://as.osa.org/abstract.cfm?URI=as-58-11-1353},
volume = {58},
year = {2004}
}
@article{Pallikaris1998,
abstract = {BACKGROUND: Corneal hydration is an important factor in laser corneal ablation. In photorefractive keratectomy (PRK), corneal ablation rate and final ablation surface quality are strongly dependent on corneal hydration. We used a spectroscopic technique for monitoring corneal hydration during PRK. METHODS: Hydroxyethlymethacrylate (HEMA) was employed for corneal hydration modeling. Hydrated HEMA samples were irradiated with a pulsed Nd:YAG laser (1064 nm, 10 mJ/pulse, pulse duration 15 nsec). Successive emission spectra corresponding to different degrees of hydration were recorded on a gated optical multichannel analyzer. The weight of the sample and hence its water content was monitored during the entire procedure with a sensitive balance. One rabbit and one human cornea were used to demonstrate the spectral analogy between the model and corneal tissue. RESULTS: The most noticeable dependence on water content of the substrate was that of atomic emission lines of Ca at 393 nm and 396 nm. CONCLUSION: Plasma emission spectra exhibited significant dependence on sample hydration. This dependence can be used for estimation of water content of irradiated model material and real cornea.},
author = {Pallikaris, I G and Ginis, H S and Kounis, G A and Anglos, D and Papazoglou, T G and Naoumidis, L P},
institution = {University of Crete, School of Health Sciences, Department of Ophthalmology, Heraklion, Greece. pallikar@med.uch.gr},
journal = {Journal of refractive surgery Thorofare NJ 1995},
keywords = {absorption,anatomic,animals,body water,cornea,excimer,humans,intraoperative,lasers,methacrylates,models,monitoring,photorefractive keratectomy,rabbits,spectrum analysis},
number = {6},
pages = {655--660},
pmid = {9866108},
title = {{Corneal hydration monitored by laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9866108},
volume = {14},
year = {1998}
}
@article{Casavola2003,
abstract = {We present a theoretical approach to interpreting optical emission spectroscopy measurements for nonequilibrium conditions. In this approach both the fluid dynamics and the kinetics of laser-induced plasma are taken into account, and the results obtained by the numerical model are applied to the spectroscopic observation of the plasma induced by the interaction between a KrF laser and a metallic Ti target. We have generalized the theoretical method to calculate the initial conditions for the plume expansion that show the best agreement with experimental results.},
author = {Casavola, Anna Rita and Colonna, Gianpiero and {De Giacomo}, Alessandro and {De Pascale}, Olga and Capitelli, Mario},
institution = {Department of Chemistry, University of Bari, 70126 Bari, Italy. casavola@chimica.uniba.it},
issn = {0003-6935},
journal = {Applied optics},
month = {oct},
number = {30},
pages = {5963--70},
pmid = {14594052},
title = {{Experimental and theoretical investigation of laser-induced plasma of a titanium target.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594052},
volume = {42},
year = {2003}
}
@article{Rehse2009,
abstract = {Nanosecond single-pulse laser-induced breakdown spectroscopy LIBS has been used to discriminate between two different genera of Gram-negative bacteria and between several strains of the Escherichia coli bacterium based on the relative concentration of trace inorganic elements in the bacteria. Of particular importance in all such studies to date has been the role of divalent cations, specifically Ca2+ and Mg2+, which are present in the membranes of Gram-negative bacteria and act to aggregate the highly polar lipopolysaccharide molecules. We have demonstrated that the source of emission from Ca and Mg atoms observed in LIBS plasmas from bacteria is at least partially located at the outer membrane by intentionally altering membrane biochemistry and correlating these changes with the observed changes in the LIBS spectra. The definitive assignment of some fraction of the LIBS emission to the outer membrane composition establishes a potential serological, or surface-antigen, basis for the laser-based identification. E. coli and Pseudomonas aeruginosa were cultured in three nutrient media: trypticase soy agar as a control, a MacConkey agar with a 0.01{\%} concentration of bile salts including sodium deoxycholate, and a trypticase soy agar with a 0.4{\%} deoxycholate concentration. The higher concentration of deoxycholate is known to disrupt bacterial outer membrane integrity and was expected to induce changes in the observed LIBS spectra. Altered LIBS emission was observed for bacteria cultured in this 0.4{\%} medium and laser ablated in an all-argon environment. These spectra evidenced a reduced calcium emission and in the case of one species, a reduced magnesium emission. Culturing on the lower 0.01{\%} concentration of bile salts altered the LIBS spectra for both the P. aeruginosa and two strains of E. coli in a highly reproducible way, although not nearly as significantly as culturing in the higher concentration of deoxycholate did. This was possibly due to the accumulation of divalent cations around the bacteria by the formation of an extracellular polysaccharide capsule. Lastly, a discriminant function analysis demonstrated that in spite of alterations in the LIBS spectrum induced by growth in the three different media, the analysis could correctly identify all samples better than 90{\%} of the time. This encouraging result illustrates the potential utility of LIBS as a rapid bacteriological identification technology. © 2009 American Institute of Physics},
author = {Rehse, Steven J. and Jeyasingham, Narmatha and Diedrich, Jonathan and Palchaudhuri, Sunil},
doi = {10.1063/1.3116141},
issn = {00218979},
journal = {Journal of Applied Physics},
number = {10},
pages = {102034},
title = {{A membrane basis for bacterial identification and discrimination using laser-induced breakdown spectroscopy}},
url = {http://link.aip.org/link/JAPIAU/v105/i10/p102034/s1{\&}Agg=doi},
volume = {105},
year = {2009}
}
@article{Alonso-Medina2010,
abstract = {In this paper, we present transition probabilities for 97 spectral lines of Sn I, corresponding to transitions n (n = 6,7,8)s 5p(2), n(n = 5,6,7)d 5p(2), 5p(3) 5p(2), n(n = 7)p 6s, determined by measuring the intensities of the emission lines of a Laser-induced breakdown (emission) spectrometry (LIBS). The optical emission spectroscopy from a laser-induced plasma generated by a 10 640 angstrom radiation, with an irradiance of 1.4 x 10(10) Wcm(-2) on an Sn-Pb alloy (an Sn content of approximately 20{\%}), in vacuum, was recorded at 0.8 mu s, and analysed between 1900 and 7000 angstrom. The population-level distribution and corresponding temperature were obtained using Boltzmann plots. The electron density of the plasma was determined using well-known Stark broadening parameters of spectral lines. The plasma under study had an electron temperature of 13,200 K and an electron number density of 2 x 10(16) cm(-3). The experimental relative transition probabilities were put on an absolute scale using the branching ratio method to calculate Sn I multiplet transition probabilities from available radiative lifetime data of their upper states and plotting the Sn I emission spectrum lines on a Boltzmann plot assuming local thermodynamic equilibrium (LTE) to be valid and following Boltzmann's law. The LTE conditions and plasma homogeneity have been checked. Special attention was paid to the possible self-absorption of the different transitions. The experimental results obtained have been compared with the experimental values given by other authors. (C) 2010 Elsevier B.V. All rights reserved.},
author = {Alonso-Medina, A},
doi = {10.1016/j.sab.2010.01.002},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {2},
pages = {158--166},
title = {{A spectroscopic study of laser-induced tin-lead plasma: Transition probabilities for spectral lines of Sn I}},
url = {http://www.sciencedirect.com/science/article/B6THN-4Y70C5N-2/2/1850f3c6090989ba6335857e8234050b},
volume = {65},
year = {2010}
}
@article{Lundin2011,
abstract = {We present optical methods at a wide range of wavelengths for remote classification of birds. The proposed methods include eye-safe fluorescence and depolarization lidar techniques, passive scattering spectroscopy, and infrared (IR) spectroscopy. In this paper we refine our previously presented method of remotely classifying birds with the help of laser-induced $\beta$-keratin fluorescence. Phenomena of excitation quenching are studied in the laboratory and are theoretically discussed in detail. It is shown how the ordered microstructures in bird feathers induce structural "colors" in the IR region with wavelengths of around 3-6 $\mu$m. We show that transmittance in this region depends on the angle of incidence of the transmitted light in a species-specific way and that the transmittance exhibits a close correlation to the spatial periodicity in the arrangement of the feather barbules. We present a method by which the microstructure of feathers can be monitored in a remote fashion by utilization of thermal radiation and the wing beating of the bird.},
author = {Lundin, Patrik and Samuelsson, Per and Svanberg, Sune and Runemark, Anna and {\AA}kesson, Susanne and Brydegaard, Mikkel},
doi = {10.1364/AO.50.003396},
institution = {Atomic Physics Division, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden. patrik.lundin@fysik.lth.se},
journal = {Applied Optics},
number = {20},
pages = {3396--3411},
pmid = {21743546},
title = {{Remote nocturnal bird classification by spectroscopy in extended wavelength ranges.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21743546},
volume = {50},
year = {2011}
}
@article{Schade2006,
abstract = {Laser-induced breakdown spectroscopy (LIBS) in combination with a conventional mine prodder is applied for remote detection of explosives and mine housing materials. High power subnanosecond laser pulses (pulse power Ep = 0.6 mJ and pulse duration Deltat = 650 ps) at 1064 nm with a typical repetition rate of 10 kHz are generated by using a passively Q-switched Cr4+:Nd3+:YAG microchip-laser as seed-laser for an Yb-fiber amplifier. In the present investigation, the ratios of late and early LIBS intensities for the cyanide (CN) plasma emission at 388 nm and for the C-emission at 248 nm are used for data analysis. This allows the classification of different explosives and mine casing materials under real time conditions and also similar applications to materials processing.},
author = {Schade, Wolfgang and Bohling, Christian and Hohmann, Konrad and Scheel, Dirk},
doi = {10.1017/S0263034606060356},
issn = {02630346},
journal = {Laser and Particle Beams},
keywords = {explosives,fiber laser,laser spectroscopy,libs,mines},
number = {02},
pages = {241--247},
title = {{Laser-induced plasma spectroscopy for mine detection and verification}},
url = {http://www.journals.cambridge.org/abstract{\_}S0263034606060356},
volume = {24},
year = {2006}
}
@article{Bicchieri2001,
abstract = {The most commonly used blue pigments in medieval manuscripts are azurite and lapis-lazuli. The first one is a copper-based pigment; the coloring compound of the latter is lazurite, a sodium silico--aluminate in a sulfur matrix. Knowledge of the chemical composition of the materials is essential for the study of illuminated manuscripts. In this paper, micro-Raman and LIBS have been used for the study of azurite and lapis-lazuli, as well as different mixtures of these pigments applied to parchment to simulate an illuminated manuscript. The results of our work show the importance of using more than one technique for a good comprehension of a manuscript. In particular, the opportunity of combining elemental information (obtained from laser induced breakdown spectroscopy) and vibrational spectroscopy information (obtained from Raman) will be fully exploited.},
author = {Bicchieri, M and Nardone, M and Russo, P A and Sodo, A and Corsi, M and Cristoforetti, G and Palleschi, V and Salvetti, A and Tognoni, E},
doi = {10.1016/S0584-8547(01)00228-2},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {1st international,congress laser induced,cultural heritage,dedicated conference,illuminations,italy,libs,october 2000,paper presented,pigment analysis,pisa,plasma spectroscopy applications,published,raman spectroscopy,special issue,spectrochimica acta part b},
number = {6},
pages = {915--922},
title = {{Characterization of azurite and lazurite based pigments by laser induced breakdown spectroscopy and micro-Raman spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701002282},
volume = {56},
year = {2001}
}
@article{Pereira2010,
abstract = {This study investigated the organic and inorganic constituents of healthy leaves and Candidatus Liberibacter asiaticus (CLas)-inoculated leaves of citrus plants. The bacteria CLas are one of the causal agents of citrus greening (or Huanglongbing) and its effect on citrus leaves was investigated using laser-induced breakdown spectroscopy (LIBS) combined with chemometrics. The information obtained from the LIBS spectra profiles with chemometrics analysis was promising for the construction of predictive models to identify healthy and infected plants. The major, macro- and microconstituents were relevant for differentiation of the sample conditions. The models were then applied to different inoculation times (from 1 to 8 months). The models were effective in the classification of 82-97{\%} of the diseased samples with a 95{\%} significance level. The novelty of this method was in the fingerprinting of healthy and diseased plants based on their organic and inorganic contents.},
author = {Pereira, Fab{\'{\i}}ola Manhas Verbi and Milori, D{\'{e}}bora Marcondes Bastos Pereira and Ven{\^{a}}ncio, Andr{\'{e}} Leonardo and Russo, Mariana De S{\'{a}} Tavares and Martins, Polyana Kelly and Freitas-Ast{\'{u}}a, Juliana},
institution = {Embrapa Instrumenta{\c{c}}{\~{a}}o Agropecu{\'{a}}ria, P.O. Box 741, Zip Code 13561-206, S{\~{a}}o Carlos, SP, Brazil. fmverbi@uol.com.br},
journal = {Talanta},
keywords = {analytical,chemistry techniques,citrus,citrus microbiology,dna,dna metabolism,lasers,light,plant diseases,plant leaves,plant leaves metabolism,plant physiological phenomena,reverse transcriptase polymerase chain reaction,rhizobiaceae,rhizobiaceae metabolism,spectrophotometry,spectrophotometry methods,time factors},
number = {2},
pages = {351--356},
pmid = {21111145},
title = {{Evaluation of the effects of Candidatus Liberibacter asiaticus on inoculated citrus plants using laser-induced breakdown spectroscopy (LIBS) and chemometrics tools.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21111145},
volume = {83},
year = {2010}
}
@article{Cowpe2011,
abstract = {Laser-Induced Breakdown Spectroscopy (LIBS) was applied to the analysis of bio-ceramic samples. The relationship between sample hardness and LIBS plasma properties was investigated, with comparison to conventional Vickers hardness measurements. The plasma excitation temperature Te was determined using the line-to-continuum ratio for the Si (I) 288.16 nm emission line; we have demonstrated a linear relationship between sample surface hardness and plasma temperature. Results indicate that hardness determination based on measurements of Te offers greater reproducibility than Vickers hardness measurements, under the conditions considered here. The validity of spectroscopic diagnostics based on LTE was confirmed.},
author = {Cowpe, JS and Moorehead, RD and Moser, D and Astin, JS and Karthikeyan, S and Kilcoyne, SH and Crofts, G and Pilkington, RD},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {energy},
number = {3-4},
pages = {290--294},
publisher = {Elsevier},
title = {{Hardness determination of bio-ceramics using laser-induced breakdown spectroscopy}},
url = {http://dx.doi.org/10.1016/j.sab.2011.03.007},
volume = {66},
year = {2011}
}
@article{Moros2010,
abstract = {A novel experimental design combining Raman spectroscopy and laser-induced breakdown spectroscopy (LIBS) in a unique integrated sensor is described. The sensor presented herein aims to demonstrate the applicability of a hybrid dual Raman-LIBS system as an analytical tool for the standoff analysis of energetic materials. Frequency-doubled 532 nm Nd:YAG nanosecond laser pulses, first expanded and then focused using a 10x beam expander on targets located at 20 m, allowed simultaneous acquisition of Raman-LIBS spectra for 4-mononitrotoluene (MNT), 2,6-dinitrotoluene (DNT), 2,4,6-trinitrotoluene (TNT), (RDX), C4 and H15 (plastic explosives containing 90{\%} and 75{\%} of RDX by weight, respectively), and Goma2-ECO (Spanish denominated dynamite class high explosive mainly composed of ammonium nitrate, nitroglycol, and dinitrotoluene among other compounds), sodium chlorate, and ammonium nitrate. With the use of a Cassegrain telescope, both Raman and LIBS signals from the same laser pulses were collected and conducted through a bifurcated optical fiber into two identical grating spectrographs coupled to intensified charge-coupled device (iCCD) detectors. With the use of the appropriate timing for each detection mode, adjustment of the laser power on the beam focal conditions is not required. The ability of the present single hybrid sensor to simultaneously acquire, in real time, both molecular and multielemental information from the same laser pulses on the same cross section of the sample at standoff distances greatly enhances the information power of this approach.},
author = {Moros, Javier and Lorenzo, Juan Antonio and Lucena, Patricia and Tobaria, Luciano Miguel and Laserna, Jos{\'{e}} Javier},
institution = {Department of Analytical Chemistry, Faculty of Sciences, University of M{\'{a}}laga, E29071 M{\'{a}}laga, Spain.},
journal = {Analytical Chemistry},
number = {4},
pages = {1389--1400},
pmid = {20085236},
publisher = {American Chemical Society},
title = {{Simultaneous Raman spectroscopy-laser-induced breakdown spectroscopy for instant standoff analysis of explosives using a mobile integrated sensor platform.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20085236},
volume = {82},
year = {2010}
}
@article{Viskup2009,
abstract = {Time-resolved photography was employed to study plasma dynamics and particle ejection of laser-irradiated iron oxide materials. Nano-particle powder, pressed powder pellets and sintered ceramics were ablated in air and Ar gas background by means of short laser pulses (Nd:YAG laser wavelength lambda =4爊m and pulse duration tauL燵approximates; KrF laser lambda =爊m and tauL燵approximatens). Plasma plume dynamics significantly depended on sample morphology. The ejection of non-luminous particles up to several hundreds of microseconds after the laser pulse was observed for powder and pressed powder target materials. Laser-induced breakdown spectroscopy (LIBS) was employed for element analysis of iron oxide powders, pressed pellets and sintered ceramics. LIBS spectra of the different targets were comparable to each other and qualitatively independent of target morphology.},
author = {Viskup, R and Praher, B and Stehrer, T and Jasik, J and Wolfmeir, H and Arenholz, E and Pedarnig, J D and Heitz, J},
doi = {10.1016/j.apsusc.2008.08.092},
issn = {01694332},
journal = {Applied Surface Science},
keywords = {laser induced breakdown spectroscopy,plasma plume photography,pulsed laser ablation},
number = {10},
pages = {5215--5219},
title = {{Plasma plume photography and spectroscopy of Fe—Oxide materials}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S016943320801862X},
volume = {255},
year = {2009}
}
@article{Nasr2011a,
abstract = {Highly toxic contaminants like Cr, As, and Pb were detected in chrome-tanning process of animal skin to produce leather by applying locally developed laser-induced breakdown spectrometer. An Nd-YAG laser with 1,064nm wavelength was focused on the surface of leather samples (natural and manufactured) to generate a plasma spark and spectrally resolved spectra were used for identification and quantification of contaminants. The leather samples were collected from a tannery located in industrial cities of Riyadh and Jeddah, Saudi Arabia. The study was carried out on fully, half manufactured (wet blue leather), and natural hide (skin). To the best of our knowledge, this is the first attempt where laser-induced breakdown spectroscopy (LIBS) technique has been applied for the analysis of leather before and after tanning process. The maximum concentration of different elements of environmental significance like chromium, lead, arsenic, sulfur, magnesium were 199, 289, 31, 38, and 39ppm, respectively, in one of the manufactured leather samples. The limit of detection (LOD) of our LIBS system for chromium, lead, arsenic, sulfur, and magnesium were 2, 3, 1.5,7, and 3ppm, respectively. The safe permissible limit for tanned leather for highly toxic elements like chromium, lead, and arsenic are 1, 0.5, 0.01ppm, respectively, as prescribed in Environmental Regulation Standards for Saudi Industries set by Royal Commission Jubail, Saudi Arabia. The LIBS technique is superior to other conventional techniques like ICP or atomic absorption that a little or no sample preparation is required, no chemicals are needed, multi-elemental analysis is possible for all kinds of samples (natural and anthropogenic materials), microgram of sample is essential, and LIBS could be applied for remote analysis. It is highly selective and sensitivity higher than ICP, and as no sample and chemicals are required, it is cost effective for multi-sample analysis per unit time as compared with other conventional techniques. The concentration of some toxic elements (Cr, Pb, As) is much higher than the safe permissible limits set by Occupational Safety and Health Administration in USA or Saudi environmental regulatory agencies. Results obtained with our LIBS systems were in close agreement with the results obtained using other standard analytical technique such as the inductively coupled plasma atomic emission spectroscopy.},
author = {Nasr, M M and Gondal, Mohammed Asharf and Seddigi, Z S},
institution = {Department of Natural Science, Riyadh College of Dentistry and Pharmacy, Mail Box 84891, Riyadh, 11681, Saudi Arabia.},
journal = {Environmental Monitoring and Assessment},
number = {1-4},
pages = {387--395},
pmid = {20556649},
title = {{Detection of hazardous pollutants in chrome-tanned leather using locally developed laser-induced breakdown spectrometer.}},
url = {http://www.springerlink.com/content/d1m2q25l70235634/},
volume = {175},
year = {2011}
}
@article{Balzer2005,
abstract = {In this study a new method for online analysis of the zinc coating of galvanized sheet steel based on laser-induced breakdown spectroscopy (LIBS) is presented. The coating is characterized with a series of single laser bursts irradiated on the traversing sheet steel, each on a different sheet steel position. To achieve an ablation depth in the range of the coating thickness of about 10 mum a Nd:YAG laser at 1064 nm in collinear double pulse mode was used. The depth information is obtained by control of the ablation depth by adjusting the burst energy using an external electro-optical attenuator. Concepts for the determination of the coating thickness and the chemical composition are presented. The achieved thickness resolution is estimated to about 400 nm for coating thicknesses of electrolytic galvanized sheet steel in the range of 3.2 to 11.2 mum. In the case of hot-dip galvanized sheet steel information about the depth profile of aluminium can be gained by the new method.},
author = {Balzer, H and Hoehne, M and Sturm, V and Noll, R},
doi = {10.1016/j.sab.2005.07.003},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {7-8},
pages = {1172--1178},
title = {{Online coating thickness measurement and depth profiling of zinc coated sheet steel by laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854705002119},
volume = {60},
year = {2005}
}
@article{Singh2011,
abstract = {We review the different spectroscopic techniques including the most recent laser-induced breakdown spectroscopy (LIBS) for the characterization of materials in any phase (solid, liquid or gas) including biological materials. A brief history of the laser and its application in bioscience is presented. The development of LIBS, its working principle and its instrumentation (different parts of the experimental set up) are briefly summarized. The generation of laser-induced plasma and detection of light emitted from this plasma are also discussed. The merit and demerits of LIBS are discussed in comparison with other conventional analytical techniques. The work done using the laser in the biomedical field is also summarized. The analysis of different tissues, mineral analysis in different organs of the human body, characterization of different types of stone formed in the human body, analysis of biological aerosols using the LIBS technique are also summarized. The unique abilities of LIBS including detection of molecular species and calibration-free LIBS are compared with those of other conventional techniques including atomic absorption spectroscopy, inductively coupled plasma atomic emission spectroscopy and mass spectroscopy, and X-ray fluorescence.},
author = {Singh, Vivek Kumar and Rai, Awadhesh Kumar},
doi = {10.1007/s10103-011-0921-2},
file = {::},
issn = {1435-604X},
journal = {Lasers in medical science},
keywords = {Aerosols,Aerosols: analysis,Biocompatible Materials,Biocompatible Materials: analysis,Biocompatible Materials: radiation effects,Calculi,Calculi: chemistry,Humans,Lasers,Lasers, Solid-State,Minerals,Minerals: analysis,Spectrophotometry, Atomic,Spectrophotometry, Atomic: instrumentation,Spectrophotometry, Atomic: methods,Spectrum Analysis,Spectrum Analysis: instrumentation,Spectrum Analysis: methods,Trace Elements,Trace Elements: analysis},
month = {sep},
number = {5},
pages = {673--87},
pmid = {21533560},
title = {{Prospects for laser-induced breakdown spectroscopy for biomedical applications: a review.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21533560},
volume = {26},
year = {2011}
}
@article{Vo-Dinh1997,
abstract = {An optical diagnostic procedure based on laser-induced fluorescence was developed for direct in vivo cancer diagnosis without requiring biopsy. The methodology was applied in a clinical study involving over 100 patients in order to differentiate normal tissue from malignant tumors of the esophagus. Endogenous fluorescence of normal and malignant tissues was measured directly with the use of a fiber-optic probe inserted through an endoscope. The measurements were performed in vivo during routine endoscopy. Detection of the fluorescence signal from the tissue was performed with the use of laser excitation. This report describes the differential normalized fluorescence (DNF) procedure using the amplified spectral differences between the normalized fluorescence of malignant tissue and normal mucosa. The results of this DNF approach were compared with histopathology results of the biopsy samples and indicated excellent agreement in the classification of normal tissue and malignant tumors for the samples investigated. Data related to various grades of Barrett's esophagus are discussed. The DNF procedure could lead to the development of a rapid and cost-effective technique for cancer diagnosis.},
author = {Vo-Dinh, Tuan and Panjehpour, Masoud and Overholt, Bergein F and Buckley, Paul},
doi = {10.1366/0003702971938768},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {1},
pages = {58--63},
title = {{Laser-Induced Differential Fluorescence for Cancer Diagnosis without Biopsy}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=51{\&}issue=1{\&}spage=58},
volume = {51},
year = {1997}
}
@article{Judge2009,
abstract = {Remote filament-induced breakdown spectroscopy (R-FIBS) using ultrashort laser pulses was used to measure the carbon/clay ratios between three graphite composites of different hardness at a standoff distance of approximately 6 m. Measurements using R-FIBS and femtosecond laser-induced breakdown (fs-LIBS) reveal similar selectivity and ability to excite emission. Comparison of the two stand-off techniques with optical microscopy and electron microprobe point detection confirmed the qualitative analysis capability of both femtosecond remote probing techniques. The R-FIBS technique produced more accurate results compared to fs-LIBS due to the intensity clamping nature of the filament ablation source. Measurement of the plasma temperatures for the metallic emission lines (approximately 8500 K) and the C(2) Swan lines (approximately 4500 K) suggest that the plasmas from different microdomains (clay and graphite) are not in equilibrium.},
author = {Judge, Elizabeth J and Heck, George and Cerkez, Elizabeth B and Levis, Robert J},
institution = {Temple University Department of Chemistry, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, USA.},
journal = {Analytical Chemistry},
number = {7},
pages = {2658--2663},
pmid = {19256525},
title = {{Discrimination of composite graphite samples using remote filament-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19256525},
volume = {81},
year = {2009}
}
@article{Deluciajr2007,
abstract = {Detecting trace explosive residues at standoff distances in real-time is a difficult problem. One method ideally suited for real-time standoff detection is laser-induced breakdown spectroscopy (LIBS). However, atmospheric oxygen and nitrogen contributes to the LIBS signal from the oxygen- and nitrogen-containing explosive compounds, complicating the discrimination of explosives from other organic materials. While bathing the sample in an inert gas will remove atmospheric oxygen and nitrogen interference, it cannot practically be applied for standoff LIBS. Alternatively, we have investigated the potential of double pulse LIBS to improve the discrimination of explosives by diminishing the contribution of atmospheric oxygen and nitrogen to the LIBS signal. These initial studies compare the close-contact 1 m) LIBS spectra of explosives using single pulse LIBS in argon with double pulse LIBS in atmosphere. We have demonstrated improved discrimination of an explosive and an organic interferent using double pulse LIBS to reduce the air entrained in the analytical plasma.},
author = {Deluciajr, F and Gottfried, J and Munson, C and Miziolek, A},
doi = {10.1016/j.sab.2007.10.036},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {double pulse,explosives,laser induced breakdown spectroscopy,libs,principal components analysis,roc curves},
number = {12},
pages = {1399--1404},
publisher = {Elsevier B.V.},
title = {{Double pulse laser-induced breakdown spectroscopy of explosives: Initial study towards improved discrimination}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707003527},
volume = {62},
year = {2007}
}
@article{Barnett2011a,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is used for the identification of the presence of hazardous bacteria in food. In this study, our main focus was centered on the identification of S. enterica serovar Typhimurium, a Gram-negative foodborne pathogen, in various liquids such as milk, chicken broth, and brain heart infusion due to the infection being most prevalent in raw meat and dairy products. A Nd:YAG laser of operating wavelength 266 nm was used to obtain the spectra from the artificially inoculated liquid samples. A series of experiments were performed to determine the effectiveness of LIBS to discriminate the bacteria from the background liquids. These results are compared with competing modern molecular methods of detection which include polymerase chain reaction (PCR) and quantitative real-time PCR. In addition to analyzing S. enterica serovar Typhimurium, another common Gram-negative, Escherichia coli, as well as Gram-positive pathogen, Staphlycoccus auerus, were used to determine the specificity of the LIBS technique.},
author = {Barnett, Cleon and Bell, Courtne{\'{e}} and Vig, Komal and Akpovo, a C and Johnson, Lewis and Pillai, Shreekumar and Singh, Shree},
doi = {10.1007/s00216-011-4844-3},
file = {::},
issn = {1618-2650},
journal = {Analytical and bioanalytical chemistry},
keywords = {Food Contamination,Food Contamination: analysis,Food Microbiology,Food Microbiology: methods,Lasers,Polymerase Chain Reaction,Salmonella typhimurium,Salmonella typhimurium: isolation {\&} purification,Spectrum Analysis,Spectrum Analysis: methods},
month = {jul},
number = {10},
pages = {3323--30},
pmid = {21424774},
title = {{Development of a LIBS assay for the detection of Salmonella enterica serovar Typhimurium from food.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21424774},
volume = {400},
year = {2011}
}
@article{Bruneau2005,
abstract = {Mechanisms of ultra-fast laser ablation during deep-drilling of metals was studied using plasma diagnostics and morphological analyses of the laser-induced craters. Fast imaging and time- and space-resolved optical emission spectroscopy were employed to characterize the ablation plume. After irradiation, the crater morphology was analyzed by scanning electron microscopy and optical microscopy. From the correlation between the ablation plume characteristics and the shape of the laser-produced craters, it is shown that the nanoparticles have an important influence on the accuracy of micromachining by ultra-short laser pulses.},
author = {Bruneau, S and Hermann, J and Dumitru, G and Sentis, M and Axente, E},
doi = {10.1016/j.apsusc.2005.03.061},
issn = {01694332},
journal = {Applied Surface Science},
keywords = {femtosecond laser ablation,laser induced plasma,micromachining},
number = {1-4},
pages = {299--303},
publisher = {Elsevier B.V.},
title = {{Ultra-fast laser ablation applied to deep-drilling of metals}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169433205004320},
volume = {248},
year = {2005}
}
@article{Hosseinimakarem2011,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is applied to analyze human fingernails using nanosecond laser pulses. Measurements on 45 nail samples are carried out and 14 key species are identified. The elements detected with the present system are: Al, C, Ca, Fe, H, K, Mg, N, Na, O, Si, Sr, Ti as well as CN molecule. Sixty three emission lines have been identified in the spectrum that are dominated by calcium lines. A discriminant function analysis is used to discriminate among different genders and age groups. This analysis demonstrates efficient discrimination among these groups. The mean concentration of each element is compared between different groups. Correlation between concentrations of elements in fingernails is calculated. A strong correlation is found between sodium and potassium while calcium and magnesium levels are inversely correlated. A case report on high levels of sodium and potassium in patients with hyperthyroidism is presented. It is shown that LIBS could be a promising technique for the analysis of nails and therefore identification of health problems.},
author = {Hosseinimakarem, Zahra and Tavassoli, Seyed Hassan},
file = {::},
institution = {Shahid Beheshti University, Laser and Plasma Research Institute, GC, Evin, Tehran 1983963113, Iran.},
journal = {Journal of Biomedical Optics},
keywords = {16,17,2010,2011,8,accepted publication mar,laser induced breakdown spectroscopy,nail analysis,paper 10440rr received aug,published,revised manuscript received mar,sex age discrimination},
number = {5},
pages = {057002},
pmid = {21639580},
title = {{Analysis of human nails by laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21639580},
volume = {16},
year = {2011}
}
@article{Gondal2010,
abstract = {Laser Induced Breakdown Spectroscopy (LIBS) technique was applied to determine the concentrations of different toxic elements like lead, chromium, cadmium and zinc in four different lipstick brands sold at local markets in Saudi Arabia. These samples contain toxic elements like lead, cadmium and chromium which are carcinogen dermatitis, allergic and eczematous. Their extraction from human body takes over 40 years and accumulation in the body cause problems like disruption of nervous systems and kidney damage. They could trigger to systemic lupus erythematosus (SLE). In order to test the validity of our LIBS results, standard technique like (ICP-AES) was also applied. To the best of our knowledge, this is the first study where LIBS technique was applied for the measurement of toxic substances in lipsticks. The maximum concentration detected in four lipstick brands was much higher than the permissible safe limits for human use and could lead to serious health problems. It is worth mentioning that the lipstick is not a solid rather is in fluid state which is not trivial to analyze using LIBS technique. For this purpose, special treatment of the lipstick samples was necessary to analyze with our LIBS method.},
author = {Gondal, M A and Seddigi, Z S and Nasr, M M and Gondal, B},
institution = {Physics Department {\&} Center of Excellence in Nanotechnology, King Fahd University of Petroleum {\&} Minerals, Dhahran 31261, Saudi Arabia. magondal@kfupm.edu.sa},
journal = {Journal of Hazardous Materials},
keywords = {cd,cr,hazardous effects cosmetic,laser induced breakdown spectroscopy,pb,products,toxic substances},
number = {1-3},
pages = {726--732},
pmid = {19926220},
publisher = {Elsevier B.V.},
title = {{Spectroscopic detection of health hazardous contaminants in lipstick using Laser Induced Breakdown Spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19926220},
volume = {175},
year = {2010}
}
@article{Smith2002,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been applied for the determination of plutonium isotope ratios through direct observation of atomic emission from laser-induced plasmas at high resolution. The Pu-239/Pu-240 isotope shift of -0.355 cm-1 from the plutonium atomic line at 594.52202 nm (Blaise et al., The Atomic Spectrum of Plutonium, Argonne National Laboratory Report ANL-83-95, 1984) is clearly resolved in our plasma conditions. Atomic emission is dispersed through a 2-m spectrometer in double pass mode and collected on an electronically gated, intensified charge-coupled device (ICCD) camera. The integrated peak areas obtained from curve-fitting closely match the Pu-239/Pu-240 isotopic ratios obtained from standard methods of thermal ionization mass spectrometry and gamma spectrometry. The observed plutonium linewidths were 0.19 cm-1 (0.0067 nm). These linewidths are within the experimental error of the ideal instrument-limited linewidth, which is calculated to be 0.15 cm-1 (0.0052 nm) based upon the known modulation transfer function for the ICCD system. This linewidth should allow LIBS to be applicable for isotopic ratio measurements for all of the light actinides.},
author = {Smith, Coleman A and Martinez, Max A and Veirs, D Kirk and Cremers, David A},
doi = {10.1016/S0584-8547(02)00023-X},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {5},
pages = {929--937},
title = {{Pu-239/Pu-240 isotope ratios determined using high resolution emission spectroscopy in a laser-induced plasma}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S058485470200023X},
volume = {57},
year = {2002}
}
@article{Radziemski1983,
abstract = {The repetitive breakdown spark from a focused laser beam was used to generate analytically useful emission spectra of aerosols In air. The apparatus Is slmple; a pulsed laser and optlcs, a spectrometer, and some method for tlme resolutlon of the spark Ilght. Tlme resolutlon Is essentlal because of the strong contlnuum emlsslon at early times (<500 ns). High temperatures In the spark result in vaporization of small particles, dlssoclatlon of molecules, and excltatlon of atomic and lonlc spectra. The plasma acts as If It were In local thermodynamic equlllbrlum, at least aRer 1 /IS. Spectroscoplc methods have been used to measure the tlme-resolved temperatures and electron densities. A slmple one-dlmenslonal hydrodynamic model predicts the temperature and diameter of the spark. Berylllum In atmospheric pressure air has been detected at 0.7 pg/m3, which Is 0.6 ng/g of alr (RSD = 30{\%}). Llmlts of detection have also been established for Na, P, As, and Hg In alr. A callbratlon curve linear over 4 orders of magnltude has been developed for Na In air. In sltu experlments have been performed on two experlmental coal gastflcatlon systems, and real-time spectral lnformatlon has been obtained In both cases.},
author = {Radziemski, L.J. and Loree, T.R. and Cremers, D.A. and Hoffman, N.M.},
doi = {0003-2700/83/0355-1246{\$}01.50/0},
file = {::},
journal = {Analytical Chemistry},
number = {8},
pages = {1246--1252},
publisher = {ACS Publications},
title = {{Time-resolved laser-induced breakdown spectrometry of aerosols}},
url = {http://pubs.acs.org/doi/abs/10.1021/ac00259a016},
volume = {55},
year = {1983}
}
@article{Osticioli2009,
abstract = {A small, potentially transportable prototype instrument capable of carrying out Raman, laser-induced breakdown (LIB), and laser-induced fluorescence (LIF) spectroscopy using a single pulsed laser source was developed for the analysis of cultural heritage objects. The purpose of this instrumentation is to perform fast and reliable analysis of surfaces with minimum damage to an object. For this purpose, a compact (51 x 203 x 76 mm) nanosecond Q-switched neodymium doped yttrium aluminum garnet laser (8 ns, 20 Hz, 0.01-115 mJ/pulse) was used as an irradiation source. The use of a nanosecond-gated detector sensitive between 180 and 900 nm allows the acquisition of elemental emissions in LIB spectroscopy and can also be employed for both LIF and time-resolved Raman spectroscopy. In this work, attention is focused on the description of the instrument and its optical components, and two examples of applications for the analysis of pigments and binding media used in works of art are presented.},
author = {Osticioli, I and Mendes, N F C and Nevin, A and Zoppi, A and Lofrumento, C and Becucci, M and Castellucci, E M},
institution = {Department of Chemistry, University of Florence, Polo Scientifico e Tecnologico, via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy.},
journal = {Review of Scientific Instruments},
number = {7},
pages = {076109},
title = {{A new compact instrument for Raman, laser-induced breakdown, and laser-induced fluorescence spectroscopy of works of art and their constituent materials.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19655994},
volume = {80},
year = {2009}
}
@article{Goueguel2010,
abstract = {Resonance-enhanced laser-induced breakdown spectroscopy (RELIBS) was investigated with the aim to improve the limit of detection of trace elements in the context of elemental analysis of aluminium alloys. A Q-switched Nd:YAG laser pulse (7 ns, 1064 nm) was used for ablation of the samples and was followed, after a suitable delay, by an Optical Parametric Oscillator (OPO) laser pulse (7 ns), tuned at 396.15 nm, to resonantly excite the aluminium host atoms. In particular, the Mg I 285.21 nm and Si I 288.16 nm lines were observed in the acquisition spectral window. We investigated the influence of the main experimental parameters, namely, the excitation wavelength, the interpulse delay and the ablation and excitation fluences, on the signal-to-noise ratio for the Mg I 285.21 nm line. We found that, at low ablation fluences, typically less than a few J cm-2, the Mg signal at 285.21 nm achieved using RELIBS was significantly enhanced when compared to LIBS using the same ablation fluence. At fluences higher than 8 J cm-2, the effect of the excitation pulse became unnoticeable and similar results were observed for both approaches. The optimum conditions were achieved for an interpulse delay of about 30 ns, an ablation fluence of about 3.8 J cm-2 and an excitation fluence of about 1.1 J cm-2. The corresponding absolute LoDs were 0.7 and 50 fg, for Mg and Si, respectively, using RELIBS. When using LIBS, they were 4 and 128 fg, instead. Finally, the applicability of RELIBS in the context of a minimally destructive elemental analysis is discussed.},
author = {Goueguel, Christian and Laville, St{\'{e}}phane and Vidal, Fran{\c{c}}ois and Sabsabi, Mohamad and Chaker, Mohamed},
doi = {10.1039/b927013b},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {5},
pages = {635},
publisher = {The Royal Society of Chemistry},
title = {{Investigation of resonance-enhanced laser-induced breakdown spectroscopy for analysis of aluminium alloys}},
url = {http://xlink.rsc.org/?DOI=b927013b},
volume = {25},
year = {2010}
}
@article{Snyder2011,
abstract = {Laser-induced breakdown spectroscopy (LIBS) using conditional data analysis was applied to aqueous suspensions of palladium particles in the reformate water of palladium-based proton exchange membrane fuel cells. A significant amount of palladium was found in the water, indicating degradation of the fuel-cell cathode catalytic layers. The palladium particle-size detection limit was found to be about 400 nm. Calibration procedures to quantify the palladium concentration are discussed.},
author = {Snyder, Stuart C and Wickun, William G and Mode, Jeremy M and Gurney, Brian D and Michels, Fred G},
institution = {Department of Biological and Physical Sciences, Montana State University-Billings, 59101, USA. ssnyder@msubillings.edu},
journal = {Applied Spectroscopy},
number = {6},
pages = {642--647},
pmid = {21639986},
title = {{The detection of palladium particles in proton exchange membrane fuel-cell water by laser-induced breakdown spectroscopy (LIBS).}},
url = {http://www.ingentaconnect.com/content/sas/sas/1994/00000048/00000011/art00002},
volume = {65},
year = {2011}
}
@article{Salle2005,
abstract = {Laser-induced Breakdown Spectroscopy (LIBS) is actively under development for future use on surface probes to Mars. The analytical method can be deployed for in-situ and/or stand-off analysis with the latter embodiment providing the greatest advantages compared to previous and current elemental analysis methods used for planetary surface analysis. For this application, LIBS must be thoroughly investigated in terms of analytical capabilities and flight-rated instruments must be developed. Because of the low pressure of the predominantly CO2 atmosphere on Mars, studies are needed to understand analytical requirements and to determine performance under these conditions. Stand-off analysis demands the most stringent requirements on instrumentation. Therefore, it must be determined if the high performance components that are normally used in a typical LIBS laboratory setup, which are generally not optimized for small size and weight, are essential to obtain the maximum scientific return from a mission. A key component of a LIBS apparatus is the detection system consisting of a spectrograph and a detector. Here we present an evaluation of one design of a compact spectrograph (Ocean Optics HR2000) for in-situ and stand-off LIBS analyses of geological samples under Mars atmospheric conditions. (c) 2005 Elsevier B.V. All rights reserved.},
author = {Salle, B and Cremers, D and Maurice, S and Wiens, R and Fichet, P},
doi = {10.1016/j.sab.2005.05.007},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {laser induced breakdown spectroscopy,libs,low pressure,mars},
number = {6},
pages = {805--815},
title = {{Evaluation of a compact spectrograph for in-situ and stand-off Laser-Induced Breakdown Spectroscopy analyses of geological samples on Mars missions}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854705001400},
volume = {60},
year = {2005}
}
@article{Mateo2007,
abstract = {In this work, the capability of laser-induced breakdown spectroscopy for process control in a thermal power plant is presented through quantitative compositional characterization of the coal used for combustion. Laser-induced emission signal of seven samples with a range of concentrations was calibrated for quantification purposes. The eighth sample was subsequently analyzed five times as unknown in order to determine the precision and accuracy of the measurements. Two modes of operation, dynamic and static and two laser wavelengths, 1064爊m and 355爊m were employed in this study for comparison. The results revealed that UV wavelength provided better results than IR radiation in terms of accuracy for the quantification of inorganic species in coal after the comparison with conventional atomic absorption spectrometry characterization.},
author = {Mateo, M P and Nicolas, G and Y{\'{a}}{\~{n}}ez, A},
doi = {10.1016/j.apsusc.2007.08.043},
issn = {01694332},
journal = {Applied Surface Science},
number = {4},
pages = {868 -- 872},
title = {{Characterization of inorganic species in coal by laser-induced breakdown spectroscopy using UV and IR radiations}},
url = {http://www.sciencedirect.com/science/article/B6THY-4PFW61S-1/2/1992fdb91c20fd77b89c92339a9a9ca8},
volume = {254},
year = {2007}
}
@article{Dalyander2008,
abstract = {The application of laser-induced breakdown spectroscopy (LIBS) to aerosol systems has been shown to provide quantitative analysis of particle-derived species; however, the exact nature of the plasma/particle interactions remains to be fully understood. Although the plasma/particle interaction may be idealized within a framework of instantaneous vaporization and analyte diffusion throughout the plasma volume, experimental evidence suggests that these processes actually occur on finite time scales relative to the plasma decay times at which measurements are frequently taken. In the present work, a numerical simulation of the temperature and species concentration fields of a plasma containing a single particle, including dissociation and diffusion on semi-empirical finite time scales, is developed. Using these results, the intensity of analyte emission is calculated as a function of time, and the standard ion/neutral ratios typical of aerosol-derived LIBS signals are calculated. Furthermore, the ratio of ion/neutral ratios for two different species was used to assess the temperature homogeneity of the particle-derived analytes in comparison to the overall plasma temperature field. From this numerical study, it is shown that the finite time scale of evaporation and diffusion of aerosol material results in a non-uniform spatial distribution in concentration. This results, in turn, in temperature and free electron density gradients within the plasma, leading to variation between the local conditions surrounding aerosol mass and the bulk conditions of the plasma as a whole. © 2007 Elsevier B.V. All rights reserved.},
author = {Dalyander, P.S. and Gornushkin, I.B. and Hahn, D.W.},
doi = {10.1016/j.sab.2007.11.023},
file = {::},
issn = {05848547},
journal = {Spectrochimica Acta Part B: Atomic Spectroscopy},
keywords = {aesorol,diffusion,laser-induced breakdown spectroscopy,libs,particle,plasma},
month = {feb},
number = {2},
pages = {293--304},
title = {{Numerical simulation of laser-induced breakdown spectroscopy: Modeling of aerosol analysis with finite diffusion and vaporization effects}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707004363},
volume = {63},
year = {2008}
}
@article{Smith2011,
abstract = {Here we demonstrate a unique optical sensing scheme based on deep-UV photochemical perturbation in combination with difference spectroscopy. Applying a sequence of optical probing, UV-laser-induced perturbation, and repeat optical probing coupled with difference spectroscopy provides a new spectral signature. We show a selective (sevenfold difference) optical response using a fluorescence probe for binary mixtures of organic dyes, and generate complementary spectral information derived from Raman scattering of the dipeptide glycine-glycine. We further extend the methodology to fluorescence-based imaging of an organic matrix.},
author = {Smith, Sarah E and Shanyfelt, Leia M and Buchanan, Katherine D and Hahn, David W},
file = {::},
issn = {1539-4794},
journal = {Optics letters},
month = {jun},
number = {11},
pages = {2116--8},
pmid = {21633467},
title = {{Differential laser-induced perturbation spectroscopy using a deep-ultraviolet excimer laser.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21633467},
volume = {36},
year = {2011}
}
@article{Rai2003,
abstract = {We have demonstrated that a fiber-optic laser-induced breakdown spectroscopy (LIBS) probe is suitable for measuring the concentration of minor constituents of a molten Al alloy in a laboratory furnace. For the first time to our knowledge we are able to record the LIBS spectra in several spectral regions of seven different molten Al alloy samples by inserting the LIBS probe inside the molten alloys, allowing us to obtain a ratio calibration curve for minor constituents (Cr, Mg, Zn, Cu, Si, etc.), using Fe as a reference element. A ratio calibration curve for Fe with a major element (Al) can also be obtained with which the concentration of Fe in the alloy can be determined. The effects of the surrounding atmosphere on the LIBS spectra of the molten alloy were investigated. Effects of focal length of the lens on the LIBS signals were also studied. LIBS spectra of a solid Al alloy recorded with the same LIBS probe were compared with the LIBS spectra of the molten alloy. Our results suggest that the LIBS probe is useful for monitoring the elemental composition of an Al melt in an industrial furnace at different depths and different positions inside the melt.},
author = {Rai, Awadhesh K and Yueh, Fang-Yu and Singh, Jagdish P},
institution = {Diagnostic Instrumentation and Analysis Laboratory, Mississippi State University, 205 Research Boulevard, Starkville, Mississippi 39759-7704, USA.},
journal = {Applied Optics},
number = {12},
pages = {2078--2084},
pmid = {12716148},
publisher = {OSA OPTICAL SOCIETY OF AMERICA},
title = {{Laser-induced breakdown spectroscopy of molten aluminum alloy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12716148},
volume = {42},
year = {2003}
}
@article{Yao2010,
abstract = {Abstract— Laser induced breakdown spectroscopy (LIBS) has been used for the determination of the species and concentration of elements in industries. However, there is less research for LIBS analysis of agricultural and environmental samples. In this work, a LIBS system has been evaluated for the determination of nutrition elements in orange leaves. The experimental setup was designed by using a Nd:YAG laser operating at 1064 nm (200 mJ per pulse and 5HZ repetition rate) and an Avantes spectrometer (200-1100nm wavelength range)with ICCD detector. The species and relative contents were identified by LIBS spectra, which belonged to qualitative analysis. The quantitive analysis will be carried combining with routine analysis such as ICP-OES.},
author = {Yao, Mingyin and Liu, Muhua and Zhao, Jinhui and Huang, Lin},
doi = {10.1109/IITSI.2010.83},
file = {::},
isbn = {978-1-4244-6730-3},
journal = {2010 Third International Symposium on Intelligent Information Technology and Security Informatics},
keywords = {-libs,nutrition elements,orange leaves},
month = {apr},
pages = {398--401},
publisher = {Ieee},
title = {{Identification of Nutrition Elements in Orange Leaves by Laser Induced Breakdown Spectroscopy}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=5453578},
year = {2010}
}
@article{Lei2009,
abstract = {Optical emission of laser-induced plasma on the surface of fresh vegetables provides sensitive analysis of trace elements for in situ or online detection of these materials. This emergent technique promises applications with expected outcomes in food security or nutrition quality, as well as environment pollution detection. Characterization of the plasma induced on such soft and humid materials represents the first step towards quantitative measurement using this technique. In this paper, we present the experimental setup and protocol that optimize the plasma generation on fresh vegetables, potatoes for instance. The temporal evolution of the plasma properties are investigated using time-resolved laser-induced breakdown spectroscopy (LIBS). In particular. the electron density and the temperatures of the plasma are reported as functions of its decay time. The temperatures are evaluated from the well known Boltzmann and Saha-Boltzmann plot methods. These temperatures are further compared to that of the typical molecular species, CN, for laser-induced plasma from plant materials. This comparison validates the local thermodynamic equilibrium (LTE) in the specific case of fresh vegetables ablated in the typical LIBS conditions. A study of the temporal evolution of the signal to noise ratio also provides practical indications for an optimized detection of trace elements. We demonstrate finally that, under certain conditions, the calibration-free LIBS procedure can be applied to determine the concentrations of trace elements in fresh vegetables. (C) 2009 Elsevier B.V. All rights reserved.},
author = {Lei, Wenqi and Motto-Ros, Vincent and Boueri, Myriam and Ma, Qianli and Zhang, Dacheng and Zheng, Lijuan and Zeng, Heping and Yu, Jin},
doi = {10.1016/j.sab.2009.07.015},
issn = {05848547},
journal = {Spectrochimica Acta Part BAtomic Spectroscopy},
number = {9},
pages = {891--898},
title = {{Time-resolved characterization of laser-induced plasma from fresh potatoes}},
volume = {64},
year = {2009}
}
@article{Cross2009,
author = {Cross, E S and Onasch, T B and Canagaratna, M and Jayne, J T and Kimmel, J and Yu, X Y and Alexander, M L and Worsnop, D R and Davidovits, P},
doi = {10.5194/acp-9-7769-2009},
file = {::},
issn = {16807324},
journal = {Atmospheric Chemistry and Physics},
number = {20},
pages = {7769--7793},
publisher = {European Geophysical Society, Max-Planck-Str. 13 Katlenburg-Lindau Germany},
title = {{Single particle characterization using a light scattering module coupled to a time-of-flight aerosol mass spectrometer}},
url = {http://www.atmos-chem-phys.net/9/7769/2009/},
volume = {9},
year = {2009}
}
@article{Rai2003b,
abstract = {Effects of a steady magnetic field on the laser-induced breakdown spectroscopy of certain elements (Mn, Mg, Cr, and Ti) in aqueous solution were studied, in which the plasma plume expanded across an external steady magnetic field (approximately 6 kilogauss). Nearly 1.6 times enhancement in the line emission intensity was observed in the presence of the magnetic field. The temporal evolution of the line emission showed a significant enhancement in plasma emission between 2- and 7- micro(s) gate delays for Mg in the presence of the magnetic field (5-30 micro(s) for Mn). This enhancement in the emission is attributed to an increase in the rate of recombination because of an increase in plasma density due to a magnetic confinement after cooling the plasma. The increase in the optical line emission due to magnetic confinement was absent when the plasma was hot with a dominant background (continuum) emission. The limits of detection of Mg and Mn were reduced by a factor of two in the presence of a steady magnetic field of 5 kilogauss.},
author = {Rai, Virendra N and Zhang, Hansheng and Yueh, Fang Y and Singh, Jagdish P and Kumar, Akshaya},
doi = {10.1016/j.optlastec.2008.07.010},
file = {::},
issn = {00036935},
journal = {Applied Optics},
number = {18},
pages = {3662--9},
pmid = {12833972},
title = {{Effect of steady magnetic field on laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12833972},
volume = {42},
year = {2003}
}
@article{Rehse2009a,
abstract = {Four Cu-Zn brass alloys with different stoichiometries and compositions have been analyzed by laser-induced breakdown spectroscopy (LIBS) using nanosecond laser pulses. The intensities of 15 emission lines of copper, zinc, lead, carbon, and aluminum (as well as the environmental contaminants sodium and calcium) were normalized and analyzed with a discriminant function analysis (DFA) to rapidly categorize the samples by alloy. The alloys were tested sequentially in two different noble gases (argon and helium) to enhance discrimination between them. When emission intensities from samples tested sequentially in both gases were combined to form a single 30-spectral line "fingerprint" of the alloy, an overall 100{\%} correct identification was achieved. This was a modest improvement over using emission intensities acquired in argon gas alone. A similar study was performed to demonstrate an enhanced discrimination between two strains of Escherichia coli (a Gram-negative bacterium) and a Gram-positive bacterium. When emission intensities from bacteria sequentially ablated in two different gas environments were combined, the DFA achieved a 100{\%} categorization accuracy. This result showed the benefit of sequentially testing highly similar samples in two different ambient gases to enhance discrimination between the samples.},
author = {Rehse, Steven J and Mohaidat, Qassem I},
doi = {10.1016/j.sab.2009.07.012},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1020--1027},
publisher = {Elsevier B.V.},
title = {{The effect of sequential dual-gas testing on laser-induced breakdown spectroscopy-based discrimination: Application to brass samples and bacterial strains}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709002225},
volume = {64},
year = {2009}
}
@article{Mukherjee2008,
abstract = {Aerosolized drug delivery methods have increasingly become popular for pharmaceutical applications. This is mainly due to their ease of application and the more recent advancements incorporating nano-sized generation of particles that find deeper penetration routes and more efficient administration of the drug to specific target organs. Their effectiveness heavily relies on the uniformity of the chemical composition of these aerosolized drugs. Thus, it calls for a real-time on-line analytical tool that can accurately characterize the chemical constituents of the drug powder particles generated to ensure a stringent quality control. We present laser-induced breakdown spectroscopy (LIBS) for the first time as an efficient analytical tool to carry out on-line quantitative chemical characterization of aerosolized drugs. We used three different carbon based aerosolized drugs, namely L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate Iron(II) L-ascorbate (C(12)H(14)FeO(12)), and DL-pantothenic acid hemicalcium salt (C(9)H(16)NO(5)0.5Ca) for our quantitative LIBS studies here. Our results show that LIBS can effectively estimate the quantitative ratios of carbon to various trace elements for each of these drugs, thereby enabling on-line unique characterization of individual aerosolized drugs. The quantitative LIBS technique predicted the C/Mg, C/Fe, and C/Ca ratios as 4.02+/-0.76, 12.42+/-2.36, and 18.47+/-4.39 for each of the above aerosolized drugs, respectively. Within error limits, we find these ratios in good agreement with the respective stoichiometric values of 4, 12, and 18 corresponding to the drugs above. Thus, the work demonstrated the utility and validity of LIBS in accurate on-line identification of drug powders during real-time manufacturing processes.},
author = {Mukherjee, Dibyendu and Cheng, Meng-Dawn},
institution = {Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.},
journal = {Applied Spectroscopy},
number = {5},
pages = {554--562},
pmid = {18498697},
title = {{Characterization of carbon-containing aerosolized drugs using laser-induced breakdown spectroscopy.}},
url = {http://www.ingentaconnect.com/content/sas/sas/2008/00000062/00000005/art00018},
volume = {62},
year = {2008}
}
@article{Buteau2010,
abstract = {A standoff bioaerosol sensor based on intensified range-gated spectrometric detection of Laser Induced Fluorescence was used to spectrally characterize bioaerosol simulants during in-chamber and open-air releases at Suffield, Canada, in August 2008 from a standoff position. In total, 42 in-chamber Bacillus atrophaeus (formerly Bacillus subtilis var globigii; BG) cloud and 27 open-air releases of either BG, Pantoea agglomerans (formerly Erwinia herbicola; EH), MS2 and ovalbumin (OV) were generated. The clouds were refereed by different point sensors including Aerodynamic Particle Sizer (APS) and slit or impingers samplers. The APS monitored the particle size distribution and concentration and the samplers characterized the viable portion of the cloud. The extracted spectral signatures show robustness to different degree. The correlation assessment showed good results in most cases where the LIF signal to noise ratio was significant. The sensor 4$\sigma$ sensitivity was evaluated to 1 300, 600, 100 and 30 ppl for BG, OV, MS2 and EH respectively. Correlation results are presented by plotting the SINBAHD metric versus the corresponding particle concentration, in which case, the obtained slope is proportional to the material fluorescence cross-section. The different acquired signal is hence compared in terms of their fluorescence cross-section additionally to their spectral characteristics.},
author = {Buteau, Sylvie and Simard, JR and Rowsell, Susan},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Buteau, Simard, Rowsell - Bioaerosol standoff detection and correlation assessment with concentration and viability point sensors - 2010.pdf:pdf},
journal = {Society of Photo-Optical},
keywords = {acpla,aerosol,biological agent simulant,laser-induced fluorescence,lif,ppl,standoff detection},
number = {August},
title = {{Bioaerosol standoff detection and correlation assessment with concentration and viability point sensors}},
url = {http://pubs.drdc.gc.ca/PDFS/unc107/p534626{\_}A1b.pdf},
volume = {2008},
year = {2010}
}
@article{Remus2010,
abstract = {Over the past quarter century, multielement chemical analysis has become a common means for attributing the provenance of archaeological materials. The Coso Volcanic Field (CVF) in California, USA, contains at least 38 high-silica rhyolite domes, many of which contain obsidian glass that has been quarried for tools by the indigenous population for more than 12,000 years. Artifacts made from CVF obsidian are found throughout the southwestern United States and geochemical sourcing of CVF obsidian has been an important tool in understanding prehistoric Native American trading patterns. Laser-induced breakdown spectroscopy (LIBS) is a simple atomic emission spectroscopic technique that has the potential for real-time man-portable chemical analysis in the field. Because LIBS is simultaneously sensitive to all elements, a single laser shot can be used to record the broadband emission spectra, which provides a chemical fingerprint of a material. Single-shot broadband LIBS spectra were collected using a commercial benchtop LIBS system for 27 obsidian samples from major sites across the CVF and four additional sites in California and western Nevada outside of CVF. Classification of the samples was performed using partial least-squares discriminant analysis (PLSDA), a common chemometric technique suitable for performing regression on high-dimensional data. Provenance identification for the obsidian samples was evaluated for three separate labeling frameworks. The first framework consisted of a binary classification problem to distinguish CVF samples from non-CVF samples. The second approach focused on the CVF samples with labels that corresponded to the eight separate Coso sites encompassed by the 27 samples. In the third analysis, non-CVF samples were excluded, and the remaining 27 CVF samples were labeled based on groupings defined from previous major and trace element chemical studies, which reduces the number of possible classes from eight to four. Different aspects of the classifier setup considered in this study include the training/testing routine (a 27-fold leave-one-sample-out setup versus a simple split of the data into separate sets for training and evaluation), the number of latent variables used in the regression model, and whether PLSDA operating on the entire broadband LIBS spectrum is superior to that using only a selected subset of LIBS emission lines. The results point to the robustness of the PLSDA technique and suggest that LIBS analysis combined with the appropriate statistical signal processing has the potential to be a useful tool for chemical analysis of archaeological artifacts and geological specimens.},
author = {Remus, Jeremiah J and Gottfried, Jennifer L and Harmon, Russell S and Draucker, Anne and Baron, Dirk and Yohe, Robert},
doi = {10.1364/AO.49.00C120},
journal = {Applied Optics},
number = {13},
pages = {C120--C131},
title = {{Archaeological applications of laser-induced breakdown spectroscopy: an example from the Coso Volcanic Field, California, using advanced statistical signal processing analysis}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-49-13-C120},
volume = {49},
year = {2010}
}
@article{Alonso-Medina2010,
abstract = {In this paper, we present transition probabilities for 97 spectral lines of Sn I, corresponding to transitions n (n = 6,7,8)s 5p(2), n(n = 5,6,7)d 5p(2), 5p(3) 5p(2), n(n = 7)p 6s, determined by measuring the intensities of the emission lines of a Laser-induced breakdown (emission) spectrometry (LIBS). The optical emission spectroscopy from a laser-induced plasma generated by a 10 640 angstrom radiation, with an irradiance of 1.4 x 10(10) Wcm(-2) on an Sn-Pb alloy (an Sn content of approximately 20{\%}), in vacuum, was recorded at 0.8 mu s, and analysed between 1900 and 7000 angstrom. The population-level distribution and corresponding temperature were obtained using Boltzmann plots. The electron density of the plasma was determined using well-known Stark broadening parameters of spectral lines. The plasma under study had an electron temperature of 13,200 K and an electron number density of 2 x 10(16) cm(-3). The experimental relative transition probabilities were put on an absolute scale using the branching ratio method to calculate Sn I multiplet transition probabilities from available radiative lifetime data of their upper states and plotting the Sn I emission spectrum lines on a Boltzmann plot assuming local thermodynamic equilibrium (LTE) to be valid and following Boltzmann's law. The LTE conditions and plasma homogeneity have been checked. Special attention was paid to the possible self-absorption of the different transitions. The experimental results obtained have been compared with the experimental values given by other authors. (C) 2010 Elsevier B.V. All rights reserved.},
author = {Alonso-Medina, A},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {2},
pages = {158--166},
title = {{A spectroscopic study of laser-induced tin-lead plasma: Transition probabilities for spectral lines of Sn I}},
url = {http://www.sciencedirect.com/science/article/B6THN-4Y70C5N-2/2/1850f3c6090989ba6335857e8234050b},
volume = {65},
year = {2010}
}
@article{Rai2003c,
abstract = {Effects of a steady magnetic field on the laser-induced breakdown spectroscopy of certain elements (Mn, Mg, Cr, and Ti) in aqueous solution were studied, in which the plasma plume expanded across an external steady magnetic field (approximately 6 kilogauss). Nearly 1.6 times enhancement in the line emission intensity was observed in the presence of the magnetic field. The temporal evolution of the line emission showed a significant enhancement in plasma emission between 2- and 7- micro(s) gate delays for Mg in the presence of the magnetic field (5-30 micro(s) for Mn). This enhancement in the emission is attributed to an increase in the rate of recombination because of an increase in plasma density due to a magnetic confinement after cooling the plasma. The increase in the optical line emission due to magnetic confinement was absent when the plasma was hot with a dominant background (continuum) emission. The limits of detection of Mg and Mn were reduced by a factor of two in the presence of a steady magnetic field of 5 kilogauss.},
author = {Rai, Virendra N and Zhang, Hansheng and Yueh, Fang Y and Singh, Jagdish P and Kumar, Akshaya},
doi = {10.1016/j.optlastec.2008.07.010},
file = {::},
issn = {00036935},
journal = {Applied Optics},
number = {18},
pages = {3662--9},
pmid = {12833972},
title = {{Effect of steady magnetic field on laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12833972},
volume = {42},
year = {2003}
}
@article{Loudyi2009,
abstract = {The combination of laser-induced breakdown spectroscopy (LIBS) and laser-induced fluorescence (LIF) was investigated to improve the limit of detection (LoD) of trace elements in liquid water, while preserving the distinctive on-line monitoring capabilities of LIBS analysis. The influence of the main experimental parameters, namely the ablation fluence, the excitation fluence, and the inter-pulse delay was studied to maximize the fluorescence signal. The plasma was produced by a 266 nm frequency-quadrupled Q-switched Nd:YAG laser and the trace elements under investigation were then re-excited by a nanosecond optical parametric oscillator (OPO) laser, delivering pulses in the sub-mJ energy range, and tuned to strong absorption lines of the trace elements. The reproducibility of the measurements was improved using a home-made flow-cell, and relative standard deviations as low as 6.7{\%} for a series of 100 shots were attained with a repetition rate of 0.7 Hz. Using the LIBS-LIF technique, we demonstrated LoDs of 39 ppb and 65 ppb for Pb and Fe, respectively, accumulating over 100 laser shots only, which correspond to an improvement of about 500 times with respect to LIBS.},
author = {Loudyi, Hakim and Rifa{\"{\i}}, Kheireddine and Laville, St{\'{e}}phane and Vidal, Fran{\c{c}}ois and Chaker, Mohamed and Sabsabi, Mohamad},
doi = {10.1039/b909485g},
file = {::},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {10},
pages = {1421},
title = {{Improving laser-induced breakdown spectroscopy (LIBS) performance for iron and lead determination in aqueous solutions with laser-induced fluorescence (LIF)}},
url = {http://xlink.rsc.org/?DOI=b909485g},
volume = {24},
year = {2009}
}
@article{Cravetchi2006,
abstract = {The analytical performance of femtosecond laser-induced breakdown spectroscopy (LIBS) for elemental microanalysis of aluminium alloys and for mapping precipitate distribution on the sample surface has been studied in detail. A Ti-sapphire laser system producing pulses of 130 fs at 800 nm was used to generate the laser-induced plasma. Multi-element microanalysis of commercially available aluminium alloys was performed in air at atmospheric pressure. Crater characteristics such as diameter and crater morphology were characterized by optical and scanning-electron microscopy. Scaling of plasma emission and limit of detection as a function of laser pulse energy was also investigated. Current experimental results are presented and are compared with previous nanosecond microLIBS measurements.},
author = {Cravetchi, Igor V and Taschuk, Mike T and Tsui, Ying Y and Fedosejevs, Robert},
file = {::},
institution = {Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada, T6G 2V4. igorc@ece.ualberta.ca},
journal = {Analytical and Bioanalytical Chemistry},
keywords = {aluminium alloy,laser induced breakdown spectroscopy,libs,precipitates,solid sampling,spectrochemical microanalysis},
number = {2},
pages = {287--294},
pmid = {16437203},
publisher = {SPRINGER HEIDELBERG},
title = {{Evaluation of femtosecond LIBS for spectrochemical microanalysis of aluminium alloys.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16437203},
volume = {385},
year = {2006}
}
@article{Baudelet2007,
abstract = {Ultraviolet pulses (266 nm) delivered by a quadrupled Nd:YAG laser were used to analyze organic samples with laser-induced breakdown spectroscopy (LIBS). We present characteristics of the spectra obtained from organic samples with special attentions on the emissions of organic elements, O and N, and molecular bonds CN. The choice of these atomic or molecular species is justified on one hand, by the importance of these species to specify organic or biological materials; and on the other hand by the possible interferences with ambient air when laser ablation takes place in the atmosphere. Time-resolved LIBS was used to determine the time-evolution of line intensity emitted from these species. We demonstrate different kinetic behaviors corresponding to different origins of emitters: native atomic or molecular species directly vaporized from the sample or those generated through dissociation or recombination due to interaction between laser-induced plasma and air molecules. Our results show the ability of time-resolved UV-LIBS for detection and identification of native atomic or molecular species from an organic sample.},
author = {Baudelet, Matthieu and Boueri, Myriam and Yu, Jin and Mao, Samuel S. and Piscitelli, Vincent and Mao, Xianglei and Russo, Richard E.},
doi = {10.1016/j.sab.2007.10.043},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Baudelet et al. - Time-resolved ultraviolet laser-induced breakdown spectroscopy for organic material analysis - 2007.pdf:pdf},
issn = {05848547},
journal = {Spectrochimica Acta Part B: Atomic Spectroscopy},
keywords = {organic material analysis,time-resolved libs,ultraviolet laser-induced breakdown spectroscopy},
month = {dec},
number = {12},
pages = {1329--1334},
title = {{Time-resolved ultraviolet laser-induced breakdown spectroscopy for organic material analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707003606},
volume = {62},
year = {2007}
}
@article{Boroumand1992,
abstract = {An adaptation of Kubelka's general model of diffuse reflectance and diffuse transmittance of light to nonideal scattering samples is proposed. It is applied to quantitative Fourier transform infrared spectrometry of nondiluted surface-derivatized silica powders. Corrections of the mea- surements are introduced in order to take into account common problems that often prevent a truly quantitative application of the DRIFTS ana- lytical method. Effects on the measured data due to the background absorption of the sample and to the specular reflection on its surface are discussed and quantitatively corrected for. The possible existence of gradients of the optical properties of the powder medium is taken into account by a numerical adaptation of the model to inhomogeneities of the phenomenological absorption and scattering coefficients K and S. Model systems constituted of two types of silica powders of very different morphology are prepared. Known concentrations of molecules carrying a cyano functional group as chromophore were covalently anchored on the powder surface. Application of the adapted model gives a quite good description of the measured diffuse reflectance and diffuse transmittance in these cases where the simple Kubelka-Munk function fails.},
author = {Boroumand, Farnaz and Moser, Jacques E and {Van Den Bergh}, Hubert},
doi = {10.1366/0003702924123502},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {12},
pages = {1874--1886},
title = {{Quantitative Diffuse Reflectance and Transmittance Infrared Spectroscopy of Nondiluted Powders}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=46{\&}issue=12{\&}spage=1874},
volume = {46},
year = {1992}
}
@article{O'Leary2010,
abstract = {This work presents a technique by which a low resolution approximately 1 nm) fiberoptic spectrometer may be used to definitively identify elements and molecular fragments in laser-induced breakdown spectroscopy. Commercial laser-induced breakdown spectroscopy (LIBS) spectrometers have high resolution in the area of spectral interest, and software is used to identify elements via a look-up table containing known spectral lines. When analyzing spectra from a lower resolution fiber-optic spectrometer, software based on look-up tables can produce erroneous results, reporting elements absent from the sample. As a solution to this problem, an analysis using the coherence function in conjunction with Welch's method is used to compare sample spectra with a library of reference spectra, which contain peaks primarily from a single element. The analysis has proved to be adept at identifying specific elemental signatures in multi-component samples. The technique leverages the increased information content of concomitant atomic emission lines, which are easily collected with a low resolution broadband (200-1100 nm) fiber-optic spectrometer. This technique alleviates the need for the user to visually verify the vicinity of individual peaks during testing. While Pearson's method is generally used for this type of analysis, we show that Welch's method has the advantage of being less susceptible to problems caused by continuum background.},
author = {O'Leary, Brendon and Kelley, Jude A},
file = {::},
institution = {College of the Holy Cross, Worcester, Massachusetts 01610, USA.},
journal = {Applied Spectroscopy},
number = {4},
pages = {370--376},
pmid = {20412620},
title = {{Utilization of the coherence function with Welch's method for signal analysis in low resolution laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20414511},
volume = {64},
year = {2010}
}
@article{Cabalin2011,
abstract = {The potential of a multi-pulse (MP) laser excitation scheme for deep stratigraphy of electrolytically galvanized steel using laser-induced breakdown spectrometry (LIBS) has been evaluated. For this purpose, a commercial electro-optically (EO) Q-switched Nd:YAG laser was employed, where by reducing the delay between the Q-switch opening and the flash lamp, a train of pulses (up to 11) separated by approximately 7.40 $\mu$s was generated during one lamp flashing. Plasma emission after each individual laser pulse of the MP sequence was detected by a spectrograph equipped with an intensified charge-coupled device (iCCD) detector. With MP excitation, the ablation efficiency was increased ten-fold on iron sample and 22.5-fold on zinc material with respect to dual-pulse or single-pulse excitation. The LIBS signal generated by MP excitation shows an analogous enhancement. Although the total energy per shot delivered to samples was only 60 mJ, it was possible using LIBS to measure the sample stratigraphy up to depths of 90 $\mu$m on zinc-coated steel sheets. A satisfactory agreement between the Zn thickness determined by the MP-LIBS system and data from the manufacturer has also been obtained.},
author = {Cabal{\'{\i}}n, Luisa Mar{\'{\i}}a and Gonz{\'{a}}lez, Alina and Lazic, Violeta and Laserna, Javier},
institution = {Department of Analytical Chemistry, University of M{\'{a}}laga, M{\'{a}}laga, Spain.},
journal = {Applied Spectroscopy},
number = {7},
pages = {797--805},
pmid = {21740642},
title = {{Deep ablation and depth profiling by laser-induced breakdown spectroscopy (LIBS) employing multi-pulse laser excitation: application to galvanized steel.}},
volume = {65},
year = {2011}
}
@article{Gizur2008,
abstract = {The medicine called Tamsulosin was produced 25 years ago and since then almost 10 new synthesis route has been known. Each process shows the researchers' workstyle, every year, which mainly differs in the way of separating the enantiomers. The applied reaction steps also reflect the development over the past 25 years and the new synthesis is influenced by the antecedents. The key-intermediate used in our new method is a racemic secondary amine derivative, which is unknown in the literature before and for resolving it, we worked out a quite advantegeous process. By using an optically active secondary amine, side reactions can be avoided.},
author = {Gizur, T and Fogassy, E and B{\'{a}}lint, J and Egri, G and T{\"{o}}rley, J and Demeter, A and Greiner, I},
institution = {Chemical Works of Gedeon Richter Ltd., Budapest, H-1475, Hungary.},
journal = {Chirality},
number = {6},
pages = {790--795},
pmid = {18306291},
title = {{New practical synthesis of Tamsulosin.}},
volume = {20},
year = {2008}
}
@article{Godoi2011,
abstract = {Quality control of toys for avoiding children exposure to potentially toxic elements is of utmost relevance and it is a common requirement in national and/or international norms for health and safety reasons. Laser-induced breakdown spectroscopy (LIBS) was recently evaluated at authors' laboratory for direct analysis of plastic toys and one of the main difficulties for the determination of Cd. Cr and Pb was the variety of mixtures and types of polymers. As most norms rely on migration (lixiviation) protocols, chemometric classification models from LIBS spectra were tested for sampling toys that present potential risk of Cd, Cr and Pb contamination. The classification models were generated from the emission spectra of 51 polymeric toys and by using Partial Least Squares - Discriminant Analysis (PLS-DA), Soft Independent Modeling of Class Analogy (SIMCA) and K-Nearest Neighbor (KNN). The classification models and validations were carried out with 40 and 11 test samples, respectively. Best results were obtained when KNN was used, with corrected predictions varying from 95{\%} for Cd to 100{\%} for Cr and Pb. (C) 2011 Elsevier B.V. All rights reserved.},
author = {Godoi, Quienly and Leme, Flavio O and Trevizan, Lilian C and {Pereira Filho}, Edenir R and Rufini, Iolanda A and {Santos Jr.}, Dario and Krug, Francisco J},
doi = {10.1016/j.sab.2011.01.001},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {chemometrics,classification models,icp oes,libs,toxic elements,toys},
number = {2},
pages = {138--143},
publisher = {Elsevier B.V.},
title = {{Laser-induced breakdown spectroscopy and chemometrics for classification of toys relying on toxic elements}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854711000036},
volume = {66},
year = {2011}
}
@article{Marquardt1996,
abstract = {On-site determination of leaded paint in houses is important for minimizing the costs of renovations. A simple fiber-optic probe suitable for remote elemental analysis using laser-induced breakdown spectroscopy has been developed for this purpose and is used to determine the lead concentration in samples of dry paint. Optical fibers transport the laser pulse to the sample and transfer the emission signal to the spectrometer. The use of separate excitation and collection fibers allows coupling of the probe to a conventional spectrometer using simple optics. The measurement takes less than 1 min to perform, requires no sample preparation, and can be made through overlayers of non-lead-containing paint. The limit of detection is 0.014{\%} Pb in latex paint, on a dry weight basis, with relative sample standard deviations of 510{\%}.},
author = {Marquardt, Brian J and Goode, Scott R and Angel, S Michael},
doi = {10.1021/ac950828h},
isbn = {8037779521},
issn = {00032700},
journal = {Analytical Chemistry},
number = {6},
pages = {977--981},
title = {{In Situ Determination of Lead in Paint by Laser-Induced Breakdown Spectroscopy Using a Fiber-Optic Probe}},
url = {http://pubs.acs.org/doi/abs/10.1021/ac950828h},
volume = {68},
year = {1996}
}
@article{Ramil2008,
abstract = {Abstract The aim of this work is to analyze the feasibility of artificial neural networks (ANN) for the classification, in function of the provenance, of archaeological ceramics Terra Sigillata analyzed by means of laser-induced breakdown spectroscopy (LIBS). In order to automate and facilitate the task of comparison of LIBS spectra, two ANN algorithms are proposed: One is fed with the whole LIBS spectra and the other with the areas of the most intense peaks of the spectra. In both cases, an analysis of the network architecture as a function of the number of hidden neurons and number of epochs of training was carried out in order to optimize the performance of the network. Following both procedures, the correct classification (higher than the 95{\%} of success) of Terra Sigillata pieces from their LIBS spectra can be achieved in a systematic and objective way.},
author = {Ramil, A and L{\'{o}}pez, A J and Y{\'{a}}{\~{n}}ez, A},
doi = {10.1007/s00339-008-4481-7},
issn = {09478396},
journal = {Applied Physics A},
number = {1},
pages = {197--202},
title = {{Application of artificial neural networks for the rapid classification of archaeological ceramics by means of laser induced breakdown spectroscopy (LIBS)}},
url = {http://www.springerlink.com/index/10.1007/s00339-008-4481-7},
volume = {92},
year = {2008}
}
@article{Michaud2007,
abstract = {Laser-Induced Breakdown Spectroscopy (LIBS) was applied to the analysis of iron ore concentrates. The objective was to determine the influence of particle size and mineral phase on the LIBS signal. The LIBS spectra of hematite and magnetite ore concentrates were qualitatively indistinguishable from each other but magnetite yielded systematically less than hematite. This behavior could be set into an empirical equation to correct the iron peak intensities according to the level of magnetite in the analyzed sample. Similarly, an increase of the LIBS signal was observed as the particle size of the ore samples decreased. Again, an equation could be written down to correct the intensity of either iron or silicon in response to a variation of the average particle size of the ore concentrate. Using these corrections, proper response of the silicon signal against the concentration of silica in the samples was restored. The observed dependence of the strength of the iron signal upon the mineral phase is attributed to oxidation of magnetite into hematite.},
author = {Michaud, Daniel and Leclerc, R{\'{e}}mi and Proulx, {\'{E}}ric},
doi = {10.1016/j.sab.2007.10.021},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {12},
pages = {1575--1581},
title = {{Influence of particle size and mineral phase in the analysis of iron ore slurries by Laser-Induced Breakdown Spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707003394},
volume = {62},
year = {2007}
}
@article{Castro2003,
abstract = {The aim of the present study was the rapid identification of alloys used in the manufacture of jewelry pieces with the help of a spectral library. The laser-induced breakdown spectra of 32 alloys were stored, with 25 of them chosen as library standards; the remaining seven spectra were used as samples. The composition of the alloys was obtained by flame atomic absorption spectrometry. A rank correlation method was applied for comparison between spectra, providing good correlation coefficients for the alloys studied. The composition of the samples was also predicted by partial least-squares regression to demonstrate the capability of this technique for the rapid analysis of this type of material.},
author = {Castro, M D Luque De},
doi = {10.1016/S0584-8547},
issn = {05848547},
journal = {Instrumentation},
keywords = {faas,flame atomic absorption spectrometry,jewellery alloys,laser induced breakdown spectroscopy,libs,rank correlation,spectral libraries},
number = {7},
pages = {1291--1299},
title = {{Rank correlation of laser-induced breakdown spectroscopic data for the identification of alloys used in jewelry manufacture}},
url = {http://www.sciencedirect.com/science/article/B6THN-48KFS5X-8/2/dd767e68a135591caf2387d34b64e2ee},
volume = {58},
year = {2003}
}
@article{Russo2009,
abstract = {In this review we discuss the application of laserinduced breakdown spectroscopy (LIBS) to the problem of detection of residues of explosives. Research in this area presented in open literature is reviewed. Both laboratory and field-tested standoff LIBS instruments have been used to detect explosive materials. Recent advances in instrumentation and data analysis techniques are discussed, including the use of double-pulse LIBS to reduce air entrainment in the analytical plasma and the application of advanced chemometric techniques such as partial leastsquares discriminant analysis to discriminate between residues of explosives and non-explosives on various surfaces. A number of challenges associated with detection of explosives residues using LIBS have been identified, along with their possible solutions. Several groups have investigated methods for improving the sensitivity and selectivity of LIBS for detection of explosives, including the use of femtosecond-pulse lasers, supplemental enhancement of the laser-induced plasma emission, and complementary orthogonal techniques. Despite the associated challenges, researchers have demonstrated the tremendous potential of LIBS for real-time detection of explosives residues at standoff distances.},
author = {Russo, Richard and Treado, Patrick J and Nelson, Matthew P},
file = {::},
journal = {Anal Bioanal Chem},
number = {I},
pages = {395:283},
title = {{A NEW STANDOFF CB DETECTION TECHNOLOGY BASED ON THE FUSION OF}},
volume = {300},
year = {2009}
}
@article{Zelenyuk2009,
abstract = {Recent improvements in single particle mass spectrometers make it possible to optically detect, size, and characterize the compositions of individual particles with diameters larger than a micron and smaller than 100 nm. In these instruments, two stages of optical detection are used to generate a precisely timed trigger pulse that is used to fire the ion generation laser or lasers. However, experience shows that the wide particle size range results in significant differences in laser trigger timing between small and large particles. If not treated these differences produce an instrument with size dependent hit-rate. In this case the operator is forced to optimize the instrument for the desired size range, while contending with a significantly lower hit-rate for other particle sizes. This article presents an analysis of the phenomenon and demonstrates that the dependence of laser trigger timing on particle size stems from the differences in the particle position within the detection laser beam at the instant of detection. We demonstrate that it is possible to compensate for these differences by generating, for each particle, a laser trigger delay coefficient that is a function of particle’s time of flight, i.e., its vacuum aerodynamic size. The study also shows that a single function can be used to eliminate the size bias for particles with a wide range of densities.},
author = {Zelenyuk, Alla and Yang, Juan and Imre, Dan and Choi, Eric},
doi = {10.1080/02786820802637915},
file = {::},
isbn = {0278682080263},
issn = {0278-6826},
journal = {Aerosol Science and Technology},
month = {mar},
number = {4},
pages = {305--310},
title = {{Achieving Size Independent Hit-Rate in Single Particle Mass Spectrometry}},
url = {http://www.tandfonline.com/doi/abs/10.1080/02786820802637915},
volume = {43},
year = {2009}
}
@article{Asgill2010,
abstract = {We explore the use of a combination of double-pulse and single-pulse laser-induced breakdown spectroscopy (LIBS) methodologies as a means of differentiating between solid-phase and gaseous-phase analytes (namely, carbon) in an aerosol stream. A range of spectral data was recorded for double-pulse and singlepulse configurations, including both ns and fs prepulse widths, while varying the gas-phase mass percentage of the carbon from about 10{\%} to 90{\%} for various fixed carbon concentrations. The carbon emission response, as measured by the peak-to-continuum ratio, was greater for the double-pulse configuration as compared with the single-pulse response and was also enhanced as the percentage of solid-phase carbon was increased. Using a combination of the double-pulse and single-pulse emission signals, a monotonically increasing response function was found to correlate with the percentage of gas-phase analyte. However, individual data points at the measured gas-phase percentages reveal considerable scatter from the predicted trend. Furthermore, the double-pulse to single-pulse ratio was only pronounced with the ns–ns configuration as compared with the fs–ns scheme. Overall, the LIBS methodology has been demonstrated as a potential means to discriminate between gas-phase and particulatephase fractions of the same elemental species in an aerosol, although future optimization of the temporal parameters should be explored to improve the precision and accuracy of this approach. © 2010 Optical Society of America},
author = {Asgill, Michael E and Brown, Michael S and Frische, Kyle and Roquemore, William M and Hahn, David W},
doi = {300.6365, 300.6210.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Asgill et al. - breakdown spectroscopy for distinguishing between gaseous and particulate phase analytes - 2010.pdf:pdf},
journal = {Applied Optics},
number = {13},
title = {breakdown spectroscopy for distinguishing between gaseous and particulate phase analytes},
volume = {49},
year = {2010}
}
@article{Malpica2005,
abstract = {BACKGROUND: As part of a program project to evaluate emerging optical technologies for cervical neoplasia, we performed fluorescence and reflectance spectroscopic examinations of patients with abnormal Papanicolaou smears. Biopsy specimens were taken from each area and measured optically, and study pathologists performed qualitative histopathologic readings. Several methodologic issues arose in this analysis: (1) the interpathologist and intrapathologist agreement between institutions for the 1790 biopsy specimens; (2) the interinstitutional agreement among the two institutions conducting the trials on 117 randomly chosen biopsy specimens; (3) the interinstitutional agreement among the two institutions and a third expert gynecologic pathologist to ensure the expert readings were comparable to those outside both institutions on 117 randomly chosen biopsy specimens; and (4) an additional three reviews of the 106 difficult biopsy specimens by all three institutions. METHODS: All 1790 specimens from 850 patients were reviewed three times at each institution in blinded fashion; those for which the first and second reviews were identical were not reviewed a third time. A randomly selected sample of 117 specimens was randomly ordered and read by study pathologists at The University of Texas M. D. Anderson Cancer Center, British Columbia Cancer Agency (BCCA), and Brigham and Women's Hospital (BWH). The 106 difficult cases were treated in the same manner as the randomized and random-ordered cases. Generalized, unweighted, and weighted kappas and their 95{\%} confidence intervals were used to assess agreement. Binary comparisons were used to compare diagnostic categories. FINDINGS: The kappas for the three readings of the overall data set using eight-category World Health Organization (WHO) criteria were as follows: 0.66 for the generalized, 0.72 for weighted, and ranged from 0.59 to 0.94 unweighted binary categories; those read using four-category Bethesda criteria: 0.70 for generalized, 0.69 for weighted, and 0.56-0.94 for unweighted binary categories. For the pool versus the study pathologist readings, the eight-category kappa was 0.51 for generalized, 0.72 for weighted, and 0.56-0.82 for unweighted binary categories; for those read using Bethesda criteria: 0.70 for generalized, 0.70 for weighted, and 0.59-0.82 for the unweighted binary categories. The interpathologist and intrapathologist readings were fair by Landis standards at the low end of the diagnostic scale (atypia, human papillomavirus, and CIN1) and substantial to almost perfect at the high end (CIN2, CIN3, and CIS). The randomly selected and randomly ordered sample of 117 specimens read with the WHO system yielded a generalized kappa of 0.45; among the three institutions (M. D. Anderson Cancer Center vs. BCCA, M. D. Anderson vs. BWH, and BCCA vs. BWH), the unweighted kappas were 0.46, 0.41, and 0.49 and the weighted were 0.65, 0.66, and 0.68, respectively; for the Bethesda, a generalized kappa of 0.65, unweighted kappas of 0.66, 0.65, and 0.47, and weighted of 0.74, 0.72, and 0.74. The difficult specimens read with the WHO system yielded a generalized kappa of 0.23; among the three institutions the unweighted kappas were 0.20, 0.30, and 0.37, and the weighted were 0.17, 0.34, and 0.31; for the Bethesda, a generalized kappa of 0.25; among the three institutions, the unweighted kappas were 0.21, 0.32, and 0.37, and the weighted were: 0.07, 0.21, and 0.37, respectively. INTERPRETATION: Kappas in this expert group of pathologists were in the moderate, substantial, and almost perfect ranges for the overall and randomized samples. The randomized sample was representative of the larger sample. The kappa of the specimens for which disagreements arose was, predictably, in the slight range. Our findings will aid both the correlations with optical measurements using fluorescence and reflectance spectroscopy and the quantitative histopathologic analysis of these study specimens.},
author = {Malpica, Anais and Matisic, Jasenka P and Niekirk, Dirk Van and Crum, Christopher P and Staerkel, Gregg A and Yamal, Jose-Miguel and Guillaud, Martial H and Cox, Dennis D and Atkinson, Edward Neely and Adler-Storthz, Karen and Poulin, Neal M and Macaulay, Calum A and Follen, Michele},
institution = {Department of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.},
journal = {Gynecologic Oncology},
number = {3 Suppl 1},
pages = {S38--S52},
pmid = {16183106},
title = {{Kappa statistics to measure interrater and intrarater agreement for 1790 cervical biopsy specimens among twelve pathologists: qualitative histopathologic analysis and methodologic issues.}},
volume = {99},
year = {2005}
}
@article{Yang2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is a rapid quantitative analytical technique that can be used to determine the elemental composition of numerous sample matrices, and it has been successfully applied in many types of samples. However, for chemically and physically complex soil samples, its quantitative analytical ability is controversial. Multivariate analytical techniques have great potential for analyzing the complex LIBS spectra. To demonstrate the feasibility of LIBS as an alternative technique to quantitatively analyze soil samples, the univariate and the partial least square (PLS) techniques are used to analyze the LIBS spectra of 12 soil samples and to build calibration models predicting Cu and Zn concentrations. The results show that PLS can significantly improve the analytical results compared with the univariate technique. The normalized root mean square error (NRMSE) and r2 of the univariate models are 16.60{\%} and 0.71 in calibration and 18.80{\%} and 0.62 in prediction for Cu and 18.97{\%} and 0.62 in calibration and 22.81{\%} and 0.45 in prediction for Zn. For the PLS models using the spectral range 300 to 350 nm, the NRMSE and r2 are 1.94{\%} and 0.99 for both Cu and Zn in calibration and 7.90{\%} and 0.94 for Cu and 8.14{\%} and 0.94 for Zn in prediction, respectively. Compared with the univariate technique, PLS improves the NRMSE 87.53{\%} and 87.78{\%} in calibration and 44.47{\%} and 53.44{\%} in prediction for Cu and Zn, respectively. The results indicate that PLS can improve the quantitative analytical ability of LIBS for soil sample analysis. (C) 2010 Lippincott Williams {\&} Wilkins, Inc.},
author = {Yang, Ningfang and Eash, Neal S and Lee, Jaehoon and Martin, Madhavi Z and Zhang, Yong-Seon and Walker, Forbes R and Yang, Jae E},
doi = {10.1097/SS.0b013e3181f516ea},
issn = {0038075X},
journal = {Soil Science},
keywords = {libs,multivariate analysis,pls,quantitative soil},
number = {9},
pages = {447--452},
title = {{Multivariate Analysis of Laser-Induced Breakdown Spectroscopy Spectra of Soil Samples}},
url = {http://content.wkhealth.com/linkback/openurl?sid=WKPTLP:landingpage{\&}an=00010694-201009000-00005},
volume = {175},
year = {2010}
}
@article{Mustafi2001,
abstract = {The catalytically competent active-site structure of a true acylenzyme reaction intermediate of TEM-1 beta-lactamase formed with the kinetically specific spin-labeled substrate 6-N-(2,2,5,5-tetramethyl-1-oxypyrrolinyl-3-carboxyl)-penicillanic acid isolated under cryoenzymologic conditions has been determined by angle-selected electron nuclear double resonance (ENDOR) spectroscopy. Cryoenzymologic experiments with use of the chromophoric substrate 6-N-3-(2-furanyl)-propen-2-oyl-penicillanic acid showed that the acylenzyme reaction intermediate could be stabilized in the -35 to -75 degrees C range with a half-life suitably long to allow freeze-quenching of the reaction species for ENDOR studies while a noncovalent Michaelis complex could be optically identified at temperatures only below -70 degrees C. The wild-type, Glu166Asn, Glu240Cys, and Met272Cys mutant forms of the mature enzyme were overexpressed in perdeuterated minimal medium to allow detection and assignment of proton resonances specific for the substrate and chemically modified amino acid residues in the active site. From analysis of the dependence of the ENDOR spectra on the setting of the static laboratory magnetic field H0, the dipolar contributions to the principal hyperfine coupling components were estimated to calculate the separations between the unpaired electron of the nitroxyl group and isotopically identified nuclei. These electron-nucleus distances were applied as constraints to assign the conformation of the substrate in the active site and of amino acid side chains by molecular modeling. Of special interest was that the ENDOR spectra revealed a water molecule sequestered in the active site of the acylenzyme of the wild-type protein that was not detected in the deacylation impaired Glu166Asn mutant. On the basis of the X-ray structure of the enzyme, the ENDOR distance constraints placed this water molecule within hydrogen-bonding distance to the carboxylate side chain of glutamate-166 as if it were poised for nucleophilic attack of the scissile ester bond. The ENDOR results provide experimental evidence of glutamate-166 in its functional role as the general base catalyst in the wild-type enzyme for hydrolytic breakdown of the acylenzyme reaction intermediate of TEM-1 beta-lactamase.},
author = {Mustafi, D and Sosa-Peinado, A and Makinen, M W},
institution = {Department of Biochemistry and Molecular Biology, The University of Chicago, Cummings Life Science Center, 920 East 58th Street, Chicago, Illinois 60637, USA.},
journal = {Biochemistry},
number = {8},
pages = {2397--2409},
pmid = {11327860},
title = {{ENDOR structural characterization of a catalytically competent acylenzyme reaction intermediate of wild-type TEM-1 beta-lactamase confirms glutamate-166 as the base catalyst.}},
volume = {40},
year = {2001}
}
@article{Zhang2008,
abstract = {In the present paper, the productions by applying laser-induced plasma spectral analysis technique in different research fields were summarized. Many examples of the application based on laser-induced breakdown spectroscopy (LIBS) and laser-induced plasma spectroscopy (LIPS) methods were introduced, including the substance composition and correlative characteristics of the solid samples (e.g. metal alloy, soil, concrete, mineral, fossil, medicine etc.), liquid samples (e.g. solution, pure water, liquid jets etc.), and gaseous samples (e.g. air, pure gas, vapor and aerosol etc.). Some other investigations and applications were also included. The factors, which influence the detection capability, were discussed. Laser wavelength, pulse energy, power density, environmental atmosphere, external electric field, carbon layer on sample surface, sample material characteristic, and so on all have effects on the precision and the limit of detection. Finally, a simple introduction of the improvements in experimental equipment and methods was also covered. The development of laser-induced plasma spectral analysis technique creates favorable conditions, such as convenience and shortcut, for many science and application researches. It plays an important role in the progress in science and technology.},
author = {Zhang, Xiao-Ping and Chen, Jin-Zhong and Guo, Qing-Lin and Huai, Su-Fang and Wei, Yan-Hong},
institution = {College of Physics Science and Technology, Hebei University, Baoding 071002, China.},
journal = {Guang pu xue yu guang pu fen xi Guang pu},
number = {3},
pages = {656--662},
pmid = {18536436},
title = {{The current development of laser-induced plasma spectral analysis technique}},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve{\&}db=PubMed{\&}dopt=Citation{\&}list{\_}uids=18536436},
volume = {28},
year = {2008}
}
@article{Ismael2011,
abstract = {Time-saving, low-cost analyses of soil contamination are required to ensure fast and efficient pollution removal and remedial operations. In this work, laser-induced breakdown spectroscopy (LIBS) has been successfully applied to in situ analyses of polluted soils, providing direct semi-quantitative information about the extent of pollution. A field campaign has been carried out in Brittany (France) on a site presenting high levels of heavy metal concentrations. Results on iron as a major component as well as on lead and copper as minor components are reported. Soil samples were dried and prepared as pressed pellets to minimize the effects of moisture and density on the results. LIBS analyses were performed with a Nd:YAG laser operating at 1064 nm, 60 mJ per 10 ns pulse, at a repetition rate of 10 Hz with a diameter of 500 $\mu$m on the sample surface. Good correlations were obtained between the LIBS signals and the values of concentrations deduced from inductively coupled plasma atomic emission spectroscopy (ICP-AES). This result proves that LIBS is an efficient method for optimizing sampling operations. Indeed, "LIBS maps" were established directly on-site, providing valuable assistance in optimizing the selection of the most relevant samples for future expensive and time-consuming laboratory analysis and avoiding useless analyses of very similar samples. Finally, it is emphasized that in situ LIBS is not described here as an alternative quantitative analytical method to the usual laboratory measurements but simply as an efficient time-saving tool to optimize sampling operations and to drastically reduce the number of soil samples to be analyzed, thus reducing costs. The detection limits of 200 ppm for lead and 80 ppm for copper reported here are compatible with the thresholds of toxicity; thus, this in situ LIBS campaign was fully validated for these two elements. Consequently, further experiments are planned to extend this study to other chemical elements and other matrices of soils.},
author = {Isma{\"{e}}l, Amina and Bousquet, Bruno and {Michel-Le Pierr{\`{e}}s}, Karine and Travaill{\'{e}}, Gr{\'{e}}goire and Canioni, Lionel and Roy, St{\'{e}}phane},
institution = {LOMA CNRS-Universit{\'{e}} Bordeaux, Talence, France.},
journal = {Applied Spectroscopy},
number = {5},
pages = {467--473},
pmid = {21513588},
title = {{In situ semi-quantitative analysis of polluted soils by laser-induced breakdown spectroscopy (LIBS).}},
volume = {65},
year = {2011}
}
@article{Mosier-Boss2005,
abstract = {At Naval Base Point Loma in San Diego, California, a canyon had been filled with construction debris and automotive scrap residue (ASR), the latter of which included lead acid batteries. A magnetic survey and induced potential (IP)/DC resistivity survey showed the presence of anomalies at the western end of the site where historic records indicated that the ASR had been placed. Lead concentration depth profiles were obtained in situ and in real time at the site using a direct push fiber-optic laser-induced breakdown spectroscopy (FO-LIBS) sensor probe. Lead, along with strontium and titanium, was detected at depths of 7 to 8 m bgs. These results provided confirmation that the magnetic/IP anomalies at the site are due to ASR.},
author = {Mosier-Boss, P A and Lieberman, S H},
institution = {SPAWAR Systems Center San Diego, Code 237, San Diego, California 92152, USA.},
journal = {Applied Spectroscopy},
number = {12},
pages = {1445--1456},
pmid = {16390582},
title = {{Detection of lead derived from automotive scrap residue using a direct push fiber-optic laser-induced breakdown spectroscopy metal sensor.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16390582},
volume = {59},
year = {2005}
}
@article{Hauser2002,
abstract = {A mobile Laser-Induced Breakdown Detection (LIBD) system is developed for the field study of the aquatic colloid migration. The principle of LIBD is based on the plasma generation at breakdown of colloids in the laser focus region, which is then observed by either photo-acoustic detection or optical monitoring. The method provides information on the number density and average size of colloids. The present instrumentation built up particularly for the field study is applied for the aquatic colloid migration in a natural granite fracture. The study is performed within the Colloid and Radionuclide Retention project (CRR) in order to investigate the role of colloids on the radionuclide migration, For this purpose, bentonite colloids dispersed in granite groundwater are injected into a rock fracture zone with a dipole distance of 5 m. After passing through the fracture, the groundwater is guided into a flow-through detection cell of LIBD for the quantification of colloids. Another experiment is performed with the same colloids traced by tetra- and tri-valent metal ions, Th(IV), Hf(IV) and Tb(III). The recovery of colloids as found by LIDB appears to be about 55 5{\%} of the injected colloid mass concentration, which is corroborated by ICP-MS analysis of Al present in bentonite colloids. An average size of recovered colloids is slightly decreased from the value of before injection and hence the relative number density increased in the course of the rock fracture migration. Recovered fractions of colloid-borne trace elements in the extracted groundwater are 78 8{\%} for both tetra-valent elements and 33 3{\%} for trivalent element of the originally traced concentrations. Plausible explanations are given for the different recoveries of heavy metal ions. (C) 2002 Elsevier Science B.V. All rights reserved.},
author = {Hauser, W and Geckeis, H and Kim, J I and Fierz, Th},
issn = {09277757},
journal = {Colloids and Surfaces A Physicochemical and Engineering Aspects},
keywords = {aquifer,colloids,laser induced breakdown detection,migration,optical detection,particles},
number = {1-3},
pages = {37--45},
title = {{A mobile laser-induced breakdown detection system and its application for the in situ-monitoring of colloid migration}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S092777570101086X},
volume = {203},
year = {2002}
}
@article{Schmidt2002,
abstract = {Elemental analysis of solutions can be achieved by concentrating and immobilizing the metal ions into a commercially available ion exchange polymer membrane followed by laser-induced breakdown spectroscopy. Two methods of sample preparation were investigated: filtering the solution through the ion exchange membrane with suction, and placing the membrane in the solution and allowing the ions to equilibrate with the membrane. The membrane was then ablated with the focused energy of a Nd:YAG laser at 1064 nm. The emitted light was collected by an echelle spectrometer through a fiber-optic cable and detected with an intensified charge-coupled device (CCD). Ten different metals, most covered by the Resource Conservation and Recovery Act (RCRA), were studied. The concentrations of barium, cadmium, chromium, cobalt, copper, silver, lead, mercury, nickel, and zinc can be measured simultaneously with limits of detection ranging from 2 $\mu$g/mL to 4 ng/mL. The linear range is 2-6 orders of magnitude depending upon the element and sampling method. The major advantages of the technique are the multielement capability and the ease of sample preparation.},
author = {Schmidt, Norman E and Goode, Scott R},
doi = {10.1366/0003702021954746},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {3},
pages = {370--374},
title = {{Analysis of Aqueous Solutions by Laser-Induced Breakdown Spectroscopy of Ion Exchange Membranes}},
url = {http://www.ingentaconnect.com/content/sas/sas/2002/00000056/00000003/art00015},
volume = {56},
year = {2002}
}
@article{Sun2009a,
abstract = {A simplified procedure for correcting self-absorption effect was proposed in calibration-free laser-induced breakdown spectroscopy (CF-LIBS). In typical LIBS measurement conditions, the plasma produced is often optically thick, especially for the strong lines of major elements. The selection of self-absorption lines destroys the performance of CF-LIBS, and the familiar correction method based on the curve of growth is complex in implementation. The procedure we proposed, named internal reference for self-absorption correction (IRSAC), first chose an internal reference line for each species, then compared other spectral line intensity of the same species with the reference line to estimate the self-absorption degrees of other spectral lines, and finally achieved an optimal correction by a regressive algorithm. The self-absorption effect of the selected reference line can be ignored, since the reference line with high excitation energy of the upper level is slightly affected by the self-absorption. Through the IRSAC method, the points on the Boltzmann plot become more regular, and the evaluations of the plasma temperature and material composition are more accurate than the basic CF-LIBS.},
author = {Sun, Lanxiang and Yu, Haibin},
institution = {Key Laboratory of Industrial Informatics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China. sunlanxiang@sia.cn},
journal = {Talanta},
number = {2},
pages = {388--395},
pmid = {19559895},
title = {{Correction of self-absorption effect in calibration-free laser-induced breakdown spectroscopy by an internal reference method.}},
url = {http://www.sciencedirect.com/science/article/B6THP-4W1BV4C-1/2/83a2682b053487810ff4fa18d1cedc03},
volume = {79},
year = {2009}
}
@article{Huang2002,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is applied to detect trace metals contained in liquids. The sample in the form of liquid droplets is generated with an electrospray ionization needle. The microdroplets are interacted with an impinging laser pulse approximately 2 mm downstream from the needle tip. A sequence of single-shot time-resolved LIB emission signals of Na, K and Al is detected, respectively. The LIB signal intensity integrated within a gate linearly correlates with the plasma current obtained simultaneously on a single-shot basis. The correlation plot exhibits a straight line, of which the slope increases with the sample concentration. Given the calibration curves and the focused cross-sections of the incident laser beam, the detection limits may be determined to be 0.630.02 (0.3 pg), 1.20.1 (0.5 pg), and 435 mg/l (21 pg) for Na, K, and Al, respectively. As compared to the correlation methods applied, our treatment is more straightforward to yield concentration information and the resulting detection limits are comparable to those reported previously. The dependence of the correlation plot on the adopted laser energy and wavelength is also characterized. The detection limits tend to be improved by applying a laser with larger pulse energy but shorter wavelengths.},
author = {Huang, Jer-Shing and Ke, Ching-Bin and Huang, Li-Shing and Lin, King-Chuen},
doi = {10.1016/S0584-8547(01)00349-4},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {correlation method,electrospray ionization,elemental analysis,laser induced breakdown spectroscopy},
number = {1},
pages = {35--48},
title = {{The correlation between ion production and emission intensity in the laser-induced breakdown spectroscopy of liquid droplets}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701003494},
volume = {57},
year = {2002}
}
@article{Sun2009,
abstract = {In laser-induced breakdown spectroscopy (LIBS), plasma emission is extremely unstable because of many factors, such as the fluctuation of laser energy, inhomogeneity of sample surfaces, and variable distance between lens and samples. Therefore, the detection and correction of varying continuum background emission are not easily accomplished. The aim of this work is to present a method that can automatically estimate and correct varying continuum background emission, which is representative in laser-induced plasma. In this method, we first find all minima on a spectrum, and then deduct the unreasonable minima by a proper threshold. Finally, we use one or multiple polynomial functions through the minima left to approximate the continuum backgrounds. The validity of this method was evaluated by using several spectra with different complexities and wavelength ranges. We also applied this method to optimize the measurement time delays of detectors. In addition, for five aluminum alloy samples, we compared their elemental calibration cures between original spectra and background-corrected spectra. Experimental results proved that the method proposed in this paper can well estimate varying continuum backgrounds over a wide range of wavelengths.},
author = {Sun, Lanxiang and Yu, Haibin},
doi = {10.1016/j.sab.2009.02.010},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {background estimation,laser induced breakdown spectroscopy},
number = {3},
pages = {278--287},
publisher = {Elsevier B.V.},
title = {{Automatic estimation of varying continuum background emission in laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709000378},
volume = {64},
year = {2009}
}
@article{Adamson2007,
abstract = {Laser-induced breakdown spectroscopy (LIBS), which is an excellent tool for trace elemental analysis, was studied as a method of detecting sub-part-per-10(6) (ppm) concentrations of aluminum in surrogates of human tissue. Tissue was modeled using a 2{\%} agarose gelatin doped with an Al(2)O(3) nanoparticle suspension. A calibration curve created with standard reference samples of known Al concentrations was used to determine the limit of detection, which was less than 1 ppm. Rates of false negative and false positive detection results for a much more realistic sampling methodology were also studied, suggesting that LIBS could be a candidate for the real-time in vivo detection of metal contamination in human soft tissue.},
author = {Adamson, Marian D and Rehse, Steven J},
file = {:C$\backslash$:/Users/LASER/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Adamson, Rehse - 2007 - Detection of trace Al in model biological tissue with laser-induced breakdown spectroscopy.pdf:pdf},
institution = {Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, USA.},
journal = {Applied Optics},
keywords = {aluminum,aluminum analysis,aluminum chemistry,aluminum oxide,aluminum oxide chemistry,biological,calcium,calcium chemistry,calibration,equipment design,false negative reactions,false positive reactions,humans,lasers,models,optics photonics,roc curve,sensitivity specificity,sepharose,sepharose chemistry,time factors,trace elements,trace elements analysis},
number = {23},
pages = {5844--5852},
pmid = {17694134},
title = {{Detection of trace Al in model biological tissue with laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17694134},
volume = {46},
year = {2007}
}
@article{Morel2003,
abstract = {A laser-induced breakdown spectroscopy technique for analyzing biological matter for the detection of biological hazards is investigated. Eight species were considered in our experiment: six bacteria and two pollens in pellet form. The experimental setup is described, then a cumulative intensity ratio is proposed as a quantitative criterion because of its linearity and reproducibility. Time-resolved laser-induced breakdown spectroscopy (TRELIBS) exhibits a good ability to differentiate among all these species, whatever the culture medium, the species or the strain. Thus we expect that TRELIBS will be a good candidate for a sensor of hazards either on surfaces or in ambient air.},
author = {Morel, S. and Leone, N. and Adam, P. and Amouroux, J.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Morel et al. - Detection of bacteria by time-resolved laser-induced breakdown spectroscopy. - 2003.pdf:pdf},
journal = {Applied optics},
number = {30},
pages = {6184--6191},
publisher = {Optical Society of America},
title = {{Detection of bacteria by time-resolved laser-induced breakdown spectroscopy}},
url = {http://www.opticsinfobase.org/abstract.cfm?{\&}amp;id=77650},
volume = {42},
year = {2003}
}
@article{Fichet1999,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was applied to detect elements in different liquids (water and oil). Spectra of plasmas generated by focusing the second harmonic $\lambda$ = 532 nm of a pulsed Nd:YAG laser on the liquids' surfaces at atmospheric pressure were recorded. Calibration curves for chromium in water and in oil were obtained, and detection limits were deduced. Springer-Verlag 1999.},
author = {Fichet, P and Toussaint, A and Wagner, J F},
doi = {10.1007/s003390051482},
issn = {09478396},
journal = {Applied Physics A Materials Science Processing},
number = {7},
pages = {591--592},
title = {{Laser-induced breakdown spectroscopy: A tool for analysis of different types of liquids}},
url = {http://dx.doi.org/10.1007/s003390051482},
volume = {69},
year = {1999}
}
@article{Goode1997,
author = {Goode, Scott R and Angel, S Michael},
journal = {Imaging},
number = {November},
title = {{A Fundamental Study of Laser-Induced Breakdown Spectroscopy Using Fiber Optics for Remote Measurements of Trace Metals}},
volume = {305},
year = {1997}
}
@article{Rehse2010,
abstract = {Laser-induced breakdown spectroscopy has been utilized to classify and identify bacterial specimens on the basis of their atomic composition. We have characterized the effect that the presence of a second bacterial species in the ablated specimen had on the identification of the majority species. Specimens with a reduced number of bacterial cells (approximately 2500) were identified with 100{\%} accuracy when compared to undiluted specimens. In addition, a linear dependence of the total spectral power as a function of cell number was determined. Lastly, a high selectivity was obtained for a LIBS-based analysis of nine separate bacterial strains from four genera.},
author = {Rehse, Steven J and Mohaidat, Qassem I and Palchaudhuri, Sunil},
doi = {10.1364/AO.49.000C27},
file = {::},
issn = {00036935},
journal = {Applied Optics},
number = {13},
pages = {27--35},
title = {{Towards the clinical application of laser-induced breakdown spectroscopy for rapid pathogen diagnosis: the effect of mixed cultures and sample dilution on bacterial identification}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=ao-49-13-C27},
volume = {49},
year = {2010}
}
@article{Whitehouse2001,
abstract = {We report on a novel design 75-m length umbilical fiber-optic LIBS (FOLIBS) system suitable for remotely determining the copper content of 316H austenitic stainless steel superheater bifurcation tubing within the pressure vessels of Advanced Gas Cooled Reactor (AGR) nuclear power stations. The system was deployed during the routine reactor outage programs for Hunterston `B' and Hinkley Point `B' stations during the summer of 1999 and used successfully to determine the copper content of the bifurcations over the range 0.04{\%}<0.60{\%} (by mass). Measurement times per bifurcation were typically less than 3 min and measurement accuracy was approximately 25{\%}.},
author = {Whitehouse, A I and Young, J and Botheroyd, I M and Lawson, S and Evans, C P and Wright, J},
doi = {10.1016/S0584-8547(01)00232-4},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {advanced gas cooled reactor,analysis,fiber optic libs {\v{z}} folibs,laser induced breakdown spectroscopy {\v{z}},libs,nuclear power station,remote inspection,semi quantitative elemental,{\v{z}} agr},
number = {6},
pages = {821--830},
title = {{Remote material analysis of nuclear power station steam generator tubes by laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701002324},
volume = {56},
year = {2001}
}
@article{Bulatov2003,
abstract = {Cavity ring-down laser absorption spectroscopy (CRLAS) was applied for the first time to detection and characterization of laser breakdown generated aerosols. The method provided time-resolved morphological information on the aerosol plume, which is of importance in laser ablation (LA) and deposition, in laser-induced breakdown spectroscopy (LIBS) analysis, and in laser ablation inductively coupled plasma (LA-ICP) methods. This method provides sensitive detection of a variety of aerosols produced under ambient conditions. The morphological investigation revealed that the aerosol density has a reproducible pattern as a function of distance from the surface, although its details depend on time, on geometrical parameters and on the surface characteristics.},
author = {Bulatov, Valery and Khalmanov, Aktam and Schechter, Israel},
institution = {Department of Chemistry, Technion-Israel Institute of Technology, 32000, Haifa, Israel.},
journal = {Analytical and Bioanalytical Chemistry},
keywords = {aerosols,cavity ring down,laser ablation,laser induced breakdown spectroscopy,libs},
number = {8},
pages = {1282--1286},
pmid = {12733051},
publisher = {Springer},
title = {{Study of the morphology of a laser-produced aerosol plume by cavity ringdown laser absorption spectroscopy.}},
url = {http://www.springerlink.com/index/PVJY29HL9NVYLVYN.pdf},
volume = {375},
year = {2003}
}
@article{Morozov2006,
abstract = {Abstract The radiation hardness and mechanical strength of single-and two-phase glasses are studied for the case when nanosecond laser pulses ($\lambda$= 1.06 $\mu$m, $\tau$0.5 12.5 ns) are focused inside the material. Laser interferometry is applied to measure the displacement of the free surface, find optical breakage thresholds, and carry out the fractographic analysis of damaged regions. It is shown that breakdown channels and damage regions develop in a nonlinear manner according to optical breakdown mechanisms, changing each other with an increase in the laser energy. The strength of the two-phase glass is found to be more than four times that of the single-phase glass, although their elastic properties differ insignificantly. Such a considerable difference in the hardness of these materials with chemically similar constitutents is attributed to the presence of the double-lattice nanometer-scale structure of the two-phase glass.},
author = {Morozov, N and Startsev, Yu and Sud’enkov, Yu and Suslikov, A and Baranov, G and Belyaev, A},
doi = {10.1134/S1063784206070097},
journal = {Technical Physics},
number = {7},
pages = {872--877},
title = {{Laser-induced breakdown threshold and fracture versus the nanostructure of two-phase glass}},
url = {http://dx.doi.org/10.1134/S1063784206070097},
volume = {51},
year = {2006}
}
@article{Sarkar2009,
abstract = {Laser induced breakdown spectroscopy (LIBS) was applied to the determination of sub-ppm levels of boron in ground water samples using spectroscopically pure graphite planchets as solid support. The data obtained by LIBS agreed well with those from ICP-AES. No spectral interference due to the possibly interfering elements Fe, Cr, Al and Mo was observed. The detection limit was 0.01 A mu g.g(-1) for boron using the B(I) 249.773 nm emission line. The method is considered to be promising for the rapid determination of boron, with an acceptable degree of accuracy and without the need for elaborate sample treatment, preconcentration and purification steps.},
author = {Sarkar, Arnab and Aggarwal, Suresh K and Sasibhusan, K and Alamelu, D},
doi = {10.1007/s00604-009-0259-7},
issn = {00263672},
journal = {Microchimica Acta},
keywords = {boron,ground water,laser induced breakdown spectroscopy,libs,spectral interference},
number = {1-2},
pages = {65--69},
title = {{Determination of sub—ppm levels of boron in ground water samples by laser induced breakdown spectroscopy}},
url = {http://www.springerlink.com/index/10.1007/s00604-009-0259-7},
volume = {168},
year = {2009}
}
@article{Martin2003,
abstract = {The technique of laser-induced breakdown spectroscopy has been used for the first time to our knowledge for the identification of metals such as palladium and silver that were dispersed in bacterial cellulose membranes. These results for palladium-dispersed films have been correlated to a calibration curve obtained by use of atomic absorption spectroscopy and were found to be in good agreement. The experiments were conducted by use of wet and dry metal-doped membranes. The metal peaks obtained with a dry membrane are greater than five times higher in signal-to-background ratio than when metals are detected by a hydrated membrane. The advantage of this laser-based technique is that minimal sample handling and sample preparation are needed and measurements are completed in real time (a few seconds). Hence this technique can be used for the detection of metals in dry membranes that would be used in the construction of electrode assemblies.},
author = {Martin, Madhavi and Evans, Barbara and O'Neill, Hugh and Woodward, Jonathan},
institution = {Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6038, USA. martinm1@ornl.gov},
journal = {Applied Optics},
keywords = {adsorption,artificial,atomic,atomic methods,cellulose,cellulose analysis,cellulose chemistry,feasibility studies,gluconacetobacter xylinus,gluconacetobacter xylinus chemistry,hot temperature,lasers,membranes,palladium,palladium analysis,palladium chemistry,silver,silver analysis,silver chemistry,spectrophotometry,spectrum analysis,spectrum analysis methods},
number = {30},
pages = {6174--6178},
pmid = {14594081},
title = {{Laser-induced breakdown spectroscopy used to detect palladium and silver metal dispersed in bacterial cellulose membranes.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594081},
volume = {42},
year = {2003}
}
@article{Windom2011,
abstract = {Molybdenum disulfide (MoS2) and molybdenum trioxide are investigated using Raman spectroscopy with emphasis on the application to tribological systems. The Raman vibrational modes were investigated for excitation wavelengths at 632.8 and 488 nm using both micro-crystalline MoS2 powder and natural MoS2 crystals. Differences are noted in the Raman spectra for these two different wavelengths, which are attributed to resonance effects due to overlap of the 632.8 nm source with electronic absorption bands. In addition, significant laser intensity effects are found that result in laser-induced transformation of MoS2 to MoO3. Finally, the transformation to molybdenum trioxide is explored as a function of temperature and atmosphere, revealing an apparent transformation at 375 K in the presence of oxygen. Overall, Raman spectroscopy is an useful tool for tribological study of MoS2 coatings, including the role of molybdenum trioxide transformations, although careful attention must be given to the laser excitation parameters (both wavelength and intensity) when interpreting Raman spectra.},
author = {Windom, Bret C. and Sawyer, W. G. and Hahn, David W.},
doi = {10.1007/s11249-011-9774-x},
file = {::},
issn = {1023-8883},
journal = {Tribology Letters},
keywords = {molybdenum disulfide {\'{a}} raman,spectroscopy,{\'{a}} oxidation resistance},
month = {mar},
number = {3},
pages = {301--310},
title = {{A Raman Spectroscopic Study of MoS2 and MoO3: Applications to Tribological Systems}},
url = {http://www.springerlink.com/index/10.1007/s11249-011-9774-x},
volume = {42},
year = {2011}
}
@article{Rehse2009,
abstract = {Nanosecond single-pulse laser-induced breakdown spectroscopy LIBS has been used to discriminate between two different genera of Gram-negative bacteria and between several strains of the Escherichia coli bacterium based on the relative concentration of trace inorganic elements in the bacteria. Of particular importance in all such studies to date has been the role of divalent cations, specifically Ca2+ and Mg2+, which are present in the membranes of Gram-negative bacteria and act to aggregate the highly polar lipopolysaccharide molecules. We have demonstrated that the source of emission from Ca and Mg atoms observed in LIBS plasmas from bacteria is at least partially located at the outer membrane by intentionally altering membrane biochemistry and correlating these changes with the observed changes in the LIBS spectra. The definitive assignment of some fraction of the LIBS emission to the outer membrane composition establishes a potential serological, or surface-antigen, basis for the laser-based identification. E. coli and Pseudomonas aeruginosa were cultured in three nutrient media: trypticase soy agar as a control, a MacConkey agar with a 0.01{\%} concentration of bile salts including sodium deoxycholate, and a trypticase soy agar with a 0.4{\%} deoxycholate concentration. The higher concentration of deoxycholate is known to disrupt bacterial outer membrane integrity and was expected to induce changes in the observed LIBS spectra. Altered LIBS emission was observed for bacteria cultured in this 0.4{\%} medium and laser ablated in an all-argon environment. These spectra evidenced a reduced calcium emission and in the case of one species, a reduced magnesium emission. Culturing on the lower 0.01{\%} concentration of bile salts altered the LIBS spectra for both the P. aeruginosa and two strains of E. coli in a highly reproducible way, although not nearly as significantly as culturing in the higher concentration of deoxycholate did. This was possibly due to the accumulation of divalent cations around the bacteria by the formation of an extracellular polysaccharide capsule. Lastly, a discriminant function analysis demonstrated that in spite of alterations in the LIBS spectrum induced by growth in the three different media, the analysis could correctly identify all samples better than 90{\%} of the time. This encouraging result illustrates the potential utility of LIBS as a rapid bacteriological identification technology. © 2009 American Institute of Physics},
author = {Rehse, Steven J. and Jeyasingham, Narmatha and Diedrich, Jonathan and Palchaudhuri, Sunil},
issn = {00218979},
journal = {Journal of Applied Physics},
number = {10},
pages = {102034},
title = {{A membrane basis for bacterial identification and discrimination using laser-induced breakdown spectroscopy}},
url = {http://link.aip.org/link/JAPIAU/v105/i10/p102034/s1{\&}Agg=doi},
volume = {105},
year = {2009}
}
@article{Babankova2006a,
abstract = {Large-scale plasma was created in molecular gases (CO, CO2, N2, H2O) and their mixtures by high-power laser-induced dielectric breakdown (LIDB). Compositions of the mixtures used are those suggested for the early earth's atmosphere of neutral and/or mildly reducing character. Time-integrated optical spectra emitted from the laser spark have been measured and analyzed. The spectra of the plasma generated in the CO-containing mixtures are dominated by emission of both C2 and CN radicals. A vibrational temperature of approximately 10(4) K was determined according to an intensity distribution in a vibronic structure of the CN (B2Sigma(+)u-X2Sigma(+)g) violet band. For comparison, the NH3-CH4-H2-H2O mixture has been irradiated as a model of the strongly reducing version of the early earth's atmosphere. In this mixture, excited CN seems to be significantly less abundant than C2. The LIDB experiments were in the molecular gases carried out not only in the static cell but also using a large, double stream pulse jet (gas puff target) placed in the vacuum interaction chamber. The obtained soft X-ray emission spectra indicate the presence of highly charged atomic ions in the hot core of high-power laser sparks.},
author = {Babankova, Dagmar and Civis, Svatopluk and Juha, Libor and Bittner, Michal and Cihelka, Jaroslav and Pfeifer, Miroslav and Skala, Jir{\'{\i}} and Bartnik, Andrzej and Fiedorowicz, Henryk and Mikolajczyk, Janusz and Ry{\'{c}}, Leszek and Sedivcova, Tereza},
institution = {J. Heyrovsk{\'{y}} Institute of Physical Chemistry, Czech Academy of Sciences, Dolejskova 3, 182 23 Prague 8, Czech Republic.},
journal = {The Journal of Physical Chemistry A},
number = {44},
pages = {12113--12120},
pmid = {17078605},
title = {{Optical and X-ray emission spectroscopy of high-power laser-induced dielectric breakdown in molecular gases and their mixtures.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17078605},
volume = {110},
year = {2006}
}
@article{Galbacs2005,
abstract = {A portable laser induced breakdown spectrometer (LIBS), built around a microscope using a Q-switched Nd:GGG laser releasing multiple pulses and a non-intensified fiber optic spectrometer, was used to investigate the signal improvement of emission data achievable by the multiple-pulse approach. LIBS experiments were carried out in air and using Al, Cu, Si and Zn metallic targets. It was found that the use of 7 laser pulses, separated by ca. 25 micro signs time intervals, enhance line emissions by a factor of 2.5 to 129 with respect to the single-pulse case, and also decrease the relative standard deviation of the signal based on five consecutive measurements to 2-5{\%}. Time-resolved emission data and the observation of ablation craters suggest that the signal enhancement is mainly attributable to the reheating of the plasma by multiple laser pulses.},
author = {Galb{\'{a}}cs, G{\'{a}}bor and Budav{\'{a}}ri, Vikt{\'{o}}ria and Geretovszky, Zsolt},
doi = {10.1039/b504373e},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {9},
pages = {974},
title = {{Multi-pulse laser-induced plasma spectroscopy using a single laser source and a compact spectrometer}},
url = {http://xlink.rsc.org/?DOI=b504373e},
volume = {20},
year = {2005}
}
@article{Yang2007,
abstract = {An acoustic transducer based on a fiber Bragg grating (FBG) is presented and characterized for use in time-resolved laser-induced photoacoustic spectroscopy (PAS) on solid samples. The photoacoustic wave was generated by pulsed laser excitation of immobilized carbon black or erbium oxide powder, and detected by recording either the transmission or reflection spectrum of a clamped fiber Bragg grating (FBG). The characterization of the FBGs photoacoustic response is based on the experimental comparison with a static lateral strain source and on theoretical analysis using the piecewise-uniform approach to photoelastic theory. The temporal resolution of the response is determined by the arrangement of the FBG with respect to the source of the acoustic wave and is better than 150 ns, as was verified in a deconvolution analysis. The method has not only a fast time response but also is simple, inexpensive, and accurate as indicated by the good agreement of the experimental photoacoustic spectrum with previous measurements. Crown Copyright (C) 2007 Published by Elsevier B.V. All rights reserved.},
author = {Yang, Qingxin and Barnes, Jack and Loock, Hans-peter and Pedersen, David},
doi = {10.1016/j.optcom.2007.03.075},
issn = {00304018},
journal = {Optics Communications},
keywords = {acousto optic spectro,chemical sensing,er 2 o 3,erbium oxide,fbg,fiber bragg grating,laser induced opto acoustic spectroscopy,lioas,pas,photoacoustic spectroscopy,scopy},
number = {1},
pages = {97--106},
title = {{Time-resolved photoacoustic spectroscopy using fiber Bragg grating acoustic transducers}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0030401807003707},
volume = {276},
year = {2007}
}
@article{Cheri2011,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been applied to the analysis of toxic metals Pb and Cd in Pb(NO3)2 and Cd(NO3)2.4H2O aqueous solutions, respectively. The plasma is generated by focusing a nanosecond Nd:YAG ($\lambda$=1064nm) laser on the surface of liquid in the homemade liquid jet configuration. With an assumption of local thermodynamic equilibrium (LTE), calibration curves of Pb and Cd were obtained at different delay times between 1 to 5$\mu$s. The temporal behavior of limit of detections (LOD) was investigated and it is shown that the minimum LODs for Pb and Cd are 4 and 68 parts in 10(6) (ppm), respectively. In order to demonstrate the correctness of the LTE assumption, plasma parameters including plasma temperature and electron density are evaluated, and it is shown that the LTE condition is satisfied at all delay times.},
author = {Cheri, M Sadegh and Tavassoli, S H},
doi = {10.1364/AO.50.001227},
file = {::},
institution = {Laser and Plasma Research Institute, Shahid Beheshti University, Tehran, Iran.},
journal = {Applied Optics},
number = {9},
pages = {1227--1233},
pmid = {21460994},
title = {{Quantitative analysis of toxic metals lead and cadmium in water jet by laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21460994},
volume = {50},
year = {2011}
}
@article{Smith2000,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has become a very popular analytical method in the last decade in view of some of its unique features such as applicability to any type of sample, practically no sample preparation, remote sensing capability, and speed of analysis. The technique has a remarkably wide applicability in many fields, and the number of applications is still growing. From an analytical point of view, the quantitative aspects of LIBS may be considered its Achilles' heel, first due to the complex nature of the laser-sample interaction processes, which depend upon both the laser characteristics and the sample material properties, and second due to the plasma-particle interaction processes, which are space and time dependent. Together, these may cause undesirable matrix effects. Ways of alleviating these problems rely upon the description of the plasma excitation-ionization processes through the use of classical equilibrium relations and therefore on the assumption that the laser-induced plasma is in local thermodynamic equilibrium (LTE). Even in this case, the transient nature of the plasma and its spatial inhomogeneity need to be considered and overcome in order to justify the theoretical assumptions made. This first article focuses on the basic diagnostics aspects and presents a review of the past and recent LIBS literature pertinent to this topic. Previous research on non-laser-based plasma literature, and the resulting knowledge, is also emphasized. The aim is, on one hand, to make the readers aware of such knowledge and on the other hand to trigger the interest of the LIBS community, as well as the larger analytical plasma community, in attempting some diagnostic approaches that have not yet been fully exploited in LIBS.},
author = {Smith, Coleman A},
doi = {10.1063/1.1292305},
issn = {0094243X},
journal = {Aip Conference Proceedings},
number = {12},
pages = {305--306},
pmid = {21144145},
publisher = {Aip},
title = {{Laser induced breakdown spectroscopy (LIBS) applied to plutonium analysis}},
url = {http://link.aip.org/link/?APC/532/305/1{\&}Agg=doi},
volume = {532},
year = {2000}
}
@article{Liu2010,
abstract = {It is shown that the continuum emission produced in the ablation of an Al target with nanosecond laser pulses is much more strongly polarized than the discrete line emission. This effect may be utilized to improve the resolution of the laser-induced breakdown spectroscopy spectrum by using a polarizer to filter out the continuum background. The effects of laser fluence and focal position are also reported. It is further shown that the lifetime of the emission closely tracks the intensity spectrum.},
author = {Liu, Yaoming and Penczak, John S and Gordon, Robert J},
doi = {10.1364/OL.35.000112},
institution = {Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607-7061, USA.},
journal = {Optics Letters},
number = {2},
pages = {112--114},
pmid = {20081938},
publisher = {OSA},
title = {{Nanosecond polarization-resolved laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20081938},
volume = {35},
year = {2010}
}
@article{Lopez2006,
abstract = {Abstract Archaeological ceramics Terra Sigillata manufactured in different production centres have been studied by laser-induced plasma spectroscopy (LIPS). The aim of this work was to establish a procedure for the rapid classification of these archaeological ceramics in function of their provenance through combination of LIPS and statistical methodologies. Representative emission spectra of the Hispanic, Gaulish and African groups of pottery were selected as references. The use of linear correlation allowed one to cluster the samples by quantitative comparison of LIP spectra, leading to a reliable assignment of Terra Sigillata pieces to origin centres.},
author = {L{\'{o}}pez, A J and Nicol{\'{a}}s, G and Mateo, M P and Ramil, A and Pi{\~{n}}{\'{o}}n, V and Y{\'{a}}{\~{n}}ez, A},
doi = {10.1007/s00339-006-3556-6},
issn = {09478396},
journal = {Applied Physics A},
number = {4},
pages = {695--698},
title = {{LIPS and linear correlation analysis applied to the classification of Roman pottery Terra Sigillata}},
url = {http://dx.doi.org/10.1007/s00339-006-3556-6},
volume = {83},
year = {2006}
}
@article{Singh2009,
abstract = {We performed laser-induced breakdown spectroscopy (LIBS) for the in situ quantitative estimation of elemental constituents distributed in different parts of kidney stones obtained directly from patients by surgery. We did this by focusing the laser light directly on the center, shell, and surface of the stones to find the spatial distribution of the elements inside the stone. The elements detected in the stones were calcium, magnesium, manganese, copper, iron, zinc, strontium, sodium, potassium, carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, and chlorine (Cl), etc. We optimized the LIBS signals by varying the laser energy from 10 mJ to 40 mJ to obtain the best signal-to-background and signal-to-noise ratios. We estimated the quantities of different elements in the stones by drawing calibration curves, plotting graphs of the analyte signal versus the absolute concentration of the elements in standard samples. The detection limits of the calibration curves were discussed. The concentrations of the different elements were found to be widely different in different stones found in different age groups of patients. It was observed that stones containing higher amounts of copper also possessed higher amounts of zinc. In general, the concentrations of trace elements present in the kidney stones decreased as we moved from center to shell and surface. Our results also revealed that the concentrations of elements present in the stones increased with the age of the patients. The results obtained from the calibration curves were compared with results from inductively coupled plasma mass spectrometry (ICP-MS). We also used the intensity ratios of different elemental lines to find the spatial distribution of different elements inside the kidney stones.},
author = {Singh, V K and Rai, A K and Rai, P K and Jindal, P K},
institution = {Department of Physics, University of Allahabad, Allahabad, India. singh{\_}vivekkumar2005@yahoo.com},
journal = {Lasers in Medical Science},
keywords = {*chemistry,*lasers,*methods,adult,analysis,humans,instrumentation,kidney calculi,male,middle aged,optical devices,optical phenomena,pathology,solid state,spectrum analysis,statist,trace elements,young adult},
number = {5},
pages = {749--759},
pmid = {19104906},
title = {{Cross-sectional study of kidney stones by laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19104906},
volume = {24},
year = {2009}
}
@article{Yin2009,
abstract = {It is vitally important for a power plant to determine the chemical composition of coal prior to combustion in order to obtain optimal boiler control. In this work, a fully software-controlled laser-induced breakdown spectroscopy (LIBS) system comprising a LIBS apparatus and sampling equipment has been designed for possible application to power plants for on-line quality analysis of pulverized coal. Special attention was given to the LIBS system, the data processing methods (especially the normalization with Bode Rule/DC Level) and the specific settings (the software-controlled triggering source, high-pressure gas cleaning device, sample-preparation module, sampling module, etc.), which gave the best direct measurement for C, H, Si, Na, Mg, Fe, Al, and Ti with measurement errors less than 10{\%} for pulverized coal. Therefore, the apparatus is accurate enough to be applied to industries for on-line monitoring of pulverized coal. The method of proximate analysis was also introduced and the experimental error of A(ad) (Ash, 'ad' is an abbreviation for 'air dried') was shown in the range of 2.29 to 13.47{\%}. The programmable logic controller (PLC) controlled on-line coal sampling equipment, which is designed based upon aerodynamics, and is capable of performing multipoint sampling and sample-preparation operation.},
author = {Yin, Wangbao and Zhang, Lei and Dong, Lei and Ma, Weiguang and Jia, Suotang},
institution = {State Key Laboratory of Quantum Optics and Quantum Optics Devices, College of Physics and Electronics Engineering, Shanxi University, Taiyuan 030006, P.R. China.},
journal = {Applied Spectroscopy},
number = {8},
pages = {865--872},
pmid = {19678982},
title = {{Design of a laser-induced breakdown spectroscopy system for on-line quality analysis of pulverized coal in power plants.}},
url = {http://www.ingentaconnect.com/content/sas/sas/2009/00000063/00000008/art00008},
volume = {63},
year = {2009}
}
@article{Hybl2003a,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is examined as a potential method for detecting airborne biological agents. A spectrally broadband LIBS system was used for laboratory measurements on some common biological agent simulants. These measurements were compared to those of common, naturally occurring biological aerosol components (pollen and fungal spores) to determine the potential of LIBS for discriminating biological agents from natural background aerosols. A principal components analysis illustrates that linear combinations of the detected atomic lines, which are present in different ratios in each of the samples tested, can be used to discriminate biological agent simulants from other biological matter. A more sensitive, narrowband LIBS instrument was used to demonstrate the detection of single simulant (Bg) particles in the size range 1–5 mm. Ca, Mg, and Na, which are present in varying concentrations between 0.3 and 11{\%} (by mass) in the Bg particles, were observed in single particles using LIBS. Index Headings: Laser-induced breakdown spectroscopy; LIBS; Plasma spectroscopy; Biological agent detection; Biological aerosols.},
author = {Hybl, John D and Lithgow, Gregg A and Buckley, Steven G},
doi = {0003-7028 / 03 / 5710-1207{\$}2.00 / 0},
file = {::},
journal = {Applied Spectroscopy},
number = {10},
pages = {1207--1215},
title = {{accelerated paper Laser-Induced Breakdown Spectroscopy Detection and Classi cation of Biological Aerosols *}},
volume = {57},
year = {2003}
}
@article{Salle2004,
abstract = {An international consortium is studying the feasibility of performing in situ geochemical analysis of Mars soils and rocks at stand-off distances up to several meters using the Laser-Induced Breakdown Spectroscopy (LIBS) technique. Stand-off analysis for Martian exploration imposes particular requirements on instrumentation, and it is necessary to first test the performance of such a system in the laboratory. In this paper, we test the capabilities of two different experimental setups. The first one is dedicated to the qualitative analysis of metals and rocks at distances between 3 and 12 m. With the second one, we have obtained quantitative results for aluminum alloys and developed a spectral database under Martian conditions for sulfur and chlorine, two elements that are geologically interesting but generally difficult to detect by LIBS under standard conditions (atmospheric pressure, close distance). These studies were carried out to determine an optimal instrumental design for in situ Mars analysis. The quality of analytical results affected by the optical elements and spectrometer has been particularly highlighted.},
author = {Salle, B},
doi = {10.1016/j.sab.2004.06.006},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {chlorine,laser induced breakdown spectroscopy,mars elemental analysis,metals,rocks,sulfur},
number = {9},
pages = {1413--1422},
title = {{Laser-Induced Breakdown Spectroscopy for Mars surface analysis: capabilities at stand-off distances and detection of chlorine and sulfur elements}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854704001569},
volume = {59},
year = {2004}
}
@article{Gornushkin2010,
abstract = {The paper describes past and present efforts in modeling of laser-induced plasma and overviews plasma diagnostics carried out by pump-probe techniques. Besides general information on existing plasma models, the emphasis is given to models relevant to spectrochemical analysis, i.e. models of radiating plasma. Special attention is paid to collisional-radiative (CR) and collisional-dominated (CD) plasma models where radiative processes play an important role. Also, calibration-free (CF) models are considered which may endow with the possibility for standardless spectroscopic analysis. In the diagnostic part, only methods based on the use of additional diagnostic tools (auxiliary lasers, optics, and probes) are described omitting those based on plasma own radiation. A short review is provided on image-based diagnostics (shadowgraphy, schlieren, and interferometry), absorption and fluorescence, Langmuir probe, and less frequently used cavity ringdown and Thomson scattering methods. (C) 2010 Elsevier B.V. All rights reserved.},
author = {Gornushkin, Igor B and Panne, Ulrich},
doi = {10.1016/j.sab.2010.03.021},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {5},
pages = {345--359},
publisher = {Elsevier B.V.},
title = {{Radiative models of laser-induced plasma and pump-probe diagnostics relevant to laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854710000911},
volume = {65},
year = {2010}
}
@article{Barnett2011,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is used for the identification of the presence of hazardous bacteria in food. In this study, our main focus was centered on the identification of S. enterica serovar Typhimurium, a Gram-negative foodborne pathogen, in various liquids such as milk, chicken broth, and brain heart infusion due to the infection being most prevalent in raw meat and dairy products. A Nd:YAG laser of operating wavelength 266 nm was used to obtain the spectra from the artificially inoculated liquid samples. A series of experiments were performed to determine the effectiveness of LIBS to discriminate the bacteria from the background liquids. These results are compared with competing modern molecular methods of detection which include polymerase chain reaction (PCR) and quantitative real-time PCR. In addition to analyzing S. enterica serovar Typhimurium, another common Gram-negative, Escherichia coli, as well as Gram-positive pathogen, Staphlycoccus auerus, were used to determine the specificity of the LIBS technique.},
author = {Barnett, Cleon and Bell, Courtne{\'{e}} and Vig, Komal and Akpovo, a C and Johnson, Lewis and Pillai, Shreekumar and Singh, Shree},
doi = {10.1007/s00216-011-4844-3},
file = {::},
issn = {1618-2650},
journal = {Analytical and bioanalytical chemistry},
keywords = {Food Contamination,Food Contamination: analysis,Food Microbiology,Food Microbiology: methods,Lasers,Polymerase Chain Reaction,Salmonella typhimurium,Salmonella typhimurium: isolation {\&} purification,Spectrum Analysis,Spectrum Analysis: methods},
month = {jul},
number = {10},
pages = {3323--30},
pmid = {21424774},
title = {{Development of a LIBS assay for the detection of Salmonella enterica serovar Typhimurium from food.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21424774},
volume = {400},
year = {2011}
}
@article{Song1999,
author = {Song, XH and Hopke, PK and Fergenson, DP},
file = {::},
journal = {Analytical},
number = {4},
pages = {860--865},
title = {{Classification of single particles analyzed by ATOFMS using an artificial neural network, ART-2A}},
url = {http://pubs.acs.org/doi/abs/10.1021/ac9809682},
volume = {71},
year = {1999}
}
@article{Virtanen2007,
abstract = {The objective of this work was to study with near infrared spectrometry (NIRS) the degree of mixing of poorly miscible binary mixtures of carbamazepine (CBZ) and alpha-lactose monohydrate (LMH). CBZ was cohesive and the particle size difference between CBZ (0.3microm) and LMH (75microm) was substantial. Mixed batches were measured directly in the mixing container with a fiber-optic probe. The spectral data were filtered by applying a novel automated selection technique during the NIRS measurement. The data analyses were performed with partial least squares modeling. Reference measurements were carried out with ultraviolet spectrophotometry. The results describe the degree of homogeneity at various depths. Some of the mixtures densified when the mixing speed increased. The densification of the batches was a source of error because it caused changes in the measuring geometry. The automated selection technique for the spectra reduced this problem. NIRS detected differences in the mixing degrees of mixtures and the method is suitable for mixing studies. However, the difference in the particle size of the materials and the densification caused problems to the measuring geometry. NIRS can be used at line, but the method requires accurate operation and method developing before it is useable.},
author = {Virtanen, Satu and Antikainen, Osmo and Yliruusi, Jouko},
institution = {Division of Pharmaceutical Technology, 00014 University of Helsinki, P.O. Box 56, Helsinki, Finland. satu.virtanen@helsinki.fi},
journal = {International Journal of Pharmaceutics},
number = {1-2},
pages = {108--115},
pmid = {17604924},
title = {{Uniformity of poorly miscible powders determined by near infrared spectroscopy.}},
volume = {345},
year = {2007}
}
@article{Herrera2009a,
abstract = {The calibration-free methodology described in the literature dealing with the technique of laser induced breakdown spectroscopy has been applied here to several samples under different operating pressures with the aim of classifying the analytical technique as quantitative, semi-quantitative or qualitative (with quantitative estimates only), depending on the relative percentage errors calculated for the major, minor and trace elemental composition of the sample. The results were obtained with a Q-switched Nd:YAG laser (1064 nm), characterized by 5.3 ns duration pulses at a maximum repetition frequency of 10 Hz and with pulse energy up to 300 mJ. The spectra were taken with a grating monochromator coupled with an intensified CCD detector, calibrated from 220 to 700 nm. The samples investigated were aluminum alloy standard disks, standard reference materials of Zn alloy, Cu-Ni alloy, Ti alloy, Ni alloy powder, Cu-Zn alloy and soils. The data are compared with those published in the literature. The results show that the best accuracy (5{\%} relative error) is usually obtained for the matrix element, while in most cases, for the remainder of the components in the sample (major, minor or trace composition), the results can only be considered semi-quantitative (<200{\%} relative error).},
author = {Herrera, Kathleen K and Tognoni, Elisabetta and Omenetto, Nicol{\'{o}} and Smith, Benjamin W and Winefordner, James D},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {4},
pages = {413--425},
title = {{Semi-quantitative analysis of metal alloys, brass and soil samples by calibration-free laser-induced breakdown spectroscopy: recent results and considerations}},
url = {http://dx.doi.org/10.1039/b820493d},
volume = {24},
year = {2009}
}
@article{Munson2008,
abstract = {The performance of a man-portable laser induced breakdown spectrometer was evaluated for the detection of biological powders on indoor office surfaces and wipe materials. Identification of pure unknown powders was performed by comparing against a library of spectra containing biological agent surrogates and confusant materials, such as dusts, diesel soot, natural and artificial sweeteners, and drink powders, using linear correlation analysis. Simple models constructed using a second technique, partial least squares discriminant analysis, successfully identified Bacillus subtilis (BG) spores on wipe materials and office surfaces. Furthermore, these models were able to identify BG on materials not used in the training of the model.},
author = {Munson, Chase A and Gottfried, Jennifer L and Snyder, Emily Gibb and {De Lucia}, Frank C and Gullett, Brian and Miziolek, Andrzej W},
institution = {U.S. Army Research Laboratory, AMSRD-ARL-WM-BD, Aberdeen Proving Ground, Maryland 21005-5069, USA. cmunson@arl.army.mil},
issn = {1539-4522},
journal = {Applied optics},
keywords = {Air Microbiology,Air Pollution,Animals,Bacillus subtilis,Bacillus subtilis: metabolism,Biological Warfare,Biological Warfare: methods,Dust,Environmental Monitoring,Environmental Monitoring: instrumentation,Environmental Monitoring: methods,Indoor,Indoor: analysis,Lasers,Models,Optics and Photonics,Particle Size,Powders,Statistical},
month = {nov},
number = {31},
pages = {G48--57},
pmid = {19122702},
title = {{Detection of indoor biological hazards using the man-portable laser induced breakdown spectrometer.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19122702},
volume = {47},
year = {2008}
}
@article{Putkiranta2010a,
author = {Putkiranta, M. and Manninen, a. and Rostedt, a. and Saarela, J. and Sorvaj{\"{a}}rvi, T. and Marjam{\"{a}}ki, M. and Hernberg, R. and Keskinen, J.},
doi = {10.1007/s00340-010-4073-z},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Putkiranta et al. - Fluorescence properties of biochemicals in dry NaCl composite aerosol particles and in solutions - 2010.pdf:pdf},
issn = {0946-2171},
journal = {Applied Physics B},
month = {may},
number = {4},
pages = {841--851},
title = {{Fluorescence properties of biochemicals in dry NaCl composite aerosol particles and in solutions}},
url = {http://www.springerlink.com/index/10.1007/s00340-010-4073-z},
volume = {99},
year = {2010}
}
@article{Asimellis2008,
abstract = {Development and application of an in-situ applicable method to provide rapid determination of platinum group metals (platinum, palladium, and rhodium) elemental concentration in automobile catalyst scrap is reported. Application is based on laser-induced breakdown spectroscopy (LIBS). Actual automobile catalyst slurry in powder form was used to develop the application. With a method requiring approximately 1.5 min of examination per sample, calibration curves are presented with linear regression coefficients close to 0.99 and stability better than 3.0{\%}.},
author = {Asimellis, George and Michos, Nikolaos and Fasaki, Ioanna and Kompitsas, Michael},
doi = {10.1016/j.sab.2008.09.016},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {laser induced breakdown spectroscopy},
number = {11},
pages = {1338--1343},
publisher = {Elsevier B.V.},
title = {{Platinum group metals bulk analysis in automobile catalyst recycling material by laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854708002693},
volume = {63},
year = {2008}
}
@book{Bachor2004,
abstract = {Laser induced breakdown spectroscopy (LIBS) has been evaluated for the determination of micronutrients (B, Cu, Fe, Mn and Zn) in pellets of plant materials, using NIST, BCR and GBW biological certified reference materials for analytical calibration. Pellets of approximately 2 mm thick and 15 mm diameter were prepared by transferring 0.5 g of powdered material to a 15 mm die set and applying 8.0 tons cm- 2. An experimental setup was designed by using a Nd:YAG laser operating at 1064 nm (200 mJ per pulse, 10 Hz) and an Echelle spectrometer with ICCD detector. Repeatability precision varied from 4 to 30{\%} from measurements obtained in 10 different positions (8 laser shots per test portion) in the same sample pellet. Limits of detection were appropriate for routine analysis of plant materials and were 2.2 mg kg- 1 B, 3.0 mg kg- 1 Cu, 3.6 mg kg- 1 Fe, 1.8 mg kg- 1 Mn and 1.2 mg kg- 1 Zn. Analysis of different plant samples were carried out by LIBS and results were compared with those obtained by ICP OES after wet acid decomposition.},
author = {Bachor, Hans-A and Ralph, Timothy C},
booktitle = {WileyVCH},
doi = {10.1017/S0263034600234125},
editor = {Textbook, Physics},
institution = {University of Minnesota},
isbn = {3527403930},
issn = {05848547},
number = {5},
pages = {434},
publisher = {Wiley-VCH},
title = {{A Guide to Experiments in Quantum Optics}},
url = {http://www.amazon.com/Guide-Experiments-Quantum-Optics/dp/3527403930},
volume = {64},
year = {2004}
}
@article{Hilbk-Kortenbruck2001,
author = {Hilbk-Kortenbruck, F and Noll, Reinhard and Wintjens, Peter},
file = {::},
journal = {B: Atomic Spectroscopy},
keywords = {and is published in,at the 1st international,congress on laser induced,dedicated to that conference,heavy metals,hyphenated technique,italy,libs,lif,october 2000,pisa,plasma spectroscopy and applications,soil,spectrochimica acta part b,the special issue of,this paper was presented},
number = {October 2000},
pages = {933--945},
title = {{Analysis of heavy metals in soils using laser-induced breakdown spectrometry combined with laser-induced fluorescence}},
url = {http://www.sciencedirect.com/science/article/pii/S0584854701002130},
year = {2001}
}
@article{Beddows2002,
abstract = {Using a novel laser-induced breakdown spectroscopy set-up, accurate quantitative analysis of samples submerged in liquids has been demonstrated. The measurements were conducted using a single-fibre plus plastic tube assembly of 20 m length. This delivered the ablation laser light pulse and a buffer gas flow to the sample surface, and collected the light emitted by the micro-plasma for analysis. No distil optics were used at the sample end of the fibre. Argon, nitrogen and compressed air were used as buffer gases; while the rare gas resulted in slightly better signal-to-noise ratios, most analytical measurements were carried out with nitrogen for convenience and to provide comparability with in-air measurements. Detection limits and reproducibility were comparable to those achieved for the same samples placed in standard ambient air, with all other experimental conditions unchanged. In standard steel samples, detection limits of 31045, 32548 and 45555 ppm for Cr, Mn and Si, respectively, could be achieved. Pattern recognition algorithms were used to identify, for classification, spectra of specimen submerged in turbid and non-transparent liquids.},
author = {Beddows, D C S and Samek, O and Liska, M and Telle, H H},
doi = {10.1016/S0584-8547(02)00260-4},
isbn = {1792295324},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {laser induced breakdown spectroscopy,remote material identification,underwater measurements},
number = {3},
pages = {1461--1471},
title = {{Single-pulse laser-induced breakdown spectroscopy of samples submerged in water using a single-fibre light delivery system}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854702002604},
volume = {57},
year = {2002}
}
@article{Corsi2006,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is a promising technique for in situ environmental analysis. The potential of this technique for accurate quantitative analysis could be greatly improved using an innovative experimental setup - based on the use of two laser pulses suitably retarded - and analyzing the results with a standard-less procedure which overcomes the problems related to matrix effects. A new mobile instrument for soil analysis, developed at the Applied Laser Spectroscopy Laboratory in Pisa, is presented, and some experimental results are given.},
author = {Corsi, M and Cristoforetti, G and Hidalgo, M and Legnaioli, S and Palleschi, V and Salvetti, A and Tognoni, E and Vallebona, C},
doi = {10.1016/j.apgeochem.2006.02.004},
issn = {08832927},
journal = {Applied Geochemistry},
number = {5},
pages = {748--755},
title = {{Double pulse, calibration-free laser-induced breakdown spectroscopy: A new technique for in situ standard-less analysis of polluted soils}},
url = {http://www.sciencedirect.com/science/article/B6VDG-4JHMY04-4/2/d0ec9c40c99251bed33ac72250da1173},
volume = {21},
year = {2006}
}
@article{Asgill2009,
abstract = {The temporal evolution of the Si atomic emission signal produced from individual silica microspheres in an aerosolized air stream was investigated using laser-induced breakdown spectroscopy (LIBS). Specifically, the temporal evolution of Si emission from 2.47 and 4.09-micrometer-sized particles is evaluated over discrete delay times ranging from 15 to 70 µs following plasma initiation. The analyte signal profile from the microspheres, taken as the silicon atomic emission peak-to-continuum ratio, was observed to follow the same profile of silicon-rich nanoparticles over the range of delay times. The ratio of analyte signals for the 2.47 and 4.09-micrometer particles was observed to be approximately constant with plasma decay time and less than the expected mass ratio, leading to the conclusion that further vaporization and enhanced analyte response do not continue with increasing delay times for these microsphere sizes. While recent research suggests that the temporal component of analyte response is important for quantitative LIBS analysis, the current study does confirm earlier research demonstrating an upper size limit for quantitative aerosol particle analysis in the diameter range of 2 to 2.5 µm for silica microspheres.},
author = {Asgill, Michael E and Hahn, David W},
doi = {10.1016/j.sab.2009.07.026},
editor = {M, Sabsabi and R, Russo},
file = {::},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1153--1158},
publisher = {Elsevier B.V.},
title = {{Particle size limits for quantitative aerosol analysis using laser-induced breakdown spectroscopy: Temporal considerations}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709002249},
volume = {64},
year = {2009}
}
@article{Apanaskevich2008a,
abstract = {Two new tick species belonging to the African Haemaphysalis (Rhipistoma) leachi subgroup, namely H. (R.) colesbergensis n. sp. and H. (R.) oliveri n. sp., are described. Haemaphysalis (R.) colesbergensis adults are easily differentiated from the other species of the H. (R.) leachi subgroup, including H. (R.) oliveri, by the spur on coxa IV, which is considerably longer than that on coxa III. The adults of the 2 new species are equal in size, but the dental formula of the hypostome of H. (R.) colesbergensis is 4/4 compared to 5/5 for H. (R.) oliveri. The dental formula of H. (R.) oliveri also distinguishes it from other ticks in the subgroup, namely H. (R.) leachi, H. (R.) elliptica, H. (R.) moreli, and H. (R.) punctaleachi (4/4 in these species), but not from H. (R.) paraleachi, which has a 5/5 dental arrangement. However, the average total length and width of H. (R.) oliveri males (2.47 x 1.20 mm) are considerably shorter and narrower than those of H. (R.) paraleachi males (3.81 x 1.79 mm). Similar differences in size apply to the females. Nymphs and larvae of H. (R.) colesbergensis and H. (R.) oliveri can be distinguished from those of other members of the H. (R.) leachi subgroup, as well as from each other, by a combination of the following characters: size and measurement ratios, length of posterodorsal and posteroventral spurs on palpal segment II, and number of denticles per file on the hypostome. Haemaphysalis (R.) colesbergensis is known only from South Africa, where it has been collected from domestic cats and dogs and medium-sized wild felids. Haemaphysalis (R.) oliveri is recorded only from Sudan, where it has been collected from small- to medium-sized wild felids and canids and an antelope. The hosts of the immature stages of H. (R.) colesbergensis are unknown, while nymphs of H. (R.) oliveri have been collected from rodents.},
author = {Apanaskevich, Dmitry A and Horak, Ivan G},
institution = {United States National Tick Collection, Institute of Arthropodology and Parasitology, Georgia Southern University, Statesboro, Georgia 30460-8056, USA. dapanaskevich@georgiasouthern.edu},
journal = {The Journal of parasitology},
number = {3},
pages = {594--607},
pmid = {18605788},
title = {{Two new species of African Haemaphysalis ticks (Acari: Ixodidae), carnivore parasites of the H. (Rhipistoma) leachi group.}},
volume = {94},
year = {2008}
}
@article{Gornushkin1999,
abstract = {The curve-of-growth (COG) method was applied to a laser-induced plasma. The plasma was produced by a Nd:YAG laser on the surface of steel samples containing 0.007-1.3{\%} of Cr. The emission was collected from the top of the plasma by means of a 45 pierced mirror and aligned onto an intensified charge-coupled device (ICCD) with a gate width of 1 mus and a variable delay time. The resonance 425.4 nm Cr line was used for construction of the COG. The temperature of the plasma ({\~{}}8000 K at 5-mus delay) was determined from a Boltzmann plot. The damping constant a, proportional to the ratio of the Lorentzian to the Doppler line widths, was found from the best fit of a series of calculated COG to the experimental data points and was 0.200.05. The number density of neutral Cr atoms which corresponded to the transition between low and high optical densities, was approximate6.51012 cm-3. The cross-section for broadening collisions of Cr atoms with atmospheric species (presumably N2) was calculated to be (6616) {\AA}. The shape of the 425.4-nm Cr line was additionally checked by scanning an ultra-narrow cw Ti:Sapphire laser across the atomic transition and found to be in agreement with preliminary estimates. The potential of the COG method for laser breakdown spectroscopy is discussed.},
author = {Gornushkin, I B and Anzano, J M and King, L A and Smith, B W and Omenetto, N and Winefordner, J D},
doi = {10.1016/S0584-8547(99)00004-X},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {177,50013 zaragoza,chromium,curve growth,departmento de quimica analitica,facultad de veterinaria,laser plasma,libs,miquel servet,present address,spain,universitidad de zaragoza},
number = {3-4},
pages = {491--503},
title = {{Curve of growth methodology applied to laser-induced plasma emission spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S058485479900004X},
volume = {54},
year = {1999}
}
@article{Salle2007,
abstract = {A review of recent results on stand-off Laser-Induced Breakdown Spectroscopy (LIBS) analysis and applications is presented. Stand-off LIBS was suggested for elemental analysis of materials located in environments where any physical access was not possible but optical access could be envisaged. This review only refers to the use of the open-path LIBS configuration in which the laser beam and the returning plasma light are transmitted through the atmosphere. It does not present the results obtained with a transportation of the laser pulses to the target through an optical fiber. Open-path stand-off LIBS has mainly been used with nanosecond laser pulses for solid sample analysis at distances of tens of meters. Liquid samples have also been analyzed at distances of a few meters. The distances achievable depend on many parameters including the laser characteristics (pulse energy and power, beam divergence, spatial profile) and the optical system used to focus the pulses at a distance. A large variety of laser focusing systems have been employed for stand-off analysis comprising refracting or reflecting telescope. Efficient collection of the plasma light is also needed to obtain analytically useful signals. For stand-off LIBS analysis, a lens or a mirror is required to increase the solid angle over which the plasma light can be collected. The light collection device can be either at an angle from the laser beam path or collinear with the optical axis of the system used to focus the laser pulses on the target surface. These different configurations have been used depending on the application such as rapid sorting of metal samples, identification of material in nuclear industry, process control and monitoring in metallurgical industry, applications in future planetary missions, detection of environmental contamination or cleaning of objects of cultural heritage. Recent stand-off analyses of metal samples have been reported using femtosecond laser pulses to extend LIBS capabilities to very long distances. The high-power densities achievable with these laser pulses can also induce self-guided filaments in the atmosphere which produce LIBS excitation of a sample. The first results obtained with remote filament-induced breakdown spectroscopy predict sample analysis at kilometer ranges.},
author = {Sall{\'{e}}, B and Mauchien, P and Maurice, S},
doi = {10.1016/j.sab.2007.07.001},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {laser induced breakdown spectroscopy,libs,stand off analysis},
number = {8},
pages = {739--768},
publisher = {Elsevier},
title = {{Laser-Induced Breakdown Spectroscopy in open-path configuration for the analysis of distant objects}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707001929},
volume = {62},
year = {2007}
}
@misc{Dobroiu2007,
abstract = {A series of experiments in the field of THz-wave spectroscopy is described. The measurement of absorption spectra of solid samples, powders, and liquids is demonstrated using various optical setups. One of the sources we used is a widely tunable coherent THz-wave generator relying on an optical parametric process: nanosecond Q-switched Nd : YAG laser light scattering from the polariton mode of a MgO-doped LiNbO3 crystal. For the measurement of the absorption of THz waves in liquids, a train of waves is allowed to oscillate inside a silicon prism. A liquid placed on a total internal reflection surface lowers the quality factor of the resonator, which allows determining the complex refraction index of the sample by frequency scanning. We have also developed a technique for THz chemical imaging, by introducing the component spatial pattern analysis. The spatial distribution of the chemicals, such as illicit drugs concealed in an envelope, is obtained from terahertz multispectral transillumination images and absorption spectra. To compensate for the low imaging speed, a prescreening step is proposed, by first detecting the presence of powders in the envelopes, which is achieved by measuring in real time the amount of scattering produced by the envelopes. Details and examples are provided.},
author = {Dobroiu, A and Sasaki, Y and Shibuya, T and Otani, C and Kawase, K},
booktitle = {Proceedings of the IEEE},
doi = {10.1109/JPROC.2007.898840},
file = {::},
issn = {00189219},
keywords = {homeland security,nondestructive testing,terahertz spectroscopy,terahertz wave sources,terahertz waves},
number = {8},
pages = {1566--1575},
title = {{THz-Wave Spectroscopy Applied to the Detection of Illicit Drugs in Mail}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4337835},
volume = {95},
year = {2007}
}
@article{Em2002,
abstract = {The U.S. Department of Energy (DOE) sponsored a technology development and field demonstration program focused on a continuous emissions monitor (CEM) capable of providing real-time measurements of metal emissions in the waste streams of thermal facilities. This project was initiated in 1993 at Sandia National Laboratories, Livermore, California, and lead to the development of a prototype CEM based on an optical emission technique referred to as Laser-Induced Breakdown Spectroscopy (LIBS). This report provides information on the LIBS technology, performance, applicability, cost, OS{\&}H, and regulatory and policy issues.},
author = {Em, D O E},
journal = {Science And Technology},
number = {September},
title = {{Laser-Induced Breakdown Spectroscopy Continuous Emissions Monitor for Metals Laser-Induced Breakdown Spectroscopy Continuous Emissions Monitor for Metals}},
year = {2002}
}
@article{Rehse2012a,
abstract = {The recent progress made in developing laser-induced breakdown spectroscopy (LIBS) has transformed LIBS from an elemental analysis technique to one that can be applied for the reagentless analysis of molecularly complex biological materials or clinical specimens. Rapid advances in the LIBS technology have spawned a growing number of recently published articles in peer-reviewed journals which have consistently demonstrated the capability of LIBS to rapidly detect, biochemically characterize and analyse, and/or accurately identify various biological, biomedical or clinical samples. These analyses are inherently real-time, require no sample preparation, and offer high sensitivity and specificity. This overview of the biomedical applications of LIBS is meant to summarize the research that has been performed to date, as well as to suggest to health care providers several possible specific future applications which, if successfully implemented, would be significantly beneficial to humankind.},
author = {Rehse, S J and Salimnia, H and Miziolek, a W},
doi = {10.3109/03091902.2011.645946},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Rehse, Salimnia, Miziolek - Laser-induced breakdown spectroscopy (LIBS) an overview of recent progress and future potential for biomedic.pdf:pdf},
issn = {1464-522X},
journal = {Journal of medical engineering {\&} technology},
keywords = {diagnostics,laser-induced breakdown spectroscopy,medical,point-of-care,rapid pathogen identification},
month = {feb},
number = {2},
pages = {77--89},
pmid = {22268995},
title = {{Laser-induced breakdown spectroscopy (LIBS): an overview of recent progress and future potential for biomedical applications.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22268995},
volume = {36},
year = {2012}
}
@article{Wenning2006,
abstract = {The species composition of microbial communities in natural habitats may be extremely complex and therefore a quantitative analysis of the fraction each species contributes to the consortium has proven to be difficult. During recent years, the identification of bacterial pure cultures based on their infrared spectra has been established. Fourier-transform infrared microspectroscopy now proceeds a step further and allows identification of microorganisms directly plated from community dilutions. Infrared spectra of microcolonies of 70-250 microm in diameter can be recorded without producing a pure culture of the isolate. We have applied this novel technique for quantitative comparative analysis of two undefined, geographically separated food-borne smear cheese microbial consortia of limited complexity. Due to the high degree of automation, up to 200 microcolonies could be identified in 1 day and, in total, 3170 infrared spectra of microcolonies were recorded. The results obtained have been verified by Fourier-transform infrared macrospectroscopy and 16S rDNA sequencing. Interestingly, although the communities were unrelated, Staphylococcus equorum, Corynebacterium casei, Arthrobacter casei and Brevibacterium linens were found to be part of both consortia, however, with different incidence. In addition, Corynebacterium variabile, Microbacterium gubbeenense, Brachybacterium alimentarium, Enterococcus faecalis and an unknown species were detected in either one of the consortia.},
author = {Wenning, Mareike and Theilmann, Vera and Scherer, Siegfried},
institution = {Lehrstuhl f{\"{u}}r Mikrobielle Okologie, Wissenschaftszentrum Weihenstephan, Technische Universit{\"{a}}t M{\"{u}}nchen, Weihenstephaner Berg 3, D-85350 Freising, Germany.},
journal = {Environmental Microbiology},
number = {5},
pages = {848--857},
pmid = {16623742},
title = {{Rapid analysis of two food-borne microbial communities at the species level by Fourier-transform infrared microspectroscopy.}},
url = {http://ovidsp.ovid.com/ovidweb.cgi?T=JS{\&}CSC=Y{\&}NEWS=N{\&}PAGE=fulltext{\&}D=med4{\&}AN=16623742},
volume = {8},
year = {2006}
}
@article{Aydin2008,
abstract = {The aim of this work is to provide a procedure to determine time-resolved electron temperatures with minimized relative errors by the Boltzmann plot method. The applied procedure consists of two parts, a systematic theoretical spectral line selection and an iterative Boltzmann plot algorithm. After a pre-selection of an appropriate non-disturbed or overlapped set of spectral lines of a particular atomic or ionic species Boltzmann plots are generated using experimentally recorded data for every time window and laser pulse energy of interest. Spectral lines with the highest average deviations from the regression function are assumed as being not representative for the considered ensemble of spectral lines and are therefore discarded gradually until a threshold value for the coefficient of determination is exceeded. Laser-induced breakdown spectroscopy (LIBS) is applied for time-resolved and spatially integrated investigations of plasmas on 1.1750 C75 steel alloy samples with laser pulse energies ranging between 200 $\mu$J and 2 mJ. For the specific chemical composition ofthese samples a selection of atomic and ionic Fe spectral lines has been carried out. In spite of the fact that onlylaser pulse energies in the low millijoule regime are applied the final sets of spectral lines comprise in total 61Fe I and 12 Fe II emission lines. By applying this method electron temperatures can be determined withaveraged relative errors of down to 1.8{\%} for Fe I and 4.4{\%} for Fe II emission lines.},
author = {Aydin, {\"{U}}mit and Roth, Peter and Gehlen, Christoph Dominic and Noll, Reinhard},
chapter = {1060},
doi = {10.1016/j.sab.2008.08.003},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1060--1065},
publisher = {Elsevier B.V.},
title = {{Spectral line selection for time-resolved investigations of laser-induced plasmas by an iterative Boltzmann plot method}},
url = {http://www.sciencedirect.com/science/article/B6THN-4T8SM0P-1/2/44f49ac3e856df67f14460ba6ae2667b},
volume = {63},
year = {2008}
}
@article{Nasr2011,
abstract = {Highly toxic contaminants like Cr, As, and Pb were detected in chrome-tanning process of animal skin to produce leather by applying locally developed laser-induced breakdown spectrometer. An Nd-YAG laser with 1,064nm wavelength was focused on the surface of leather samples (natural and manufactured) to generate a plasma spark and spectrally resolved spectra were used for identification and quantification of contaminants. The leather samples were collected from a tannery located in industrial cities of Riyadh and Jeddah, Saudi Arabia. The study was carried out on fully, half manufactured (wet blue leather), and natural hide (skin). To the best of our knowledge, this is the first attempt where laser-induced breakdown spectroscopy (LIBS) technique has been applied for the analysis of leather before and after tanning process. The maximum concentration of different elements of environmental significance like chromium, lead, arsenic, sulfur, magnesium were 199, 289, 31, 38, and 39ppm, respectively, in one of the manufactured leather samples. The limit of detection (LOD) of our LIBS system for chromium, lead, arsenic, sulfur, and magnesium were 2, 3, 1.5,7, and 3ppm, respectively. The safe permissible limit for tanned leather for highly toxic elements like chromium, lead, and arsenic are 1, 0.5, 0.01ppm, respectively, as prescribed in Environmental Regulation Standards for Saudi Industries set by Royal Commission Jubail, Saudi Arabia. The LIBS technique is superior to other conventional techniques like ICP or atomic absorption that a little or no sample preparation is required, no chemicals are needed, multi-elemental analysis is possible for all kinds of samples (natural and anthropogenic materials), microgram of sample is essential, and LIBS could be applied for remote analysis. It is highly selective and sensitivity higher than ICP, and as no sample and chemicals are required, it is cost effective for multi-sample analysis per unit time as compared with other conventional techniques. The concentration of some toxic elements (Cr, Pb, As) is much higher than the safe permissible limits set by Occupational Safety and Health Administration in USA or Saudi environmental regulatory agencies. Results obtained with our LIBS systems were in close agreement with the results obtained using other standard analytical technique such as the inductively coupled plasma atomic emission spectroscopy.},
author = {Nasr, M M and Gondal, Mohammed Asharf and Seddigi, Z S},
institution = {Department of Natural Science, Riyadh College of Dentistry and Pharmacy, Mail Box 84891, Riyadh, 11681, Saudi Arabia.},
journal = {Environmental Monitoring and Assessment},
number = {1-4},
pages = {387--395},
pmid = {20556649},
title = {{Detection of hazardous pollutants in chrome-tanned leather using locally developed laser-induced breakdown spectrometer.}},
url = {http://www.springerlink.com/content/d1m2q25l70235634/},
volume = {175},
year = {2011}
}
@article{Yao2011,
abstract = {Laser-induced breakdown spectroscopy (LIBS) combined with partial least squares (PLS) analysis has been applied for the quantitative analysis of the ash content of coal in this paper. The multivariate analysis method was employed to extract coal ash content information from LIBS spectra rather than from the concentrations of the main ash-forming elements. In order to construct a rigorous partial least squares regression model and reduce the calculation time, different spectral range data were used to construct partial least squares regression models, and then the performances of these models were compared in terms of the correlation coefficients of calibration and validation and the root mean square errors of calibration and cross-validation. Afterwards, the prediction accuracy, reproducibility, and the limit of detection of the partial least squares regression model were validated with independent laser-induced breakdown spectroscopy measurements of four unknown samples. The results show that a good agreement is observed between the ash content provided by thermo-gravimetric analyzer and the LIBS measurements coupled to the PLS regression model for the unknown samples. The feasibility of extracting coal ash content from LIBS spectra is approved. It is also confirmed that this technique has good potential for quantitative analysis of the ash content of coal.},
author = {Yao, S and Lu, J and Dong, M and Chen, K and Li, J},
doi = {10.1366/10-06190},
issn = {19433530},
journal = {Applied Spectroscopy},
number = {10},
pages = {1197--201},
pmid = {21986081},
title = {{Extracting coal ash content from laser-induced breakdown spectroscopy (LIBS) spectra by multivariate analysis}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21986081},
volume = {65},
year = {2011}
}
@article{Hariri2007,
abstract = {Optical coherence tomography (OCT) and laser-induced fluorescence (LIF) spectroscopy each have clinical potential in identifying human gastrointestinal (GI) pathologies, yet their diagnostic capability in mouse models is unknown. In this study, we combined the 2 modalities to survey the GI tract of a variety of mouse strains and ages and to sample dysplasias and inflammatory bowel disease (IBD) of the intestines. Segments (length, 2.5 cm) of duodenum and lower colon and the entire esophagus were imaged ex-vivo with combined OCT and LIE We evaluated 30 normal mice (A/J and 10- and 21-wk-old and retired breeder C57BL/6J) and 10 mice each of 2 strains modeling colon cancer and IBD (Apc(Min) and IL2-deficient mice, respectively). Histology was used to classify tissue regions as normal, Peyer patch, dysplasia, adenoma, or IBD. Features in corresponding OCT images were analyzed. Spectra from each category were averaged and compared via Student t tests. OCT provided structural information that led to identification of the imaging characteristics of healthy mouse GI. With histology as the 'gold standard,' we developed preliminary image criteria for early disease in the form of adenomas, dysplasias, and IBD. LIF characterized the endogenous fluorescence of mouse GI tract, with spectral features corresponding to collagen, NADH, and hemoglobin. In the IBD sample, LIF emission spectra displayed potentially diagnostic peaks at 635 and 670 nm, which we attributed to increased porphyrin production by bacteria associated with IBD. OCT and LIF appear to be useful and complementary modalities for ex vivo imaging of mouse GI tissues.},
author = {Hariri, Lida P and Tumlinson, Alexandre R and Wade, Norman H and Besselsen, David G and Utzinger, Urs and Gerner, Eugene W and Barton, Jennifer K},
institution = {Division of Biomedical Engineering, The University of Arizona, Tucson, AZ, USA. lphariri@u.arizona.edu},
journal = {Comparative Medicine},
number = {2},
pages = {175--185},
pmid = {17536618},
publisher = {American Association for Laboratory Animal Science},
title = {{Ex vivo optical coherence tomography and laser-induced fluorescence spectroscopy imaging of murine gastrointestinal tract.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17536618},
volume = {57},
year = {2007}
}
@article{Anglos1997,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was employed for the in situ analysis of pigments used in painting. LIBS spectra were collected from a wide variety of pigments in powder form and in oil color test samples. Appropriate emission lines for the identi - cation of the metallic elements in the pigments examined are pro- posed. Under optimal experimental parameters, the technique is minimally destructive; two pulses from a laser beam focused on the sample surface result in the formation of a small crater with typical diameter around 40 m m and depth of no more than 10 m m. Fur- thermore, recording LIBS spectra from successive laser pulses on the same spot of a model oil painting resulted in information re- garding the pigment composition of several paint layers, showing the capability of the technique in performing depth pro le analysis. Finally, a test case is presented in which an 18th century oil paint- ing, subjected to partial restoration, was examined by LIBS, and the different pigments used in the original and in the restored part of the work were clearly identi ed. The results of our studies dem- onstrate the applicability of LIBS in the rapid, in situ, and practi- cally nondestructive determination of pigments in painted artworks. Index Headings: Laser-induced breakdown spectroscopy (LIBS); Artwork diagnostics; Pigment analysis; Painting.},
author = {Anglos, Demetrios and Couris, Stelios and Fotakis, Costas},
doi = {10.1366/0003702971941421},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {7},
pages = {1025--1030},
title = {{Laser Diagnostics of Painted Artworks: Laser-Induced Breakdown Spectroscopy in Pigment Identification}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=51{\&}issue=7{\&}spage=1025},
volume = {51},
year = {1997}
}
@article{Ito1995,
abstract = {Laser-induced breakdown spectroscopy was applied to the determination of FeO(OH) in water and successfully determined the concentration of the turbid solution down to a few ppm (mug ml-1). A Q-switched Nd:YAG laser, which delivered 8 ns pulses, was used as an excitation source. Cell-less measurement was achieved using a coaxial nozzle flow system which allowed to study the effect of ambient gas on emission intensity and decay lifetime of the breakdown plasma. Using helium gas and with a proper timing gate, the FeO(OH) concentration in water was determined in the ppm range.},
author = {Ito, Yoshiro and Ueki, Osamu and Nakamura, Susumu},
doi = {10.1016/0003-2670(94)00313-B},
issn = {00032670},
journal = {Analytica Chimica Acta},
number = {3},
pages = {401--405},
title = {{Determination of colloidal iron in water by laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/000326709400313B},
volume = {299},
year = {1995}
}
@article{Hedwig2006,
abstract = {The applicability of spectrochemical analysis for liquid and powder samples of minute amount in the form of thin film was investigated using ultraviolet Nd-YAG laser (355nm) and low-pressure ambient air. A variety of organic samples such as commercial black ink usually used for stamp pad, ginseng extract, human blood, liquid milk and ginseng powder was prepared as film deposited on the surface of an appropriate hard substrate such as copper plate or glass slide. It was demonstrated that in all cases studied, good quality spectra were obtained with very low background and free from undesirable contamination by the substrate elements, featuring ppm or even sub-ppm sensitivity and worthy of application for quantitative analysis of organic samples. The proper preparation of the films was found to be crucial in achieving the high quality spectra. It was further shown that much inferior results were obtained when the atmospheric-pressure (101kPa) operating condition of laser-induced breakdown spectroscopy or the fundamental wavelength of the Nd-YAG laser was employed due to the excessive or improper laser ablation process},
author = {Hedwig, Rinda and Budi, Wahyu Setia and Abdulmadjid, Syahrun Nur and Pardede, Marincan and Suliyanti, Maria Margaretha and Lie, Tjung Jie and Kurniawan, Davy Putra and Kurniawan, Koo Hendrik and Kagawa, Kiichiro and Tjia, May On},
doi = {10.1016/j.sab.2006.10.012},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {12},
pages = {1285--1293},
title = {{Film analysis employing subtarget effect using 355 nm Nd-YAG laser-induced plasma at low pressure}},
url = {http://www.sciencedirect.com/science/article/B6THN-4MD9G4T-6/2/360e717542c3ddf8ad59238f0e9faee9},
volume = {61},
year = {2006}
}
@article{DeGiacomo2008,
abstract = {We present measurements of the Stark broadening of several Mn lines in the conditions of typical laser-induced plasmas. Single-and double-pulse Laser-Induced Breakdown spectroscopy (LIBS) configurations are studied on a series of Fe-Mn alloy samples with Mn concentration ranging from 6{\%} to 30{\%}. The effects of self-absorption on the measured line broadenings are discussed in detail. In particular, the experimental results evidence that self-absorption is much higher in laser-induced plasmas generated with double pulses, compared to the case of single pulse. After measurement of the electron density, the Stark coefficients of several neutral and ionic Mn lines are derived through the measure of the broadening in conditions of optically thin plasma. The results obtained for singly ionized Mn lines are compared with the theoretical and experimental data present in the literature. For the first time, experimental measurements of the Stark coefficient for several neutral Mn lines are also presented.},
author = {{De Giacomo}, A and Dell'Aglio, M and Gaudiuso, R and Cristoforetti, G and Legnaioli, S and Palleschi, V and Tognoni, E},
doi = {10.1016/j.sab.2008.06.010},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {9},
pages = {980--987},
title = {{Spatial distribution of hydrogen and other emitters in aluminum laser-induced plasma in air and consequences on spatially integrated Laser-Induced Breakdown Spectroscopy measurements}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854708002073},
volume = {63},
year = {2008}
}
@article{Naes2008,
abstract = {Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), micro X-ray fluorescence spectroscopy ($\mu$XRF), and laser induced breakdown spectroscopy (LIBS) are compared in terms of discrimination power for a glass sample set consisting of 41 fragments. Excellent discrimination results (N99{\%} discrimination) were obtained for each of the methods. In addition, all three analytical methods produced very similar discrimination results in terms of the number of pairs found to be indistinguishable. The small number of indistinguishable pairs that were identified all originated from the same vehicle. The results also show a strong correlation between the data generated from the use of $\mu$XRF and LA-ICP-MS, when comparing $\mu$XRF strontium intensities to LA-ICP-MS strontium concentrations. A 266 nm laser was utilized for all LIBS analyses, which provided excellent precision (b10{\%} RSD for all elements and b10{\%} RSD for all ratios, N=5). The paper also presents a thorough data analysis review for forensic glass examinations by LIBS and suggests several element ratios that provide accurate discrimination results related to the LIBS system used for this study. Different combinations of 10 ratios were used for discrimination, all of which assisted with eliminating Type I errors (false exclusions) and reducing Type II errors (false inclusions). The results demonstrate that the LIBS experimental setup described, when combined with a comprehensive data analysis protocol, provides comparable discrimination when compared to LA-ICP-MS and $\mu$XRF for the application of forensic glass examinations. Given the many advantages that LIBS offers, most notably reduced complexity and reduced cost of the instrumentation, LIBS is a viable alternative to LA-ICP-MS and $\mu$XRF for use in the forensic laboratory.},
author = {Naes, Benjamin E. and Umpierrez, Sayuri and Ryland, Scott and Barnett, Cleon and Almirall, Jose R.},
doi = {10.1016/j.sab.2008.07.005},
issn = {05848547},
journal = {Spectrochimica Acta Part B: Atomic Spectroscopy},
month = {oct},
number = {10},
pages = {1145--1150},
title = {{A comparison of laser ablation inductively coupled plasma mass spectrometry, micro X-ray fluorescence spectroscopy, and laser induced breakdown spectroscopy for the discrimination of automotive glass}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854708002176},
volume = {63},
year = {2008}
}
@article{Fichet2003,
abstract = {One of the most promising approaches to laser-induced breakdown spectroscopy (LIBS) experiments involves the use of an echelle spectrometer coupled with an intensified CCD. Even if drawbacks remain with its use, the echelle spectrometer facilitates a multielemental analysis that is more rapid than can be obtained with the more-conventional Czerny-Turner spectrometer and, moreover, does not sacrifice reliability. Quantitative results obtained with such apparatus for solids, liquids, powders, and gases are described and when possible compared with results from Czerny-Turner spectrometers. Liquid analysis by LIBS with echelle spectrometers has allowed a spectral database to be compiled. Once the qualitative spectra of pure elements in aqueous solutions, are obtained, they can be used for qualitative analysis of unknown samples.},
author = {Fichet, Pascal and Menut, Denis and Brennetot, Ren{\'{e}} and Vors, Evelyne and Rivoallan, Annie},
institution = {Commissariat {\`{a}} l'Energie Atomique Saclay, Fuel Cycle Division, Laboratoire d'Analyse par Laser et d'Etude de Surface, B{\^{a}}timent 391, 91191 Gif Sur Yvette, France. fichet@carnac.cea.fr},
journal = {Applied Optics},
number = {30},
pages = {6029--6035},
pmid = {14594061},
title = {{Analysis by laser-induced breakdown spectroscopy of complex solids, liquids, and powders with an echelle spectrometer.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594061},
volume = {42},
year = {2003}
}
@article{Ohta2009,
abstract = {We demonstrate the monitoring of plant nutrients in leaves of Citrus unshiu and Rhododendron obtusum using low-energy (<1 mJ) laser-induced breakdown spectroscopy. The raw plant leaf was successfully ablated without desiccation before laser irradiation, by applying metallic colloidal particles to the leaf surface. The emission intensity with the metallic particles was larger than that without the particles. This result indicates an improvement of the sensitivity and the detection limit of laser-induced breakdown spectroscopy. The emission enhancement was caused by localized surface plasmon resonance and was dependent on the size and material of metallic particles.},
author = {Ohta, Takayuki and Ito, Masafumi and Kotani, Takashi and Hattori, Takeaki},
institution = {Department of Opto-Mechatronics, Faculty of Systems Engineering, Wakayama University, Wakayama, Japan. ohta@sys.wakayama-u.ac.jp},
journal = {Applied Spectroscopy},
number = {5},
pages = {555--558},
pmid = {19470213},
title = {{Emission enhancement of laser-induced breakdown spectroscopy by localized surface plasmon resonance for analyzing plant nutrients.}},
url = {http://www.ingentaconnect.com/content/sas/sas/2009/00000063/00000005/art00015},
volume = {63},
year = {2009}
}
@article{Burakov2007,
abstract = {In the present work, the possibilities of application of laser-induced breakdown spectroscopy for the diagnosis and analysis of uncorroded and artificially weathered glasses have been studied. Optimization of the laser-induced breakdown spectroscopy parameters included the energy per pulse and number of pulses. Analysis of spectra allowed the identification, not only of the major components but also of the chromophores of the glass samples considered. Stratigraphic analyses, performed by applying successive laser pulses on the same spot, allowed the detection of the different corrosion layers built up during weathering (corrosion crust, gel layer and unaltered glass bulk). Finally, the comparison of the laser-induced breakdown spectroscopy results with the conventional techniques Scanning Electron Microscopy/Energy Dispersive X-ray analysis, X-ray fluorescence and ultraviolet-visible spectroscopy revealed the advantages of this spectroscopic technique for the practice of glass conservation.},
author = {Burakov, V S and Raikov, S N},
doi = {10.1016/j.sab.2007.03.021},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {12},
pages = {1419--1425},
title = {{Quantitative analysis of alloys and glasses by a calibration-free method using laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707000882},
volume = {62},
year = {2007}
}
@article{Aguilera2009a,
abstract = {Optical emission of laser-induced plasma on the surface of fresh vegetables provides sensitive analysis of trace elements for in situ or online detection of these materials. This emergent technique promises applications with expected outcomes in food security or nutrition quality, as well as environment pollution detection. Characterization of the plasma induced on such soft and humid materials represents the first step towards quantitative measurement using this technique. In this paper, we present the experimental setup and protocol that optimize the plasma generation on fresh vegetables, potatoes for instance. The temporal evolution of the plasma properties are investigated using time-resolved laser-induced breakdown spectroscopy (LIBS). In particular, the electron density and the temperatures of the plasma are reported as functions of its decay time. The temperatures are evaluated from the well known Boltzmann and Saha-Boltzmann plot methods. These temperatures are further compared to that of the typical molecular species, CN, for laser-induced plasma from plant materials. This comparison validates the local thermodynamic equilibrium (LTE) in the specific case of fresh vegetables ablated in the typical LIBS conditions. A study of the temporal evolution of the signal to noise ratio also provides practical indications for an optimized detection of trace elements. We demonstrate finally that, under certain conditions, the calibration-free LIBS procedure can be applied to determine the concentrations of trace elements in fresh vegetables.},
author = {Aguilera, J A and Arag{\'{o}}n, C and Cristoforetti, G and Tognoni, E},
doi = {10.1016/j.sab.2009.06.002},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {7},
pages = {685--689},
publisher = {Elsevier B.V.},
title = {{Application of calibration-free laser-induced breakdown spectroscopy to radially resolved spectra from a copper-based alloy laser-induced plasma}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709001414},
volume = {64},
year = {2009}
}
@article{Li2010,
abstract = {Aerosol particles in the atmosphere are important participants in the formation of cloud droplets and have significant impact on cloud albedo and global climate. According to the K¨ ohler theory which describes the nucleation and the equilibrium growth of cloud 5 droplets, the surface tension of an aerosol droplet is one of the most important factors that determine the critical supersaturation of droplet activation. In this paper, with specific interest to remote marine aerosol, we predict the surface tension of aerosol droplets by performing molecular dynamics simulations on two model systems; the pure water droplets and glycine in water droplets. The curvature dependence of the 10 surface tension is interpolated by a quadratic polynomial over the nano-sized droplets and the limiting case of a planar interface, so that the so-called Aitken mode particles which are critical for droplet formation could be covered and the K¨ ohler equation could be improved by incorporating surface tension corrections.},
author = {Li, X. and Hede, T. and Tu, Y. and Leck, C. and {\AA}gren, H.},
doi = {10.5194/acpd-10-23169-2010},
file = {::},
issn = {1680-7375},
journal = {Atmospheric Chemistry and Physics Discussions},
month = {oct},
number = {10},
pages = {23169--23196},
title = {{Glycine in aerosol water droplets: a critical assessment of K{\"{o}}hler theory by predicting surface tension from molecular dynamics simulations}},
url = {http://www.atmos-chem-phys-discuss.net/10/23169/2010/},
volume = {10},
year = {2010}
}
@article{Wang2008,
abstract = {Comparative measurements of Laser-Induced Breakdown Spectroscopy (LIBS) for ultraviolet (UV) and near infrared (NIR) excitationwavelengths on a wide range of plastics and one kind of explosive are presented. The focus of work is on the influence of laser wavelength on the Signal-to-peak to peak noise ratio (SPPNR) for selected emission lines as well as the plasma thresholds for NIR and UV excitation wavelengths. The merits of both excitation wavelengths are discussed with respect to the detection of explosives.},
author = {Wang, Qianqian and Jander, Peter and Fricke-Begemann, Cord and Noll, Reinhard},
doi = {10.1016/j.sab.2008.06.008},
file = {::},
issn = {05848547},
journal = {Spectrochimica Acta Part B: Atomic Spectroscopy},
month = {oct},
number = {10},
pages = {1011--1015},
publisher = {Elsevier B.V.},
title = {{Comparison of 1064 nm and 266 nm excitation of laser-induced plasmas for several types of plastics and one explosive}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854708002097},
volume = {63},
year = {2008}
}
@article{Santos2008,
abstract = {The aim of this work was to evaluate the performance of femtosecond laser-induced breakdown spectroscopy (fs-LIBS) for the determination of elements in animal tissues. Sample pellets were prepared from certified reference materials, such as liver, kidney, muscle, hepatopancreas, and oyster, after cryogenic grinding assisted homogenization. Individual samples were placed in a two-axis computer-controlled translation stage that moved in the plane orthogonal to a beam originating from a Ti:Sapphire chirped-pulse amplification (CPA) laser system operating at 800 nm and producing a train of 840 microJ and 40 fs pulses at 90 Hz. The plasma emission was coupled into the optical fiber of a high-resolution intensified charge-coupled device (ICCD)-echelle spectrometer. Time-resolved characteristics of the laser-produced plasmas showed that the best results were obtained with delay times between 80 and 120 ns. Data obtained indicate both that it is a matrix-independent sampling process and that fs-LIBS can be used for the determination of Ca, Cu, Fe, K, Mg, Na, and P, but efforts must be made to obtain more appropriate detection limits for Al, Sr, and Zn.},
author = {Santos, D{\'{a}}rio and Samad, Ricardo Elgul and Trevizan, L{\'{\i}}lian Cristina and {De Freitas}, Anderson Zanardi and Vieira, Nilson Dias and Krug, Francisco Jos{\'{e}}},
institution = {Centro de Lasers e Aplica{\c{c}}{\~{o}}es, Instituto de Pesquisas Energ{\'{e}}ticas e Nucleares-CNEN, Av. Prof. Lineu Prestes 2242, Cidade Universit{\'{a}}ria, 05508-000 S{\~{a}}o Paulo-SP, Brazil. dario@cena.usp.br},
journal = {Applied Spectroscopy},
number = {10},
pages = {1137--1143},
pmid = {18926024},
title = {{Evaluation of femtosecond laser-induced breakdown spectroscopy for analysis of animal tissues.}},
url = {http://apps.isiknowledge.com/full{\_}record.do?product=UA{\&}search{\_}mode=GeneralSearch{\&}qid=3{\&}SID=1BbIdABkjB33AOo9iD4{\&}page=1{\&}doc=5{\&}colname=WOS},
volume = {62},
year = {2008}
}
@article{Fujimoto1985,
abstract = {The use of high intensity ultrashort pulsed laser radiation to produce optical breakdown is an important approach for the surgical treatment of intraocular structures. We have investigated the transient properties of Nd:YAG laser induced breakdown in a saline model using time-resolved spectroscopic techniques. Spatially resolved pump and probe techniques are applied to study the dynamic behavior of the plasma formation, acoustic wave generation, and cavitation processes which accompany the optical breakdown. Measurements of plasma shielding and luminescence indicate that the laser induced plasma forms on a subnanosecond time scale and has a lifetime of several nanoseconds. An acoustic transient is generated at the breakdown site and propagates spherically outward with an initial hypersonic velocity, then loses energy and propagates at sound velocity. Transient heating following the plasma formation produces a liquid-gas phase change and gives rise to cavitation or gas bubble formation. This gas bubble expands rapidly for several microseconds, then slows to reach its maximum size and finally collapses.},
author = {Fujimoto, J G and Lin, W Z and Ippen, E P and Puliafito, C A and Steinert, R F},
journal = {Investigative Ophthalmology {\&} Visual Science},
number = {12},
pages = {1771--1777},
pmid = {4066213},
title = {{Time-resolved studies of Nd:YAG laser-induced breakdown. Plasma formation, acoustic wave generation, and cavitation.}},
url = {http://www.iovs.org/cgi/content/abstract/26/12/1771},
volume = {26},
year = {1985}
}
@article{Gleason2001,
abstract = {A systematic study of the processes associated with mercury atomic emission in a laser-induced plasma and the interactions of mercury with oxygen species is presented. At early plasma decay times, on the order of 510 s, no significant variation in mercury atomic emission was observed with the addition of oxygen-containing species. At intermediate and long decay times {\v{Z}}10100 s., a significant reduction in the 253.7-nm mercury emission intensity was recorded with the introduction of oxygen-containing species. The decrease in mercury emission was temporally coincident with the recombination of atomic oxygen, as measured by the O{\v{Z}}I. emission. The decreased mercury emission was not due to thermal effects, based on plasma temperature measurements, and was independent of the molecular source of oxygen, for similar concentrations of oxygen as air, carbon dioxide, and carbon monoxide. Analysis of additional mercury atomic emission lines revealed that the reduction in mercury emission in the presence of oxygen species is limited primarily to the 253.7-nm transition. In concert, the data lead to the conclusion that the 253.7-nm mercury emission line is selectively quenched by oxygen species, primarily O2 and NO, that are formed during the plasma recombination process. Implications for laser-induced breakdown spectroscopy-based emissions monitoring of mercury species are discussed.  2001 Elsevier Science B.V. All rights reserved.},
author = {Gleason, R.L and Hahn, D.W},
doi = {10.1016/S0584-8547(01)00169-0},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Gleason, Hahn - The effects of oxygen on the detection of mercury using laser-induced breakdown spectroscopy - 2001.pdf:pdf},
issn = {05848547},
journal = {Spectrochimica Acta Part B: Atomic Spectroscopy},
keywords = {emissions monitoring,laser-induced breakdown spectroscopy,mercury},
month = {apr},
number = {4},
pages = {419--430},
title = {{The effects of oxygen on the detection of mercury using laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701001690},
volume = {56},
year = {2001}
}
@article{Hybl2003,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is examined as a potential method for detecting airborne biological agents. A spectrally broadband LIBS system was used for laboratory measurements on some common biological agent simulants. These measurements were compared to those of common, naturally occurring biological aerosol components (pollen and fungal spores) to determine the potential of LIBS for discriminating biological agents from natural background aerosols. A principal components analysis illustrates that linear combinations of the detected atomic lines, which are present in different ratios in each of the samples tested, can be used to discriminate biological agent simulants from other biological matter. A more sensitive, narrowband LIBS instrument was used to demonstrate the detection of single simulant (Bg) particles in the size range 1–5 mm. Ca, Mg, and Na, which are present in varying concentrations between 0.3 and 11{\%} (by mass) in the Bg particles, were observed in single particles using LIBS. Index Headings: Laser-induced breakdown spectroscopy; LIBS; Plasma spectroscopy; Biological agent detection; Biological aerosols},
author = {Hybl, John D and Lithgow, Gregg A and Buckley, Steven G},
file = {::},
journal = {Applied Spectroscopy},
number = {10},
pages = {1207--1215},
title = {{accelerated paper Laser-Induced Breakdown Spectroscopy Detection and Classi cation of Biological Aerosols *}},
volume = {57},
year = {2003}
}
@book{Bachor2004a,
abstract = {Laser induced breakdown spectroscopy (LIBS) has been evaluated for the determination of micronutrients (B, Cu, Fe, Mn and Zn) in pellets of plant materials, using NIST, BCR and GBW biological certified reference materials for analytical calibration. Pellets of approximately 2 mm thick and 15 mm diameter were prepared by transferring 0.5 g of powdered material to a 15 mm die set and applying 8.0 tons cm- 2. An experimental setup was designed by using a Nd:YAG laser operating at 1064 nm (200 mJ per pulse, 10 Hz) and an Echelle spectrometer with ICCD detector. Repeatability precision varied from 4 to 30{\%} from measurements obtained in 10 different positions (8 laser shots per test portion) in the same sample pellet. Limits of detection were appropriate for routine analysis of plant materials and were 2.2 mg kg- 1 B, 3.0 mg kg- 1 Cu, 3.6 mg kg- 1 Fe, 1.8 mg kg- 1 Mn and 1.2 mg kg- 1 Zn. Analysis of different plant samples were carried out by LIBS and results were compared with those obtained by ICP OES after wet acid decomposition.},
author = {Bachor, Hans-A and Ralph, Timothy C},
booktitle = {WileyVCH},
doi = {10.1017/S0263034600234125},
editor = {Textbook, Physics},
institution = {University of Minnesota},
isbn = {3527403930},
issn = {05848547},
number = {5},
pages = {434},
publisher = {Wiley-VCH},
title = {{A Guide to Experiments in Quantum Optics}},
url = {http://www.amazon.com/Guide-Experiments-Quantum-Optics/dp/3527403930},
volume = {64},
year = {2004}
}
@article{Cristoforetti,
author = {Cristoforetti, Gabriele and Legnaioli, Stefano and Palleschi, Vincenzo and Salvetti, A},
file = {::},
journal = {essex.ac.uk},
title = {{A new self-calibrated method for precise quantitative analysis by laser induced breakdown spectroscopy}},
url = {http://www.essex.ac.uk/bs/libs/papersLIBS/palleschi.pdf}
}
@article{U2001,
author = {U, A I Whitehouse and Young, J and Botheroyd, I M and Lawson, S and Evans, C P and Wright, J},
journal = {System},
keywords = {advanced gas cooled reactor,analysis,fiber optic libs {\v{z}} folibs,laser induced breakdown spectroscopy {\v{z}},libs,nuclear power station,remote inspection,semi quantitative elemental,{\v{z}} agr},
pages = {821--830},
title = {{Remote material analysis of nuclear power station steam generator tubes by laser-induced breakdown}},
year = {2001}
}
@article{Bol'shakov2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) offers rapid, localized chemical analysis of solid or liquid materials with high spatial resolution in lateral and depth profiling, without the need for sample preparation. Principal component analysis and partial least squares algorithms were applied to identify a variety of complex organic and inorganic samples. This work illustrates how LIBS analyzers can answer a multitude of real-world needs for rapid analysis, such as determination of lead in paint and children's toys, analysis of electronic and solder materials, quality control of fiberglass panels, discrimination of coffee beans from different vendors, and identification of generic versus brand-name drugs. Lateral and depth profiling was performed on children's toys and paint layers. Traditional one-element calibration or multivariate chemometric procedures were applied for elemental quantification, from single laser shot determination of metal traces at {\~{}}10 $\mu$g/g to determination of halogens at 90 $\mu$g/g using 50-shot spectral accumulation. The effectiveness of LIBS for security applications was demonstrated in the field by testing the 50-m standoff LIBS rasterizing detector.},
author = {Bol'shakov, Alexander A and Yoo, Jong H and Liu, Chunyi and Plumer, John R and Russo, Richard E},
doi = {10.1364/AO.49.00C132},
journal = {Applied Optics},
number = {13},
pages = {C132--C142},
title = {{Laser-induced breakdown spectroscopy in industrial and security applications}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-49-13-C132},
volume = {49},
year = {2010}
}
@article{Alvira2010a,
abstract = {Two of the main items from which to retrieve data in anthropology are teeth and bones. Identification of trace elements in their composition allows valuable information to be obtained about alimentary habits and community life conditions of groups and individuals. Conventional methods used to determine the presence of trace elements require sample preparation, with partial or total destruction of the pieces, which in most cases are unique. In this work we show the possibilities of laser-induced breakdown spectroscopy (LIBS) as a nearly nondestructive tool in anthropology and paleontology for the measurement of the presence and distribution of trace elements in teeth. We applied LIBS to the determination of strontium and magnesium in dentin and enamel of Neolithic, middle age, and modern Homo sapiens teeth. Mg/Ca and Sr/Ca distribution maps of dentin and enamel in modern teeth were created using the data obtained. Ablation threshold fluences of dentin and enamel were also measured using the photoacoustic signal induced by laser ablation. Significant variations were found in the Mg/Ca and Sr/Ca ratios in the tooth dental tissue and between the teeth of the groups and individuals studied. These results can be useful for evolutionary anthropology studies as they can provide information regarding early nutrition, seasonality, and residential mobility.},
author = {Alvira, F C and {Ramirez Rozzi}, F and Bilmes, G M},
institution = {Centro de Investigaciones Opticas-CIOp (CONICET La Plata -CIC) C.C.3,1897, La Plata, Argentina.},
journal = {Applied Spectroscopy},
number = {3},
pages = {313--319},
pmid = {20223067},
title = {{Laser-induced breakdown spectroscopy microanalysis of trace elements in Homo sapiens teeth.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20223067},
volume = {64},
year = {2010}
}
@article{Corsi2006,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is a promising technique for in situ environmental analysis. The potential of this technique for accurate quantitative analysis could be greatly improved using an innovative experimental setup - based on the use of two laser pulses suitably retarded - and analyzing the results with a standard-less procedure which overcomes the problems related to matrix effects. A new mobile instrument for soil analysis, developed at the Applied Laser Spectroscopy Laboratory in Pisa, is presented, and some experimental results are given.},
author = {Corsi, M and Cristoforetti, G and Hidalgo, M and Legnaioli, S and Palleschi, V and Salvetti, A and Tognoni, E and Vallebona, C},
doi = {10.1016/j.apgeochem.2006.02.004},
issn = {08832927},
journal = {Applied Geochemistry},
number = {5},
pages = {748--755},
title = {{Double pulse, calibration-free laser-induced breakdown spectroscopy: A new technique for in situ standard-less analysis of polluted soils}},
url = {http://www.sciencedirect.com/science/article/B6VDG-4JHMY04-4/2/d0ec9c40c99251bed33ac72250da1173},
volume = {21},
year = {2006}
}
@article{Kim1998,
abstract = {A sensitive optical technique for compositional mapping of solid surfaces using laser-induced breakdown spectroscopy (LIBS) is described. A pulsed Nd:YAG laser with second harmonic module was focused on the solid surface, giving a small ablation area, to produce plasma emission. Copper and magnesium emissions from a standard sample were carefully analyzed and assigned in the wavelength range 500520 nm. The assigned spectral information was selected to construct an image of 100 100 pixels by mapping the measured emission intensity values from the analyzed points. The time required for image construction and image sharpness depends on the number of laser shots per point of analysis and the number of analyzed points per image. A clear image of a copper conductor pattern from a printed circuit board was generated. In addition, some copper contaminations around the conductor area are clearly visible in the scanning LIBS map. The contaminated copper salt probably resulted from the incomplete washing step during manufacturing that could cause a short circuit in an electronic device.},
author = {Kim, Taesam and Lin, C T and Yoon, Yoonyeol},
doi = {10.1021/jp980245m},
issn = {15206106},
journal = {The Journal of Physical Chemistry B},
number = {22},
pages = {4284--4287},
title = {{Compositional Mapping by Laser-Induced Breakdown Spectroscopy}},
url = {http://dx.doi.org/10.1021/jp980245m},
volume = {102},
year = {1998}
}
@article{Bulajic2002,
abstract = {A model of the self-absorption effect in laser-induced plasma has been developed, with the aim of providing a tool for its automatic correction in the Calibration-Free algorithm recently developed for standardless analysis of materials by LIBS (Laser Induced Breakdown Spectroscopy). As a test of the model, the algorithm for self-absorption correction is applied to three different certified steel NIST samples and to three ternary alloys (Au, Ag, Cu) of known composition. The experimental results show that the self-absorption corrected Calibration-Free method gives reliable results, improving the precision and the accuracy of the CF-LIBS procedure by approximately one order of magnitude.},
author = {Bulajic, D},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {curve growth,elemental analysis,libs,lips,self absorption},
number = {2},
pages = {339--353},
title = {{A procedure for correcting self-absorption in calibration free-laser induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701003986},
volume = {57},
year = {2002}
}
@article{Radziemski1981,
abstract = {We have added time resolution to laser-induced breakdown spectroscopy in two forms, by gating an optical multichannel analyzer (OMA) and by time-resolving the output of a photomultiplier with a boxcar amplifier. Spectra were obtained for temporal segments of 25 to 100 ns, from 25 ns to 50 µs after initiation of the breakdown. OMA spectra of oxygen illustrate the power of this technique for survey purposes. The photomultiplier-boxcar arrangement was used to detect phosphorus atoms from diisopropylmethyl phosphonate in air, and also to detect chlorine in air, both in real time. In the former experiments we detected 690 ppm (w/w) of phosphorus and project a limit of detection with our current apparatus of 15 ppm (w/w). For chlorine, we observed signal from 120 ppm (w/w) and project a limit of detection of 60 ppm (w/w).},
author = {Radziemski, L J and Loree, T R},
doi = {10.1007/BF00568836},
issn = {02724324},
journal = {Plasma Chemistry and Plasma Processing},
keywords = {1,a p e r,chlorine detection,i n t r,laser induced,laser induced breakdown,o d u c,phosphorus detection,previous p,spectrochemistry,spectroscopy,t i o n,time resolved,we reported time integrated},
number = {3},
pages = {281--293},
title = {{Laser-induced breakdown spectroscopy: Time-resolved spectrochemical applications}},
url = {http://www.springerlink.com/index/10.1007/BF00568836},
volume = {1},
year = {1981}
}
@article{Death2009,
abstract = {In the mining industry the quality and extent of an ore body is determined on the basis of routine assays conducted on drill core and chip samples. Both the elemental composition and the mineralogical classification are important in the characterisation of an ore body for commercial exploitation. Mining industry laboratories typically analyse large numbers of samples from both exploration and mine production environments. At CSIRO we have explored the application of chemometric methods of analysis in combination with laser induced breakdown spectroscopy (LIBS) in order to produce routine quantitative analysis of several ore types including iron, nickel and lead/zinc ores. In particular, principal components regression (PCR) has been applied to perform multi-element analysis of iron ore samples from Australia and West Africa. Calibration models for iron (4.8{\%} Av. Relative Error), aluminium (2.2{\%}), silicon (3.7{\%}) and potassium (1.4{\%}) were determined for the Australian ores. In addition phosphorous measurements were made at trace level for samples from West Africa (5.5{\%} Av. Relative Error). LIBS measurements of segments of a nickel drill core were also analysed using PCR. Mineralogical classification using a combination of LIBS and principal components analysis (PCA) has also been explored. Broad discrimination of ore mineralogy was demonstrated on the basis of the PCA of LIBS spectra in selected emission wavelength bands. The combination of PCA and PCR offers potential for both broad mineralogical and elemental analysis for the minerals industry in exploration and in mine production for the on-line monitoring of ore quality.},
author = {Death, D L and Cunningham, A P and Pollard, L J},
doi = {10.1016/j.sab.2009.07.017},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1048--1058},
publisher = {Elsevier B.V.},
title = {{Multi-element and mineralogical analysis of mineral ores using laser induced breakdown spectroscopy and chemometric analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709002298},
volume = {64},
year = {2009}
}
@article{Cho2001,
abstract = {Spatially resolved laser-induced breakdown spectrometry (LIBS) was investigated to evaluate the feasibility as a quick and simple method to analyze trace elemental concentrations in starch-based flour samples. A NdratioYAG laser beam (small lambda=1064nm, 30mJpulse-1) has been used for generation of laser-induced plasma on sample surface under reduced pressure of argon atmosphere. A series of starch powder samples containing different concentrations of Sr, Mg, Al, Cu, Cr, K, Mn, Rb, Cd, and Pb were used to construct the calibration curves and estimate detection limits of measurements. The calibration graphs for all elements show good linearity (correlation coefficient, r>0.99) in the range 0-160micro signgg-1 or within three orders of magnitude. Detection limits achieved were below 18micro signgg-1 for all elements studied in this work. The lowest detection limit (0.3micro signgg-1) was obtained from Sr measurement. Precision ({\%}RSD) for the selected analysis was in the range 2-10{\%}. The standard addition method was applied to assess the accuracy of LIBS using a NIES standard rice sample. The concentrations of Mg and Mn in NIES standard rice sample determined by spatially resolved LIBS technique have good agreements with those of certified value within an error range. The results indicate that spatially resolved LIBS has been shown to be an accurate technique for determining trace elements of ppm (micro signgg-1) level in starch-based food samples directly with an acceptable precision without any tedious digestion and dilution procedure.},
author = {Cho, HyoHyun and Kim, YoungJu and Jo, YoungSoo and Kitagawa, Kuniyuki and Arai, Norio and Lee, YongIll},
doi = {10.1039/b100754h},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {6},
pages = {622--627},
title = {{Application of laser-induced breakdown spectrometry for direct determination of trace elements in starch-based flours}},
url = {http://xlink.rsc.org/?DOI=b100754h},
volume = {16},
year = {2001}
}
@article{Kossakovski2000,
abstract = {Spatially resolved chemical imaging is achieved by combining a fiber-optic scanning probe microscope with laser-induced breakdown spectroscopy in a single instrument, TOPOLIBS. Elemental composition of surfaces can be mapped and correlated with topographical data. The experiment is conducted in air with minimal sample preparation. In a typical experiment, surface topography is analyzed by scanning a sharp fiber-optic probe across the sample using shear force feedback. The probe is then positioned over a feature of interest and pulsed radiation is delivered to the surface using a nitrogen laser. The pulse vaporizes material from the surface and generates a localized plasma plume. Optical emission from the plume is analyzed with a compact UV/visible spectrometer. Ablation crater size is controlled by the amount of laser power coupled into the probe. Sampling areas with submicrometer dimensions are achieved by using reduced laser power.},
author = {Kossakovski, Dmitri and Beauchamp, J L},
doi = {10.1021/ac0005058},
issn = {00032700},
journal = {Analytical Chemistry},
number = {19},
pages = {4731--7},
pmid = {11028639},
title = {{Topographical and chemical microanalysis of surfaces with a scanning probe microscope and laser-induced breakdown spectroscopy}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11028639},
volume = {72},
year = {2000}
}
@article{Salt1996,
abstract = {Measurement of scattered light intensity and aerodynamic particle sizing are two methods that have recently been coupled with time-of-flight mass spectrometry for real-time determination of aerosol particle size and composition. An aerosol analysis technique recently developed in our laboratory, aerosol time-of-flight mass spectrometry, offers a unique experimental platform to evaluate both of these sizing techniques. This paper presents a comparison of results obtained with these two methods.},
author = {Salt, K and Noble, C a and Prather, K a},
doi = {10.1021/ac950396a},
file = {::},
issn = {0003-2700},
journal = {Analytical chemistry},
month = {jan},
number = {1},
pages = {230--4},
pmid = {21619241},
title = {{Aerodynamic Particle Sizing versus Light Scattering Intensity Measurement as Methods for Real-Time Particle Sizing Coupled with Time-of-Flight Mass Spectrometry.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21619241},
volume = {68},
year = {1996}
}
@article{Praher2000,
abstract = {Calibration-free laser-induced breakdown spectroscopy (CF-LIBS) method is employed for quantitative determination of oxide concentrations in multi-component materials. Industrial oxide materials from steel industry are laser ablated in air, and the optical plasma emission is collected by spectrometers and gated detectors. The temperature and electron number density of laser-induced plasma are determined from measured LIBS spectra. Emission lines of aluminium (Al), calcium (Ca), iron (Fe), manganese (Mn), magnesium (Mg), silicon (Si), titanium (Ti), and chromium (Cr) of low self-absorption are selected, and the concentration of oxides CaO, Al(2)O(3), MgO, SiO(2), FeO, MnO, TiO(2), and Cr(2)O(3) is calculated by CF-LIBS analysis. For all sample materials investigated, we find good match of calculated concentration values (C (CF)) with nominal concentration values (C (N)). The relative error in oxide concentration, e (r)=C (CF)-C (N)/C (N), decreases with increasing concentration and it is e (r)100{\%} for concentration C (N)1wt.{\%}. The CF-LIBS results are stable against fluctuations of experimental parameters. The variation of laser pulse energy over a large range changes the error by less than 10{\%} for major oxides (C (N)10wt.{\%}). The results indicate that CF-LIBS method can be employed for fast and stable quantitative compositional analysis of multi-component materials.},
author = {Praher, B and R{\"{o}}ssler, R and Arenholz, E and Heitz, J and Pedarnig, J D},
issn = {16182650},
journal = {Analytical and Bioanalytical Chemistry},
number = {2002},
pages = {245--250},
title = {{A note on testing for nonlinearity with partially observed time series}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21527623},
year = {2000}
}
@article{Vors2008,
abstract = {This work is devoted to the study of the gas pressure effect on the laser-induced breakdown spectroscopy signal intensity of carbon. Experiments are performed, using a 1064 nm Nd:YAG laser, with carbon solid samples placed inside a high pressure chamber filled with helium or nitrogen, the gas pressure varying from 1 to 80 atm. The signal intensity of the carbon line (247.86 nm) decreases with increasing pressure. As the plasma size strongly decreases with pressure, two collection optical setups are used, showing different raw results. To take into account the plasma size evolution with pressure, calculated corrections are applied to the collected light intensity. Carbon line emission is measured and corrected as a function of pressure in both gases. At 1 atm, the emission line is found to be greater in helium than in nitrogen by a factor of approximately 3, whereas the intensities in the two gases become close to each other at 80 atm.},
author = {Vors, Evelyne and Gallou, Catherine and Salmon, Laurent},
doi = {10.1016/j.sab.2008.08.015},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1198--1204},
title = {{Laser-induced breakdown spectroscopy of carbon in helium and nitrogen at high pressure}},
url = {http://www.sciencedirect.com/science/article/B6THN-4TB1851-2/2/32e28d596c6eb9daa479e56b1696151a},
volume = {63},
year = {2008}
}
@article{Clegg2009,
abstract = {Quantitative analysis with laser-induced breakdown spectroscopy traditionally employs calibration curves that are complicated by chemical matrix effects. These chemical matrix effects influence the laser-induced breakdown spectroscopy plasma and the ratio of elemental composition to elemental emission line intensity. Consequently, laser-induced breakdown spectroscopy calibration typically requires a priori knowledge of the unknown, in order for a series of calibration standards similar to the unknown to be employed. In this paper, three new Multivariate Analysis techniques are employed to analyze the laser-induced breakdown spectroscopy spectra of 18 disparate igneous and highly-metamorphosed rock samples. Partial Least Squares analysis is used to generate a calibration model from which unknown samples can be analyzed. Principal Components Analysis and Soft Independent Modeling of Class Analogy are employed to generate a model and predict the rock type of the samples. These Multivariate Analysis techniques appear to exploit the matrix effects associated with the chemistries of these 18 samples.},
author = {Clegg, Samuel M and Sklute, Elizabeth and Dyar, M Darby and Barefield, James E and Wiens, Roger C},
doi = {10.1016/j.sab.2008.10.045},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {remote laser induced breakdown},
number = {1},
pages = {79--88},
publisher = {Elsevier B.V.},
title = {{Multivariate analysis of remote laser-induced breakdown spectroscopy spectra using partial least squares, principal component analysis, and related techniques}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854708003443},
volume = {64},
year = {2009}
}
@article{Harmon2011,
abstract = {Conflict minerals is a term applied to ores mined in conditions of armed conflict and human rights abuse. Niobium and tantalum are two rare metals whose primary natural occurrence is in the complex oxide minerals columbite and tantalite, the ore of which is commonly referred to as coltan. The illicit export of coltan ore from the Democratic Republic of the Congo is thought to be responsible for financing the ongoing civil conflicts in this region. Determining the chemical composition of an ore is one of the means of ascertaining its provenance. Laser-induced breakdown spectroscopy (LIBS) offers a means of rapidly distinguishing different geographic sources for a mineral because the LIBS plasma emission spectrum provides the complete chemical composition (i.e., "chemical fingerprint") of any material in real time. To test this idea for columbite-tantalite, three sample sets were analyzed. Partial least squares discriminant analysis (PLSDA) allows correct sample-level geographic discrimination at a success rate exceeding 90{\%}.},
author = {Harmon, Russell S and Shughrue, Katrina M and Remus, Jeremiah J and Wise, Michael A and East, Lucille J and Hark, Richard R},
institution = {Environmental Sciences Division, ARL Army Research Office, Durham, NC 27709, USA.},
journal = {Analytical and Bioanalytical Chemistry},
number = {10},
pages = {3377--3382},
pmid = {21537914},
publisher = {Springer Berlin / Heidelberg},
title = {{Can the provenance of the conflict minerals columbite and tantalite be ascertained by laser-induced breakdown spectroscopy?}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21537914},
volume = {400},
year = {2011}
}
@article{Yaroshchyk2004,
abstract = {A laser-induced breakdown spectroscopy (LIBS) analog of a dual beam spectrometer is described and applied to the determination of trace components present in aqueous samples. It is shown that the complexity of such an instrument can be greatly reduced by using a single imaging spectrograph and two-dimensional detector to record the LIBS spectrum from the analyte and reference channels simultaneously. Implementation of the dual beam technique results in substantial spectral simplification and corresponding lower detection limits in LIBS analysis of liquids.},
author = {Yaroshchyk, Pavel and Morrison, Richard J S and Body, Doug and Chadwick, Bruce L},
doi = {10.1063/1.1805211},
issn = {00346748},
journal = {Review of Scientific Instruments},
number = {11},
pages = {5050},
title = {{Dual beam spectrometer using laser-induced breakdown spectroscopy}},
url = {http://link.aip.org/link/?RSI/75/5050/1},
volume = {75},
year = {2004}
}
@article{Mohaidat2011,
abstract = {In this paper we investigate the effect that adverse environmental and metabolic stresses have on the laser-induced breakdown spectroscopy (LIBS) identification of bacterial specimens. Single-pulse LIBS spectra were acquired from a non-pathogenic strain of Escherichia coli cultured in two different nutrient media: a trypticase soy agar and a MacConkey agar with a 0.01{\%} concentration of deoxycholate. A chemometric discriminant function analysis showed that the LIBS spectra acquired from bacteria grown in these two media were indistinguishable and easily discriminated from spectra acquired from two other non-pathogenic E. coli strains. LIBS spectra were obtained from specimens of a nonpathogenic E. coli strain and an avirulent derivative of the pathogen Streptococcus viridans in three different metabolic situations: live bacteria reproducing in the log-phase, bacteria inactivated on an abiotic surface by exposure to bactericidal ultraviolet irradiation, and bacteria killed via autoclaving. All bacteria were correctly identified regardless of their metabolic state. This successful identification suggests the possibility of testing specimens that have been rendered safe for handling prior to LIBS identification. This would greatly enhance personnel safety and lower the cost of a LIBS-based diagnostic test. LIBS spectra were obtained from pathogenic and non-pathogenic bacteria that were deprived of nutrition for a period of time ranging from one day to nine days by deposition on an abiotic surface at room temperature. All specimens were successfully classified by species regardless of the duration of nutrient deprivation.},
author = {Mohaidat, Qassem and Palchaudhuri, Sunil and Rehse, Steven J},
doi = {10.1366/10-06178},
file = {::},
issn = {1943-3530},
journal = {Applied spectroscopy},
keywords = {Bacteriological Techniques,Bacteriological Techniques: methods,Computational Biology,Computational Biology: methods,Culture Media,Discriminant Analysis,Escherichia coli,Escherichia coli: chemistry,Escherichia coli: classification,Escherichia coli: metabolism,Lasers,Spectrum Analysis,Spectrum Analysis: methods,Stress, Physiological,Viridans Streptococci,Viridans Streptococci: chemistry,Viridans Streptococci: classification,Viridans Streptococci: metabolism},
month = {apr},
number = {4},
pages = {386--92},
pmid = {21396185},
title = {{The effect of bacterial environmental and metabolic stresses on a laser-induced breakdown spectroscopy (LIBS) based identification of Escherichia coli and Streptococcus viridans.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21396185},
volume = {65},
year = {2011}
}
@article{Brown2007,
abstract = {An intensive multi-disciplinary research effort is underway at Wayne State University to synthesize and characterize magnetic nanoparticles in a biocompatible matrix for biomedical applications. The particular system being studied consists of 3-10 nm gamma-Fe2O3 nanoparticles in an alginate matrix, which is being studied for applications in targeted drug delivery, as a magnetic-resonance imaging (MRI) contrast agent, and for hyperthermic treatments of malignant tumors. In the present work we report on our efforts to determine if laser-induced breakdown spectroscopy (LIBS) can offer a more accurate and substantially faster determination of iron content in such nanoparticle-containing materials than competing technologies such as inductively-coupled plasma (ICP). Standardized samples of alpha-Fe2O3 nanoparticles (5-25 nm diameter) and silver micropowder (2-3.5 mu m diameter) were created with thirteen precisely known concentrations and pressed hydraulically to create solid "pellets" for LIBS analysis. The ratio of the intensity of an Fe(I) emission line at 37 1.994 nm to that of an Ag(I) line at 328.069 nm was used to create a calibration curve exhibiting an exponential dependence on Fe mass fraction. Using this curve, an "unknown" gamma-Fe2O3/alginate/silver pellet was tested, leading to a measurement of the mass fraction of Fe in the nanoparticle/alginate matrix of 51 3 wt.{\%}, which is in very good agreement with expectations and previous determinations of its iron concentration. (C) 2007 Elsevier B.V. All rights reserved.},
author = {Brown, E and Rehse, S J},
doi = {10.1016/j.sab.2007.10.023},
issn = {05848547},
journal = {Spectrochimica Acta Part B},
number = {12},
pages = {1475--1483},
title = {{Laser-induced breakdown spectroscopy of gamma-Fe2O3 nanoparticles in a biocompatible alginate matrix}},
url = {http://www.sciencedirect.com/science/article/B6THN-4PYP70S-3/2/c03aae30c83305f7f06532d2ddf10962},
volume = {62},
year = {2007}
}
@article{Gaudiuso2010,
abstract = {Analytical applications of Laser Induced Breakdown Spectroscopy (LIBS), namely optical emission spectroscopy of laser-induced plasmas, have been constantly growing thanks to its intrinsic conceptual simplicity and versatility. Qualitative and quantitative analysis can be performed by LIBS both by drawing calibration lines and by using calibration-free methods and some of its features, so as fast multi-elemental response, micro-destructiveness, instrumentation portability, have rendered it particularly suitable for analytical applications in the field of environmental science, space exploration and cultural heritage. This review reports and discusses LIBS achievements in these areas and results obtained for soils and aqueous samples, meteorites and terrestrial samples simulating extraterrestrial planets, and cultural heritage samples, including buildings and objects of various kinds.},
author = {Gaudiuso, Rosalba and Dell’Aglio, Marcella and Pascale, Olga De and Senesi, Giorgio S. and Giacomo, Alessandro De},
doi = {10.3390/s100807434},
file = {::},
issn = {1424-8220},
journal = {Sensors},
keywords = {Laser Induced Breakdown Spectroscopy (LIBS),cultural heritage,elemental,elemental analysis,laser induced breakdown spectroscopy,libs,meteorites,optical emission,soils,space exploration},
month = {aug},
number = {8},
pages = {7434--7468},
title = {{Laser Induced Breakdown Spectroscopy for Elemental Analysis in Environmental, Cultural Heritage and Space Applications: A Review of Methods and Results}},
url = {http://www.mdpi.com/1424-8220/10/8/7434/},
volume = {10},
year = {2010}
}
@article{Montenegro2003,
abstract = {High density 50 $\mu$s pulses of the UV dyes PPF, POPOP and BBO and of two dyes in the visible region, Xanthen N92 and Fluorol 7GA were generated by laser ablation. Dye powders were pressed with 7800 kp/cm2 in round pellets which were ablated by exposure to KrF excimer laser radiation (248 nm) at a fluence of 100 mJ/cm2. The ablation cloud was optically activated with a XeCl excimer laser. Its fluorescence spectrum was measured and was identified as a dye vapour fluorescence spectrum by comparison to conventional dye solution and dye vapour spectra. The dye cloud is not deflected in an electric field (106 V/m). By changing the delay time between the ablation laser and the focused activation laser, the velocity distribution of the ablated dye was measured. Its maximum is at 600 m/s for PPF. Knowing the thickness of the ablated dye layer per shot (300 {\AA}) and the size of the ablation cloud (pictures of a video camera), one can estimate the maximum density of the dye in the gas pulse to be 10-5 mol/l in the range of concentration of lasing dyes. However, no lasing was observed up to now. 1992.},
author = {Montenegro, M.J. and Clerc, C. and Lippert, T. and M{\"{u}}ller, S. and Willmott, P.R. and Weidenkaff, A. and Wokaun, A.},
doi = {10.1016/S0169-4332(02)01334-X},
issn = {01694332},
journal = {Applied Surface Science},
keywords = {aromatic compounds,dye vapor fluorescence spectroscopy,excimer radiation effects,fluorescence measurements,laser ablation vapor clouds,laser induced dye pellet ablation,laser pulses effects,lasers,optically activated ablation clouds,powders etching,pulsed excimer laser ablation,vapors spectroscopic analysis},
month = {mar},
number = {C},
pages = {45--51},
title = {{Analysis of the plasma produced by pulsed reactive crossed-beam laser ablation of La0.6Ca0.4CoO3}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S016943320201334X},
volume = {208-209},
year = {2003}
}
@article{Taylor2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was evaluated as a means for quantitative analys is of the s ize, mass, and compos ition of individual micron-to submicron-s ized aerosol particles over a range of well-characterized experimental conditions. Conditional data analys is was used to identify LIBS spectra that correspond to discrete aerosol particles under low aerosol particle loadings. The s ize distributions of monodisperse particle source  ows were measured using the LIBS technique for calcium- and magnes ium-based aerosols. The resulting s ize distributions were in good agreement with independently measured s ize distribution data. A lower s ize detection limit of 175 nm was determined for the calcium- and magnes ium-based particles, which corresponds to a detectable mass of approximately 3 femtograms. In addition, the accuracy of the LIBS technique for the interference-free analys is of different particle types was veri ed using a binary aerosol system of calcium-based and chromium particles.},
author = {Taylor, Publisher and Hahn, D W and Lunden, M M},
file = {::},
isbn = {0278682004108},
journal = {Aerosol Science and Technology},
number = {30 Nov 2010},
pages = {37--41},
title = {{Aerosol Science and Technology Detection and Analysis of Aerosol Particles by Laser-Induced Breakdown Spectroscopy Detection and Analysis of Aerosol Particles}},
url = {http://dx.doi.org/10.1080/027868200410831},
volume = {33:1-2},
year = {2010}
}
@article{Wang2010,
abstract = {This paper presents a new approach of applying partial least squares method combined with a physical principle based dominant factor. The characteristic line intensity of the specific element was taken to build up the dominant factor to reflect the major elemental concentration and partial least squares (PLS) approach was then applied to further improve the model accuracy. The deviation evolution of characteristic line intensity from the ideal condition was depicted and according to the deviation understanding, efforts were taken to model the non-linear self-absorption and inter-element interference effects to improve the accuracy of dominant factor model. With a dominant factor to carry the main quantitative information, the novel multivariate model combines advantages of both the conventional univariate and PLS models and partially avoids the overuse of the unrelated noise in the spectrum for PLS application. The dominant factor makes the combination model more robust over a wide concentration range and PLS application improves the model accuracy for samples with matrices within the calibration sample set. Results show that RMSEP of the final dominant factor based PLS model decreased to 2.33{\%} from 5.25{\%} when using the conventional PLS approach with full spectral information. Furthermore, with the development in understanding the physics of the laser-induced plasma, there is potential to easily improve the accuracy of the dominant factor model as well as the proposed novel multivariate model.},
author = {Wang, Zhe and Feng, Jie and Li, Lizhi and Ni, Weidou and Li, Zheng},
journal = {Journal Of Analytical Atomic Spectrometry},
pages = {17},
title = {{A Novel Multivariate Model Based on Dominant Factor for Laser-induced Breakdown Spectroscopy Measurements}},
url = {http://arxiv.org/abs/1012.2735},
year = {2010}
}
@article{Galbacs2001,
abstract = {A new calibration approach to analyze binary solid samples at the percentage level is proposed, and its application to laser-induced breakdown spectroscopy (LIBS) is presented. The method is based on the observed dependence of the linear correlation coefficient on the analyte concentration in a binary sample. The linear correlation coefficient is calculated between spectra of a range of certified standards and the spectrum of a reference sample (the analyte in the form of a pure metal), and the resulting curve is used as a calibration curve. It was found that a quadratic function could be adequately used to fit the calibration points. The first part of this paper characterizes the proposed calibration method providing mathematical and simulational data, and also describes a possibility to extend it to multicomponent samples. In the second part, the method is successfully applied to the LIBS analysis of Cu in brass samples as well as Al, Si and Cu in aluminum alloys. The new method was found to give rise to results accurate to 1-5{\%} for major components, and usually outperformed conventional calibration in terms of both precision and accuracy.},
author = {Galb{\'{a}}cs, G and Gornushkin, I B and Smith, B W and Winefordner, J D},
doi = {10.1016/S0584-8547(01)00205-1},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {binary alloys,calibration method,laser induced breakdown {\v{z}} libs,linear correlation},
number = {7},
pages = {1159--1173},
title = {{Semi-quantitative analysis of binary alloys using laser-induced breakdown spectroscopy and a new calibration approach based on linear correlation}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701002051},
volume = {56},
year = {2001}
}
@article{Ferrero2008,
abstract = {A theoretical study of atmospheric extinction mechanisms of optical radiation (molecular/aerosol scattering and absorption) has been carried out in order to assess their influences on stand-off laser-induced breakdown spectroscopy (LIBS) measurements. The atmospheric extinction of laser radiation at wavelengths commonly used in laser-induced breakdown spectroscopy (1064 nm and 532 nm) and of the laser-induced breakdown spectroscopy plasma emission beyond 250 nm is small compared to the attenuation with range due to the inverse square law. The fundamental problem with light propagation through the atmosphere is that the atmospheric transmittance does not remain constant within the whole spectral interval, and that this variation results in a change in the spectral distribution of the light received by the detector. Knowledge of atmospheric transmittance would allow for compensation of this effect.},
author = {Ferrero, A and Laserna, J J},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {2},
pages = {305--311},
title = {{A theoretical study of atmospheric propagation of laser and return light for stand-off laser induced breakdown spectroscopy purposes}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707003916},
volume = {63},
year = {2008}
}
@article{Rock2004,
abstract = {The effect of various parameters on the accuracy of the laser-induced breakdown spectroscopy (LIBS) data taken from pellet samples has been investigated. The dependence of the standard deviation of the LIBS data on the amount and nature of the binder used, pressure used to press the powder into a pellet, and the position of the focal spot on the pellet has been investigated. Pellets made from industrially important materials such as silica, alumina, and lime with polyvinyl alcohol, sucrose, and starch as binders have been studied. The results thus obtained are tested by preparation of the calibration curves for Si, Fe, and B in the pellets made from the powder glass batch used as a surrogate for the batch employed for the vitrification of radioactive waste.},
author = {Rock, Steven and Marcano, Aristides and Markushin, Yuri and Sabanayagam, Chandran and Melikechi, Noureddine},
institution = {Center for Research and Education in Optical Sciences and Applications, Department of Physics and Pre-Engineering, Delaware State University, 1200 North DuPont Hwy Dover, Delaware 19901, USA.},
journal = {Applied Optics},
number = {31},
pages = {2792--2797},
pmid = {19122709},
title = {{Elemental analysis of laser induced breakdown spectroscopy aided by an empirical spectral database.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19122709},
volume = {43},
year = {2004}
}
@article{Hamatani2003,
abstract = {Low-pressure plasma spraying (LPPS) is a promising method of applying coatings to surfaces for thermal, chemical, and mechanical protection. The deposition of coatings with superior properties requires an improved understanding of this complex spray process, including the detailed understanding of the time-temperature and chemical history to which an injected particle is exposed during its travel through the high-temperature and high-velocity plasma jet. In this paper, we report on measurements of the temperatures and velocities within the plasma in a low-pressure argon-hydrogen arcjet spray plasma being developed for mesoscale manufacturing of mechanical components. The measurements reported here make use of laser absorption, laser-induced fluorescence, and optical emission spectroscopy of the H-alpha Balmer transition in atomic hydrogen. Both the absorption and fluorescence methods take advantage of the well-known spectral line broadening of atomic hydrogen, to extract the arcjet. temperature and electron density. Jet axial velocities are measured via the time of flight, as detected by optical emission, of convected disturbances caused by intrinsic fluctuations in the arc voltage. Measurements made for various anode (nozzle) geometries indicate that relatively low (similar to1 km s(-1) mm(-1)) velocity gradients in the axial direction could be achieved with nozzles that include an expanding section of 10degrees half-angles. The measured temperatures and velocities suggest the presence of complex gas-dynamic shock structures in the arcjet plume, depending on the particular nozzle length and expansion section. (C) 2002 Elsevier Science B.V. All rights reserved.},
author = {Hamatani, H and Crawford, W S and Cappelli, M A},
doi = {10.1016/S0257-8972(02)00565-0},
issn = {02578972},
journal = {Surface and Coatings Technology},
keywords = {arcjet temperature,electron density,jet axial velocity,laser absorption,laser induced fluorescence,low pressure plasma spraying},
number = {1},
pages = {79--92},
title = {{Optical measurements of plasma velocity and temperature in a low-rate, low-power LPPS system}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0257897202005650},
volume = {162},
year = {2003}
}
@article{Yun2001,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was applied to selectively analyze the aqueous suspension of Eu2O3(s) particles in the presence of the Eu3+ aquo ion. A plasma was generated by focusing a pulsed Nd:YAG laser beam ($\lambda$ = 532 nm) into the sample. The light emission from the plasma was detected by a spectrograph equipped with a gated intensified charge-coupled device (ICCD) in the wavelength range of 275-525 nm. The atomic emission intensity of the Eu2O3(s) suspension was about two orders of magnitude higher than that of the Eu3+ aquo ion. The detection limits for Eu3+(aq) and Eu2O3(s) were found to be 3.3 10-5 mol/L and 2.0 10-7 mol/L, respectively. Such a difference allows the selective determination of colloidal europium particles. This capability of LIBS was used to study the formation of Eu(OH)3(s) colloids in the aqueous Eu3+ solution by varying pH until the solubility limit was exceeded. The appraisal of the threshold pH for the solubility limit led to the determination of the solubility product of colloidal Eu(OH)3(s), which was then calculated to be log K0sp = -25.5 0.4.},
author = {Yun, Jong-Il and Bundschuh, Tobias and Neck, Volker and Kim, Jae-Il},
doi = {10.1366/0003702011951885},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {3},
pages = {273--278},
title = {{Selective Determination of Europium(III) Oxide and Hydroxide Colloids in Aqueous Solution by Laser-Induced Breakdown Spectroscopy}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=55{\&}issue=3{\&}spage=273},
volume = {55},
year = {2001}
}
@article{Goode1997,
author = {Goode, Scott R and Angel, S Michael},
journal = {Imaging},
number = {November},
title = {{A Fundamental Study of Laser-Induced Breakdown Spectroscopy Using Fiber Optics for Remote Measurements of Trace Metals}},
volume = {305},
year = {1997}
}
@article{Hybl2006,
abstract = {Methods for accurately characterizing aerosols are required for detecting biological warfare agents. Currently, fluorescence-based biological agent sensors provide adequate detection sensitivity but suffer from high false-alarm rates. Combining single-particle fluorescence analysis with laser-induced breakdown spectroscopy (LIBS) provides additional discrimination and potentially reduces false-alarm rates. A transportable UV laser-induced fluorescence-cued LIBS test bed has been developed and used to evaluate the utility of LIBS for biological-agent detection. Analysis of these data indicates that LIBS adds discrimination capability to fluorescence-based biological-agent detectors. However, the data also show that LIBS signatures of biological agent simulants are affected by washing. This may limit the specificity of LIBS and narrow the scope of its applicability in biological-agent detection. © 2006 Optical Society of America},
author = {Hybl, John D and Tysk, Shane M and Berry, Shaun R and Jordan, Michael P},
doi = {140.3440, 300.6210, 300.6360.},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Hybl et al. - breakdown spectroscopy biological-agent detection - 2006.pdf:pdf},
journal = {Applied Optics},
number = {34},
pages = {6--8},
title = {breakdown spectroscopy biological-agent detection},
volume = {45},
year = {2006}
}
@article{Bulajic2002,
abstract = {A model of the self-absorption effect in laser-induced plasma has been developed, with the aim of providing a tool for its automatic correction in the Calibration-Free algorithm recently developed for standardless analysis of materials by LIBS (Laser Induced Breakdown Spectroscopy). As a test of the model, the algorithm for self-absorption correction is applied to three different certified steel NIST samples and to three ternary alloys (Au, Ag, Cu) of known composition. The experimental results show that the self-absorption corrected Calibration-Free method gives reliable results, improving the precision and the accuracy of the CF-LIBS procedure by approximately one order of magnitude.},
author = {Bulajic, D},
doi = {10.1016/S0584-8547(01)00398-6},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {curve growth,elemental analysis,libs,lips,self absorption},
number = {2},
pages = {339--353},
title = {{A procedure for correcting self-absorption in calibration free-laser induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701003986},
volume = {57},
year = {2002}
}
@article{Lazzari1994,
abstract = {For several years the laser-induced breakdown spectroscopy (LIBS) technique has been applied successfully to the problem of detecting small traces of pollutants in gases. The possible application of this method for the individuation of mercury in air is discussed. The laboratory prototype of the detection system is described in detail, and the sensitivity of the system for the diagnostics of small traces of mercury is determined. The reduced dimensions of the experimental apparatus and its relatively low cost make the LIBS method competitive with other laser-based methods for in situ analysis.},
author = {Lazzari, C and Rosa, M De and Rastelli, S and Ciucci, A and Palleschi, V and Salvetti, A},
doi = {10.1017/S0263034600008387},
journal = {Laser and Particle Beams},
number = {03},
pages = {525--530},
title = {{Detection of mercury in air by time-resolved laser-induced breakdown spectroscopy technique}},
volume = {12},
year = {1994}
}
@article{Friberg1998,
abstract = {This special issue of Pure and Applied Optics is devoted to physical optics and coherence theory in honour of Professor Emil Wolf, one of the world's most distinguished scientists in these fields, whose 75th birthday fell on 30 July last year. IMG http://ej.iop.org/images/0963-9659/7/5/001/img1.gif Professor Emil Wolf Emil Wolf was born and grew up in Prague in Czechoslovakia. Being of Jewish origin, he fled the country after it was occupied by Nazi Germany in 1939. After brief periods in Italy and France (where he worked for the Czech government in exile), he arrived in Great Britain in the summer of 1940. He resumed his education the following year at the University of Bristol, where he earned a BSc degree in mathematics in 1945. It was as a postgraduate student that he began his studies in optics, designing the aspheric corrector 1 Wolf47 . After receiving a PhD degree from Bristol in 1948, he moved with his thesis supervisor, Dr E H Linfoot, to Cambridge University as a research assistant at the university observatory. It was during this period that he made several important contributions to the diffraction theory of aberrations 2 wolf51 and to the study of the structure of optical fields in focal regions, a subject which he still continues to work on today. Also at that time his association with the exiled Hungarian scientist Professor Dennis Gabor began. Gabor, who was awarded the 1971 Nobel Prize in Physics for the invention of holography, was then at Imperial College. With the help of Gabor, Wolf obtained his next position, assistant to Nobel Laureate Max Born, who was then the Tait Professor of Mathematical Physics at the University of Edinburgh in Scotland. Born wanted to produce a revised English translation of his 1933 work Optik , and needed an assistant to help in this task. However, as the project progressed, the book evolved into an entirely more comprehensive and authoritative text. Since its publication in 1959 Principles of Optics by Max Born and Emil Wolf 3 bornwolf or as it is more widely known `Born and Wolf', has become one of the most widely cited books in physical science, having been reprinted 15 times, and at the time of writing, a 7th edition is under preparation for publication by Cambridge University Press. Following his years at Edinburgh (1951 - 54), from which university he received a DSc degree in 1955, Wolf was a research fellow at the University of Manchester (1954 - 59). Here Wolf published his seminal papers on coherence, a subject which he had begun investigating at Edinburgh. The theory of optical coherence, which had been largely originated by Fritz Zernike and others, was at that time a rather empirical series of formulae by which the visibility of interference fringes could be calculated. Wolf's 1955 paper 4 Wolf55 placed the theory on a firm theoretical basis, and established that the two-point correlation function IMG http://ej.iop.org/images/0963-9659/7/5/001/img2.gif obeys in free space the pair of wave equations IMG http://ej.iop.org/images/0963-9659/7/5/001/img3.gif Also while at Manchester, Wolf worked with Brian Thompson, then a PhD student (who later became Director of the Institute of Optics and Provost of the University of Rochester), to produce a well-known experimental paper 5 Thompson57 which confirmed the calculations of fringe visibilities based on Wolf and Zernicke's earlier theoretical work. In 1957 Wolf spent a sabbatical year at New York University, and in 1959 he was invited by Professor Robert Hopkins, director of the Institute of Optics, to join the faculty of the University of Rochester in New York State, where he has remained ever since, except for a year as a Guggenheim fellow at the University of California, Berkeley (1966 - 67), a year as a visiting Professor at the University of Toronto (1974 - 75) and a semester as a Distinguished Visiting Professor at the University of Central Florida (spring 1998). In recognition of his outstanding accomplishments, he was appointed to the Wilson Chair of Optical Physics at the University of Rochester in 1987. He has supervised (and continues to supervise) about 30 PhD students, including the editors of this special issue, many of whom have made contributions to this special issue, and also continues the regular academic activities of a full time professor of physics at the University of Rochester. Wolf's work at Rochester in coherence theory, a good deal of it in collaboration with Professor Leonard Mandel, led to a classic review article on the subject in 1965 6 Mandel65 . This article, which is one of the 100 most cited articles published by Reviews of Modern Physics since 1955, proved so popular that the authors decided to expand it into a full length book which finally appeared in 1995 7 mandelwolf95 . His important investigations into the foundations of radiometry and its connection with coherence theory 8 Wolf78 and into the frequency representation of stationary random fields 9 Wolf81 led to the discovery of a new mechanism by means of which the spectrum of radiation can be changed on propagation even in free space. In particular, spectral lines can be shifted independently of the relative motion of the source and the observer 10 Wolf87 . This phenomenon, which has come to be known as `the Wolf effect', and is discussed in some of the articles of this special issue, may have very profound implications in cosmology. It also has applications to such fields as optical radiometric standards, communications and remote sensing (for a recent review of this subject, see 11 Wolf96 ). Other research areas that Professor Wolf has pursued include the reconstruction of objects from diffracted and scattered light: he published the seminal paper on diffraction tomography in 1969 12 Wolf69 . He also continued his work on focused fields 13 Boivin65 , 14 Wolf97 and, with Y Li, gave the first explanation of the focal shift, by which the position of the focal spot can be displaced towards the focusing lens by diffractive effects 15 Li84 . He has also made important contributions to diffraction theory (for example the theory of the boundary diffraction wave 16 Miya the theory of non-radiating sources, phase retrieval in inverse problems and the Ewald - Oseen extinction theorem. Lack of space forbids us from citing all of his papers (over 280 at last count), so we have confined ourselves to mentioning a few representative examples of his work. Professor Wolf has been awarded five honorary doctorates, from the University of Groningen, Netherlands (1989), from the University of Edinburgh, Scotland (1990), from Palacky University, Czechoslovakia (1992), from the University of Bristol, England (1997) and from Laval University, Canada (1997). In addition he is one of eight lifetime honorary members of the Optical Society of America, of which he served as president in 1978, and which he helped save from itself when it rather pointlessly attempted to change its name in 1989. He is also a fellow of the American Physical Society, the British Institute of Physics and the Franklin Institute and an honorary member of the Optical Society of India, the Optical Society of Australia and the Czech Academy of Sciences. He has also been the Editor since its founding in 1961 of the review series Progress in Optics , which now consists of 38 volumes, and he has also received many awards for his contributions, including the Ives Medal, the highest award of the Optical Society of America. The subjects covered by the papers in this special issue, like Professor Wolf's research interests, range over a wide variety of fields. Many of the papers are written versions of talks presented at the Workshop on Physical Optics and Coherence Theory, also organized in honour of Professor Wolf, which was held at Long Beach, California, on 17 October 1997. We have arranged the papers into topical sections, as follows: coherence theory, the Wolf effect and spatial coherence spectroscopy, scattering and propagation in turbulent media, propagation in nonlinear media, propagation in dispersive media, periodicities in propagation, optical signal processing and the fractional Fourier transform, inverse problems and diffraction tomography, non-radiating sources, beam propagation and characterization and, finally, focused optical fields. In the spirit of fairness, the papers are arranged in these sections in the order in which they were received. We are sure that we express the sentiments of all our contributors and readers when we wish Emil many more years of productive research. If there were any articles which were too late for inclusion in this special issue, we are most willing to consider them for the special issue we are planning for his 100th birthday in 2022, provided the article is likely to become of equally lasting value as those of Professor Wolf! The editors would like to express their deep appreciation to Professor Mario Bertolotti, Michele Bouchareine and the editorial staff of the Journal of the European Optical Society, as well as to Tom Spicer, Elizabeth Martin and the staff of IOP Publishing for their untiring and highly professional help in preparing this special issue. This issue could not have been produced without the expert help of the various anonymous referees who reviewed the manuscripts. 1 Wolf E and Preddy W S 1947 On the determination of aspheric profiles Proc. Phys. Soc. 59 704 - 11 2 Wolf E 1951 The diffraction theory of aberrations Rep. Prog. Phys. 14 95 - 120 3 Born M and Wolf E 1959 Principles of Optics (Oxford: Pergamon); reprinted 1998 6th edition (Cambridge: Cambridge University Press); Japanese translation 1974 - 75 (Tokyo: Tokai University Press). There have also been several unauthorized editions and translations: Russian 1970 (Moscow: Nauka); Chinese 1978 - 81 (Peking: Science); and various T},
author = {Friberg, A T and James, D F V},
issn = {09639659},
journal = {PURE AND APPLIED OPTICS},
number = {5},
pages = {U3--U6},
title = {{Physical optics and coherence theory}},
url = {http://stacks.iop.org/0963-9659/7/i=5/a=001},
volume = {7},
year = {1998}
}
@article{Brouard2007,
abstract = {Silicon, zirconium and aluminum sol-gels were investigated as suitable starting materials for tunable matrix calibration standards for laser-induced breakdown spectroscopy. A fast and simple preparation method was developed, using aluminum i-propoxide as the precursor in the sol-gel synthesis, which allows one to quickly prepare solid calibration standards offering very homogenous analyte distribution in the matrix, low optical spectral background, as well as reproducible behavior towards laser ablation and vaporization. The surface of the calibration targets and the morphology of the ablation craters were examined by optical and scanning electron microscopy, and the material ejection process was observed by shadowgraph imaging. Low mug/g detection limits and 4-15{\%} relative standard deviation were measured by laser induced breakdown spectroscopy for Pb, Cr and Be used as internal standards.},
author = {Brouard, D and Gravel, J F Y and Viger, M L and Boudreau, D},
doi = {10.1016/j.sab.2007.10.047},
editor = {M, Sabsabi and R, Russo},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {12},
pages = {1361--1369},
title = {{Use of sol-gels as solid matrixes for laser-induced breakdown spectroscopy}},
url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-36749087072{\&}partnerID=40{\&}md5=01c63ab612851c7a1eb497a3a68855ea},
volume = {62},
year = {2007}
}
@article{Oh2009,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was applied to the analysis of simulant slurry samples used in the vitrification process of liquid radioactive wastes. A spectroscopic analysis was performed by two different detection systems: Czerny-Turner spectrometer coupled with intensified diode array detector (IDAD) and an Echelle spectrometer with intensified charge coupled device (ICCD). For the Czerny-Turner detection system, the normalized intensity method, which is the normalization of the atomic emission intensity by the released whole plasma emission area intensity, was employed to improve the reproducibility of LIBS signals. The Echelle detection system showed a high efficiency in simultaneous multi-element detection and determination of the physical quantities of the simulant.},
author = {Oh, Seong Yong and Yueh, Fang Yu and Singh, Jagdish P and Herman, Connie C and Zeigler, Kristine},
doi = {10.1016/j.sab.2008.10.023},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {1},
pages = {113--118},
publisher = {Elsevier B.V.},
title = {{Preliminary evaluation of laser induced breakdown spectroscopy for slurry samples}},
url = {http://www.sciencedirect.com/science/article/B6THN-4TTMNBC-6/2/25717454f80116dd4a54ab5efc6c2456},
volume = {64},
year = {2009}
}
@article{Cabalin2011,
abstract = {The potential of a multi-pulse (MP) laser excitation scheme for deep stratigraphy of electrolytically galvanized steel using laser-induced breakdown spectrometry (LIBS) has been evaluated. For this purpose, a commercial electro-optically (EO) Q-switched Nd:YAG laser was employed, where by reducing the delay between the Q-switch opening and the flash lamp, a train of pulses (up to 11) separated by approximately 7.40 $\mu$s was generated during one lamp flashing. Plasma emission after each individual laser pulse of the MP sequence was detected by a spectrograph equipped with an intensified charge-coupled device (iCCD) detector. With MP excitation, the ablation efficiency was increased ten-fold on iron sample and 22.5-fold on zinc material with respect to dual-pulse or single-pulse excitation. The LIBS signal generated by MP excitation shows an analogous enhancement. Although the total energy per shot delivered to samples was only 60 mJ, it was possible using LIBS to measure the sample stratigraphy up to depths of 90 $\mu$m on zinc-coated steel sheets. A satisfactory agreement between the Zn thickness determined by the MP-LIBS system and data from the manufacturer has also been obtained.},
author = {Cabal{\'{\i}}n, Luisa Mar{\'{\i}}a and Gonz{\'{a}}lez, Alina and Lazic, Violeta and Laserna, Javier},
institution = {Department of Analytical Chemistry, University of M{\'{a}}laga, M{\'{a}}laga, Spain.},
journal = {Applied Spectroscopy},
number = {7},
pages = {797--805},
pmid = {21740642},
title = {{Deep ablation and depth profiling by laser-induced breakdown spectroscopy (LIBS) employing multi-pulse laser excitation: application to galvanized steel.}},
volume = {65},
year = {2011}
}
@article{Stratis2001,
abstract = {In this paper, we report the first time-resolved laser-induced plasma images acquired using a liquid crystal tunable filter (LCTF). We also compare the use of LCTFs and acousto-optic tunable filters (AOTFs) for time-resolved plasma imaging applications in terms of resolution, out-of-band rejection, and image quality. Application of tunable filter technologies to plasma imaging is unlike other spectroscopic imaging methods because of the intense and spectrally broad background generated by a laser-induced plasma. High quality images of the distribution of atomic emission within a laser-induced plasma can be achieved using both AOTFs and LCTFs. However, additional filters are needed for rejection of wavelengths outside the tuning ranges of the devices. Both devices exhibited superior resolution in the lower working range of the filters ({\~{}}500 nm) with the LCTF exhibiting superior spectral resolution to the AOTF.},
author = {Stratis, D I M Itra N and Eland, Kristine L and Carter, J Chance and Uel, S A M and Linson, J T O M and Angel, S M Ichael},
doi = {10.1366/0003702011953144},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {8},
pages = {999--1004},
title = {{Comparison of Acousto-optic and Liquid Crystal Tunable Filters for Laser-Induced Breakdown Spectroscopy}},
url = {http://www.ingentaconnect.com/content/sas/sas/2001/00000055/00000008/art00007},
volume = {55},
year = {2001}
}
@article{Naes2008,
abstract = {Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), micro X-ray fluorescence spectroscopy ($\mu$XRF), and laser induced breakdown spectroscopy (LIBS) are compared in terms of discrimination power for a glass sample set consisting of 41 fragments. Excellent discrimination results (N99{\%} discrimination) were obtained for each of the methods. In addition, all three analytical methods produced very similar discrimination results in terms of the number of pairs found to be indistinguishable. The small number of indistinguishable pairs that were identified all originated from the same vehicle. The results also show a strong correlation between the data generated from the use of $\mu$XRF and LA-ICP-MS, when comparing $\mu$XRF strontium intensities to LA-ICP-MS strontium concentrations. A 266 nm laser was utilized for all LIBS analyses, which provided excellent precision (b10{\%} RSD for all elements and b10{\%} RSD for all ratios, N=5). The paper also presents a thorough data analysis review for forensic glass examinations by LIBS and suggests several element ratios that provide accurate discrimination results related to the LIBS system used for this study. Different combinations of 10 ratios were used for discrimination, all of which assisted with eliminating Type I errors (false exclusions) and reducing Type II errors (false inclusions). The results demonstrate that the LIBS experimental setup described, when combined with a comprehensive data analysis protocol, provides comparable discrimination when compared to LA-ICP-MS and $\mu$XRF for the application of forensic glass examinations. Given the many advantages that LIBS offers, most notably reduced complexity and reduced cost of the instrumentation, LIBS is a viable alternative to LA-ICP-MS and $\mu$XRF for use in the forensic laboratory.},
author = {Naes, Benjamin E. and Umpierrez, Sayuri and Ryland, Scott and Barnett, Cleon and Almirall, Jose R.},
issn = {05848547},
journal = {Spectrochimica Acta Part B: Atomic Spectroscopy},
month = {oct},
number = {10},
pages = {1145--1150},
title = {{A comparison of laser ablation inductively coupled plasma mass spectrometry, micro X-ray fluorescence spectroscopy, and laser induced breakdown spectroscopy for the discrimination of automotive glass}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854708002176},
volume = {63},
year = {2008}
}
@article{Snyder2008,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was used to discern between two biological agent surrogates (Bacillus atrophaeus and ovalbumin) and potential interferent compounds (mold spores, humic acid, house dust, and Arizona road dust). Multiple linear regression and neural network analysis models were constructed by using B. atrophaeus and ovalbumin spectra, and limits of detection were calculated. Classification of the agent surrogates' LIBS spectra was attempted by using a neural network model. False negative rates of 0{\%} were observed for B. atrophaeus (100 colony forming units) spore spectra with the neural network model used for classification.},
author = {Snyder, Emily Gibb and Munson, Chase A and Gottfried, Jennifer L and {De Lucia}, Frank C and Gullett, Brian and Miziolek, Andrzej},
institution = {U.S. EPA Office of Research and Development, National Homeland Security Research Center, E343-06, 109 TW Alexander Drive, Research Triangle Park, North Carolina 27711, USA. snyder.emily@epa.gov},
journal = {Applied Optics},
keywords = {bacillus,bacillus metabolism,calibration,dust,equipment design,fiber optic technology,humans,humic substances,lasers,models,neural networks (computer),optics photonics,ovalbumin,ovalbumin chemistry,powders,regression analysis,spectrum analysis,spectrum analysis methods,statistical},
number = {31},
pages = {G80--G87},
pmid = {19122707},
publisher = {OSA},
title = {{Laser-induced breakdown spectroscopy for the classification of unknown powders.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19122707},
volume = {47},
year = {2008}
}
@article{Ehlerding2010,
abstract = {Stand-off measurements on nitromethane (NM), 2,4-DNT and 2,4,6-TNT in vapor phase using resonance Raman spectroscopy have been performed. The Raman cross sections for NM, DNT and TNT in vapor phase have been measured in the wavelength range 210-300 nm under laboratory conditions, in order to estimate how large resonance enhancement factors can be achieved for these explosives. The measurements show that the signal is greatly enhanced, up to 250.000 times for 2,4-DNT and 60.000 times for 2,4,6-TNT compared to the non-resonant signal at 532 nm. For NM the resonance enhancement enabled realistic outdoor measurements in vapor phase at 13 m distance. This all indicate a potential for resonance Raman spectroscopy as a stand-off technique for detection of vapor phase explosives.},
author = {Ehlerding, Anneli and Johansson, Ida and Wallin, Sara and Ostmark, Henric},
doi = {10.1117/12.865012},
file = {::},
journal = {Proc. of SPIE},
keywords = {explosives,raman spectroscopy,resonance enhancement,resonance raman,stand-off detection},
pages = {783507--783507--9},
title = {{Stand-off detection of vapor phase explosives by resonance enhanced Raman spectroscopy}},
url = {http://link.aip.org/link/PSISDG/v7835/i1/p783507/s1{\&}Agg=doi},
volume = {7835},
year = {2010}
}
@article{Gottfried2009b,
abstract = {A large suite of natural carbonate, fluorite and silicate geological materials was studied using laser-induced breakdown spectroscopy (LIBS). Both single- and double-pulse LIBS spectra were acquired using close-contact benchtop and standoff (25 m) LIBS systems. Principal components analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to identify the distinguishing characteristics of the geological samples and to classify the materials. Excellent discrimination was achieved with all sample types using PLS-DA and several techniques for improving sample classification were identified. The laboratory double-pulse LIBS system did not provide any advantage for sample classification over the single-pulse LIBS system, except in the case of the soil samples. The standoff LIBS system provided comparable results to the laboratory systems. This work also demonstrates how PCA can be used to identify spectral differences between similar sample types based on minor impurities. Published by Elsevier B.V},
author = {Gottfried, Jennifer L and Harmon, Russell S and {De Lucia Jr.}, Frank C and Miziolek, Andrzej W},
doi = {10.1016/j.sab.2009.07.005},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1009--1019},
publisher = {Elsevier B.V.},
title = {{Multivariate analysis of laser-induced breakdown spectroscopy chemical signatures for geomaterial classification}},
url = {http://www.sciencedirect.com/science/article/B6THN-4WSHK3D-2/2/6111b29f8eebdd413e7d530fa0268e3e},
volume = {64},
year = {2009}
}
@article{Novotny2007,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been applied to the direct analysis of powdered tungsten carbide hard-metal precursors and cemented tungsten carbides. The aim of this work was to examine the possibility of quantitative determination of the niobium, titanium, tantalum and cobalt. The investigated samples were in the form of pellets, pressed with and without binder (powdered silver) and in the form of cemented tungsten carbides. The pellets were prepared by pressing the powdered material in a hydraulic press. Cemented tungsten carbides were embedded in resin for easier manipulation. Several lasers and detection systems were utilized. The Nd:YAG laser working at a basic wavelength of 1064 nm and fourth-harmonic frequency of 266 nm with a gated photomultiplier or ICCD detector HORIBA JY was used for the determination of niobium which was chosen as a model element. Different types of surrounding gases (air, He, Ar) were investigated for analysis. The ICCD detector DICAM PRO with Mechelle 7500 spectrometer with ArF laser (193 nm) and KrF laser (248 nm) were employed for the determination of niobium, titanium, tantalum and cobalt in samples under air atmosphere. Good calibration curves were obtained for Nb, Ti, and Ta (coefficients of determination r2 > 0.96). Acceptable calibration curves were acquired for the determination of cobalt (coefficient of determination r2 = 0.7994) but only for the cemented samples. In the case of powdered carbide precursors, the calibration for cobalt was found to be problematic.},
author = {Novotn{\'{y}}, K and Stankov{\'{a}}, A and H{\"{a}}kk{\"{a}}nen, H and Korppi-Tommola, J and Otruba, V and Kanick{\'{y}}, V},
doi = {10.1016/j.sab.2007.10.020},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {12},
pages = {1567--1574},
title = {{Analysis of powdered tungsten carbide hard-metal precursors and cemented compact tungsten carbides using laser-induced breakdown spectroscopy}},
url = {http://www.sciencedirect.com/science/article/B6THN-4PYGVVN-1/2/86624baee9d348ae5a8ed283fb05bf2b},
volume = {62},
year = {2007}
}
@article{Schenk2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been applied to the elemental characterization of unprocessed cotton. This research is important in forensic and fraud detection applications to establish an elemental fingerprint of U.S. cotton by region, which can be used to determine the source of the cotton. To the best of our knowledge, this is the first report of a LIBS method for the elemental analysis of cotton. The experimental setup consists of a Nd:YAG laser that operates at the fundamental wavelength as the LIBS excitation source and an echelle spectrometer equipped with an intensified CCD camera. The relative concentrations of elements Al, Ba, Ca, Cr, Cu, Fe, Mg, and Sr from both nutrients and environmental contributions were determined by LIBS. Principal component analysis was used to visualize the differences between cotton samples based on the elemental composition by region in the U.S. Linear discriminant analysis of the LIBS data resulted in the correct classification of >97{\%} of the cotton samples by U.S. region and >81{\%} correct classification by state of origin.},
author = {Schenk, Emily R and Almirall, Jose R},
doi = {10.1364/AO.49.00C153},
journal = {Applied Optics},
number = {13},
pages = {C153--C160},
title = {{Elemental analysis of cotton by laser-induced breakdown spectroscopy}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-49-13-C153},
volume = {49},
year = {2010}
}
@article{Pandhija2008,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is an emerging technique for simultaneous multi-elemental analysis of solids, liquids and gases with minute or no sample preparation and thus revolutionized the area of on-line analysis technologies. The foundation for LIBS is a solid state, short-pulsed laser that is focused on a sample to generate a high-temperature plasma, and the emitted radiation from the excited atomic and ionic fragments produced within the plasma is characteristic of the elemental composition of the sample that can be detected and analyzed using a suitable optical spectrograph. In the present paper, the applicability of LIBS for different solid samples having homogeneous (silver ornament, aluminum plate) or heterogeneous composition (soil) using nanosecond laser pulses is discussed. Nanosecond pulse laser makes plasma at the sample surface even at very low pulse energies and also allows for precise ablation of the substrate material with little damage to the surrounding area. We have also studied the penetration of different heavy metals inside the soil surface.},
author = {Pandhija, Shiwani and Rai, A K},
doi = {10.1007/s12043-008-0070-8},
issn = {03044289},
journal = {Pramana},
keywords = {laser induced breakdown spectroscopy,leaching,nanosecond pulse laser},
number = {3},
pages = {553--563},
title = {{Laser-induced breakdown spectroscopy: A versatile tool for monitoring traces in materials}},
url = {http://www.springerlink.com/index/10.1007/s12043-008-0070-8},
volume = {70},
year = {2008}
}
@article{Ctvrtnickova2009,
abstract = {The high sensitivity of laser-induced breakdown spectroscopy (LIBS) for the detection of most of the fly ash components enables the analysis of these residues produced during the combustion of coal. Fly ash consists of oxides (SiO2, Al2O3, Fe2O3, CaO...) and unburnt carbon which is the major determinant of combustion efficiency in coal fired boilers. For example, an excessive amount of residual carbon dispersed in the fly ash means a significant loss of energy (Styszko et al., 2004 1). Standard methods employed for the analysis of fly ash make not possible a control of boiler in real time. LIBS technique can significantly reduce the time of analysis, in some cases even an online detection can be performed. For this reason, some studies have been addressed in order to demonstrate the capability of the laser-induced breakdown spectroscopy technique for the detection of carbon content in high pressure conditions typical of thermal power plants (Noda et al., 2002 2) and for the monitoring of unburnt carbon for the boiler control in real time (Kurihara et al., 20033). In particular, the content of unburnt carbon is a valuable indicator for the control of fly ash quality and for the boiler combustion. Depending on this unburnt carbon content, fly ash can be disposed as an industrial waste or as a raw material for the production of concrete in the construction sector. In this study, analyses were performed on specimens of various forms of preparation. Pressed pellets were prepared with two different binders. Presented results concern the nature and amount of the binder used to pelletize the powder, and the laser-induced breakdown spectroscopy parameters and procedure required to draw calibration curves of elements from the fly ash. Analysis "on tape" was performed in order to establish the experimental conditions for the future "online analysis".},
author = {Ctvrtnickova, Tereza and Mateo, Mari-Paz and Ya{\~{n}}ez, Armando and Nicolas, G},
doi = {10.1016/j.sab.2009.07.032},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1093--1097},
title = {{Characterization of coal fly ash components by laser-induced breakdown spectroscopy}},
url = {http://www.sciencedirect.com/science/article/B6THN-4WYDN08-4/2/0b003ce4c8feec9108d08ba47ce7ca41},
volume = {64},
year = {2009}
}
@article{Galiova2008,
abstract = {Abstract Single-pulse Laser-Induced Breakdown Spectroscopy (LIBS) and Laser-Ablation Inductively Coupled Plasma Mass-Spectrometry (LA-ICP-MS) were applied for mapping the silver and copper distribution in Helianthus Annuus L. samples treated with contaminant in controlled conditions. For Ag and Cu detection the 328.07 nm Ag(I) and 324.75 nm Cu(I) lines were used, respectively. The LIBS experimental conditions (mainly the laser energy and the observation window) were optimized in order to avoid self-absorption effect in the measured spectra. In the LA-ICP-MS analysis the Ag 107 and Cu 63 isotopes were detected. The capability of these two analytical techniques for high-resolution mapping of selected trace chemical elements was demonstrated.},
author = {Galiov{\'{a}}, M and Kaiser, J and Novotn{\'{y}}, K and Novotn{\'{y}}, J and Vaculovi{\v{c}}, T and Li{\v{s}}ka, M and Malina, R and Stejskal, K and Adam, V and Kizek, R},
doi = {10.1007/s00339-008-4747-0},
issn = {09478396},
journal = {Applied Physics A},
number = {4},
pages = {917--922},
title = {{Investigation of heavy-metal accumulation in selected plant samples using laser induced breakdown spectroscopy and laser ablation inductively coupled plasma mass spectrometry}},
url = {http://www.springerlink.com/index/10.1007/s00339-007-4211-6},
volume = {93},
year = {2008}
}
@article{Noda2002,
abstract = {A laser-induced breakdown spectroscopy (LIBS) technique has been applied to detect the carbon content in fly ash, char and pulverized coal under high-pressure and high-temperature conditions. An automated LIBS unit has been developed and applied in this experiment to demonstrate its capability in actual power plant monitoring. Gas composition effects were examined to obtain the best operating parameters under actual plant conditions. The results were compared to those obtained using the conventional method, showing satisfactory agreement. LIBS can detect carbon content even under the high-pressure conditions typical of gasification thermal power plants. LIBS is capable of a detection time of 1 min, as compared to over 30 min of sampling and analysis time required by the conventional methods (JIS-M8814 and JIS-M8815), and offers various merits as a tool for actual power-plant monitoring.},
author = {Noda, M and Deguchi, Y and Iwasaki, S and Yoshikawa, N},
doi = {10.1016/S0584-8547(01)00403-7},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {4},
pages = {701--709},
publisher = {Elsevier Science},
title = {{Detection of carbon content in a high-temperature and high-pressure environment using laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701004037},
volume = {57},
year = {2002}
}
@article{Alonso-Medina2010a,
abstract = {In this paper, we present transition probabilities for 97 spectral lines of Sn I, corresponding to transitions n (n = 6,7,8)s 5p(2), n(n = 5,6,7)d 5p(2), 5p(3) 5p(2), n(n = 7)p 6s, determined by measuring the intensities of the emission lines of a Laser-induced breakdown (emission) spectrometry (LIBS). The optical emission spectroscopy from a laser-induced plasma generated by a 10 640 angstrom radiation, with an irradiance of 1.4 x 10(10) Wcm(-2) on an Sn-Pb alloy (an Sn content of approximately 20{\%}), in vacuum, was recorded at 0.8 mu s, and analysed between 1900 and 7000 angstrom. The population-level distribution and corresponding temperature were obtained using Boltzmann plots. The electron density of the plasma was determined using well-known Stark broadening parameters of spectral lines. The plasma under study had an electron temperature of 13,200 K and an electron number density of 2 x 10(16) cm(-3). The experimental relative transition probabilities were put on an absolute scale using the branching ratio method to calculate Sn I multiplet transition probabilities from available radiative lifetime data of their upper states and plotting the Sn I emission spectrum lines on a Boltzmann plot assuming local thermodynamic equilibrium (LTE) to be valid and following Boltzmann's law. The LTE conditions and plasma homogeneity have been checked. Special attention was paid to the possible self-absorption of the different transitions. The experimental results obtained have been compared with the experimental values given by other authors. (C) 2010 Elsevier B.V. All rights reserved.},
author = {Alonso-Medina, A},
doi = {10.1016/j.sab.2010.01.002},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {2},
pages = {158--166},
title = {{A spectroscopic study of laser-induced tin-lead plasma: Transition probabilities for spectral lines of Sn I}},
url = {http://www.sciencedirect.com/science/article/B6THN-4Y70C5N-2/2/1850f3c6090989ba6335857e8234050b},
volume = {65},
year = {2010}
}
@article{Cristoforetti2009,
abstract = {The problem of finding new methods for the analysis of precious alloys has stimulated, in recent years, a number of different proposals for improving the analytical procedures introducing more robust calibration (or calibration-free) methods. In the paper "Accurate quantitative analysis of gold alloys using multi-pulse laser-induced breakdown spectroscopy and a correlation-based calibration method" by G. Galb{\'{a}}cs, N.Jedinski, G.Cseh, Z. Galb{\'{a}}cs and L. T{\'{u}}ri Spectrochimica Acta Part B, Volume 63, Issue 5, 591-597 (May 2008) the authors proposed the use of multiple-pulse LIBS and a correlation-based method for building calibration curves for quantitative analysis of gold alloys. The method is proposed for gold alloys prepared using a fixed proportion of the alloying element. The general case where the relative concentration of the elements of the matrix is not a priori known is not discussed in the paper. In this communication, we will demonstrate that the method proposed is extremely fragile against matrix effects, and therefore cannot be usefully applied for the purpose of actual analytical measurements on gold alloys without a previous knowledge of the matrix composition.},
author = {Cristoforetti, G and Legnaioli, S and Palleschi, V and Tognoni, E},
doi = {10.1016/j.sab.2009.03.005},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {4},
pages = {357--358},
title = {{Comments on the paper: "Accurate quantitative analysis of gold alloys using multi-pulse laser-induced breakdown spectroscopy and a correlation-based calibration method"}},
url = {http://www.sciencedirect.com/science/article/B6THN-4W4S33S-1/2/d758cf91b774ee3b9256f63e740af3a7},
volume = {64},
year = {2009}
}
@article{Marquardt1998,
abstract = {A fiber-optic probe designed for remote laser-induced breakdown spectroscopy (LIBS), Raman spectroscopy, and Raman imaging has been developed for the microanalysis of solid samples. The probe incorporates both single-strand optical fibers and an image guide and allows atomic emission and Raman analysis of any spot on a solid sample within a 5 mm diameter field of view. The real-time sample imaging aspects of the probe are demonstrated by measuring LIBS spectra from different regions of a granite sample and by measuring the Raman spectra of individual TiO2 and Sr(NO3)2 particles on a soil substrate. The ability to obtain remote Raman images of the TiO2 and Sr(NO3)2 particles on the soil substrate is also demonstrated. In this paper we discuss the design and implementation of the fiber-optic probe for obtaining LIBS spectra, Raman spectra, and Raman images.},
author = {Marquardt, Brian J and Stratis, Dimitra N and Cremers, David A and Angel, S Michael},
doi = {10.1366/0003702981945147},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {9},
pages = {1148--1153},
publisher = {Soc for Applied Spectroscopy, Frederick, MD, USA},
series = {Appl. Spectrosc. (USA)},
title = {{Novel Probe for Laser-Induced Breakdown Spectroscopy and Raman Measurements Using an Imaging Optical Fiber}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=52{\&}issue=9{\&}spage=1148},
volume = {52},
year = {1998}
}
@article{Kim2004,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is used to record the plasma emission for the colonies of vegetative cells or spores of five bacterial strains: Bacillus thuringiensis T34, Escherichia coli IHII/pHT315, Bacillus subtilis 168, Bacillus megaterium QM B1551, and Bacillus megaterium PV361. The major inorganic components of the bacterial samples, including Ca, Mn, K, Na, Fe, and phosphate, are clearly identified from the breakdown emission spectra. The bacterial spores accumulate a lot of calcium that shows strong LIBS emission at 393.7 and 396.9 nm. The diverse emissions from the phosphate component at 588.1 and 588.7 nm provide a fingerprint for bacterial strains. The relative change of inclusions in the bacteria is clearly distinguished by two-dimensional charts of the bacterial components. The results demonstrate the potential of the LIBS method for the rapid and low false-positive classification of bacteria with minimum sample preparation.},
author = {Kim, T and Specht, ZG and Vary, PS and Lin, CT},
file = {::},
journal = {The Journal of Physical Chemistry B},
number = {17},
pages = {5477--5482},
publisher = {ACS Publications},
title = {{Spectral fingerprints of bacterial strains by laser-induced breakdown spectroscopy}},
url = {http://pubs.acs.org/doi/abs/10.1021/jp031269i},
volume = {108},
year = {2004}
}
@article{Hrdlicka2009,
abstract = {An acoustic signal was used for the internal standardization of laser-induced breakdown spectroscopy (LIBS) of a glazed wall tile. For the LIBS analyses, 1064 nm and 532 nm wavelengths of the Nd:YAG laser were utilized. The tile was depth profiled by a single-spot ablation from the glaze into the substrate. Some lines of major elements Si(I) 252.418, Si(I) 252.851, Al(I) 257.509, Cr(I) 295.368, Al(I) 309.271 nm and Ti(II) 334.904 nm were monitored. The decrease in the optical emissions during the ablation was successfully compensated for by normalization to the square power of the acoustic signal in the interval of 290-340 nm. This approach failed for the lines between 250-270 nm. The results were the same for both lasing wavelengths despite different irradiances. The acquired profiles are in good agreement with the reference X-ray fluorescence measurement.},
author = {Hrdlicka, Ales and Zaor{\'{a}}lkov{\'{a}}, Linda and Galiov{\'{a}}, Michaela and Ctvrtn{\'{\i}}ckov{\'{a}}, Tereza and Kanick{\'{y}}, Viktor and Otruba, V{\'{\i}}tezslav and Novotn{\'{y}}, Karel and Kr{\'{a}}sensk{\'{y}}, Pavel and Kaiser, Jozef and Malina, Radom{\'{\i}}r and P{\'{a}}len{\'{\i}}kov{\'{a}}, Katerina},
doi = {10.1016/j.sab.2008.10.043},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {1},
pages = {74--78},
title = {{Correlation of acoustic and optical emission signals produced at 1064 and 532 nm laser-induced breakdown spectroscopy (LIBS) of glazed wall tiles}},
url = {http://www.sciencedirect.com/science/article/B6THN-4TX33KJ-1/2/59decf62fc217f8409f5985b7bbf2fa2},
volume = {64},
year = {2009}
}
@article{Russo2009,
abstract = {In this review we discuss the application of laserinduced breakdown spectroscopy (LIBS) to the problem of detection of residues of explosives. Research in this area presented in open literature is reviewed. Both laboratory and field-tested standoff LIBS instruments have been used to detect explosive materials. Recent advances in instrumentation and data analysis techniques are discussed, including the use of double-pulse LIBS to reduce air entrainment in the analytical plasma and the application of advanced chemometric techniques such as partial leastsquares discriminant analysis to discriminate between residues of explosives and non-explosives on various surfaces. A number of challenges associated with detection of explosives residues using LIBS have been identified, along with their possible solutions. Several groups have investigated methods for improving the sensitivity and selectivity of LIBS for detection of explosives, including the use of femtosecond-pulse lasers, supplemental enhancement of the laser-induced plasma emission, and complementary orthogonal techniques. Despite the associated challenges, researchers have demonstrated the tremendous potential of LIBS for real-time detection of explosives residues at standoff distances.},
author = {Russo, Richard and Treado, Patrick J and Nelson, Matthew P},
doi = {DOI 10.1007/s00216-009-2802-0},
file = {::},
journal = {Anal Bioanal Chem},
number = {I},
pages = {395:283},
title = {{A NEW STANDOFF CB DETECTION TECHNOLOGY BASED ON THE FUSION OF}},
volume = {300},
year = {2009}
}
@article{Schechter2002,
abstract = {Matrix effects limit the performance of LIBS in absolute elemental analysis, since the spectral intensity of an emission line at a given concentration depends on the matrix. On the other hand, several characteristics of the plasma morphology depend on the matrix as well. Therefore, understanding the interrelation between plasma morphology and the matrix effects may result in releasing LIBS analysis from the necessity of obtaining independent information on the sample matrix. Preliminary results indicate that morphological data, which can be readily obtained, may provide the necessary information on the most important matrix characteristics, such that the proper calibration plot can be utilized for obtaining the required concentration. Moreover, once the interrelations between the matrix effects and plasma morphology have been established, one can utilize this information for performing sophisticated LIBS analysis. For example, the organic carbon content of soils can be distinguished from the total carbon, using a specific emission line, which is affected be the organic content. This way, the matrix effect is utilized for obtaining analytical information that could not be obtained by traditional LIBS.},
author = {Schechter, Israel and Bulatov, Valery},
file = {::},
journal = {Laser Induced Plasma},
pages = {6200},
title = {{Plasma morphology and matrix effects interrelation in LIBS analysis}},
url = {http://www.opticsinfobase.org/abstract.cfm?id=113437},
year = {2002}
}
@article{Beddows2005,
abstract = {In this paper we discuss the prospects of real-time, in situ laser-induced breakdown spectroscopy applied for the identification and classification of bio-aerosols (including species of potential bio-hazard) within common urban aerosol mixtures. In particular, we address the issues associated with the picking out of bio-aerosols against common background aerosol particles, comparing laser-induced breakdown spectroscopy measurements with data from a mobile single-particle aerosol mass spectrometer (ATOFMS). The data from the latter provide statistical data over an extended period of time, highlighting the variation of the background composition. While single-particle bio-aerosols are detectable in principle, potential problems with small (similar to 1 mu m size) bio-aerosols have been identified; constituents of the air mass other than background aerosols, e.g. gaseous CO2 in conjunction with common background aerosols, may prevent unique recognition of the bio-particles. We discuss whether it is likely that laser-induced breakdown spectroscopy on its own can provide reliable, real-time identification of bio-aerosol in an urban environment, and it is suggested that more than one technique should be or would have to be used. A case for using a combination of laser-induced breakdown spectroscopy and Raman (and/or) laser-induced fluorescence spectroscopy is made. (c) 2005 Elsevier B.V. All rights reserved.},
author = {Beddows, D and Telle, H},
doi = {10.1016/j.sab.2005.05.018},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {aerosol,aerosol time flight mass spectroscopy,biological,laser induced breakdown spectroscopy,raman spectroscopy},
number = {7-8},
pages = {1040--1059},
title = {{Prospects of real-time single-particle biological aerosol analysis: A comparison between laser-induced breakdown spectroscopy and aerosol time-of-flight mass spectrometry}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854705001503},
volume = {60},
year = {2005}
}
@article{Sirven2007,
abstract = {The ChemCam instrument that will equip the Mars Science Laboratory (MSL) rover uses laser-induced breakdown spectroscopy (LIBS) to remotely identify Martian rocks in the proximity of the rover, and to quantitatively assess their composition. Sample identification is then the first step of the chemical analysis, as a decision aid for monitoring the rover and/or before a subsequent composition measurement. In this paper we analyze our experimental spectra obtained in the laboratory by three chemometric methods-principal components analysis (PCA), soft independent modeling of class analogy (SIMCA) and partial least-squares discriminant analysis (PLS-DA)-to investigate the feasibility of rocks classification by remote LIBS. If PCA is very interesting for data visualization, SIMCA and PLS-DA enable the making of automatic predictions. We show that SIMCA is less sensitive than PLS-DA, but also more robust when it encounters spectra of an unknown rock. The instrument accuracy during MSL operations will benefit from a combination of the two approaches.},
author = {Sirven, Jean-Baptiste and Salle, Beatrice and Mauchien, Patrick and Lacour, Jean-Luc and Maurice, Sylvestre and Manhes, Gerard},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {12},
pages = {1471--1480},
title = {{Feasibility study of rock identification at the surface of Mars by remote laser-induced breakdown spectroscopy and three chemometric methods}},
url = {http://dx.doi.org/10.1039/b704868h},
volume = {22},
year = {2007}
}
@article{Blevins2003,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was applied (1) near the superheater of an electric power generation boiler burning biomass, coal, or both; (2) at the exit of a glass-melting furnace burning natural gas and oxygen; and (3) near the nose arches of two paper mill recovery boilers burning black liquor. Difficulties associated with the high temperatures and high particle loadings in these environments were surmounted by use of novel LIBS probes. Echelle and linear spectrometers coupled to intensified CCD cameras were used individually and sometimes simultaneously. Elements detected include Na, K, Ca, Mg, C, B, Si, Mn, Al, Fe, Rb, Cl, and Ti.},
author = {Blevins, Linda G and Shaddix, Christopher R and Sickafoose, Shane M and Walsh, Peter M},
institution = {Sandia National Laboratories, Livermore, California 94550, USA. lgblevi@sandia.gov},
journal = {Applied Optics},
number = {30},
pages = {6107--6118},
pmid = {14594073},
title = {{Laser-induced breakdown spectroscopy at high temperatures in industrial boilers and furnaces.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594073},
volume = {42},
year = {2003}
}
@article{Chadwick2002,
abstract = {An instrumentation variation on laser-induced breakdown spectroscopy (LIBS) has been developed and applied in the operations of power generating companies utilizing low-ash lignite as the fuel source. The instrument design allows simultaneous determination of all detectable elements using a multiple spectrograph and a synchronized, multiple charge-coupled device (CCD) spectral acquisition system. The application of internal ratio analysis has enabled the development of a stable system that can be operated routinely for over a month without recalibration. Detection limits vary depending on the element but are typically on the order of 0.01{\%} by weight for heterogeneous materials such as the moist lignite used in these power stations. Independent testing of the instrument has shown good correlation between the routine LIBS analysis and the analysis of the coal via acid extraction techniques for key ash-forming elements. Testing over a one month period shows excellent correlation between the two methods for elements such as Al (R = 0.96) and Na (R = 0.92). The principle limitation is not the accuracy of the LIBS method but rather the inherent errors in sampling heterogeneous materials such as lignite. Because the LIBS analysis takes less than 30 seconds it has clear advantages over traditional methods used in elemental analysis for these materials.},
author = {Chadwick, Bruce L and Body, Doug},
doi = {10.1366/0003702021954232},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {1},
pages = {70--74},
title = {{Development and Commercial Evaluation of Laser-Induced Breakdown Spectroscopy Chemical Analysis Technology in the Coal Power Generation Industry}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=56{\&}issue=1{\&}spage=70},
volume = {56},
year = {2002}
}
@article{He2011,
abstract = {Improved spectral resolutions were achieved in laser-induced breakdown spectroscopy (LIBS) through generation of high-temperature and low-density plasmas. A first pulse from a KrF excimer laser was used to produce particles by perpendicularly irradiating targets in air. A second pulse from a 532 nm Nd:YAG laser was introduced parallel to the sample surface to reablate the particles. Optical scattering from the first-pulse plasmas was imaged to elucidate particle formation in the plasmas. Narrower line widths (full width at half maximums: FWHMs) and weaker self-absorption were observed from time-integrated LIBS spectra. Estimation of plasma temperatures and densities indicates that high temperature and low density can be achieved simultaneously in plasmas to improve LIBS resolutions.},
author = {He, X N and Hu, W and Li, C M and Guo, L B and Lu, Y F},
doi = {10.1364/OE.19.010997},
file = {::},
institution = {Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0511 USA.},
journal = {Optics Express},
number = {11},
pages = {10997--11006},
pmid = {21643361},
title = {{Generation of high-temperature and low-density plasmas for improved spectral resolutions in laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21643361},
volume = {19},
year = {2011}
}
@article{Migliorini2011,
abstract = {Laser-induced Breakdown spectroscopy was applied for the elemental analysis of aerosols. Particular care has been taken in optimizing the time resolution of the LIBS spectra and the detection limit of the technique has been evaluated for Na, Ca and Mg atoms. The applicability of the technique has been extended to the case of fly ash generated from coal combustion.},
author = {Migliorini, F and Vercelli, B and Giassi, D and {De Iuliis}, S. and Zizak, G},
doi = {10.4405/34proci2011.I2},
file = {::},
journal = {Meeting of the Italian Section of the Combustion Institute},
pages = {1--6},
title = {{LASER-INDUCED BREAKDOWN SPECTROSCOPY (LIBS) FOR ELEMENTAL COMPOSITION ANALYSIS OF AEROSOLS}},
url = {http://www.combustion-institute.it/proceedings/XXXIV-ASICI/papers/34proci2011.I2.pdf},
year = {2011}
}
@article{Bolger2000,
abstract = {An investigation is reported in the use of time-resolved laser-induced breakdown spectroscopy (LIBS) for mineral assaying applications. LIBS has potential for the rapid on-line determination of the major and minor constituents of mineral drill core samples. In this work a Q-switched Nd:YAG laser is used to test as-received lengths of drill core, with remote LIBS signal acquisition via a bare optical fiber bundle coupled to a spectrometer. A novel normalization scheme, based on integrating the total plasma emission, is demonstrated as a method for correction of signal variations due to the uneven surface geometry of rock. Averaged intensities of atomic emission for the elements Cr, Cu, Fe, Mn, and Ni show good linear correlations, with coefficients of R2 = 0.92-0.99, against laboratory assay values. Limitations in the comparison of the results of surface analysis to bulk compositions are discussed, with emphasis on mining applications of LIBS.},
author = {Bolger, J A},
doi = {10.1366/0003702001949375},
journal = {Applied Spectroscopy},
number = {2},
pages = {181--189},
title = {{Semi-quantitative Laser-Induced Breakdown Spectroscopy for Analysis of Mineral Drill Core}},
url = {http://www.ingentaconnect.com/content/sas/sas/2000/00000054/00000002/art00004},
volume = {54},
year = {2000}
}
@article{Cabalin2011,
abstract = {The potential of a multi-pulse (MP) laser excitation scheme for deep stratigraphy of electrolytically galvanized steel using laser-induced breakdown spectrometry (LIBS) has been evaluated. For this purpose, a commercial electro-optically (EO) Q-switched Nd:YAG laser was employed, where by reducing the delay between the Q-switch opening and the flash lamp, a train of pulses (up to 11) separated by approximately 7.40 $\mu$s was generated during one lamp flashing. Plasma emission after each individual laser pulse of the MP sequence was detected by a spectrograph equipped with an intensified charge-coupled device (iCCD) detector. With MP excitation, the ablation efficiency was increased ten-fold on iron sample and 22.5-fold on zinc material with respect to dual-pulse or single-pulse excitation. The LIBS signal generated by MP excitation shows an analogous enhancement. Although the total energy per shot delivered to samples was only 60 mJ, it was possible using LIBS to measure the sample stratigraphy up to depths of 90 $\mu$m on zinc-coated steel sheets. A satisfactory agreement between the Zn thickness determined by the MP-LIBS system and data from the manufacturer has also been obtained.},
author = {Cabal{\'{\i}}n, Luisa Mar{\'{\i}}a and Gonz{\'{a}}lez, Alina and Lazic, Violeta and Laserna, Javier},
institution = {Department of Analytical Chemistry, University of M{\'{a}}laga, M{\'{a}}laga, Spain.},
journal = {Applied Spectroscopy},
number = {7},
pages = {797--805},
pmid = {21740642},
title = {{Deep ablation and depth profiling by laser-induced breakdown spectroscopy (LIBS) employing multi-pulse laser excitation: application to galvanized steel.}},
volume = {65},
year = {2011}
}
@article{Panjehpour2002,
abstract = {BACKGROUND AND OBJECTIVES: Laser-induced fluorescence spectroscopy is a non-invasive technique previously used for detection of cancer in a variety of organ systems. The objective of this study was to determine whether in vivo laser-induced fluorescence spectroscopy alone at the visible excitation wavelength of 410 nm could be used to detect non-melanoma skin cancers. STUDY DESIGN/MATERIALS AND METHODS: The system consisted of a nitrogen/dye laser tuned at 410 nm, an optical multichannel analyzer, and a fiber optic probe for excitation of tissue and collection of fluorescence emission. Two hundred and seventy nine measurements were performed from normal and abnormal tissues in 49 patients. Patients were classified as having either skin types I, II, or III. Biopsy of the abnormal tissues were then performed. Each measurement was assigned as either normal, basal cell carcinoma (BCC), squamous cell carcinoma (SCC), pre-cancerous, or benign. Total emission photon count was used as the discriminating index. A threshold value was calculated to separate normal tissue indices from indices of cancer tissues. The classification accuracy of each data point was determined using the threshold value. RESULTS: Cancers were classified 93, 89, and 78{\%} correctly in patients with skin types I, II, and III, respectively. Normal tissues were classified 93, 88, and 50{\%} correctly in patients with skin types I, II, and III, respectively. Using the same threshold, pre-cancerous spectra were classified 78 and 100{\%} correctly in skin types I and III, respectively. Benign lesions were classified 100, 46, and 27{\%} correctly in patient with skin types I, II, and III, respectively. CONCLUSIONS: In vivo laser induced fluorescence spectroscopy at 410 nm excitation and using the intensity of emission signal is effective for detection of BCC, SCC, and actinic keratosis, specially in patients with light colored skin.},
author = {Panjehpour, Masoud and Julius, Clark E and Phan, Mary N and Vo-Dinh, Tuan and Overholt, Suzanne},
institution = {Thompson Cancer Survival Center, Knoxville, Tennessee 37916, USA. mpanjehp@covhlth.com},
journal = {Lasers in Surgery and Medicine},
keywords = {basal cell,basal cell diagnosis,carcinoma,fluorescence,humans,keratosis,keratosis diagnosis,keratosis etiology,lasers,lasers diagnostic use,photosensitivity disorders,photosensitivity disorders complications,photosensitivity disorders diagnosis,reproducibility results,sensitivity specificity,skin,skin neoplasms,skin neoplasms diagnosis,skin radiation effects,spectrometry,squamous cell,squamous cell diagnosis},
number = {5},
pages = {367--373},
pmid = {12430156},
title = {{Laser-induced fluorescence spectroscopy for in vivo diagnosis of non-melanoma skin cancers.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12430156},
volume = {31},
year = {2002}
}
@article{Brai2009,
abstract = {The laser-induced breakdown spectroscopy (LIBS) is an applied physical technique that has shown in recent years its great potential for rapid qualitative analysis of materials. Thanks to the possibility to implement a portable instrument that perform LIBS analysis, this technique is revealed to be particularly useful for in situ analysis in the field of cultural heritages. The purpose of this work is to evaluate the potentiality of LIBS technique in the field of cultural heritages, with respect to the chemical characterization of complex matrix as calcareous and refractory materials for further quantitative analyses on cultural heritages. X-Ray Fluorescence (XRF) analyses were used as reference. Calibration curves of certified materials used as standards were obtained by XRF analyses. The LIBS measurements were performed with a new mobile instrument called Mod{\`{\i}} (Mobile Double pulse Instrument for LIBS Analysis). The XRF analyses were performed with a portable instrument ArtTAX. LIBS and XRF measurement were performed on both reference materials and samples (bricks and mortars) sampled in the ancient Greek-Roman Theatre of Taormina. Although LIBS measurements performed on reference materials have shown non linear response to concentrations, and so we were not able to obtain quantitative results, an integrated study of XRF and LIBS signals permitted us to distinguish among chemical features and degradation state of measured building materials.},
author = {Brai, Maria and Gennaro, Gaetano and Schillaci, Tiziano and Tranchina, Luigi},
doi = {10.1016/j.sab.2009.07.027},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1119--1127},
publisher = {Elsevier B.V.},
title = {{Double pulse laser induced breakdown spectroscopy applied to natural and artificial materials from cultural heritages: A comparison with micro-X-ray fluorescence analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709002316},
volume = {64},
year = {2009}
}
@article{Sirven2009,
abstract = {Yellow cake is a commonly used name for powdered uranium concentrate, produced with the uranium ore. It is the first step in the fabrication of nuclear fuel. As it contains fissile material its circulation needs to be controlled in order to avoid proliferation. In particular there is an interest in onsite determination of the geographical origin of a sample. The yellow cake elemental composition depends on its production site and can therefore be used to identify its origin. In this work laser-induced breakdown spectroscopy (LIBS) associated with chemometrics techniques is used to discriminate yellow cake samples of different geographical origin. 11 samples, one per origin, are analyzed by a commercial equipment in laboratory experimental conditions. Spectra are then processed by multivariate techniques like Principal Components Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA). Successive global PCAs are first performed on the whole spectra and enable one to discriminate all samples. The method is then refined by selecting several emission lines in the spectra and by using them as input data of the chemometric treatments. With a SIMCA model applied to these data a rate of correct identification of 100{\%} is obtained for all classes. Then to define the specifications of a future onsite LIBS system, the use of a more compact spectrometer is simulated by a numerical treatment of experimental spectra. Simultaneously the reduction of spectral data used by the model is also investigated to decrease the spectral bandwidth of the measurement. The rate of correct identification remains very high. This work shows the very good ability of SIMCA associated with LIBS to discriminate yellow cake samples with a very high rate of success, in controlled laboratory conditions.},
author = {Sirven, Jean-Baptiste and Pailloux, Agn{\`{e}}s and M'Baye, Yacine and Coulon, Nadine and Alpettaz, Thierry and Goss{\'{e}}, St{\'{e}}phane},
doi = {10.1039/b821405k},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {4},
pages = {451},
title = {{Towards the determination of the geographical origin of yellow cake samples by laser-induced breakdown spectroscopy and chemometrics}},
url = {http://xlink.rsc.org/?DOI=b821405k},
volume = {24},
year = {2009}
}
@article{Patel1981,
abstract = {The authors discuss the theory and experiments dealing with the pulsed optoacoustic effect (i.e., generation of a transient acoustic wave by absorption of an optical pulse) in condensed matter. Their primary interest lies in the measurement of small absorption coefficients (10-1 cm-1). At present an experimental capability of measuring absorption coefficients as small as 10-6 cm-1 has been demonstrated, and further improvement is foreseen. The pulsed optoacoustic absorption measurement technique has been applied to the following linear spectroscopic studies: (1) precise measurements of the optical absorption spectra of H2O and D2O; (b) accurate determination of absorption strengths and profiles of high harmonics (n=6, 7, and 8) of vibrational modes in transparent organic liquids (e.g., benzene); (c) quantitative absorption spectra of thin 1-10 $\mu$m) liquid films; and (d) quantitative absorption spectra of solids and finely powdered crystals. The usefulness of the pulsed optoacoustic technique to nonlinear spectroscopy has been demonstrated in the following studies: (a) quantitative two-photon absorption spectroscopy of the weak two-photon (1B2$\mu$1A1g) transition in benzene; and (b) optoacoustic Raman-gain spectra for a variety of liquids where an ability to measure Raman gains as small as 10-5 cm-1 has been demonstrated. In addition to reviewing the above studies the authors discuss future possible applications and compare the pulsed optoacoustic spectroscopy technique with other optoacoustic absorption measurement techniques.},
author = {Patel, C K N and Tam, A C},
doi = {10.1103/RevModPhys.53.517},
issn = {15390756},
journal = {Reviews of Modern Physics},
number = {3},
pages = {517},
publisher = {American Physical Society},
title = {{Pulsed optoacoustic spectroscopy of condensed matter}},
url = {http://link.aps.org/doi/10.1103/RevModPhys.53.517},
volume = {53},
year = {1981}
}
@article{Yueh2002,
abstract = {The analytical figure of merit of the potential of laser-induced breakdown spectroscopy (LIBS) has been evaluated for detection of trace element in liquid. LIBS data of Mg, Cr, Mn, and Re were studied. Various optical geometries, which produce the laser spark in and at the liquid sample, were tested. The calibration curves for Mg, Cr, Mn, and Re were obtained at the optimized experimental conditions with bulk liquid and in liquid jet. It was found that measurements using a liquid jet provide better detection limits than bulk liquid measurements. The limits of detection (LOD) of Mg, Cr, Mn, and Re in the present liquid jet measurement are found to be 0.1, 0.4, 0.7, and 8 ppm, respectively. The LOD of Mg using Mg 279.55 nm was compared with the values found in other liquid work.},
author = {Yueh, Fang-Yu and Sharma, Ramesh C and Singh, Jagdish P and Zhang, Hansheng and Spencer, William A},
institution = {Diagnostic Instrumentation and Analysis Laboratory, Mississippi State University, Starkville, Mississippi 39759-7704, USA.},
journal = {Journal of the Air Waste Management Association 1995},
number = {11},
pages = {1307--1315},
pmid = {12469717},
title = {{Evaluation of the potential of laser-induced breakdown spectroscopy for detection of trace element in liquid.}},
volume = {52},
year = {2002}
}
@article{Ortiz2004,
abstract = {A procedure for estimating the minimum value assured by an analytical method has been developed. It is applied to the determination of gold in jewellery alloys by means of a recently proposed spectroscopy technique. The laser-induced breakdown spectroscopic data of 17 gold alloys, with gold concentration ranging between 50 and 100{\%} were used as calibration set for carrying out the partial least-squares regression (PLS). Ninety alloys, with known gold concentration, were used to evaluate the method's accuracy. Finally, the minimum guaranteed value of the gold content was analysed, taking into account the values for gold hallmark in Spanish regulations.},
author = {Ortiz, M C and Sarabia, L and Jurado-L{\'{o}}pez, A and {Luque De Castro}, M D},
doi = {10.1016/j.aca.2004.01.003},
issn = {00032670},
journal = {Analytica Chimica Acta},
keywords = {false compliance,false non compliance,iso,laser induced breakdown spectroscopy,pls,robust testing,validation},
number = {1},
pages = {151--157},
title = {{Minimum value assured by a method to determine gold in alloys by using laser-induced breakdown spectroscopy and partial least-squares calibration model}},
url = {http://www.sciencedirect.com/science/article/B6TF4-4BS0FRP-2/2/784c8f36d4bd771239d9bdd6d2c1d862},
volume = {515},
year = {2004}
}
@article{Margetic2000,
abstract = {The ablation of brass samples in argon shield gas by 170 fs and 6 ns laser pulses has been studied by optical emission spectroscopy of the evolving plasmas. Differences observed in the temporal behavior of the spectral line intensities are explained by the shielding effect of the Ar plasma for ns-pulses and the free expansion of the plasma of the ablated material in case of fs-pulses. Brass with different Zn/Cu ratios were used as samples. Different types of crater formation mechanisms in the case of ns- and fs-pulses were observed. At 40 mbar argon pressure the thresholds of ablation were found to be {\~{}}0.1 and {\~{}}1.5 J cm-2 for fs- and ns-pulses, respectively. With an internal standardization of zinc to copper it is possible to correct for differences in the ablation rates and to obtain linear calibration curves. For optimum experimental conditions, narrower confidence intervals for the determination of unknown concentrations were found in case of fs-pulses. Within the range of the laser intensities used, no dependence of the Zn/Cu line intensity ratio on the number of laser pulses applied to the same ablation spot was observed, neither for fs- nor for ns-pulses, which is interpreted as the absence of fractional vaporization.},
author = {Margetic, V and Pakulev, A and Stockhaus, A and Bolshov, M and Niemax, K and Hergenr{\"{o}}der, R},
doi = {10.1016/S0584-8547(00)00275-5},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {brass material,corresponding author,de {\v{z}} r,e mail address,fax,femtosecond,hergenroder,hergenroeder,isas dortmund,laser ablation,optical emission spectroscopy,q49 231 1392 120,q49 231 1392 178,tel},
number = {11},
pages = {1771--1785},
title = {{A comparison of nanosecond and femtosecond laser-induced plasma spectroscopy of brass samples}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854700002755},
volume = {55},
year = {2000}
}
@article{Zheng2008,
abstract = {Laser-induced breakdown spectroscopy was used to determine the elemental composition of a CeO2 composite powder for process control verification during lanthanide borosilicate glass fabrication. Cerium oxide is used as a surrogate for plutonium oxide, which along with other canister contents will be combined with frit to make glass. Laser-induced breakdown spectroscopy data for the composition of the CeO2 batch containing concentrations of Ce, Cr, Si, Fe, Ta, Ni, Zn, Al Mg, Gd, and W were quantitatively determined from laser-induced breakdown spectroscopy spectra of both pellet and powder samples. The results of both forms were compared and it was determined that the pellet data gave slightly better precision than the powder sample.},
author = {Zheng, Hongbo and Yueh, Fang Yu and Miller, Tracy and Singh, Jagdish P and Zeigler, Kristine E and Marra, James C},
doi = {10.1016/j.sab.2008.06.005},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {9},
pages = {968--974},
publisher = {Elsevier},
title = {{Analysis of plutonium oxide surrogate residue using laser-induced breakdown spectroscopy}},
url = {http://www.sciencedirect.com/science/article/B6THN-4SVC5M8-1/2/3a86646eb225e7a50239b6a28cf54a5c},
volume = {63},
year = {2008}
}
@article{Jeys2007,
abstract = {The deadliest form of a biological attack is aerosolized agents dispersed into the atmosphere. Early detection of aerosolized biological agents is important for defense against these agents. Because of the wide range of possible attack scenarios and attack responses, there is also a wide range of detector requirements. This article focuses on real-time, single-particle, optically based bio-agent trigger detectors—the first responder to an aerosol attack—and how to engineer these detectors to achieve optimal detection performance.},
author = {Jeys, T.H. and Herzog, W.D. and Hybl, J.D. and Czerwinski, R.N. and Sanchez, Antonio},
file = {::},
journal = {Linc. Lab. J},
number = {1},
pages = {29--62},
title = {{Advanced trigger development}},
url = {http://www.ll.mit.edu/publications/journal/pdf/vol17{\_}no1/17{\_}1{\_}2Jeys.pdf},
volume = {17},
year = {2007}
}
@article{Maravelaki-Kalaitzaki2001,
abstract = {This study deals with the analysis of encrustation on marble by laser induced breakdown spectroscopy (LIBS), with the aim to obtain quick in-situ information on the in-depth profiling of the encrustation before advancing to conservation treatments. The encrustation examined is formed on exposed marble: (a) as products of the interaction between the stone surface and atmospheric pollutants (dendritic black and thin black encrustation, of approximately 300 and 200 mum thicknesses, respectively); (b) from deposition of soil-dust on marble surfaces (soil-dust crust, 300 mum thick); and (c) from treatments conducted in the past for aesthetic and/or protective purposes (patina samples, 300 mum thick). The crusts examined are multilayer encrustations on un-weathered marble, as revealed by studying cross sections with optical microscopy and scanning electron microscopy coupled with energy dispersive X-ray analysis. The elemental LIBS profiles of black encrustation based on relative spectral line intensity values show that the Fe, Si, Al and Ti content relative to Ca content decrease significantly with depth, expressing, thus, contamination decreasing within the alteration layers, since these elements originate from atmospheric pollution and deposition. In the cases of soil-dust encrustation and patina samples Si I and Al I emissions identified throughout the analyzed crust, indicate deposition of soil-dust and remnants of previous treatments, respectively. Therefore, LIBS, a micro-destructive technique can be used as an autonomous in-situ diagnostic technique to obtain in-depth elemental profiling of encrustation even in cases of highly in-homogeneous layered crusts, such those of un-weathered Pentelic marble.},
author = {Maravelaki-Kalaitzaki, P and Anglos, D and Kilikoglou, V and Zafiropulos, V},
doi = {10.1016/S0584-8547(01)00226-9},
editor = {Bally, A W and Bender, P L and McGetchin, R and Walcott, R I},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {1st international,congress laser induced,dedicated conference,elemental depth profiling,encrustation,italy,laser induced breakdown spectroscopy,marble,october 2000,paper presented,pisa,plasma spectroscopy applications,published,special issue,spectrochimca acta part b,{\v{z}} libs},
number = {6},
pages = {887--903},
publisher = {Am. Geophys. Un. {\&} Geol. Soc. Am.},
series = {Geodynamics Series},
title = {{Compositional characterization of encrustation on marble with laser induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854701002269},
volume = {56},
year = {2001}
}
@article{Hussain2008,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was applied for the detection of toxic metals in oil spill contaminated soil (OSCS). The OSCS samples were collected from Khursania Saudi Arabia along the coast of Persian Gulf exposed to oil spills in 1991 Gulf war. Environmentally important elements like Aluminum Magnesium, Calcium, Chromium, Titanium, Strontium, Iron, Barium, Sodium, potassium, Zirconium and Vanadium from the contaminated soil have been detected. Optimal experimental conditions for analysis were investigated. The LIBS system was calibrated using standard samples containing these trace elements. The results obtained using Laser-Induced Breakdown Spectroscopy (LIBS) were compared with the results obtained using Inductively Coupled Plasma Emission Spectroscopy (ICP). The concentrations of some elements (Ba and Cr) were found higher than permissible safe limits. Health risks associated with exposure to such toxic elements are also discussed.},
author = {Hussain, T and Gondal, M A},
doi = {10.1007/s10661-007-9694-2},
issn = {15732959},
journal = {Environmental Monitoring and Assessment},
keywords = {animals,environmental monitoring,environmental monitoring instrumentation,environmental monitoring methods,environmental pollution,humans,lasers,metals,metals analysis,petroleum,petroleum analysis,reproducibility results,saudi arabia,sensitivity specificity,soil pollutants,soil pollutants analysis,spectrum analysis,spectrum analysis instrumentation,spectrum analysis methods},
number = {1-3},
pages = {391--399},
pmid = {17406995},
title = {{Monitoring and assessment of toxic metals in Gulf War oil spill contaminated soil using laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17406995},
volume = {136},
year = {2008}
}
@article{Baudelet2006,
abstract = {Bacterial samples Escherichia coli and Bacillus subtilis have been analyzed by laser-induced breakdown spectroscopy LIBS using femtosecond pulses. We compare the obtained spectra with those resulting from the classical nanosecond LIBS. Specific features of femtosecond LIBS have been demonstrated, very attractive for analyzing biological sample: i a lower plasma temperature leading to negligible nitrogen and oxygen emissions from excited ambient air and a better contrast in detection of trace mineral species; and ii a specific ablation regime that favors intramolecular bonds emission with respect to atomic emission. A precise kinetic study of molecular band head intensities allows distinguishing the contribution of native CN bonds released by the sample from that due to carbon recombination with atmospheric nitrogen. Furthermore a sensitive detection of trace mineral elements provide specific spectral signature of different bacteria. An example is given for the Gram test provided by different magnesium emissions from Escherichia coli and Bacillus subtilis. An entire spectrum consists of hundred resolved lines belonging to 13 atomic or molecular species, which provides an ensemble of valuable data to identify different bacteria. © 2006 American Institute of Physics},
author = {Baudelet, Matthieu and Guyon, Laurent and Yu, Jin and Wolf, Jean-Pierre and Amodeo, Tanguy and Fréjafon, Emeric and Laloi, Patrick},
doi = {10.1063/1.2187107},
file = {::},
issn = {00218979},
journal = {Journal of Applied Physics},
number = {8},
pages = {084701},
title = {{Femtosecond time-resolved laser-induced breakdown spectroscopy for detection and identification of bacteria: A comparison to the nanosecond regime}},
url = {http://link.aip.org/link/JAPIAU/v99/i8/p084701/s1{\&}Agg=doi},
volume = {99},
year = {2006}
}
@article{Rodero2008,
abstract = {This work aims the diagnostic differentiation of chronic inflammation (CC), low-grade Intraepithelial squamous lesions (LGSIL) and high-grade intraepithelial squamous lesions (HGSIL) in biopsies of cervix of uterus from patients with atypias (ASC-US and ASC-H) and lesions (LGSIL and HGSIL), traced in the cervical/vaginal cytology by using Laser-Induced Fluorescence Spectroscopy (LIFS), with 488 nm excitation wavelength. Ninety seven biopsies from 32 patients with atypical cervical/vaginal cytology were collected. The biopsies were guided by colposcopy and taken at the squamous-columnar junction. Fluorescence emission spectra of each biopsy were collected by means of an optical fiber cable coupled to an argon laser at 488 nm as excitation source and addressed to a spectrograph and CCD camera/controller. Spectra were separated into three groups, CC, LGSIL and HGSIL, based on the cytopathology. It was detected similar mean spectra profiles for CC and LGSIL, and differences for HGSIL. An algorithm was developed for tissue classification based on the intensity of the multiplication of each spectrum by the mean spectrum of each group, searching for a discriminator that would address this spectral difference. The sensitivity and specificity of HGSIL identification, compared to CC and LGSIL was 89{\%} and 100{\%}, respectively. The LIFS using excitation wavelength of 488 nm could be used to differentiate HGSIL lesions from LGSIL and CC inflammation, and could help a precocious and less invasive diagnosis of cervix lesions.},
author = {Rodero, Ademir Barianni and Silveira, Landulfo and Rodero, David Augusto and Racanicchi, Roberto and Pacheco, Marcos Tadeu T},
institution = {Faculdade de Medicina, Universidade Camilo Castelo Branco-UNICASTELO, Estrada Projetada F-1, s/n, Fernand{\'{o}}polis, SP, 15600-000, Brazil.},
journal = {Journal of Fluorescence},
number = {5},
pages = {979--985},
pmid = {18363079},
title = {{Fluorescence spectroscopy for diagnostic differentiation in uteri's cervix biopsies with cervical/vaginal atypical cytology.}},
url = {http://www.springerlink.com/index/a1327765u00q3731.pdf},
volume = {18},
year = {2008}
}
@article{Ferrero2008,
abstract = {A theoretical study of atmospheric extinction mechanisms of optical radiation (molecular/aerosol scattering and absorption) has been carried out in order to assess their influences on stand-off laser-induced breakdown spectroscopy (LIBS) measurements. The atmospheric extinction of laser radiation at wavelengths commonly used in laser-induced breakdown spectroscopy (1064 nm and 532 nm) and of the laser-induced breakdown spectroscopy plasma emission beyond 250 nm is small compared to the attenuation with range due to the inverse square law. The fundamental problem with light propagation through the atmosphere is that the atmospheric transmittance does not remain constant within the whole spectral interval, and that this variation results in a change in the spectral distribution of the light received by the detector. Knowledge of atmospheric transmittance would allow for compensation of this effect.},
author = {Ferrero, A and Laserna, J J},
doi = {10.1016/j.sab.2007.11.020},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {2},
pages = {305--311},
title = {{A theoretical study of atmospheric propagation of laser and return light for stand-off laser induced breakdown spectroscopy purposes}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707003916},
volume = {63},
year = {2008}
}
@article{Parigger2003,
abstract = {The measured emission spectra of the OH radical subsequent to laser-induced optical breakdown in air are analyzed to infer spectroscopic temperature and species number density. Emissions from the UV A2sigma+ X2IIi transition dominate the spectra in the wavelength range of 306-322 nm and for time delays from the optical breakdown of 30-300 micros. Contributions from other species to the recorded OH emission spectra were also investigated for spectroscopic temperature measurements in the range of 2000-6000 K and for OH number densities in the range of 10(14) - 2 x 10(16) cm(-3). Monte Carlo simulations are applied to estimate errors in the analysis of the hydroxyl spectra.},
author = {Parigger, Christian G and Guan, Guoming and Hornkohl, James O},
institution = {Center for Laser Applications, The University of Tennessee Space Institute, 411 B. H. Goethert Parkway, Tullahoma, Tennessee 37388, USA.},
journal = {Applied Optics},
number = {30},
pages = {5986--5991},
pmid = {14594055},
title = {{Measurement and analysis of OH emission spectra following laser-induced optical breakdown in air.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594055},
volume = {42},
year = {2003}
}
@article{Gornushkin2003,
abstract = {The goal of this work was the development and evaluation of an algorithm for the approximation and automatic subtraction of continuum backgrounds in laser-induced breakdown and Raman spectra. The background correction algorithm was applied to simple and complex spectra and its effect on identification accuracy was studied. Linear correlation was used for the identification of plastic samples using both laser-induced breakdown and Raman spectra. For both techniques, the algorithm successfully eliminated continuum background without compromising spectral integrity. A significant improvement in the percentage of correct plastic identifications was observed for Raman spectra. The approach should be applicable to a wide range of background correction problems in atomic and molecular spectroscopy.},
author = {Gornushkin, I B and Eagan, P E and Novikov, A B and Smith, B W and Winefordner, J D},
institution = {Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, Florida 32611, USA.},
journal = {Applied Spectroscopy},
keywords = {algorithms,artifacts,lasers,plastics,plastics analysis,plastics chemistry,quality control,raman,raman methods,reproducibility results,sensitivity specificity,spectrum analysis},
number = {2},
pages = {197--207},
pmid = {14610958},
title = {{Automatic correction of continuum background in laser-induced breakdown and Raman spectrometry.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14610958},
volume = {57},
year = {2003}
}
@article{Kleefsman2008,
author = {Kleefsman, WA and Stowers, MA and Verheijen, PJT},
file = {::},
journal = {KONA Powder Part},
keywords = {aerosol mass spectrometry,bioaerosols,maldi ms,on-line analysis,single particle analysis},
number = {26},
pages = {205--214},
title = {{Single Particle Mass Spectrometry Bioaerosol Analysis by MALDI MS}},
url = {http://www.kona.or.jp/search/26{\_}205.pdf},
volume = {26},
year = {2008}
}
@article{Salt1996,
abstract = {Measurement of scattered light intensity and aerodynamic particle sizing are two methods that have recently been coupled with time-of-flight mass spectrometry for real-time determination of aerosol particle size and composition. An aerosol analysis technique recently developed in our laboratory, aerosol time-of-flight mass spectrometry, offers a unique experimental platform to evaluate both of these sizing techniques. This paper presents a comparison of results obtained with these two methods.},
author = {Salt, K and Noble, C a and Prather, K a},
doi = {10.1021/ac950396a},
file = {::},
issn = {0003-2700},
journal = {Analytical chemistry},
month = {jan},
number = {1},
pages = {230--4},
pmid = {21619241},
title = {{Aerodynamic Particle Sizing versus Light Scattering Intensity Measurement as Methods for Real-Time Particle Sizing Coupled with Time-of-Flight Mass Spectrometry.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21619241},
volume = {68},
year = {1996}
}
@article{Baudelet2009,
abstract = {We demonstrate in this paper that laser ablation allows efficient analysis of organic and biological materials. Such analysis is based on laser-induced breakdown spectroscopy (LIBS) which consists in the detection of the optical emission from the plasma induced by a high intensity laser pulse focused on the sample surface. The optimization of the ablation regime in terms of laser parameters (pulse duration, wavelength, fluence) is important to generate a plasma suitable for the analysis. We first present the results of a study of laser ablation of organic samples with different laser parameters using time-resolved shadowgraph. We correlate the early stage expansion of the plasma to its optical emission properties, which allows us to choose suitable laser parameters for an efficient analysis of organic or biological samples by LIBS. As an illustration of the analytical ability of LIBS for biological materials, we show that the emission from CN molecules can be used to distinguish between biological and inorganic samples. Native CN molecular fragment directly ablated from a biological sample are identified using time-resolved LIBS. Those due to recombination with nitrogen contained in atmospheric air can be distinguished with their specific time evolution behavior.},
author = {Baudelet, Matthieu and Boueri, Myriam and Yu, Jin and Mao, Xianglei and Mao, Samuel S. and Russo, Richard},
doi = {10.1117/12.808485},
file = {::},
journal = {Proceedings of SPIE},
keywords = {biological material,laser-induced breakdown spectroscopy,laser-induced plasma,organic materials},
pages = {72140J--72140J--10},
publisher = {Spie},
title = {{Laser ablation of organic materials for discrimination of bacteria in an inorganic background}},
url = {http://link.aip.org/link/PSISDG/v7214/i1/p72140J/s1{\&}Agg=doi},
volume = {7214},
year = {2009}
}
@article{Groh2010,
abstract = {Recently, nanoflow nebulizers with low-volume drain-free spray chambers became available for inductively coupled plasma-mass spectrometry application for analysis of very small sampling volumes. The present technical note reports on a different approach for 100{\%} efficient subnanoliter sample introduction, the application of monodisperse piezoelectric microdroplet dispensers which generate 40-50 microm droplets with high reproducibility if nozzles of 30 microm diameter are applied. The droplets having volumes below 0.1 nL can be introduced loss-free and without plasma loading, with frequencies up to approximately 100 Hz into analytical plasmas. In this technical note, the analytical figures of merit of laser-induced breakdown spectroscopy and inductively coupled plasma-optical emission spectrometry with single droplet introduction are reported using Ca and Au standard solutions as examples. Future engineering is required to reduce the total sample volumes from the relatively large sample reservoir of the current study, thereby reducing potential issues of washout while enabling analysis of ultralow total sample volumes.},
author = {Groh, S and Diwakar, P K and Garcia, C C and Murtazin, A and Hahn, D W and Niemax, K},
institution = {ISAS-Institute for Analytical Sciences at Technische Universit{\"{a}}t Dortmund, Germany.},
journal = {Analytical Chemistry},
number = {6},
pages = {2568--2573},
publisher = {American Chemical Society},
title = {100{\%} efficient sub-nanoliter sample introduction in laser-induced breakdown spectroscopy and inductively coupled plasma spectrometry: implications for ultralow sample volumes.},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20151662},
volume = {82},
year = {2010}
}
@article{Sugiyama2010,
abstract = {The chlorine concentration in concrete samples was measured by laser-induced breakdown spectroscopy (LIBS). One or two pulsed second harmonic Nd:YAG lasers ( =532 nm) were used for the generation of laser-induced breakdown, and an intensified CCD camera, spectrometer, and optical bundle fiber were used for spectral measurement. To maximize the spectral intensity of the chlorine fluorescence line at a wavelength of 837.59 nm, the time delay between laser irradiation and spectral measurement, the time delay between the two laser pulses in double-pulse measurement, and the gate width of the spectral measurement were optimized. The linear relationship between the spectral intensity of the chlorine fluorescence line and the chlorine concentration was verified for pressed samples with chlorine concentrations from 0.18 to 5.4 kg/m3. The signal-to-noise ratio was higher than 2 for the sample with a chlorine concentration of 0.18 kg/m3 (0.008 wt. {\%}). Thus, a chlorine concentration of 0.6 kg/m3, at which the reinforcing bars in concrete structures start to corrode, can be detected. These results show that LIBS is effective for the quantitative measurement of chlorine concentration in concrete with high sensitivity.},
author = {Sugiyama, K and Fujii, T and Matsumura, T and Shiogama, Y and Yamaguchi, M and Nemoto, K},
doi = {10.1364/AO.49.00C181},
journal = {Applied Optics},
number = {13},
pages = {C181--C190},
title = {{Detection of chlorine with concentration of 0.18 kg/m3 in concrete by laser-induced breakdown spectroscopy}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-49-13-C181},
volume = {49},
year = {2010}
}
@article{Ayyalasomayajula2011a,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been employed for the analysis of slurry samples. Quantitative analysis of slurry samples is crucial and challenging. The problems associated with slurry samples include splashing, surface turbulence, and the difficulties of obtaining reproducible samples due to sedimentation. The LIBS analysis has achieved limited success due to inherent disadvantages when applied to slurry samples. In order to achieve improved measurement precision and accuracy, a spin-on-glass sampling method was evaluated. Five elements (Al, Ca, Fe, Ni, and Si) were examined in five slurry simulants containing varying amounts of each ion. Three calibration models were developed by using univariate calibration, multiple linear regression, and partial least square regression. LIBS analysis results obtained from the partial least square regression model were determined to be the best fit to results obtained from inductively coupled plasma optical emission spectroscopy analysis.},
author = {Ayyalasomayajula, Krishna K and Dikshit, Vivek and Yueh, Fang Yu and Singh, Jagdish P and Smith, Laura T},
institution = {Institute for Clean Energy Technology, Mississippi State University, Starkville, MS 39759, USA.},
journal = {Analytical and Bioanalytical Chemistry},
number = {10},
pages = {3315--3322},
pmid = {21424178},
title = {{Quantitative analysis of slurry sample by laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21424178},
volume = {400},
year = {2011}
}
@article{Howard2006,
abstract = {Yersinia enterocolitica, an important cause of human gastroenteritis generally caused by the consumption of livestock, has traditionally been categorized into three groups with respect to pathogenicity, i.e., nonpathogenic (biotype 1A), low pathogenicity (biotypes 2 to 5), and highly pathogenic (biotype 1B). However, genetic differences that explain variation in pathogenesis and whether different biotypes are associated with specific nonhuman hosts are largely unknown. In this study, we applied comparative phylogenomics (whole-genome comparisons of microbes with DNA microarrays combined with Bayesian phylogenies) to investigate a diverse collection of 94 strains of Y. enterocolitica consisting of 35 human, 35 pig, 15 sheep, and 9 cattle isolates from nonpathogenic, low-pathogenicity, and highly pathogenic biotypes. Analysis confirmed three distinct statistically supported clusters composed of a nonpathogenic clade, a low-pathogenicity clade, and a highly pathogenic clade. Genetic differences revealed 125 predicted coding sequences (CDSs) present in all highly pathogenic strains but absent from the other clades. These included several previously uncharacterized CDSs that may encode novel virulence determinants including a hemolysin, a metalloprotease, and a type III secretion effector protein. Additionally, 27 CDSs were identified which were present in all 47 low-pathogenicity strains and Y. enterocolitica 8081 but absent from all nonpathogenic 1A isolates. Analysis of the core gene set for Y. enterocolitica revealed that 20.8{\%} of the genes were shared by all of the strains, confirming this species as highly heterogeneous, adding to the case for the existence of three subspecies of Y. enterocolitica. Further analysis revealed that Y. enterocolitica does not cluster according to source (host).},
author = {Howard, Sarah L and Gaunt, Michael W and Hinds, Jason and Witney, Adam A and Stabler, Richard and Wren, Brendan W},
doi = {10.1128/JB.188.10.3645-3653.2006},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Howard et al. - Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic diffe.pdf:pdf},
issn = {00219193},
journal = {Journal Of Bacteriology},
keywords = {animals,bayes theorem,evolution,gastroenteritis,gastroenteritis microbiology,genomics,humans,meat,meat microbiology,molecular,oligonucleotide array sequence analysis,phylogeny,yersinia enterocolitica,yersinia enterocolitica classification,yersinia enterocolitica genetics,yersinia enterocolitica pathogenicity,yersinia infections,yersinia infections etiology},
number = {10},
pages = {3645--53},
pmid = {16672618},
title = {{Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16672618},
volume = {188},
year = {2006}
}
@article{Greenwood2009,
abstract = {Rapid and accurate detection and identification of biological agents is an objective of various national security programs. Detection in general is difficult owing to natural clutter and anticipated low concentrations of subject material. Typical detection architectures comprise a nonspecific trigger, a rapid identifier, and a confirming step, often in a laboratory. High-confidence identification must be made prior to taking action, though this must be traded against regrets stemming from delay. Sensing requirements are best established by positing plausible scenarios, two of which are suggested herein. Modern technologies include the use of elastic scatter and ultraviolet laser-induced fluorescence for triggering and standoff detection. Optical and nonoptical techniques are used routinely in analyzing clinical samples used to confirminfection and illness resulting from a biological attack. Today, environmental sensing serves at best as an alert to medical authorities for possible action, which would include sample collection and detailed analysis. This paper surveys the state of the art of sensing at all levels.},
author = {Greenwood, DP and Jeys, TH and Johnson, Bernadette},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Greenwood, Jeys, Johnson - Optical techniques for detecting and identifying biological-warfare agents - 2009.pdf:pdf},
journal = {Proceedings of the},
keywords = {biological agents,fluorescence,medical diagnos-,particles,scatter,standoff sensing,tics},
number = {6},
title = {{Optical techniques for detecting and identifying biological-warfare agents}},
url = {http://ieeexplore.ieee.org/xpls/abs{\_}all.jsp?arnumber=4939401},
volume = {97},
year = {2009}
}
@article{Alvira2010,
abstract = {Two of the main items from which to retrieve data in anthropology are teeth and bones. Identification of trace elements in their composition allows valuable information to be obtained about alimentary habits and community life conditions of groups and individuals. Conventional methods used to determine the presence of trace elements require sample preparation, with partial or total destruction of the pieces, which in most cases are unique. In this work we show the possibilities of laser-induced breakdown spectroscopy (LIBS) as a nearly nondestructive tool in anthropology and paleontology for the measurement of the presence and distribution of trace elements in teeth. We applied LIBS to the determination of strontium and magnesium in dentin and enamel of Neolithic, middle age, and modern Homo sapiens teeth. Mg/Ca and Sr/Ca distribution maps of dentin and enamel in modern teeth were created using the data obtained. Ablation threshold fluences of dentin and enamel were also measured using the photoacoustic signal induced by laser ablation. Significant variations were found in the Mg/Ca and Sr/Ca ratios in the tooth dental tissue and between the teeth of the groups and individuals studied. These results can be useful for evolutionary anthropology studies as they can provide information regarding early nutrition, seasonality, and residential mobility.},
author = {Alvira, F C and {Ramirez Rozzi}, F and Bilmes, G M},
institution = {Centro de Investigaciones Opticas-CIOp (CONICET La Plata -CIC) C.C.3,1897, La Plata, Argentina.},
journal = {Applied Spectroscopy},
number = {3},
pages = {313--319},
pmid = {20223067},
title = {{Laser-induced breakdown spectroscopy microanalysis of trace elements in Homo sapiens teeth.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20223067},
volume = {64},
year = {2010}
}
@article{Weidman2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) using double-pulse irradiation with Nd:YAG and CO(2) lasers was applied to the analysis of a polystyrene film on a silicon substrate. An enhanced emission signal, compared to single-pulse LIBS using a Nd:YAG laser, was observed from atomic carbon, as well as enhanced molecular emission from C(2) and CN. This double-pulse technique was further applied to 2,4,6-trinitrotoluene residues, and enhanced LIBS signals for both atomic carbon and molecular CN emission were observed; however, no molecular C(2) emission was detected.},
author = {Weidman, Matthew and Baudelet, Matthieu and Palanco, Santiago and Sigman, Michael and Dagdigian, Paul J and Richardson, Martin},
doi = {10.1364/OE.18.000259},
institution = {Townes Laser Institute, CREOL - The College of Optics and Photonics, University of Central Florida, Orlando, FL, USA. mweidman@creol.ucf.edu},
journal = {Optics Express},
number = {1},
pages = {259--266},
pmid = {20173846},
title = {{Nd:YAG-CO(2) double-pulse laser induced breakdown spectroscopy of organic films.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20173846},
volume = {18},
year = {2010}
}
@article{Nassef2005,
abstract = {Laser induced breakdown spectroscopy is combined with a spark discharge to operate in a laser triggered spark discharge mode. This spark discharge laser induced breakdown spectroscopy (SD-LIBS) is evaluated for Al and Cu targets in air under atmospheric pressure. Significant enhancement in the measured line intensities and the signal-to-background ratios, which depend on the spark discharge voltage and the laser fluence, is observed in spark discharge laser induced breakdown spectroscopy when compared to laser induced breakdown spectroscopy alone for similar laser conditions. The measured line intensities increase with the applied voltage for both targets, and the ratio of the measured line intensity using spark discharge laser induced breakdown spectroscopy to that using laser induced breakdown spectroscopy is found to increase as the laser fluence is decreased. For Al II 358.56, such intensity enhancement ratio increases from {\~{}}50 to {\~{}}400 as the laser fluence is decreased from 48 to 4 J/cm2 at an applied voltage of 3.5 kV. Thus, spark discharge laser induced breakdown spectroscopy allows for using laser pulses with relatively low energy to ablate the studied material, causing less ablation, and hence less damage to its surface. Moreover, applying spark discharge laser induced breakdown spectroscopy gives up to 6-fold enhancement in the S B ratio, compared to those obtained with laser induced breakdown spectroscopy for the investigated spectral emission lines.},
author = {Nassef, O Ayed and Elsayed-Ali, Hani E},
doi = {10.1016/j.sab.2005.10.010},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {12},
pages = {1564--1572},
title = {{Spark discharge assisted laser induced breakdown spectroscopy}},
url = {http://www.sciencedirect.com/science/article/B6THN-4HNSB2T-2/2/03f16d2530b3e21daf1d2129ca297b0c},
volume = {60},
year = {2005}
}
@article{Goode2000,
abstract = {Laser-induced breakdown spectroscopy (LIBS) produces line spectra from solid samples without any pre-treatment. The spectra were reduced to a matrix of intensities for the most intense lines and a number of different methods of identification were applied to determine if metal alloys could be distinguished by their spectra. The methods included principal component analysis, cluster analysis, multiple discriminant analysis, and spectral matching with a similarity index. The unsupervised methods, principal component analysis and cluster analysis, showed that the samples can be divided into groups based on their LIBS spectra. Discriminant analysis achieved an overall 97{\%} correct classification into metal groups. Finally, a spectral matching approach was used to compare 234 individual spectra to a library of 39 average spectra. The accuracy of the matches varied from 97.4{\%} correct prediction of the class of material to 79.9{\%} correct identification of the specific alloy.},
author = {Goode, Scott R and Morgan, Stephen L and Hoskins, Richard and Oxsher, Allison},
doi = {10.1039/b002190n},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {9},
pages = {1133--1138},
publisher = {Royal Society of Chemistry},
title = {{Identifying alloys by laser-induced breakdown spectroscopy with a time-resolved high resolution echelle spectrometer}},
url = {http://xlink.rsc.org/?DOI=b002190n},
volume = {15},
year = {2000}
}
@article{Merdes2007,
abstract = {The potential utility of laser-induced breakdown spectroscopy (LIBS) as a means to detect biological contaminants on painted surfaces is investigated. Issues involving the use of LIBS for detection of biologicals are discussed. The apparatus assembled for this work is described, as is the manner in which samples of bare copper and painted substrates onto which thin layers of bacterial spores, pollen, molds, and contaminants were prepared. A chemometric analysis methodology consisting of spectral preprocessing, principal components analysis, linear discriminant analysis, and hierarchical cluster analysis yields an automated classification tool that was able to identify bacterial spores with a false positive rate of 1{\%} and a false negative rate of 3{\%}.},
author = {Merdes, DW and Suhan, JM and Keay, JM and Hadka, DM and Bradley, WR},
file = {::},
journal = {SPECTROSCOPY-SPRINGFIELD THEN EUGENE THEN DULUTH-},
number = {4},
pages = {28},
publisher = {ASTER PUBLISHING CORPORATION},
title = {{The investigation of laser-induced breakdown spectroscopy for detection of biological contaminants on surfaces}},
url = {http://spectroscopyonline.findanalytichem.com/spectroscopy/data/articlestandard/spectroscopy/172007/421870/article.pdf},
volume = {22},
year = {2007}
}
@article{Gottfried2008,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is a promising technique for real-time chemical and biological warfare agent detection in the field. We have demonstrated the detection and discrimination of the biological warfare agent surrogates Bacillus subtilis (BG) (2{\%} false negatives, 0{\%} false positives) and ovalbumin (0{\%} false negatives, 1{\%} false positives) at 20 meters using standoff laser-induced breakdown spectroscopy (ST-LIBS) and linear correlation. Unknown interferent samples (not included in the model), samples on different substrates, and mixtures of BG and Arizona road dust have been classified with reasonable success using partial least squares discriminant analysis (PLS-DA). A few of the samples tested such as the soot (not included in the model) and the 25{\%} BG:75{\%} dust mixture resulted in a significant number of false positives or false negatives, respectively. Our preliminary results indicate that while LIBS is able to discriminate biomaterials with similar elemental compositions at standoff distances based on differences in key intensity ratios, further work is needed to reduce the number of false positives/negatives by refining the PLS-DA model to include a sufficient range of material classes and carefully selecting a detection threshold. In addition, we have demonstrated that LIBS can distinguish five different organophosphate nerve agent simulants at 20 meters, despite their similar stoichiometric formulas. Finally, a combined PLS-DA model for chemical, biological, and explosives detection using a single ST-LIBS sensor has been developed in order to demonstrate the potential of standoff LIBS for universal hazardous materials detection.},
author = {Gottfried, Jennifer L and {De Lucia}, Frank C and Munson, Chase A and Miziolek, Andrzej W},
institution = {US Army Research Laboratory, AMSRD-ARL-WM-BD, Aberdeen Proving Ground, Maryland 21005-5069, USA. gottfried@arl.army.mil},
journal = {Applied Spectroscopy},
number = {4},
pages = {353--363},
pmid = {18416891},
title = {{Standoff detection of chemical and biological threats using laser-induced breakdown spectroscopy.}},
url = {http://www.ingentaconnect.com/content/sas/sas/2008/00000062/00000004/art00007},
volume = {62},
year = {2008}
}
@article{Fisher2001,
abstract = {Optimal temporal gating for laser-induced breakdown spectroscopy (LIBS) analysis was investigated for a select group of toxic metals, namely the Resource Conservation and Recovery Act (RCRA) metals arsenic, beryllium, cadmium, chromium, lead, and mercury. The differing rates of decay between the continuum plasma emission and the atomic emission were used as a means to maximize the signalto- noise ratio of the atomic emission lines for these six metal species. Detection windows were investigated corresponding to delay times from 2 to 50 m s following the plasma-initiating laser pulse. For the current experimental conditions, it is concluded that the relatively short delay time of 12 m s is optimal for the detection of arsenic, beryllium, cadmium, and mercury, while a longer delay time of 50 m s is optimal for the detection of chromium and lead. The reduced atomic emission intensity at relatively long delay times is compensated for by the use of long detector gate widths. Estimated detection limits are reported for the six metal species based on the optimized temporal gating and ensemble averaging of multiple laser pulses, and the implications for simultaneous metals monitoring are discussed.},
author = {Fisher, Brian T. and Johnsen, Howard a. and Buckley, Steven G. and Hahn, David W.},
doi = {10.1366/0003702011953667},
issn = {00037028},
journal = {Applied Spectroscopy},
month = {oct},
number = {10},
pages = {1312--1319},
title = {{Temporal Gating for the Optimization of Laser-Induced Breakdown Spectroscopy Detection and Analysis of Toxic Metals}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=55{\&}issue=10{\&}spage=1312},
volume = {55},
year = {2001}
}
@article{Zhao2009,
author = {Zhao, Youbo and Singha, Sima and Liu, Yaoming and Gordon, Robert J},
journal = {Optics Letters},
number = {4},
pages = {494--496},
title = {breakdown spectroscopy},
volume = {34},
year = {2009}
}
@article{Fichet2006,
abstract = {In the framework of the development of new techniques, the ability of laser-induced breakdown spectroscopy (LIBS) to analyse remotely complex aqueous solutions was investigated. The jet configuration with a collimated gas stream was chosen because it appeared to be the most promising method for the LIBS probe, particularly in terms of sensitivity and repeatability. For emission collection, the echelle spectrometer offers a simultaneously recorded wavelength range from the UV to the near IR and is interesting for multielemental analysis for LIBS and also for inductively coupled plasma (ICP) optical emission spectroscopy (OES). The importance of parameters influencing the quantitative results of LIBS such as multispecies analysis, sheath gas, use of an internal standard and temporal parameters for analysis is described. LIBS quantitative data have been directly compared with results from the more standard ICP/OES technique.},
author = {Fichet, P and Tabarant, M and Salle, B and Gautier, C},
institution = {Commissariat {\`{a}} l'Energie Atomique Saclay, Nuclear Energy Department/DPC/SECR/LANIE, B{\^{a}}t 391, 91191, Gif Sur Yvette, France. pascal.fichet@cea.fr},
journal = {Analytical and Bioanalytical Chemistry},
keywords = {echelle spectrometer,emission spectroscopy,inductively coupled plasma optical,laser,laser induced breakdown,spectroscopy},
number = {2},
pages = {338--344},
pmid = {16609842},
title = {{Comparisons between LIBS and ICP/OES.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16609842},
volume = {385},
year = {2006}
}
@article{Hauser2002,
abstract = {A mobile Laser-Induced Breakdown Detection (LIBD) system is developed for the field study of the aquatic colloid migration. The principle of LIBD is based on the plasma generation at breakdown of colloids in the laser focus region, which is then observed by either photo-acoustic detection or optical monitoring. The method provides information on the number density and average size of colloids. The present instrumentation built up particularly for the field study is applied for the aquatic colloid migration in a natural granite fracture. The study is performed within the Colloid and Radionuclide Retention project (CRR) in order to investigate the role of colloids on the radionuclide migration, For this purpose, bentonite colloids dispersed in granite groundwater are injected into a rock fracture zone with a dipole distance of 5 m. After passing through the fracture, the groundwater is guided into a flow-through detection cell of LIBD for the quantification of colloids. Another experiment is performed with the same colloids traced by tetra- and tri-valent metal ions, Th(IV), Hf(IV) and Tb(III). The recovery of colloids as found by LIDB appears to be about 55 5{\%} of the injected colloid mass concentration, which is corroborated by ICP-MS analysis of Al present in bentonite colloids. An average size of recovered colloids is slightly decreased from the value of before injection and hence the relative number density increased in the course of the rock fracture migration. Recovered fractions of colloid-borne trace elements in the extracted groundwater are 78 8{\%} for both tetra-valent elements and 33 3{\%} for trivalent element of the originally traced concentrations. Plausible explanations are given for the different recoveries of heavy metal ions. (C) 2002 Elsevier Science B.V. All rights reserved.},
author = {Hauser, W and Geckeis, H and Kim, J I and Fierz, Th},
doi = {10.1016/S0927-7757(01)01086-X},
issn = {09277757},
journal = {Colloids and Surfaces A Physicochemical and Engineering Aspects},
keywords = {aquifer,colloids,laser induced breakdown detection,migration,optical detection,particles},
number = {1-3},
pages = {37--45},
title = {{A mobile laser-induced breakdown detection system and its application for the in situ-monitoring of colloid migration}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S092777570101086X},
volume = {203},
year = {2002}
}
@article{Siegel2005,
abstract = {We report a technique that is able to achieve high spatial resolution in the measurement of the temporal and spectral emission characteristics of laser-induced expanding plasmas. The plasma is imaged directly onto the slit of an imaging spectrograph coupled to a time-gated intensified camera, with the plasma expansion direction being parallel to the slit extension. In this way, a single hybrid detection system is used to acquire the spatial, spectral and temporal characteristics of the laser induced plasma. The parallel acquisition approach of this technique ensures a much better spatial resolution in the expansion direction, reproducibility and data acquisition speed than commonly obtained by sequential measurements at different distances from the target. We have applied this technique to study the laser-induced plasma in LiNbO3 and Bi12Ge1O20, revealing phenomena not seen in such detail with standard instruments. These include extreme line broadening up to a few nanometers accompanied by self-absorption near the target surface, as well as different ablation and expansion dynamics for the different species ejected. Overall, the high precision and wealth of quantitative information accessible with this technique open up new possibilities for the study of fundamental plasma expansion processes during pulsed laser ablation.},
author = {Siegel, J and Epurescu, G and Perea, A and Gordillovazquez, F and Gonzalo, J and Afonso, C},
doi = {10.1016/j.sab.2005.05.020},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {imaging,lithium niobate,plasma,self absorption,spectroscopy,stark effect},
number = {7-8},
pages = {915--919},
title = {{High spatial resolution in laser-induced breakdown spectroscopy of expanding plasmas}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854705001527},
volume = {60},
year = {2005}
}
@article{DeFreez2009,
abstract = {Bio-aerosol terrorist attacks have been carried out against civilians in the United States and elsewhere. Unfortunately, recurrence appears inevitable. A fast, reliable, and inexpensive bioaerosol threat detection trigger can be an important tool for detect-to-protect and detect-to-treat countermeasure scenarios. Bio-aerosol threat detection triggers employing light, historically laser light but recently LED light, for induced native- or auto-fluorescence (LIF) have been developed for well over a decade without a generally accepted solution being found. This paper presents a brief history of LIF triggers and reviews many vendor efforts, past and current. Various technical approaches and design considerations are discussed. Triggers from ICx technology, currently available or in development, are also discussed.},
author = {DeFreez, Richard},
doi = {10.1117/12.835088},
file = {:E$\backslash$:/Mina Dokument/Mendeley/DeFreez - LIF bio-aerosol threat triggers then and now - 2009.pdf:pdf},
journal = {Proceedings of SPIE},
keywords = {bio-terrorism,bio-warfare,detection,fluorescence,lif,triggers},
pages = {74840H--74840H--15},
publisher = {Spie},
title = {{LIF bio-aerosol threat triggers: then and now}},
url = {http://link.aip.org/link/PSISDG/v7484/i1/p74840H/s1{\&}Agg=doi},
volume = {7484},
year = {2009}
}
@article{Freedman2005,
abstract = {A laser induced breakdown spectroscopy-based apparatus for the analysis of aluminum alloys which employs a microchip laser and a handheld spectrometer with an ungated, non-intensified CCD array has been built and tested. The microchip laser, which emits low energy pulses (4-15 muJ) at high repetition rates (1-10 kHz) at 1064 nm, produces, when focused, an ablation crater with a radius on the order of only 10 mum. The resulting emission is focused onto an optical fiber connected to 0.10 m focal length spectrometer with a spectral range of 275-413 nm. The apparatus was tested using 30 different aluminum alloy reference samples. Two techniques for constructing calibration curves from the data, peak integration and partial least squares regression, were quantitatively evaluated. Results for Fe, Mg, Mn, Ni, Si, and Zn indicated limits of detection (LOD) that ranged from 0.05 to 0.14 wt.{\%} and overall measurement errors which varied from 0.06 to 0.18 wt.{\%}. Higher limits of detection and overall error for Cu 0.3 wt.{\%}) were attributed to analysis problems associated with the presence of optically thick lines and a spectral interference from Zn. Improvements in design and component sensitivity should increase overall performance by at least a factor of 2, allowing for dependable aluminum alloy classification.},
author = {Freedman, A and Iannarillijr, F and Wormhoudt, J},
doi = {10.1016/j.sab.2005.03.020},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {alloy classification,aluminum alloy,breakdown spectroscopy,microchip laser,miniature spectrometer,partial least squares},
number = {7-8},
pages = {1076--1082},
title = {{Aluminum alloy analysis using microchip-laser induced breakdown spectroscopy}},
url = {http://www.sciencedirect.com/science/article/B6THN-4G7JXPJ-1/2/0db18ad5874186761af5c4759fcfc5b6},
volume = {60},
year = {2005}
}
@article{Hoyt1987,
abstract = {We have performed a quantitative analysis of epitaxial quality and arsenic diffUSion in ion implanted polycrystaHine silicon (polysilicon) layers on 000) Si, and find a clear advantage for the use of high-temperature rapid thermal annealing (RTA) in the 10-8 regime to induce intentional, complete epitaxial alignment. The RTA-induced alignment kinetics and associated arsenic diffusion were studied in the 1050-1150 °C temperature range for arsenic doping concentrations between 1 X 1020 and 1 X 102 I em - 3, and were characterized by Rutherford backscattering, ion channeling, and cross-sectional transmission electron microscopy. The information about the relationship between arsenic diffusion, arsenic concentration, and epitaxial quality resulting from Ii given RT A cycle will be useful for optimizing bipolar transistors with realigned poly silicon emitter contacts. PolycrystaUine silicon (polysilicon) films formed by low pressure chemical vapor deposition (LPCVD) are widely used in advanced bipolar integrated circuit technology. When deposited directly on the single-crystal silicon, polysilicon serves as both a diffusion source and self-aligned contact to the extrinsic base and emitter regions. The LPCVD process produces a thin, continuous interfacial layer between the poly- and single-crystal silicon. I • 2 Subsequent furnace annealing in a standard high-speed bipolar transistor process results in partial breakup of this layer, allowing an uncontrolled amount of epitaxial regrowth of the polysilicon to take place. The transistor base current and emitter resistance are strongly dependent on the morphology of the interfacial1ayer.3 ,4 A short, high-temperature emitter drivein which intentionally induces complete epitaxial alignment of the polysilicon with the substrate will alleviate this process sensitivity and reduce the emitter contact resistance. Epitaxial alignment of undoped polysilicon deposited on (l00) silicon has been induced by furnace5 and rapid thermal annealing6 (R T A). Alignment of arsenicimplanted emitters has been realized in high-frequency devices using fast furnace annealing at 1150 0c.7 • S These authors report that high arsenic doping enhances the alignment. In this letter we establish the relative importance of the key process parameters for epitaxial alignment of arsenic implanted, 0.5- 11m polysilicon films. We also show that to obtain Me V ion channeling yields comparable to bare silicon, high temperatures are necessary, while short times are required to minimize arsenic diffusion. Starting substrates were boron doped, 11-15 !l em (100) silicon. U ndoped polysilicon films of thickness O. 51lm were deposited in a conventional LPCVD reactor at 620°C. Prior to loading, wafers were given a standard RCA clean followed by an etch in 50:! HF with no subsequent rinse. As+- was implanted at low beam current densities into some wafers at 150 keVto a dose of5 X 1015 cm--2 , and others at 60 keY to doses of2.S and 5 X 1016 em --2. Liquid nitrogen cooling was used for the two highest dose implants to avoid in situ annealing. Because arsenic diffuses so rapidly in polysilicon, uniform doping},
author = {Hoyt, J. L. and Crabbé, E. and Gibbons, J. F. and Pease, R. F. W.},
doi = {10.1063/1.98034},
issn = {00036951},
journal = {Applied Physics Letters},
number = {12},
pages = {751},
title = {{Epitaxial alignment of arsenic implanted polycrystalline silicon films on 〈100〉 silicon obtained by rapid thermal annealing}},
url = {http://link.aip.org/link/APPLAB/v50/i12/p751/s1{\&}Agg=doi},
volume = {50},
year = {1987}
}
@article{Gottfried2009a,
abstract = {In this review we discuss the application of laser-induced breakdown spectroscopy (LIBS) to the problem of detection of residues of explosives. Research in this area presented in open literature is reviewed. Both laboratory and field-tested standoff LIBS instruments have been used to detect explosive materials. Recent advances in instrumentation and data analysis techniques are discussed, including the use of double-pulse LIBS to reduce air entrainment in the analytical plasma and the application of advanced chemometric techniques such as partial least-squares discriminant analysis to discriminate between residues of explosives and non-explosives on various surfaces. A number of challenges associated with detection of explosives residues using LIBS have been identified, along with their possible solutions. Several groups have investigated methods for improving the sensitivity and selectivity of LIBS for detection of explosives, including the use of femtosecond-pulse lasers, supplemental enhancement of the laser-induced plasma emission, and complementary orthogonal techniques. Despite the associated challenges, researchers have demonstrated the tremendous potential of LIBS for real-time detection of explosives residues at standoff distances.},
author = {Gottfried, Jennifer L and {De Lucia}, Frank C and Munson, Chase a and Miziolek, Andrzej W},
doi = {10.1007/s00216-009-2802-0},
file = {:C$\backslash$:/Users/LASER/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Gottfried et al. - 2009 - Laser-induced breakdown spectroscopy for detection of explosives residues a review of recent advances, challenges, and future prospects.pdf:pdf},
isbn = {0021600928020},
issn = {1618-2650},
journal = {Analytical and bioanalytical chemistry},
keywords = {chemometric analysis,double-pulse libs,explosives detection,laser-induced breakdown,spectroscopy},
month = {sep},
number = {2},
pages = {283--300},
pmid = {19418042},
title = {{Laser-induced breakdown spectroscopy for detection of explosives residues: a review of recent advances, challenges, and future prospects.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19418042},
volume = {395},
year = {2009}
}
@article{Jasik2009,
abstract = {Laser-induced breakdown spectroscopy (LIBS) in the vacuum ultraviolet range (VUV, lambda < 200 nm) is employed for the detection of trace elements in polyethylene (PE) that are difficult to detect in the UV/VIS range. For effective laser ablation of PE, we use a F2 laser (wavelength lambda = 157 nm) with a laser pulse length of 20 ns, a pulse energy up to 50 mJ, and pulse repetition rate of 10 Hz. The optical radiation of the laser-induced plasma is measured by a VUV spectrometer with detection range down to lambda = 115 nm. A gated photon-counting system is used to acquire time-resolved spectra. From LIBS measurements of certified polymer reference materials, we obtained a limit of detection (LOD) of 50 µg/g for sulphur and 215 µg/g for zinc, respectively. The VUV LIBS spectra of PE are dominated by strong emission lines of neutral and ionized carbon atoms. From time-resolved measurements of the carbon line intensities, we determine the temporal evolution of the electronic plasma temperature, Te. For this, we use Saha-Boltzmann plots with the electron density in the plasma, Ne, derived from the broadening of the hydrogen H-alpha line. With the parameters Te and Ne, we calculate the intensity ratio of the atomic sulphur and carbon lines at 180.7 nm and at 175.2 nm, respectively. The calculated intensity ratios are in good agreement with the experimentally measured results.},
author = {Jasik, Juraj and Heitz, Johannes and Pedarnig, Johannes D and Veis, Pavel},
doi = {10.1016/j.sab.2009.07.013},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {laser induced breakdown spectroscopy},
number = {10},
pages = {1128--1134},
publisher = {Elsevier B.V.},
title = {{Vacuum ultraviolet laser-induced breakdown spectroscopy analysis of polymers}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709002250},
volume = {64},
year = {2009}
}
@article{Ayyalasomayajula2011,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been employed for the analysis of slurry samples. Quantitative analysis of slurry samples is crucial and challenging. The problems associated with slurry samples include splashing, surface turbulence, and the difficulties of obtaining reproducible samples due to sedimentation. The LIBS analysis has achieved limited success due to inherent disadvantages when applied to slurry samples. In order to achieve improved measurement precision and accuracy, a spin-on-glass sampling method was evaluated. Five elements (Al, Ca, Fe, Ni, and Si) were examined in five slurry simulants containing varying amounts of each ion. Three calibration models were developed by using univariate calibration, multiple linear regression, and partial least square regression. LIBS analysis results obtained from the partial least square regression model were determined to be the best fit to results obtained from inductively coupled plasma optical emission spectroscopy analysis.},
author = {Ayyalasomayajula, Krishna K and Dikshit, Vivek and Yueh, Fang Yu and Singh, Jagdish P and Smith, Laura T},
institution = {Institute for Clean Energy Technology, Mississippi State University, Starkville, MS 39759, USA.},
journal = {Analytical and Bioanalytical Chemistry},
number = {10},
pages = {3315--3322},
pmid = {21424178},
title = {{Quantitative analysis of slurry sample by laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21424178},
volume = {400},
year = {2011}
}
@article{Moros2011,
abstract = {In general, any standoff sensor for the effective detection of explosives must meet two basic requirements: first, a capacity to detect the response generated from only a small amount of material located at a distance of several meters (high sensitivity) and second, the ability to provide easily distinguishable responses for different materials (high specificity). Raman spectroscopy and laser-induced breakdown spectroscopy (LIBS) are two analytical techniques which share similar instrumentation and, at the same time, generate complementary data. These factors have been taken into account recently for the design of sensors used in the detection of explosives. Similarly, research on the proper integration of both techniques has been around for a while. A priori, the different operational conditions required by the two techniques oblige the acquisition of the response for each sensor through sequential analysis, previously necessary to define the proper hierarchy of actuation. However, such an approach does not guarantee that Raman and LIBS responses obtained may relate to each other. Nonetheless, the possible advantages arising from the integration of the molecular and elemental spectroscopic information come with an obvious underlying requirement, simultaneous data acquisition. In the present paper, strong and weak points of Raman spectroscopy and LIBS for solving explosives detection problems, in terms of selectivity, sensitivity, and throughput, are critically examined, discussed, and compared for assessing the ensuing options on the fusion of the responses of both sensing technologies.},
author = {Moros, J and Lorenzo, J a and Laserna, J J},
doi = {10.1007/s00216-011-4999-y},
file = {::},
issn = {1618-2650},
journal = {Analytical and bioanalytical chemistry},
keywords = {libs,raman spectroscopy,standoff sensor},
month = {jul},
number = {10},
pages = {3353--65},
pmid = {21533640},
title = {{Standoff detection of explosives: critical comparison for ensuing options on Raman spectroscopy-LIBS sensor fusion.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21533640},
volume = {400},
year = {2011}
}
@article{Death2008,
abstract = {Laser-induced Breakdown Spectroscopy (LIBS) in combination with Principal Components Regression (PCR) has been applied to determine the elemental composition of a series of run-of-mine (ROM) iron ore samples. The samples were presented for measurement both as compressed pellets and as loose chipped material. The present paper details the results of the measurements of the compressed pellets. Results from ore chips will be reported separately. LIBS spectral data was recorded in three separate spectral regions to measure major, minor and trace components of the iron ore sample pellets. Background stripping, normalization and spectral cleaning were applied to minimize the relative standard deviations of the LIBS data. PCR analysis was then applied to produce calibration models for iron, aluminum, silicon, manganese, potassium and phosphorous. These calibration models were then validated using independent LIBS measurements. Robust calibration models were determined for iron, aluminum, silicon and potassium, whilst the results for manganese were encouraging. Phosphorous, present at low levels in the ores measured, remained the most difficult element to determine accurately. The combination of LIBS and PCR shows potential for in-situ on-line determination of ore composition.},
author = {Death, D L and Cunningham, A P and Pollard, L J},
doi = {10.1016/j.sab.2008.04.014},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {laser induced breakdown spectroscopy,principal components analysis,principal components regression},
number = {7},
pages = {763--769},
title = {{Multi-element analysis of iron ore pellets by Laser-induced Breakdown Spectroscopy and Principal Components Regression}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854708001006},
volume = {63},
year = {2008}
}
@article{Stavropoulos2005,
abstract = {Laser-Induced Breakdown Spectroscopy has been applied to laminar premixed methane-air flames in order to obtain, for the first time, quantitative measurements of atomic species densities in a reacting flow. The electron density and the plasma temperature were determined and it was shown that the hypothesis of local thermodynamic equilibrium is valid under the present experimental conditions. It was further shown, that the equivalence ratio phi of methane-air mixtures can be quantitatively determined from the ratio of the number densities NH/NO, the latter being obtained from the ratio of the hydrogen (Halpha at 656 nm) and oxygen (O(I) at 777 nm) atomic lines intensities.},
author = {Stavropoulos, P and Michalakou, A and Skevis, G and Couris, S},
doi = {10.1016/j.sab.2005.03.021},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {7-8},
pages = {1092--1097},
title = {{Laser-induced breakdown spectroscopy as an analytical tool for equivalence ratio measurement in methane-air premixed flames}},
url = {http://www.sciencedirect.com/science/article/B6THN-4G7NSX1-1/2/a2319ba20775502ee4ce7bf152d5f3e5},
volume = {60},
year = {2005}
}
@article{Margetic2000,
abstract = {The ablation of brass samples in argon shield gas by 170 fs and 6 ns laser pulses has been studied by optical emission spectroscopy of the evolving plasmas. Differences observed in the temporal behavior of the spectral line intensities are explained by the shielding effect of the Ar plasma for ns-pulses and the free expansion of the plasma of the ablated material in case of fs-pulses. Brass with different Zn/Cu ratios were used as samples. Different types of crater formation mechanisms in the case of ns- and fs-pulses were observed. At 40 mbar argon pressure the thresholds of ablation were found to be {\~{}}0.1 and {\~{}}1.5 J cm-2 for fs- and ns-pulses, respectively. With an internal standardization of zinc to copper it is possible to correct for differences in the ablation rates and to obtain linear calibration curves. For optimum experimental conditions, narrower confidence intervals for the determination of unknown concentrations were found in case of fs-pulses. Within the range of the laser intensities used, no dependence of the Zn/Cu line intensity ratio on the number of laser pulses applied to the same ablation spot was observed, neither for fs- nor for ns-pulses, which is interpreted as the absence of fractional vaporization.},
author = {Margetic, V and Pakulev, A and Stockhaus, A and Bolshov, M and Niemax, K and Hergenr{\"{o}}der, R},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {brass material,corresponding author,de {\v{z}} r,e mail address,fax,femtosecond,hergenroder,hergenroeder,isas dortmund,laser ablation,optical emission spectroscopy,q49 231 1392 120,q49 231 1392 178,tel},
number = {11},
pages = {1771--1785},
title = {{A comparison of nanosecond and femtosecond laser-induced plasma spectroscopy of brass samples}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854700002755},
volume = {55},
year = {2000}
}
@article{Balzer2005a,
abstract = {In this study a new method for online analysis of the zinc coating of galvanized sheet steel based on laser-induced breakdown spectroscopy (LIBS) is presented. The coating is characterized with a series of single laser bursts irradiated on the traversing sheet steel, each on a different sheet steel position. To achieve an ablation depth in the range of the coating thickness of about 10 mum a Nd:YAG laser at 1064 nm in collinear double pulse mode was used. The depth information is obtained by control of the ablation depth by adjusting the burst energy using an external electro-optical attenuator. Concepts for the determination of the coating thickness and the chemical composition are presented. The achieved thickness resolution is estimated to about 400 nm for coating thicknesses of electrolytic galvanized sheet steel in the range of 3.2 to 11.2 mum. In the case of hot-dip galvanized sheet steel information about the depth profile of aluminium can be gained by the new method.},
author = {Balzer, H and Hoehne, M and Sturm, V and Noll, R},
doi = {10.1016/j.sab.2005.07.003},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {7-8},
pages = {1172--1178},
title = {{Online coating thickness measurement and depth profiling of zinc coated sheet steel by laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854705002119},
volume = {60},
year = {2005}
}
@article{Eseller2008,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been applied to measure the equivalence ratio of CH(4)/air flames using gated detection. In this work, we have developed an ungated, miniature LIBS-based sensor for studying CH(4)/air and biodiesel flames. We have used this sensor to characterize the biodiesel flame. LIBS spectra of biodiesel flames were recorded with different ethanol concentrations in the biodiesel and also at different axial locations within the flame. The sensor performance was evaluated with a CH(4)/air flame. LIBS signals of N, O, and H from a CH(4)/air flame were used to determine the equivalence ratio. A linear relationship between the intensity ratio of H and O lines and the calculated equivalence ratio were obtained with this sensor.},
author = {Eseller, Kemal E and Yueh, Fang Y and Singh, Jagdish P},
institution = {Institute for Clean Energy Technology, Mississippi State University, 205 Research Boulevard, Starkville, Mississippi 39759, USA.},
journal = {Applied Optics},
number = {31},
pages = {G144--G148},
pmid = {19122695},
title = {{Laser-induced breakdown spectroscopy measurement in methane and biodiesel flames using an ungated detector.}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-47-31-G144},
volume = {47},
year = {2008}
}
@article{Rehse2012b,
abstract = {The recent progress made in developing laser-induced breakdown spectroscopy (LIBS) has transformed LIBS from an elemental analysis technique to one that can be applied for the reagentless analysis of molecularly complex biological materials or clinical specimens. Rapid advances in the LIBS technology have spawned a growing number of recently published articles in peer-reviewed journals which have consistently demonstrated the capability of LIBS to rapidly detect, biochemically characterize and analyse, and/or accurately identify various biological, biomedical or clinical samples. These analyses are inherently real-time, require no sample preparation, and offer high sensitivity and specificity. This overview of the biomedical applications of LIBS is meant to summarize the research that has been performed to date, as well as to suggest to health care providers several possible specific future applications which, if successfully implemented, would be significantly beneficial to humankind.},
author = {Rehse, S J and Salimnia, H and Miziolek, a W},
doi = {10.3109/03091902.2011.645946},
file = {:E$\backslash$:/Mina Dokument/Mendeley//Rehse, Salimnia, Miziolek - Laser-induced breakdown spectroscopy (LIBS) an overview of recent progress and future potential for biomedic.pdf:pdf},
issn = {1464-522X},
journal = {Journal of medical engineering {\&} technology},
keywords = {diagnostics,laser-induced breakdown spectroscopy,medical,point-of-care,rapid pathogen identification},
month = {feb},
number = {2},
pages = {77--89},
pmid = {22268995},
title = {{Laser-induced breakdown spectroscopy (LIBS): an overview of recent progress and future potential for biomedical applications.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22268995},
volume = {36},
year = {2012}
}
@article{Kumar2004,
abstract = {Cancer diagnosis and classification is extremely complicated and, for the most part, relies on subjective interpretation of biopsy material. Such methods are laborious and in some cases might result in different results depending on the histopathologist doing the examination. Automated, real-time diagnostic procedures would greatly facilitate cancer diagnosis and classification. Laser-induced breakdown spectroscopy (LIBS) is used for the first time to our knowledge to distinguish normal and malignant tumor cells from histological sections. We found that the concentration of trace elements in normal and tumor cells was significantly different. For comparison, the tissue samples were also analyzed by an inductively coupled plasma emission spectroscopy (ICPES) system. The results from the LIBS measurement and ICPES analysis were in good agreement.},
author = {Kumar, Akshaya and Yueh, Fang-Yu and Singh, Jagdish P and Burgess, Shane},
institution = {Mississippi State University, Mississippi State, Mississippi 39762, USA.},
journal = {Applied Optics},
number = {28},
pages = {5399--5403},
pmid = {15495432},
publisher = {OSA},
title = {{Characterization of malignant tissue cells by laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15495432},
volume = {43},
year = {2004}
}
@article{Astin2006,
abstract = {The University of Salford has led the way in the fundamental research that has underpinned the development of thin film copper indium diselenide (CIS) based photovoltaics. These devices have demonstrated exceptional energy conversion efficiencies (>19{\%}) and a high tolerance to radiation damage and are thus leading researchers towards the 20{\%} efficiency barrier. Conventional CIS thin film growth processes require a post-selenisation step to incorporate Se into the as-grown material. This helps to achieve stoichometry, improves the crystallinity, controls the defect structure and also can be used to convert the semiconductor type. This paper will report the use of pulsed dc magnetron sputtering from a CIS powder target. This approach has resulted in asgrown stoichiometric thin films consisting of pinhole free, densely packed grains. An important consideration in the thin film growth of complex materials is that stoichiometry is maintained throughout the film. Conventionally, secondary ion mass spectrometry (SIMS) is used to depth profile thin films but it has been reported that laser induced breakdown spectrometry (LIBS) can also be used. We will report the initial results comparing and contrasting these two techniques and show that LIBS can produce meaningful data.},
author = {Astin, JS and Cowpe, JS and Hill, A and Hisek, J and Lucas, N and Pilkington, RD},
file = {::},
journal = {In Proceedings of Photon 06},
keywords = {other,qc350 467 optics. light},
publisher = {IOP Publishing Ltd.},
title = {{A comparative study of laser induced breakdown spectroscopy and secondary ion mass spectrometry applied to dc magnetron sputtered as-grown copper indium diselenide.}},
url = {http://usir.salford.ac.uk/2572/},
year = {2006}
}
@article{Bublitz2001,
abstract = {Laser-optical measurements and fibre optics are potentially attractive tools for applications in soil science because of their great sensitivity and selectivity and their capabilities for on-line and in situ analysis. We have investigated laser-induced breakdown spectroscopy (LIBS) for the quantitative detection of metal ions on the surface of natural soil samples from two sites (Hohenschulen and Oderbruch, Germany). The LIBS technique allows the spatially resolved investigation of adsorption and desorption effects of ions in sail. A frequency doubled (532nm) and Q-switched Nd:YAG laser with a pulse duration of 8ns is focused on the soil surface and induces a plasma. Typical power densities are 150 mJ mm(-2). The plasma emission is recorded in time and spectrally resolved by a gateable optical multichannel analyser (OMA). A delay time of about 500 ns between laser pulse and OMA gate was used to resolve single atomic and ionic spectral lines from the intense and spectrally broad light that is emitted by the plasma itself. The dependency of the LIBS signal of a single spectral line on the amount of water in the sample is investigated in detail. The results indicate that quenching of water in the plasma plume reduces the line intensities, while the interaction with aquatic colloids increases the intensity. The two processes compete with each other, and a non-linear correlation between measured line intensities and the amount of water in the sample is obtained. This is verified by a simple computer simulation and has to be taken into account for the quantitative interpretation of LIBS signals, e.g. when absolute concentrations are estimated. In the present investigation natural calcium concentrations g kg(-1) were measured with the LIBS technique in the samples for the two test sites. In addition, measurements were made with dry and water-saturated BaCl2 mixed soil samples, and no significant difference in the detection limit for barium was obtained.},
author = {Bublitz, J and D{\"{o}}lle, C and Schade, W and Hartmann, A and Horn, R},
doi = {10.1046/j.1365-2389.2001.00375.x},
issn = {13510754},
journal = {European Journal of Soil Science},
number = {2},
pages = {305--312},
title = {{Laser-induced breakdown spectroscopy for soil diagnostics}},
url = {http://doi.wiley.com/10.1046/j.1365-2389.2001.00375.x},
volume = {52},
year = {2001}
}
@article{Yaroshchyk2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) and partial least squares regression (PLSR) have been applied to perform quantitative measurements of a multiple-species parameter known as loss on ignition (LOI), in a combined set of run-of-mine (ROM) iron ore samples originating from five different iron ore deposits. Global calibration models based on 65 samples and their duplicates from all the deposits with LOI ranging from 0.5 to 10 wt{\%} are shown to be successful for prediction of LOI content in pressed pellets as well as bulk ore samples. A global independent dataset comprising a further 60 samples was used to validate the model resulting in the best validation R(2) of 0.87 and root mean square error of prediction (RMSEP) of 1.1 wt{\%} for bulk samples. A validation R(2) of 0.90 and an RMSEP of 1.0 wt{\%} were demonstrated for pressed pellets. Data preprocessing is shown to improve the quality of the analysis. Spectra normalization options, automatic outlier removal and automatic continuum background correction, which were used to improve the performance of the PLSR method, are discussed in detail.},
author = {Yaroshchyk, Pavel and Death, David L and Spencer, Steven J},
institution = {CSIRO Process Science and Engineering, Lucas Heights Science and Technology Centre, Locked Bag 2005, Kirrawee NSW 2232 Australia. pavel.yaroshchyk@csiro.au},
journal = {Applied Spectroscopy},
number = {12},
pages = {1335--1341},
pmid = {21144150},
title = {{Quantitative measurements of loss on ignition in iron ore using laser-induced breakdown spectroscopy and partial least squares regression analysis.}},
url = {http://www.ingentaconnect.com/content/sas/sas/1999/00000053/00000010/art00014},
volume = {64},
year = {2010}
}
@article{Caneve2005a,
abstract = {The use of laser induced breakdown spectroscopy (LIBS) as a possible diagnostic tool for thin films elemental composition has been investigated. For this kind of application, LIBS can be advantageous with respect to other conventional techniques of analysis routinely used to determine thin films stoichiometry. LIBS was applied to ferromagnetic thin films of FeHfO in which the electric and magnetic properties are strictly correlated to the stoichiometry. The influence of the laser parameters on the ablation process of a thin film on a substrate has been investigated, together with a study of different substrates in order to identify the film-substrate coupling that would make the LIBS technique applicable also to films whose thickness is less than the laser ablation depth. Finally, the possibility of obtaining semi-quantitative data from the analysis of FeHfO thin films using the evaluated Fe/Hf atomic ratio was investigated.},
author = {Caneve, L and Colao, F and Sarto, F and Spizzichino, V and Vadrucci, M},
doi = {10.1016/j.sab.2005.05.011},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {7-8},
pages = {109},
title = {{Laser-induced breakdown spectroscopy as a diagnostic tool for thin films elemental composition}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854705001424},
volume = {60},
year = {2005}
}
@article{Sugita2003,
abstract = {Our previous research showed that lipophilic yeasts, Malassezia species, colonize the skin of patients with atopic dermatitis (AD) at a high frequency. In this study, we found that two basidiomycetous yeasts, Cryptococcus diffluens and C. liquefaciens, colonize the skin significantly more frequently in AD patients than in healthy subjects. Transparent dressings were applied to the skin of 36 AD patients and 30 healthy subjects and then transferred onto Sabouraud dextrose agar. Colonies recovered from the medium were identified by DNA sequence analysis of internal transcribed spacer regions and the D1/D2 26S rRNA gene. C. diffluens and C. liquefaciens were isolated from 42{\%} (15/36) and 33{\%} (12/36) of AD patients and from 20{\%} (6/30) and 20{\%} (6/30) of healthy subjects, respectively. In addition, fungal DNA was extracted directly from the dressings and amplified in a specific nested PCR assay. C. diffluens and C. liquefaciens DNA were detected in dressings from 97{\%} (35/36) and 86{\%} (31/36) of the AD patients and 47{\%} (14/30) and 37{\%} (11/30) of the healthy subjects, respectively. These findings show that Malassezia spp. are not the only yeasts that colonize the skin of AD patients; Cryptococcus spp. also are present in a high proportion of patients. The role of these microorganisms in AD is as yet unknown, but the current findings, in combination with previous results, indicate that C. diffluens, C. liquefaciens, M. globosa, and M. restricta together colonize the skin surface of AD patients at a high frequency.},
author = {Sugita, Takashi and Saito, Masuyoshi and Ito, Tomonobu and Kato, Yukihiko and Tsuboi, Ryoji and Takeuchi, Shohei and Nishikawa, Akemi},
institution = {Department of Immunobiology, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan.},
journal = {Microbiology and immunology},
keywords = {adult,atopic,atopic microbiology,cryptococcus,cryptococcus growth {\&} development,cryptococcus isolation {\&} purification,dermatitis,dna,female,fungal,fungal chemistry,fungal isolation {\&} purification,humans,male,middle aged,molecular sequence data,polymerase chain reaction,ribosomal spacer,ribosomal spacer chemistry,ribosomal spacer isolation {\&} purification,sequence analysis,skin,skin microbiology},
number = {10},
pages = {945--950},
pmid = {17951984},
title = {{Evaluation of the levels of specific IgE against Cryptococcus diffluens and Cryptococcus liquefaciens in patients with atopic dermatitis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14695444},
volume = {47},
year = {2003}
}
@article{Lal2004,
abstract = {The effect of various parameters on the accuracy of the laser-induced breakdown spectroscopy (LIBS) data taken from pellet samples has been investigated. The dependence of the standard deviation of the LIBS data on the amount and nature of the binder used, pressure used to press the powder into a pellet, and the position of the focal spot on the pellet has been investigated. Pellets made from industrially important materials such as silica, alumina, and lime with polyvinyl alcohol, sucrose, and starch as binders have been studied. The results thus obtained are tested by preparation of the calibration curves for Si, Fe, and B in the pellets made from the powder glass batch used as a surrogate for the batch employed for the vitrification of radioactive waste.},
author = {Lal, Bansi and Zheng, Hongbo and Yueh, Fang-Yu and Singh, Jagdish P},
issn = {00036935},
journal = {Applied Optics},
number = {13},
pages = {2792--7},
pmid = {15130021},
title = {{Parametric study of pellets for elemental analysis with laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15130021},
volume = {43},
year = {2004}
}
@article{Sturm2003,
abstract = {Laser-induced breakdown spectroscopy (LIBS) was applied for simultaneous measurement of the elements C, H, N, and O in CO2-air, C3H8-CO2, and C3H8-N2 gas mixtures at atmospheric pressure. A single 7-mm-diameter aperture at the sample chamber was used for 1064-nm Nd:YAG laser irradiation and plasma signal output to an echelle spectrometer. Double-pulse laser bursts of approximately 8-ns pulse width (FWHM) and 250-ns interpulse separation were applied to increase the plasma signal. Calibration curves of the LIBS signal versus the partial pressure or the atomic abundance ratios were taken by dilution series in intervals that are relevant in the combustion of heptane (C7H16) near an equivalence ratio of 1.},
author = {Sturm, Volker and Noll, Reinhard},
institution = {Fraunhofer-Institut f{\"{u}}r Lasertechnik, Steinbachstrasse 15, D-52074 Aachen, Germany. sturm@ilt.fraunhofer.de},
journal = {Applied Optics},
number = {30},
pages = {6221--6225},
pmid = {14594088},
publisher = {OPTICAL SOC AMER},
title = {{Laser-induced breakdown spectroscopy of gas mixtures of air, CO2, N2, and C3H8 for simultaneous C, H, O, and N measurement.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594088},
volume = {42},
year = {2003}
}
@article{Aguilera2009,
abstract = {Optical emission of laser-induced plasma on the surface of fresh vegetables provides sensitive analysis of trace elements for in situ or online detection of these materials. This emergent technique promises applications with expected outcomes in food security or nutrition quality, as well as environment pollution detection. Characterization of the plasma induced on such soft and humid materials represents the first step towards quantitative measurement using this technique. In this paper, we present the experimental setup and protocol that optimize the plasma generation on fresh vegetables, potatoes for instance. The temporal evolution of the plasma properties are investigated using time-resolved laser-induced breakdown spectroscopy (LIBS). In particular, the electron density and the temperatures of the plasma are reported as functions of its decay time. The temperatures are evaluated from the well known Boltzmann and Saha-Boltzmann plot methods. These temperatures are further compared to that of the typical molecular species, CN, for laser-induced plasma from plant materials. This comparison validates the local thermodynamic equilibrium (LTE) in the specific case of fresh vegetables ablated in the typical LIBS conditions. A study of the temporal evolution of the signal to noise ratio also provides practical indications for an optimized detection of trace elements. We demonstrate finally that, under certain conditions, the calibration-free LIBS procedure can be applied to determine the concentrations of trace elements in fresh vegetables.},
author = {Aguilera, J A and Arag{\'{o}}n, C and Cristoforetti, G and Tognoni, E},
doi = {10.1016/j.sab.2009.06.002},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {7},
pages = {685--689},
publisher = {Elsevier B.V.},
title = {{Application of calibration-free laser-induced breakdown spectroscopy to radially resolved spectra from a copper-based alloy laser-induced plasma}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709001414},
volume = {64},
year = {2009}
}
@article{Burgio2000,
abstract = {The combined application of two laser-based analytical techniques-laser-induced breakdown spectroscopy (LIBS) and Raman microscopy-for pigment identification on painted artworks is demonstrated. Detailed spectral data are presented from analyses performed on a 19th century Byzantine icon, which was examined in order to identify the pigments used in the original painted structure, as well as in interventions carried out subsequently for restorative purposes. LIBS measurements yielded elemental analytical data which suggest the presence of certain pigments and, in addition, provide information on the stratigraphy of the paint layers. Identification of most pigments and of the materials used in the preparation layer was performed by Raman microscopy. Index Headings: Laser-induced breakdown spectroscopy; LIBS; Raman microscopy; Artwork analysis; Pigment identification.},
author = {Burgio, Lucia and Clark, Robin J H and Stratoudaki, Theodosia and Doulgeridis, Michael and Anglos, Demetrios},
journal = {Applied Spectroscopy},
number = {4},
pages = {463--469},
publisher = {OSA},
title = {{Optics InfoBase - Pigment Identification in Painted Artworks: A Dual Analytical Approach Employing Laser-Induced Breakdown Spectroscopy and Raman Microscopy}},
url = {http://as.osa.org/abstract.cfm?URI=as-54-4-463},
volume = {54},
year = {2000}
}
@article{Chang1989,
abstract = {To evaluate the diagnostic merit of fiberoptic bronchoscopy in pleural effusions, we performed fiberoptic bronchoscopy in addition to thoracocentesis and closed pleural biopsy in 140 patients who were admitted for diagnostic investigation of the causes of pleural effusions. The patients were divided into subgroups based on clinical features and roentgenographic findings of chest x-ray films. In 39 patients, the pleural effusions were due to various nonneoplastic disorders and in 95 patients it was caused by malignancy. In six patients, the causes of the pleural effusions remained undetermined. A final diagnosis was made by pleural examination in 68 patients, by fiberoptic bronchoscopy in 58 patients, and by either one or both in 100 patients. In 82 patients who had no hemoptysis, a final diagnosis was made by pleural examination in 57 cases and by fiberoptic bronchoscopy in 11 cases only. The diagnostic yield of fiberoptic bronchoscopy (47/58) was superior to that of pleural examination (11/58) in 58 patients presenting with hemoptysis. In 74 patients who had pleural effusions as the sole roentgenographic abnormality, the final entity was established by pleural examination in 45 and by fiberoptic bronchoscopy in 12. The diagnostic merit of fiberoptic bronchoscopy was significantly higher in 59 patients who had concurrent pulmonary abnormalities on their chest roentgenograms. A final diagnosis was made in 43 cases by fiberoptic bronchoscopy in comparison with 21 cases by pleural examination. For patients with unknown pleural effusions, fiberoptic bronchoscopy was more likely to yield a diagnosis than thoracocentesis with closed pleural biopsy in those who had hemoptysis or pulmonary abnormality on chest x-ray films, whereas the reverse applied when these features were absent.},
author = {Chang, S C and Perng, R P},
institution = {Department of Chest Medicine, Veterans General Hospital, Taipei, Taiwan, Republic of China.},
journal = {Archives of Internal Medicine},
number = {4},
pages = {855--857},
pmid = {2705835},
title = {{The role of fiberoptic bronchoscopy in evaluating the causes of pleural effusions.}},
volume = {149},
year = {1989}
}
@article{Drakaki2009,
abstract = {The object of this study was to investigate whether laser-induced skin autofluorescence (LIF) and/or light reflectance spectra could provide a useful contrast between basal cell carcinoma (BCC) tissues and the surrounding healthy skin. Unstained human skin samples, excised from humans undergoing biopsy examination, were irradiated with a nitrogen laser (lambda = 337 nm) for excitation of autofluorescence and a tungsten halogen lamp for the reflectance measurements. The ex vivo spectroscopic results were correlated with the histopathology images to distinguish the areas of BCC from those of the surrounding health skin. A simple spectral analysis technique was also applied for better skin diagnosis. In conclusion, it seems that LIF and reflectance spectra could be used to differentiate neoplastic from normal skin tissue using an appropriate classification model analysis.},
author = {Drakaki, E and Kaselouris, E and Makropoulou, M and Serafetinides, A A and Tsenga, A and Stratigos, A J and Katsambas, A D and Antoniou, C},
institution = {Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou Campus, Athens, Greece. edrakaki@central.ntua.gr},
journal = {Skin Pharmacology and Physiology},
keywords = {basal cell,basal cell diagnosis,basal cell pathology,biopsy,carcinoma,fluorescence,humans,lasers,light,skin,skin neoplasms,skin neoplasms diagnosis,skin neoplasms pathology,skin pathology,spectrometry,spectrum analysis},
number = {3},
pages = {158--165},
pmid = {19365155},
title = {{Laser-induced fluorescence and reflectance spectroscopy for the discrimination of basal cell carcinoma from the surrounding normal skin tissue.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19365155},
volume = {22},
year = {2009}
}
@article{Ferreira2008,
abstract = {Laser Induced Breakdown Spectroscopy (LIBS) is an advanced analytical technique for elemental determination based on direct measurement of optical emission of excited species on a laser induced plasma. In the realm of elemental analysis, LIBS has great potential to accomplish direct analysis independently of physical sample state (solid, liquid or gas). Presently, LIBS has been easily employed for qualitative analysis, nevertheless, in order to perform quantitative analysis, some effort is still required since calibration represents a difficult issue. Artificial neural network (ANN) is a machine learning paradigm inspired on biological nervous systems. Recently, ANNs have been used in many applications and its classification and prediction capabilities are especially useful for spectral analysis. In this paper an ANN was used as calibration strategy for LIBS, aiming Cu determination in soil samples. Spectra of 59 samples from a heterogenic set of reference soil samples and their respective Cu concentration were used for calibration and validation. Simple linear regression (SLR) and wrapper approach were the two strategies employed to select a set of wavelengths for ANN learning. Cross validation was applied, following ANN training, for verification of prediction accuracy. The ANN showed good efficiency for Cu predictions although the features of portable instrumentation employed. The proposed method presented a limit of detection (LOD) of 2.3爉g dm-? of Cu and a mean squared error (MSE) of 0.5 for the predictions.},
author = {Ferreira, Edilene C and Milori, D{\'{e}}bora M B P and Ferreira, Ednaldo J and {Da Silva}, Robson M and Martin-Neto, Ladislau},
doi = {10.1016/j.sab.2008.08.016},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1216--1220},
publisher = {Elsevier B.V.},
title = {{Artificial neural network for Cu quantitative determination in soil using a portable Laser Induced Breakdown Spectroscopy system}},
url = {http://www.sciencedirect.com/science/article/B6THN-4TB1851-3/2/5208aa074297f7b9a69860c11c54b9ec},
volume = {63},
year = {2008}
}
@article{Mosier-Boss2001,
abstract = {Traditional methods for delineating metal contaminated soils rely on the collection of soil samples followed by lab. analyses. Frequently, addnl. sampling efforts are required to complete the characterization of the site. Not only is this approach time consuming and expensive, but the spatial resoln. of the contaminant distribution is very coarse. In this communication, we describe a direct push fiber-optic laser-induced breakdown spectroscopy (FO-LIBS) sensor probe for the real-time, in situ measurement of metals in soil. The sensor system is capable of making very high resoln. vertical measurements (cm spatial scales). Because data is available in real-time, sampling plans can be modified as the data is being collected, to more effectively delineate the extent of the contamination. Results will be presented from field tests of the FO-LIBS sensor system. Effects of variable soil matrix and soil moisture conditions on sensor performance will be discussed. on SciFinder(R)},
author = {Mosier-Boss, Pamela A and Lieberman, Stephen H},
issn = {00657727},
journal = {Abstracts Of Papers Of The American Chemical Society},
pages = {U432--U432},
publisher = {American Chemical Society},
title = {{Direct push fiber-optic laser induced breakdown spectroscopy sensor probe for real-time, in situ measurement of metals in soil.}},
volume = {222},
year = {2001}
}
@article{Babankova2006,
abstract = {Large-scale plasma was created in molecular gases (CO, CO2, N2, H2O) and their mixtures by high-power laser-induced dielectric breakdown (LIDB). Compositions of the mixtures used are those suggested for the early earth's atmosphere of neutral and/or mildly reducing character. Time-integrated optical spectra emitted from the laser spark have been measured and analyzed. The spectra of the plasma generated in the CO-containing mixtures are dominated by emission of both C2 and CN radicals. A vibrational temperature of approximately 10(4) K was determined according to an intensity distribution in a vibronic structure of the CN (B2Sigma(+)u-X2Sigma(+)g) violet band. For comparison, the NH3-CH4-H2-H2O mixture has been irradiated as a model of the strongly reducing version of the early earth's atmosphere. In this mixture, excited CN seems to be significantly less abundant than C2. The LIDB experiments were in the molecular gases carried out not only in the static cell but also using a large, double stream pulse jet (gas puff target) placed in the vacuum interaction chamber. The obtained soft X-ray emission spectra indicate the presence of highly charged atomic ions in the hot core of high-power laser sparks.},
author = {Babankova, Dagmar and Civis, Svatopluk and Juha, Libor and Bittner, Michal and Cihelka, Jaroslav and Pfeifer, Miroslav and Skala, Jir{\'{\i}} and Bartnik, Andrzej and Fiedorowicz, Henryk and Mikolajczyk, Janusz and Ry{\'{c}}, Leszek and Sedivcova, Tereza},
institution = {J. Heyrovsk{\'{y}} Institute of Physical Chemistry, Czech Academy of Sciences, Dolejskova 3, 182 23 Prague 8, Czech Republic.},
journal = {The Journal of Physical Chemistry A},
number = {44},
pages = {12113--12120},
pmid = {17078605},
title = {{Optical and X-ray emission spectroscopy of high-power laser-induced dielectric breakdown in molecular gases and their mixtures.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17078605},
volume = {110},
year = {2006}
}
@article{Nelson1999,
abstract = {A single-frame approach to chemical imaging with high spectroscopic resolution is described that makes use of a second-generation dimension-reduction fiber-optic array. Laser-induced plume images are focused onto a 17 X 32 rectangular array of square close-packed 25 mu m cross-sectional f/2 optical fibers that are drawn into a 544 X 1 distal array with serpentine ordering. The 544 X 1 side of the array is imaged with an f/2 spectrograph equipped with a holographic grating and a gated intensified charge-coupled device (ICCD) camera for spectral analysis. Software is used to extract the spatial/spectral information contained in the ICCD images and deconvolute them into wavelength-specific univariate reconstructed images or position-specific spectra that span an 86 nm wavelength space. Temporal resolution is provided by imaging sequential laser plumes with varying time delays after each laser pulse on the gated intensifier.},
author = {Nelson, Matthew P and Myrick, M L},
doi = {10.1366/0003702991947450},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {7},
pages = {751--759},
publisher = {Society for Applied Spectroscopy},
title = {{Single-frame chemical imaging: Dimension reduction fiber-optic array improvements and application to laser-induced breakdown spectroscopy}},
url = {http://www.opticsinfobase.org/abstract.cfm?id=122862},
volume = {53},
year = {1999}
}
@article{Choi2009,
abstract = {We have observed dynamic effects of a pre-ablation spark on the signal intensity in the orthogonal dual-pulse laser-induced breakdown spectroscopy. We applied pre-ablation and ablation laser pulses with significantly reduced energy for an aluminum metal in open air. Under this experimental condition, the well-known signal enhancement through the increase in ablated mass was negligible. The Al I and II emissions were investigated by both top-view and spatially-resolved side-view collection modes. In this low laser power regime, dynamic effects of a pre-ablation spark on the signal intensity were clearly revealed. The principal factor of signal enhancement is the increase in temperature. Without the mass removal enhancement, effective rarefaction leads to decrease in the Al I emission intensity and simultaneous increase in the Al II emission intensity. This is attributed to the role of Saha equilibrium. Selective prolongation of emission lifetime only for the enclosed part of the analyte plasma in the rarefied region and other fluid-dynamic effects of a pre-ablation spark have been visualized by wavelength-selected time-space correlation maps of plasma emissions.},
author = {Choi, Sung-Chul and Oh, Myoung-Kyu and Lee, Yonghoon and Nam, Sungmo and Ko, Do-Kyeong and Lee, Jongmin},
doi = {10.1016/j.sab.2009.05.008},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {5},
pages = {427--435},
title = {{Dynamic effects of a pre-ablation spark in the orthogonal dual-pulse laser induced breakdown spectroscopy}},
url = {http://www.sciencedirect.com/science/article/B6THN-4W9XG7P-1/2/91eae3aac29805e7a4f84e945b0bcd67},
volume = {64},
year = {2009}
}
@article{Thakur2007,
author = {Thakur, S N and Singh, J P},
journal = {Spectroscopy},
title = {{Fundamentals of Laser Induced Breakdown Spectroscopy}},
year = {2007}
}
@article{Feng2011,
abstract = {Thirty-three bituminous coal samples were utilized to test the application of laser-induced breakdown spectroscopy technique for coal elemental concentration measurement in the air. The heterogeneity of the samples and the pyrolysis or combustion of coal during the laser-sample interaction processes were analyzed to be the main reason for large fluctuation of detected spectra and low calibration quality. Compared with the generally applied normalization with the whole spectral area, normalization with segmental spectral area was found to largely improve the measurement precision and accuracy. The concentrations of major element C in coal were determined by a novel partial least squares (PLS) model based on dominant factor. Dominant C concentration information was taken from the carbon characteristic line intensity since it contains the most-related information, even if not accurately. This dominant factor model was further improved by inducting non-linear relation by partially modeling the inter-element interference effect. The residuals were further corrected by PLS with the full spectrum information. With the physical-principle-based dominant factor to calculate the main quantitative information and to partially explicitly include the non-linear relation, the proposed PLS model avoids the overuse of unrelated noise to some extent and becomes more robust over a wider C concentration range. Results show that RMSEP in the proposed PLS model decreased to 4.47{\%} from 5.52{\%} for the conventional PLS with full spectrum input, while R(2) remained as high as 0.999, and RMSEC{\&}P was reduced from 3.60{\%} to 2.92{\%}, showing the overall improvement of the proposed PLS model.},
author = {Feng, Jie and Wang, Zhe and West, Logan and Li, Zheng and Ni, Weidou},
institution = {State Key Laboratory of Power Systems, Department of Thermal Engineering, Tsinghua-BP Clean Energy Center, Tsinghua University, Beijing, China.},
journal = {Analytical and Bioanalytical Chemistry},
keywords = {bituminous coal,dominant factor,laser induced breakdown spectroscopy,partial least squares},
number = {10},
pages = {3261--3271},
title = {{A PLS model based on dominant factor for coal analysis using laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21416399},
volume = {400},
year = {2011}
}
@article{Failloux2003,
abstract = {An apparatus has been investigated based on laser-induced breakdown spectroscopy (LIBS) for the rapid determination of the spatial distribution of elements on surfaces. Cylindrical optics are used to create a linear spark approximately 1 cm in length. Light emitted by atoms excited along the spark is collected and provides a spatial profile of elemental composition in the sample when analyzed with a spectrometer and gated charge-coupled device (ICCD) detector. Moving the spark across the sample surface as spectral data is recorded at regularly spaced intervals allows for the development of a three-dimensional elemental distribution map (emission intensity versus spatial distribution across an area). An analysis of the spatial resolution of this methodology is presented along with representative data from several sample types. Application of full-image analysis allowing for simultaneous investigations into the spatial distributions of multiple elements is also discussed and results are presented.},
author = {Failloux, Nelly and Bonnet, Isabelle and Baron, Marie-H{\'{e}}l{\`{e}}ne and Perrier, Eric},
institution = {Nuclear Materials Management Division, Group NMT-15, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.},
journal = {Applied Spectroscopy},
number = {4},
pages = {367--375},
pmid = {17140490},
title = {{Capabilities of surface composition analysis using a long laser-induced breakdown spectroscopy spark.}},
url = {http://www.ingentaconnect.com/content/sas/sas/2004/00000058/00000004/art00002},
volume = {58},
year = {2003}
}
@article{Das2011,
author = {Das, Ruchita S. and Agrawal, Y.K.},
doi = {10.1016/j.vibspec.2011.08.003},
file = {::},
issn = {09242031},
journal = {Vibrational Spectroscopy},
keywords = {vibrational spectroscopy},
month = {nov},
number = {2},
pages = {163--176},
publisher = {Elsevier B.V.},
title = {{Raman spectroscopy: Recent advancements, techniques and applications}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0924203111001111},
volume = {57},
year = {2011}
}
@article{Gottfried2009,
abstract = {We have demonstrated the detection and discrimination of explosive residues on a variety of surfaces using laser-induced breakdown spectroscopy and partial least squares discriminant analysis. The correlation between the hardness of a substrate and the ability to discriminate residues on that substrate is discussed. We have also shown that while using the full spectra in the chemometric model improves the classification of sample types in the model, the use of intensities and ratios specific to explosive residues improves the classification of sample types that are not part of the model. In the first case, differences in the laser-induced plasma (and resulting spectral features) attributable to the laser-material interaction contribute to the sample discrimination, while using intensities and ratios specific to explosive residues focuses on the chemical composition of the sample for discrimination. Combining the results of the two models for a given sample set decreases the overall false positive rate for all test samples.},
author = {Gottfried, Jennifer L and {De Lucia Jr.}, Frank C and Miziolek, Andrzej W},
doi = {10.1039/b818481j},
file = {::},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {3},
pages = {288},
publisher = {ROYAL SOC CHEMISTRY},
title = {{Discrimination of explosive residues on organic and inorganic substrates using laser-induced breakdown spectroscopy}},
url = {http://xlink.rsc.org/?DOI=b818481j},
volume = {24},
year = {2009}
}
@article{Shen2009,
abstract = {Monitoring of light-element concentration in steel is very important for quality assurance in the steel industry. In this work, detection in open air of trace phosphorus (P) in steel using laser-induced breakdown spectroscopy (LIBS) combined with laser-induced fluorescence (LIF) has been investigated. An optical parametric oscillator wavelength-tunable laser was used to resonantly excite the P atoms within plasma plumes generated by a Q-switched Nd:YAG laser. A set of steel samples with P concentrations from 3.9 to 720 parts in 10(6) (ppm) were analyzed using LIBS-LIF at wavelengths of 253.40 and 253.56 nm for resonant excitation of P atoms and fluorescence lines at wavelengths of 213.55 and 213.62 nm. The calibration curves were measured to determine the limit of detection for P in steel, which is estimated to be around 0.7 ppm. The results demonstrate the potential of LIBS-LIF to meet the requirements for on-line analyses in open air in the steel industry.},
author = {Shen, X K and Wang, H and Xie, Z Q and Gao, Y and Ling, H and Lu, Y F},
institution = {Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0511, USA. ylu2@unl.edu},
journal = {Applied Optics},
number = {13},
pages = {2551--2558},
pmid = {19412215},
title = {{Detection of trace phosphorus in steel using laser-induced breakdown spectroscopy combined with laser-induced fluorescence.}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-48-13-2551},
volume = {48},
year = {2009}
}
@article{Hohreiter2005,
abstract = {The effects of analyte phase on the calibration response for laser-induced breakdown spectroscopy is investigated for a range of carbon species. Significant differences in the atomic emission signal from carbon were observed when comparing calibration streams of gas-phase and submicrometer-sized solid-phase carbon species. The resulting calibration curve slopes varied by a factor of 8 over a comparable range of atomic carbon concentrations for five different analyte sources, while the plasma electron density and temperature remained essentially constant. The current findings challenge a widely held assumption that complete dissociation of constituent species within a highly energetic laser-induced plasma results in independence of the analyte atomic emission signal on the analyte source. A physical model of the plasma-analyte interaction is proposed that provides a framework to account for the observed dependence on the physical state of the analyte.},
author = {Hohreiter, V and Hahn, D W},
file = {::},
issn = {0003-2700},
journal = {Analytical chemistry},
month = {feb},
number = {4},
pages = {1118--24},
pmid = {15858994},
title = {{Calibration effects for laser-induced breakdown spectroscopy of gaseous sample streams: analyte response of gas-phase species versus solid-phase species.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15858994},
volume = {77},
year = {2005}
}
@article{Zhang2001,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been evaluated as a multimetal continuous emissions monitor (CEM) at the U.S. Environmental Protection Agency (EPA) rotary kiln incinerator simulator (RKIS) facility in Raleigh, NC. Two detection systems with a bifurcated optical fiber bundle were used for simultaneously monitoring the concentrations of Be, Cd, Cr, and Hg in the test. Two calibration techniques were evaluated in the laboratory for the field measurements. On-line calibration of relative metal concentration was also performed in the simulated incinerator gas stream. Toxic metal concentrations measured with LIBS have been compared with the EPA reference method (RM) results.},
author = {Zhang, H and Yueh, F Y and Singh, J P},
institution = {Diagnostic Instrumentation and Analysis Laboratory, Mississippi State University, Starkville, Mississippi, USA.},
journal = {Applied Optics},
number = {5},
pages = {1459--1466},
pmid = {11355455},
publisher = {OPTICAL SOC AMER},
title = {{Laser-induced breakdown spectrometry as a multimetal continuous-emission monitor.}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-38-9-1459},
volume = {51},
year = {2001}
}
@article{Carranza2002,
abstract = {Three distinct characteristic plasma volumes were experimentally measured and are discussed in the context of the analysis of gaseous and aerosol systems using laser-induced breakdown spectroscopy. The resulting statistical sample volume, emission-based plasma volume, and the physical plasma volume, range between 1.2 times 10-3 and 2.4 times 10-3 cm3, and the variations are interpreted in terms of the intrinsic behavior of laser-induced plasma-particle interactions. Due to plasma non-homogeneity, the particle vaporization necessary for subsequent detection is limited to a plasma region somewhat smaller than the region defined by the physical plasma volume based on optical absorption. In contrast, the emission-based plasma volume, the largest of the three recorded volumes, reflects analyte emission following particle vaporization and diffusion, and is considered in terms of an equivalent emitting plasma volume.},
author = {Carranza, J E and Hahn, D W},
doi = {10.1039/b206140f},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {11},
pages = {1534--1539},
title = {{Plasma volume considerations for analysis of gaseous and aerosol samples using laser-induced breakdown spectroscopy}},
url = {http://xlink.rsc.org/?DOI=b206140f},
volume = {17},
year = {2002}
}
@inproceedings{Michel2005,
abstract = {New chemical sensors are needed for both present day expeditionary oceanography and an emerging new phase involving long term in situ ocean observations. Over the past four decades, a new spectrochemical technique, Laser Induced Breakdown Spectroscopy (LIBS), has been under development for the identification of the elemental constituents of materials. This technique uses a laser to create a spark or plasma on a sample. The plasma emission is then analyzed with a spectrometer to determine its elemental composition. Recently, LIBS has been identified as a viable tool for in situ field measurements because it is able to analyze all forms of matter (solids, liquids, and gases), can operate in a stand-off mode, and is non-invasive and non-destructive. A marine LIBS sensor would be a useful tool for studying many environments in the ocean, especially midocean ridge hydrothermal vents where in situ measurements are difficult due to the presence of high-temperature, corrosive fluids. A feasibility assessment of oceanic LIBS in the laboratory has been initiated. A high pressure chamber was designed and built for investigating the effect of realistic ocean environments on the LIBS signal. Preliminary work shows that LIBS can successfully detect Li, Na, K, Ca, Mn, and Zn in bulk aqueous solutions at pressures up to 272 atm, making LIBS a viable technique for deep ocean chemical sensing.},
author = {Michel, A.P.M. and Lawrence-Snyder, M.J. and Angel, S.M. and Chave, A.D.},
booktitle = {OCEANS, 2005. Proceedings of MTS/IEEE},
file = {::},
pages = {741--747},
publisher = {IEEE},
title = {{Oceanic applications of laser induced breakdown spectroscopy: laboratory validation}},
url = {http://ieeexplore.ieee.org/xpls/abs{\_}all.jsp?arnumber=1639841},
year = {2005}
}
@article{Groh2010,
abstract = {Recently, nanoflow nebulizers with low-volume drain-free spray chambers became available for inductively coupled plasma-mass spectrometry application for analysis of very small sampling volumes. The present technical note reports on a different approach for 100{\%} efficient subnanoliter sample introduction, the application of monodisperse piezoelectric microdroplet dispensers which generate 40-50 microm droplets with high reproducibility if nozzles of 30 microm diameter are applied. The droplets having volumes below 0.1 nL can be introduced loss-free and without plasma loading, with frequencies up to approximately 100 Hz into analytical plasmas. In this technical note, the analytical figures of merit of laser-induced breakdown spectroscopy and inductively coupled plasma-optical emission spectrometry with single droplet introduction are reported using Ca and Au standard solutions as examples. Future engineering is required to reduce the total sample volumes from the relatively large sample reservoir of the current study, thereby reducing potential issues of washout while enabling analysis of ultralow total sample volumes.},
author = {Groh, S and Diwakar, P K and Garcia, C C and Murtazin, A and Hahn, D W and Niemax, K},
institution = {ISAS-Institute for Analytical Sciences at Technische Universit{\"{a}}t Dortmund, Germany.},
journal = {Analytical Chemistry},
number = {6},
pages = {2568--2573},
pmid = {20151662},
publisher = {American Chemical Society},
title = {100{\%} efficient sub-nanoliter sample introduction in laser-induced breakdown spectroscopy and inductively coupled plasma spectrometry: implications for ultralow sample volumes.},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20151662},
volume = {82},
year = {2010}
}
@article{Tucker2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is demonstrated as a quantitative technique for geochemical analysis. This study demonstrates the applicability of LIBS to bulk elemental analysis of igneous rock powders. LIBS spectra of 100 igneous rocks with highly varying compositions were acquired at 9 m standoff distance under Mars atmospheric conditions. LIBS spectra were modeled using partial least squares regressions to predict major element compositions. A series of comparative tests determined the most effective methodologies for pre-processing of spectral and compositional data, and choice of calibration set. In the best cases, calculated 1-sigma errors are 1.6 wt.{\%} SiO2, 1.5 wt.{\%} Al2O3, 0.4 wt.{\%} TiO2, 1.2 wt.{\%} Fe2O3T, 1.6 wt.{\%} MgO, 0.02 wt.{\%} MnO, 1.1 wt.{\%} CaO, 0.5 wt.{\%} Na2O, 0.2 wt.{\%} P2O5, and 0.4 wt.{\%} K2O, with totals near 100{\%}. The largest improvement came as a result of scaling the elemental distributions to equalize the ranges of variability. Optimal predictions for this data set were produced with calibration set compositions input as weight {\%} oxides and not atomic fractions. Predictions were also improved when calibration sets represented the smallest range of compositional variability possible, and completely encompassed the compositional range encountered. Multiple calibration sets relevant to different rock types are preferred over a single all-encompassing calibration set. Baseline removal and transforming spectral data by their first derivative do not improve predictions and can even have negative effects. These results are directly applicable to spectra that will be acquired by the ChemCam experiment on Mars Science Laboratory, but also apply more broadly to terrestrial LIBS applications.},
author = {Tucker, J M and Dyar, M D and Schaefer, M W and Clegg, S M and Wiens, R C},
doi = {10.1016/j.chemgeo.2010.07.016},
issn = {00092541},
journal = {Chemical Geology},
number = {1-2},
pages = {137--148},
publisher = {Elsevier B.V.},
title = {{Optimization of laser-induced breakdown spectroscopy for rapid geochemical analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0009254110002664},
volume = {277},
year = {2010}
}
@article{Menut2003,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been applied mainly to bulk analysis of solids, liquids, and gases and less frequently for elemental microanalysis of solid surfaces. A micro-LIBS device devoted to analysis of the distribution of elements on surfaces is described. This device offers rapid access with a 3-microm spatial resolution to the microchemical structures of both conductive and nonconductive samples. Quantitative microchemical results of applications to ceramics are reported. By the use of a time-resolved acquisition spectrum, cerium in a uranium matrix was characterized with a cerium detection limit of 1.14{\%}. Calibration curves obtained with manipulations during 1 year facilitated evaluations of reproducibility and repeatability. A 2{\%} single-shot repeatability with a calibration reproducibility of approximately 7{\%} is reported.},
author = {Menut, Denis and Fichet, Pascal and Lacour, Jean-Luc and Rivoallan, Annie and Mauchien, Patrick},
institution = {Commissariat {\`{a}} l'Energie Atomique de Saclay, Nuclear Energy Division, Laboratoire d'Analyse par Laser et d'Etude de Surface, B{\^{a}}timent 391, 91 191 Gif sur Yvette, France. menut@carnac.cea.fr},
journal = {Applied Optics},
number = {30},
pages = {6063--6071},
pmid = {14594067},
title = {{Micro-laser-induced breakdown spectroscopy technique: a powerful method for performing quantitative surface mapping on conductive and nonconductive samples.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594067},
volume = {42},
year = {2003}
}
@article{Balmer1990a,
abstract = {Atomic Absorption Spectrometry 3313 Flame Atomic Absorption Spectrometry 3313 Graphite Furnace Atomic Absorption Spectrometry 3314 Hydride Generation Atomic Absorption Spectrometry 3315 Atomic Fluorescence Spectrometry 3315 Atomic Emission Spectrometry 3316 Arcs and Sparks 3316 Microwave Plasmas 3316 Inductively Coupled Plasmas 3316 Laser-Induced Plasmas 3317 Microplasmas 3318 Inductively Coupled Plasma Mass Spectrometry 3318 Fundamental Studies 3318 Instrumental Developments and Applications 3322 Glow Discharge Atomic Emission and Mass Spectrometry 3328 Fundamental Studies 3328 Methodological Developments 3330 Applications of GDMS and GD-OES 3331 Literature Cited 3333 Methodological developments in atomic spectrometry are related to new techniques in optical spectrometry as well as in elemental mass spectrometry especially, as the sources used in atomic spectrometry are prominent sources of electromagnetic radiation, absorption reservoirs for atomic absorption, and ion sources for elemental mass spectrometry. Developments in the field are related to the sources themselves and their improvement and optimization as well as with the different types of spectrometers and detectors and the different ways for optimal sampling of the analytes. Improvements in the different fields have regularly been published in the journals Analytical Chemistry, Analytical and Bioanalytical Chemistry, Analytical Sciences, Analyst, Analytica Chimica Acta, Applied Spectroscopy, Journal of Analytical Atomic Spectrometry, Mikrochimica Acta, Spectrochimica Acta, Part B, and Talanta as well as to a lesser extent in a number of other journals. These progress reports published have been considered for noting the trends of development in the fields mentioned, at the hand of a selection of the papers published in the journals named in the period January 2002 to December 2003 for the case of atomic absorption and atomic emission work, whereas for inductively coupled plasma mass spectrometry and for glow discharge atomic emission and mass spectrometry, the selection of the papers considered the journals as indicated in the respective chapters. Results in the field of atomic spectrometry in the last biannual period also were reported on the following important conferences: Winter Conference on Plasma Spectrochemistry, Scottsdale, AZ (2002), the International Conference on Atomic Spectroscopy (ICAS), Tokyo (2002), the Colloquium Spectroscopicum Internationale, Granada (2003), the European Winter Conference on Plasma Spectrochemistry, Garmisch Partenkirchen (2003), and the annual Meeting of the Federation of Analytical Chemistry and Spectroscopy Societies, in Nashville, TN (2002) and Fort Lauderdale, FL (2003) as well as in many other meetings. Progress made in the field of atomic spectrometry is discussed for the following fields: optical atomic spectrometry (atomic absorption and atomic emission spectrometry with sparks, arcs, and plasma sources at atmospheric pressure including laser plasmas); plasma mass spectrometry and optical atomic and mass spectrometry with glow discharge sources.},
author = {Balmer, The},
doi = {10.1016/0584-8547(90)80097-3},
issn = {00032700},
journal = {Atomic Spectroscopy},
number = {12},
pages = {i--ii},
pmid = {15193111},
publisher = {Marcel Dekker, Inc.},
title = {{Atomic spectroscopy}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15193111},
volume = {21},
year = {1990}
}
@article{Cravetchi2006,
abstract = {The analytical performance of femtosecond laser-induced breakdown spectroscopy (LIBS) for elemental microanalysis of aluminium alloys and for mapping precipitate distribution on the sample surface has been studied in detail. A Ti-sapphire laser system producing pulses of 130 fs at 800 nm was used to generate the laser-induced plasma. Multi-element microanalysis of commercially available aluminium alloys was performed in air at atmospheric pressure. Crater characteristics such as diameter and crater morphology were characterized by optical and scanning-electron microscopy. Scaling of plasma emission and limit of detection as a function of laser pulse energy was also investigated. Current experimental results are presented and are compared with previous nanosecond microLIBS measurements.},
author = {Cravetchi, Igor V and Taschuk, Mike T and Tsui, Ying Y and Fedosejevs, Robert},
file = {::},
institution = {Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada, T6G 2V4. igorc@ece.ualberta.ca},
journal = {Analytical and Bioanalytical Chemistry},
keywords = {aluminium alloy,laser induced breakdown spectroscopy,libs,precipitates,solid sampling,spectrochemical microanalysis},
number = {2},
pages = {287--294},
pmid = {16437203},
publisher = {SPRINGER HEIDELBERG},
title = {{Evaluation of femtosecond LIBS for spectrochemical microanalysis of aluminium alloys.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16437203},
volume = {385},
year = {2006}
}
@article{Yamamoto1996,
abstract = {A portable instrument, based on laser-induced breakdown spectroscopy (LIES), has been developed for the detection of metal contaminants on surfaces. The instrument has a weight of 14.6 kg, fits completely into a small suitcase (46 x 33 x 24 cm), and operates from 115 V ac. The instrument consists of a sampling probe connected to the main analysis unit by electrical and optical cabling. The hand-held probe contains a small laser to generate laser sparks on a surface and a fiber-optic cable to collect the spark light. The collected light is spectrally resolved and detected with the use of a compact spectrograph/CCD detector system. The instrument has been evaluated for the analysis of metals in the environment: Ba, Be, Pb, and Sr in soils; Pb in paint; and Be and Pb particles collected on filters. Detection limits in ppm for metals in soils were 265 (Ba), 9.3 (Be), 298 (Pb), and 42 (Sr). The detection limit for Pb in paint was 0.8{\%} (8000 ppm), corresponding to 0.052 mg/cm(2). The higher limit obtained for Pb in paint is attributed to the use of the 220.35-nm Pb(II) line instead of the stronger 405.78-nm Pb(I) line used for soils. Spectral interferences prevented use of the 405.78-nm line to determine Pb in paint. The surface detection limit for Be particles on filters was dependent on particle size and ranged from 21 to 63 ng/cm(2). The detection limit for Pb particles on filters was 5.6 mu g/cm(2).},
author = {Yamamoto, Karen Y and Cremers, David A and Ferris, Monty J and Foster, Leeann E},
doi = {10.1366/0003702963906519},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {2},
pages = {222--233},
publisher = {Society for Applied Spectroscopy},
title = {{Detection of Metals in the Environment Using a Portable Laser-Induced Breakdown Spectroscopy Instrument}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=50{\&}issue=2{\&}spage=222},
volume = {50},
year = {1996}
}
@article{Lazic2003,
abstract = {In the present work, we report the analyses of glaze and decorations present on the surface of Renaissance Umbrian pottery, performed by means of different spectroscopic and optical techniques. Two types of ancient lustre have been considered: red and gold, coming from Deruta and Gubbio. The time resolved laser induced fluorescence (LIF) signatures of the red and gold lustre were identified by applying a laser excitation at 355 nm. Laser induced breakdown spectroscopy (LIBS) technique was applied on all the ceramic layers, i.e. bisque, glaze, and both lustre and blue coloured decorations, to determine semi-quantitatively their elemental composition. The results of colorimetric measurements are also compared to the measured composition of decorative layers.},
author = {Lazic, Violeta and Colao, Francesco and Fantoni, Roberta and Palucci, Antonio and Spizzichino, Valeria and Borgia, Ilaria and Brunetti, Brunetto G and Sgamellotti, Antonio},
doi = {10.1016/S1296-2074(02)01212-8},
issn = {12962074},
journal = {Journal of Cultural Heritage},
keywords = {ancient pottery,libs,lif,lustre,pigments},
number = {Supplement 1},
pages = {303--308},
publisher = {Elsevier},
title = {{Characterisation of lustre and pigment composition in ancient pottery by laser induced fluorescence and breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S1296207402012128},
volume = {4},
year = {2003}
}
@article{Asimellis2006,
abstract = {We report development and application of an in-situ applicable method to determine phosphate ore rock quality based on Laser-Induced Breakdown Spectroscopy (LIBS). This is an economically viable method for real-time evaluation of ore phosphate rocks in order to separate high-silica pebbles prior to deep beneficiation. This is achieved by monitoring relative emission line intensities from key probe elements via single laser ablation shots: the ratio of the phosphorous to silica line intensities (P/Si ratio) provides a simple and reliable indicator of ore rock quality. This is a unique LIBS application where no other current analytical spectroscopic method (ICP or XRF) can be applied. Method development is discussed, and results with actual ore samples are presented.},
author = {Asimellis, G and Giannoudakos, A and Kompitsas, M},
doi = {10.1016/j.sab.2006.10.011},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {laser induced breakdown spectroscopy,phosphate mine beneficiation,phosphorus detection},
number = {12},
pages = {1253--1259},
title = {{Phosphate ore beneficiation via determination of phosphorus-to-silica ratios by Laser Induced Breakdown Spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854706002928},
volume = {61},
year = {2006}
}
@article{Carranza2002a,
abstract = {A statistical analysis of single-shot spectral data is reported for laser-induced breakdown spectroscopy (LIBS). Fluctuations in both atomic emission and plasma continuum emission are investigated in concert for a homogenous gaseous flow, and fluctuations in plasma temperature are reported based on iron atomic emission in an aerosol-seeded flow.Thr eshold irradiance for plasma initiation and plasma absorption were investigated for pure gaseous and aerosol streams, with detailed statistical measurements performed as a function of pulse energy in the breakdown regime. The ratio of the analyte atomic emission intensity to the continuum emission intensity (peakybase) provided a robust signal for single-shot LIBS analysis.Mor eover, at optimal temporal delay, the precision of the LIBS signal was maximized for pulse energies within the saturation regime with respect to plasma absorption of incident energy. Finally, single-shot temperature measurements were analyzed, leading to the conclusion that spatial variations in the plasma volume formation and subsequent plasma emission collection, play important roles in the overall shot-to-shot precision of the LIBS technique for gaseous and aerosol analysis.  2002 Elsevier Science B.V. All rights reserved},
author = {Carranza, JE},
journal = {Acta Part B: Atomic Spectroscopy},
keywords = {aerosol,laser-induced breakdown spectroscopy,libs,single-shot},
pages = {779--790},
title = {{Sampling statistics and considerations for single-shot analysis using laser-induced breakdown spectroscopy}},
url = {http://www.sciencedirect.com/science/article/pii/S0584854702000071},
volume = {57},
year = {2002}
}
@article{Myakalwar2011,
abstract = {We report the effectiveness of laser-induced breakdown spectroscopy (LIBS) in probing the content of pharmaceutical tablets and also investigate its feasibility for routine classification. This method is particularly beneficial in applications where its exquisite chemical specificity and suitability for remote and on site characterization significantly improves the speed and accuracy of quality control and assurance process. Our experiments reveal that in addition to the presence of carbon, hydrogen, nitrogen and oxygen, which can be primarily attributed to the active pharmaceutical ingredients, specific inorganic atoms were also present in all the tablets. Initial attempts at classification by a ratiometric approach using oxygen (777nm) to nitrogen (742.36nm, 744.23nm and 746.83nm) compositional values yielded an optimal value at 746.83nm with the least relative standard deviation but nevertheless failed to provide an acceptable classification. To overcome this bottleneck in the detection process, two chemometric algorithms, i.e. principal component analysis (PCA) and soft independent modeling of class analogy (SIMCA), were implemented to exploit the multivariate nature of the LIBS data demonstrating that LIBS has the potential to differentiate and discriminate among pharmaceutical tablets. We report excellent prospective classification accuracy using supervised classification via the SIMCA algorithm, demonstrating its potential for future applications in process analytical technology, especially for fast on-line process control monitoring applications in the pharmaceutical industry.},
author = {Myakalwar, Ashwin Kumar and Sreedhar, S and Barman, Ishan and Dingari, Narahara Chari and {Venugopal Rao}, S and {Prem Kiran}, P and Tewari, Surya P and {Manoj Kumar}, G},
doi = {10.1016/j.talanta.2011.09.040},
issn = {18733573},
journal = {Talanta},
number = {3},
pages = {53--9},
pmid = {22099648},
title = {{Laser-induced breakdown spectroscopy-based investigation and classification of pharmaceutical tablets using multivariate chemometric analysis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22099648},
volume = {87},
year = {2011}
}
@article{Dixon2005,
abstract = {The detection and identification of individual bioaerosols using laser-induced breakdown spectroscopy (LIBS) is investigated using aerosolized Bacillus spores. Spores of Bacillus atrophaeous, Bacillus pumilus, and Bacillus stearothemophilus were introduced into an aerosol flow stream in a prescribed manner such that single-particle LIBS detection was realized. Bacillus spores were successfully detected based on the presence of the 393.4- and 396.9-nm calcium atomic emission lines. Statistical analyses based on the aerosol number density, the LIBS-based spore sampling frequency, and the distribution of the resulting calcium mass loadings support the conclusion of individual spore detection within single-shot laser-induced plasmas. The average mass loadings were in the range of 2-3 fg of calcium/Bacillus spore, which corresponds to a calcium mass percentage of approximately 0.5{\%}. While individual spores were detected based on calcium emission, the resulting Bacillus spectra were free from CN emission bands, which has implications for the detection of elemental carbon, and LIBS-based detection of single spores based on the presence of magnesium or sodium atomic emission was unsuccessful. Based on the current instrumental setup and analyses, real-time LIBS-based detection and identification of single Bacillus spores in ambient (i.e., real life) conditions appears unfeasible.},
author = {Dixon, P B and Hahn, D W},
doi = {10.1021/ac048838i},
file = {::},
issn = {0003-2700},
journal = {Analytical chemistry},
keywords = {Aerosols,Aerosols: analysis,Air Microbiology,Bacillus,Bacillus: ultrastructure,Calcium,Calcium: analysis,Environmental Monitoring,Environmental Monitoring: methods,Feasibility Studies,Lasers,Particle Size,Spectrum Analysis,Spectrum Analysis: methods,Spores, Bacterial,Spores, Bacterial: chemistry,Spores, Bacterial: isolation {\&} purification,Trace Elements,Trace Elements: analysis},
month = {jan},
number = {2},
pages = {631--8},
pmid = {15649064},
title = {{Feasibility of detection and identification of individual bioaerosols using laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15649064},
volume = {77},
year = {2005}
}
@article{Corsi2003,
abstract = {The space and time evolution of a laser-induced plasma from a steel target has been studied using optical time-of-flight and shadowgraphic techniques. The results, obtained for two distinct laser energy regimes, allow us to individuate two different regions in the plume, one characterized by air and continuum emissions produced by the shock wave ionization and the other characterized by emissions from ablated material. Moreover, it was shown that a sufficiently high laser fluence and short delay time of acquisition are needed to avoid inhomogeneous effects in the plasma, as required in analytical applications such as laser-induced breakdown spectroscopy.},
author = {Corsi, M and Cristoforetti, G and Hidalgo, M and Iriarte, D and Legnaioli, S and Palleschi, V and Salvetti, A and Tognoni, E},
doi = {10.1366/000370203322005436},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {6},
pages = {715--21},
pmid = {14658707},
publisher = {Optical Society of America},
series = {OSA Trends in Optics and Photonics Series},
title = {{Temporal and spatial evolution of a laser-induced plasma from a steel target.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14658707},
volume = {57},
year = {2003}
}
@article{Taylor2006,
abstract = {Laser-induced breakdown spectroscopy is reviewed by dividing the literature into three categories according to target phase: solid, liquid, or gas. Within each category, the literature is further divided into a fundamental studies section and an analytical results and applications section. KEY},
author = {Taylor, Publisher},
journal = {Critical Reviews in Analytical Chemistry},
keywords = {laser-induced breakdown spectroscopy},
number = {March 2012},
pages = {37--41},
title = {{Critical Reviews in Analytical Chemistry Fundamentals and Applications of Laser-Induced Breakdown Spectroscopy Fundamentals and Applications of Laser-Induced Breakdown Spectroscopy}},
year = {2006}
}
@article{Astin2006,
abstract = {The University of Salford has led the way in the fundamental research that has underpinned the development of thin film copper indium diselenide (CIS) based photovoltaics. These devices have demonstrated exceptional energy conversion efficiencies (>19{\%}) and a high tolerance to radiation damage and are thus leading researchers towards the 20{\%} efficiency barrier. Conventional CIS thin film growth processes require a post-selenisation step to incorporate Se into the as-grown material. This helps to achieve stoichometry, improves the crystallinity, controls the defect structure and also can be used to convert the semiconductor type. This paper will report the use of pulsed dc magnetron sputtering from a CIS powder target. This approach has resulted in asgrown stoichiometric thin films consisting of pinhole free, densely packed grains. An important consideration in the thin film growth of complex materials is that stoichiometry is maintained throughout the film. Conventionally, secondary ion mass spectrometry (SIMS) is used to depth profile thin films but it has been reported that laser induced breakdown spectrometry (LIBS) can also be used. We will report the initial results comparing and contrasting these two techniques and show that LIBS can produce meaningful data.},
author = {Astin, JS and Cowpe, JS and Hill, A and Hisek, J and Lucas, N and Pilkington, RD},
file = {::},
journal = {In Proceedings of Photon 06},
keywords = {other,qc350 467 optics. light},
publisher = {IOP Publishing Ltd.},
title = {{A comparative study of laser induced breakdown spectroscopy and secondary ion mass spectrometry applied to dc magnetron sputtered as-grown copper indium diselenide.}},
url = {http://usir.salford.ac.uk/2572/},
year = {2006}
}
@article{Nasrazadani2006,
abstract = {Synthetic magnetite (Fe3O4) was heated in air at 200-500 C for different time periods to study its phase transformation to maghemite (gamma-Fe2O3) and hematite (alpha-Fe2O3). Laser Induced Breakdown Spectroscopy (LIBS) was used to take the spectra of these samples which were then compared to the spectra of standard iron oxide powders using linear correlation. The linear correlation procedure used showed probabilities of identification close to unity. Complementary techniques to LIBS, Fourier Transform Infrared (FTIR) spectroscopy and X-ray Diffraction (XRD) analysis were also used to characterize iron oxides. By taking advantage of the time gated detector capability of LIBS, the identification of iron oxide phases was found to be in good agreement with FTIR and XRD analysis. This study demonstrates that LIBS can be successfully applied to the characterization of the oxidation states of multivalent oxides of elements like Fe, Cr, Pb, and others.},
author = {Nasrazadani, S and Namduri, H},
doi = {10.1016/j.sab.2006.04.001},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {correlation,ftir,iron oxide,laser induced breakdown spectroscopy,xrd},
number = {5},
pages = {565--571},
title = {{Study of phase transformation in iron oxides using Laser Induced Breakdown Spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854706001157},
volume = {61},
year = {2006}
}
@article{Hybl2003b,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is examined as a potential method for detecting airborne biological agents. A spectrally broadband LIBS system was used for laboratory measurements on some common biological agent simulants. These measurements were compared to those of common, naturally occurring biological aerosol components (pollen and fungal spores) to determine the potential of LIBS for discriminating biological agents from natural background aerosols. A principal components analysis illustrates that linear combinations of the detected atomic lines, which are present in different ratios in each of the samples tested, can be used to discriminate biological agent simulants from other biological matter. A more sensitive, narrowband LIBS instrument was used to demonstrate the detection of single simulant (Bg) particles in the size range 1-5 microns. Ca, Mg, and Na, which are present in varying concentrations between 0.3 and 11{\%} (by mass) in the Bg particles, were observed in single particles using LIBS.},
author = {Hybl, John D and Lithgow, Gregg A and Buckley, Steven G},
institution = {MIT Lincoln Laboratory, 244 Wood Street, Lexington, Massachusetts 02420-9108, USA.},
journal = {Applied Spectroscopy},
number = {10},
pages = {1207--1215},
pmid = {14639747},
publisher = {OSA},
title = {{Laser-induced breakdown spectroscopy detection and classification of biological aerosols.}},
url = {http://www.opticsinfobase.org/viewmedia.cfm?id=117987{\&}amp;seq=0},
volume = {57},
year = {2003}
}
@article{Gondal2007,
abstract = {Study of various binding materials like potassium bromide, poly(vinyl alcohol), starch, silver and aluminum has been carried out using laser-induced breakdown spectroscopy (LIBS). The role of matrix effects using these five binders on LIBS signal intensity was investigated for better performance of LIBS technique as a quantitative analytical tool. For comparative study of different binders, the signal intensity of different Mg lines at 518.3, 517.2, 383.8 and 279.5nm wavelengths were recorded for pellets prepared with known concentrations of Mg in these binders. The influence of laser energy on ablated mass under different binding materials and its correlation with LIBS signal intensity has been explored. Optical scanning microscopy images of the ablated crater were studied to understand the laser ablation process. The study revealed that the binding material plays an important role in the generation of LIBS signal. The relative signal intensity measured for a standard Mg line (at 518.3nm) were 735, 538, 387, 227 and 130 for potassium bromide, starch, poly(vinyl alcohol), silver and aluminum as binders, respectively. This indicates clearly that potassium bromide is better as a binder for LIBS studies of powder samples.},
author = {Gondal, M A and Hussain, T and Yamani, Z H and Baig, M A},
institution = {Laser Research Laboratory, Physics Department, King Fahd University of Petroleum {\&} Minerals, Dhahran 31261, Saudi Arabia.},
journal = {Talanta},
number = {2},
pages = {642--649},
pmid = {19071667},
title = {{The role of various binding materials for trace elemental analysis of powder samples using laser-induced breakdown spectroscopy.}},
url = {http://www.sciencedirect.com/science/article/B6THP-4MM8B89-2/2/346e4c090a022c07b54535c29e2461c2},
volume = {72},
year = {2007}
}
@article{Adamson,
author = {Adamson, Marian D and Rehse, Steven J and Ca, Al},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Adamson, Rehse, Ca - Detection of Trace Aluminum in Model Biological Tissue with Laser-Induced Breakdown Spectroscopy Limit of Detection.pdf:pdf},
journal = {Energy},
title = {{Detection of Trace Aluminum in Model Biological Tissue with Laser-Induced Breakdown Spectroscopy Limit of Detection Calibration Curves Few Accumulation Measurements}}
}
@article{Wise2008,
abstract = {A commercially available chemical identification taggant that imparts a unique elemental fingerprint to any object and can be analytically distinguished from billions of possible combinations has been developed. The liquid tag is easily applied and, once dry, can be removed and analyzed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to determine the combination of elements present in the sample. The current study investigates the use of laser-induced breakdown spectroscopy (LIBS) as an alternative, and perhaps more practical, analysis scheme to LA-ICP-MS for this taggant. LIBS provides excellent discrimination potential, sensitivity, and repeatability of analysis for up to 17 rare-earth elements using a Nd:YAG 266 nm or 1064 nm laser and an intensified CCD detector.},
author = {Wise, Steven H and Almirall, Jose R},
institution = {Department of Chemistry and Biochemistry and International Forensic Research Institute, Florida International University, 11200 SW 8 Street, Miami, Florida 33199, USA.},
journal = {Applied Optics},
number = {31},
pages = {G15--G20},
pmid = {19122697},
title = {{Chemical taggant detection and analysis by laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19122697},
volume = {47},
year = {2008}
}
@article{Lopez-Moreno2005,
abstract = {The development of a compact laser induced breakdown spectroscopy (LIBS) system increases the possibilities of applying the technique in industrial arenas, field applications and process monitoring. Significant progress has been achieved in miniaturization of optical detectors and lasers, allowing portable, low-cost LIBS equipment to be devised. Conventional lasers for LIBS, like actively Q-switched Nd:YAG lasers are limited by their bulkiness, the need for a cooling system and high power consumption. The use of a miniature solid state microchip laser overcomes these drawbacks and offers further advantages of good beam quality, high pulse repetition frequency and less damage to target. In this work we studied the quantification of elemental composition of low alloy steel samples using a higher power microchip ("powerchip") laser. The possibility of real time, in situ quantification of such materials by powerchip LIBS enhances the applicability of the technique to process monitoring in the steelmaking industry. The performance of the LIBS technique based on a powerchip laser and a portable non-intensified, non-gated detector for elemental quantification is evaluated and compared to that obtained using an intensified detector. Calibrations were achieved for Cr, Mo, Ni, Mn and Si with linear regression coefficients between 0.98-0.99 and limits of detection below 100 ppm in most cases.},
author = {Lopez-Moreno, C and Amponsah-Manager, K and Smith, B W and Gornushkin, I B and Omenetto, N and Palanco, S and Laserna, J J and Winefordner, J D},
doi = {10.1039/b419173k},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {6},
pages = {552},
title = {{Quantitative analysis of low-alloy steel by microchip laser induced breakdown spectroscopy}},
url = {http://xlink.rsc.org/?DOI=b419173k},
volume = {20},
year = {2005}
}
@article{Carranza2002b,
abstract = {The laser-induced plasma vaporization of individual silica microspheres in an aerosolized air stream was investigated. The upper size limit for complete particle vaporization corresponds to a silica particle diameter of 2.1 {\'{\i}}m for a laser pulse energy of 320 mJ, as determined by the deviation from a linear mass response of the silicon atomic emission signal. Comparison of the measured silica particle sampling rates and those predicted based on Poisson sampling statistics and the overall laserinduced plasma volume suggests that the primary mechanism of particle vaporization is related to direct plasmaparticle interactions as opposed to a laser beam-particle interaction. Finally, temporal and spatial plasma evolution is discussed in concert with factors that may influence the vaporization dynamics of individual aerosol particles, such as thermophoretic forces and vapor expulsion.},
author = {Carranza, Jorge E and Hahn, David W},
issn = {0003-2700},
journal = {Analytical chemistry},
keywords = {Aerosols,Aerosols: chemistry,Laser Therapy,Microspheres,Nebulizers and Vaporizers,Particle Size,Silicon,Silicon: chemistry,Spectrum Analysis,Spectrum Analysis: methods,Statistics as Topic},
month = {nov},
number = {21},
pages = {5450--4},
pmid = {12433072},
title = {{Assessment of the upper particle size limit for quantitative analysis of aerosols using laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12433072},
volume = {74},
year = {2002}
}
@article{Joshi2009,
abstract = {In this contribution we present the first demonstration of simultaneous use of laser sparks for engine ignition and laser-induced breakdown spectroscopy (LIBS) measurements of in-cylinder equivalence ratios. A 1064 nm neodynium yttrium aluminum garnet (Nd:YAG) laser beam is used with an optical spark plug to ignite a single cylinder natural gas engine. The optical emission from the combustion initiating laser spark is collected through the optical spark plug and cycle-by-cycle spectra are analyzed for H(alpha)(656 nm), O(777 nm), and N(742 nm, 744 nm, and 746 nm) neutral atomic lines. The line area ratios of H(alpha)/O(777), H(alpha)/N(746), and H(alpha)/N(tot) (where N(tot) is the sum of areas of the aforementioned N lines) are correlated with equivalence ratios measured by a wide band universal exhaust gas oxygen (UEGO) sensor. Experiments are performed for input laser energy levels of 21 mJ and 26 mJ, compression ratios of 9 and 11, and equivalence ratios between 0.6 and 0.95. The results show a linear correlation (R(2) > 0.99) of line intensity ratio with equivalence ratio, thereby suggesting an engine diagnostic method for cylinder resolved equivalence ratio measurements.},
author = {Joshi, Sachin and Olsen, Daniel B and Dumitrescu, Cosmin and Puzinauskas, Paulius V and Yalin, Azer P},
institution = {Engines and Energy Conversion Laboratory, Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80521, USA.},
journal = {Applied Spectroscopy},
number = {5},
pages = {549--554},
pmid = {19470212},
title = {{Laser-induced breakdown spectroscopy for in-cylinder equivalence ratio measurements in laser-ignited natural gas engines.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16053554},
volume = {63},
year = {2009}
}
@article{Jantzi2011,
abstract = {A method for the quantitative elemental analysis of surface soil samples using laser-induced breakdown spectroscopy (LIBS) was developed and applied to the analysis of bulk soil samples for discrimination between specimens. The use of a 266 nm laser for LIBS analysis is reported for the first time in forensic soil analysis. Optimization of the LIBS method is discussed, and the results compared favorably to a laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) method previously developed. Precision for both methods was <10{\%} for most elements. LIBS limits of detection were <33 ppm and bias <40{\%} for most elements. In a proof of principle study, the LIBS method successfully discriminated samples from two different sites in Dade County, FL. Analysis of variance, Tukey's post hoc test and Student's t test resulted in 100{\%} discrimination with no type I or type II errors. Principal components analysis (PCA) resulted in clear groupings of the two sites. A correct classification rate of 99.4{\%} was obtained with linear discriminant analysis using leave-one-out validation. Similar results were obtained when the same samples were analyzed by LA-ICP-MS, showing that LIBS can provide similar information to LA-ICP-MS. In a forensic sampling/spatial heterogeneity study, the variation between sites, between sub-plots, between samples and within samples was examined on three similar Dade sites. The closer the sampling locations, the closer the grouping on a PCA plot and the higher the misclassification rate. These results underscore the importance of careful sampling for geographic site characterization.},
author = {Jantzi, Sarah C and Almirall, Jos{\'{e}} R},
institution = {Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.},
journal = {Analytical and Bioanalytical Chemistry},
number = {10},
pages = {3341--3351},
pmid = {21461623},
title = {{Characterization and forensic analysis of soil samples using laser-induced breakdown spectroscopy (LIBS).}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21461623},
volume = {400},
year = {2011}
}
@article{Astin2006a,
abstract = {The University of Salford has led the way in the fundamental research that has underpinned the development of thin film copper indium diselenide (CIS) based photovoltaics. These devices have demonstrated exceptional energy conversion efficiencies (>19{\%}) and a high tolerance to radiation damage and are thus leading researchers towards the 20{\%} efficiency barrier. Conventional CIS thin film growth processes require a post-selenisation step to incorporate Se into the as-grown material. This helps to achieve stoichometry, improves the crystallinity, controls the defect structure and also can be used to convert the semiconductor type. This paper will report the use of pulsed dc magnetron sputtering from a CIS powder target. This approach has resulted in asgrown stoichiometric thin films consisting of pinhole free, densely packed grains. An important consideration in the thin film growth of complex materials is that stoichiometry is maintained throughout the film. Conventionally, secondary ion mass spectrometry (SIMS) is used to depth profile thin films but it has been reported that laser induced breakdown spectrometry (LIBS) can also be used. We will report the initial results comparing and contrasting these two techniques and show that LIBS can produce meaningful data.},
author = {Astin, JS and Cowpe, JS and Hill, A and Hisek, J and Lucas, N and Pilkington, RD},
file = {::},
journal = {In Proceedings of Photon 06},
keywords = {other,qc350 467 optics. light},
publisher = {IOP Publishing Ltd.},
title = {{A comparative study of laser induced breakdown spectroscopy and secondary ion mass spectrometry applied to dc magnetron sputtered as-grown copper indium diselenide.}},
url = {http://usir.salford.ac.uk/2572/},
year = {2006}
}
@article{Osticioli2009,
abstract = {A small, potentially transportable prototype instrument capable of carrying out Raman, laser-induced breakdown (LIB), and laser-induced fluorescence (LIF) spectroscopy using a single pulsed laser source was developed for the analysis of cultural heritage objects. The purpose of this instrumentation is to perform fast and reliable analysis of surfaces with minimum damage to an object. For this purpose, a compact (51 x 203 x 76 mm) nanosecond Q-switched neodymium doped yttrium aluminum garnet laser (8 ns, 20 Hz, 0.01-115 mJ/pulse) was used as an irradiation source. The use of a nanosecond-gated detector sensitive between 180 and 900 nm allows the acquisition of elemental emissions in LIB spectroscopy and can also be employed for both LIF and time-resolved Raman spectroscopy. In this work, attention is focused on the description of the instrument and its optical components, and two examples of applications for the analysis of pigments and binding media used in works of art are presented.},
author = {Osticioli, I and Mendes, N F C and Nevin, A and Zoppi, A and Lofrumento, C and Becucci, M and Castellucci, E M},
institution = {Department of Chemistry, University of Florence, Polo Scientifico e Tecnologico, via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy.},
journal = {Review of Scientific Instruments},
number = {7},
pages = {076109},
pmid = {19655994},
title = {{A new compact instrument for Raman, laser-induced breakdown, and laser-induced fluorescence spectroscopy of works of art and their constituent materials.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19655994},
volume = {80},
year = {2009}
}
@article{Da-Cheng2010,
author = {Da-Cheng, Zhang and Xin-Wen, Ma and Wei-Qiang, Wen and Peng-Ju, Zhang and Xiao-Long, Zhu and Bin, Li and Hui-Ping, Liu},
journal = {Chinese Physics Letters},
number = {6},
pages = {63202},
title = {{Influence of Laser Wavelength on Laser-induced Breakdown Spectroscopy Applied to Semi-Quantitative Analysis of Trace-Elements in a Plant Sample}},
volume = {27},
year = {2010}
}
@article{Dixon2005a,
abstract = {The detection and identification of individual bioaerosols using laser-induced breakdown spectroscopy (LIBS) is investigated using aerosolized Bacillus spores. Spores of Bacillus atrophaeous, Bacillus pumilus, and Bacillus stearothemophilus were introduced into an aerosol flow stream in a prescribed manner such that single-particle LIBS detection was realized. Bacillus spores were successfully detected based on the presence of the 393.4- and 396.9-nm calcium atomic emission lines. Statistical analyses based on the aerosol number density, the LIBS-based spore sampling frequency, and the distribution of the resulting calcium mass loadings support the conclusion of individual spore detection within single-shot laser-induced plasmas. The average mass loadings were in the range of 2-3 fg of calcium/Bacillus spore, which corresponds to a calcium mass percentage of approximately 0.5{\%}. While individual spores were detected based on calcium emission, the resulting Bacillus spectra were free from CN emission bands, which has implications for the detection of elemental carbon, and LIBS-based detection of single spores based on the presence of magnesium or sodium atomic emission was unsuccessful. Based on the current instrumental setup and analyses, real-time LIBS-based detection and identification of single Bacillus spores in ambient (i.e., real life) conditions appears unfeasible.},
author = {Dixon, P B and Hahn, D W},
doi = {10.1021/ac048838i},
file = {::},
issn = {0003-2700},
journal = {Analytical chemistry},
keywords = {Aerosols,Aerosols: analysis,Air Microbiology,Bacillus,Bacillus: ultrastructure,Calcium,Calcium: analysis,Environmental Monitoring,Environmental Monitoring: methods,Feasibility Studies,Lasers,Particle Size,Spectrum Analysis,Spectrum Analysis: methods,Spores, Bacterial,Spores, Bacterial: chemistry,Spores, Bacterial: isolation {\&} purification,Trace Elements,Trace Elements: analysis},
month = {jan},
number = {2},
pages = {631--8},
pmid = {15649064},
title = {{Feasibility of detection and identification of individual bioaerosols using laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15649064},
volume = {77},
year = {2005}
}
@article{Chang2007,
abstract = {A brief review is made of the status of °uorescence techniques to detect and par- tially identify bio-aerosols. The potential and frustrations in extracting morphology information from the angularly-resolved elastic scattering pattern is summarized. The latest advancements in the measurement of angularly-resolved elastic-light scattering for single aerosol particles on-the- °y are surveyed. Special emphasis is placed on our more recent e®orts to simultaneously measure the scattering patterns of aerosol particles in both the forward and backward hemispheres.},
author = {Chang, RK and Fernandes, GE and Pan, YL and Aptowicz, Kevin},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Chang et al. - The Quest for Detection and Identification of Bio-aerosols - 2007.pdf:pdf},
journal = {vertilon.com},
keywords = {bio-aerosol fluorescence detection,light scattering,multianode photomultiplier 8 x 8 anodes,pmt},
pages = {622--625},
title = {{The Quest for Detection and Identification of Bio-aerosols}},
url = {http://www.vertilon.com/pdf/PP6202.pdf},
year = {2007}
}
@article{Hahn2010,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has become a very popular analytical method in the last decade in view of some of its unique features such as applicability to any type of sample, practically no sample preparation, remote sensing capability, and speed of analysis. The technique has a remarkably wide applicability in many fields, and the number of applications is still growing. From an analytical point of view, the quantitative aspects of LIBS may be considered its Achilles' heel, first due to the complex nature of the laser-sample interaction processes, which depend upon both the laser characteristics and the sample material properties, and second due to the plasma-particle interaction processes, which are space and time dependent. Together, these may cause undesirable matrix effects. Ways of alleviating these problems rely upon the description of the plasma excitation-ionization processes through the use of classical equilibrium relations and therefore on the assumption that the laser-induced plasma is in local thermodynamic equilibrium (LTE). Even in this case, the transient nature of the plasma and its spatial inhomogeneity need to be considered and overcome in order to justify the theoretical assumptions made. This first article focuses on the basic diagnostics aspects and presents a review of the past and recent LIBS literature pertinent to this topic. Previous research on non-laser-based plasma literature, and the resulting knowledge, is also emphasized. The aim is, on one hand, to make the readers aware of such knowledge and on the other hand to trigger the interest of the LIBS community, as well as the larger analytical plasma community, in attempting some diagnostic approaches that have not yet been fully exploited in LIBS.},
author = {Hahn, David W and Omenetto, Nicol{\'{o}}},
doi = {10.1366/000370210793561691},
file = {::},
issn = {1943-3530},
journal = {Applied spectroscopy},
month = {dec},
number = {12},
pages = {335--66},
pmid = {21144145},
title = {{Laser-induced breakdown spectroscopy (LIBS), part I: review of basic diagnostics and plasma-particle interactions: still-challenging issues within the analytical plasma community.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21144145},
volume = {64},
year = {2010}
}
@article{Swaminathan2008,
abstract = {OBJECTIVE: To measure the bias in absolute cancer survival estimates in the absence of active follow-up of cancer patients in developing countries. METHODS: Included in the study were all incident cases of the 10 most common cancers and corresponding subtypes plus all tobacco-related cancers not ranked among the top 10 that were registered in the population-based cancer registry in Chennai, India, during 1990-1999 and followed through 2001. Registered incident cases were first matched with those in the all-cause mortality database from the vital statistics division of the Corporation of Chennai. Unmatched incident cancer cases were then actively followed up to determine their survival status. Absolute survival was estimated by using an actuarial method and applying different assumptions regarding the survival status (alive/dead) of cases under passive and active follow-up. FINDINGS: Before active follow-up, matches between cases ranged from 20{\%} to 66{\%}, depending on the site of the primary tumour. Active follow-up of unmatched incident cases revealed that 15{\%} to 43{\%} had died by the end of the follow-up period, while the survival status of 4{\%} to 38{\%} remained unknown. Before active follow-up of cancer patients, 5-year absolute survival was estimated to be between 22{\%} and 47{\%} higher, than when conventional actuarial assumption methods were applied to cases that were lost to follow-up. The smallest survival estimates were obtained when cases lost to follow-up were excluded from the analysis. CONCLUSION: Under the conditions that prevail in India and other developing countries, active follow-up of cancer patients yields the most reliable estimates of cancer survival rates. Passive case follow-up alone or applying standard methods to estimate survival is likely to result in an upward bias.},
author = {Swaminathan, Rajaraman and Rama, Ranganathan and Shanta, Viswanathan},
institution = {Division of Epidemiology and Cancer Registry, Cancer Institute, Women's India Association, Chennai, India. iarcsurvival@yahoo.co.uk},
journal = {Bulletin of the World Health Organization},
number = {7},
pages = {509--515},
publisher = {World Health Organization},
title = {{Lack of active follow-up of cancer patients in Chennai, India: implications for population-based survival estimates.}},
volume = {86},
year = {2008}
}
@article{Rai2003a,
abstract = {The optical properties of laser-induced plasma generated firm solid (Al alloy) and liquid (Mn, Cr, Mg, or Ti solutions) samples expanded across an external, steady magnetic field have been studied by atomic-emission spectroscopy. Various line emissions obtained from the constituents of the Al alloy and of the aqueous solution show an enhancement in intensity in the presence of an approximately 5-kG magnetic field. The enhancement of the signal was nearly a factor of 2 for the minor constituents of the solid samples and a factor of 1.5 for the elements in liquid phase. Temporal evolution of the emission from the solid sample showed maximum enhancement in emission intensity at 3-10-micros time delay after plasma formation in the laser energy range 10-50 mJ. However, for the liquid sample the maximum signal was for a gate delay of 3-25 micros the energy range 50-200 mJ. This enhancement in the emission intensity was found to be due to an increase in effective density of the plasma as a result of magnetic confinement when the plasma cooled after expansion. This enhanced emission was due to an increase in the rate of radiative recombination in the plasma.},
author = {Rai, Virendra N and Rai, Awadhesh K and Yueh, Fang-Yu and Singh, Jagdish P},
institution = {Diagnostic Instrumentation and Analysis Laboratory, Mississippi State University, 205 Research Boulevard, Starkville, Mississippi 89759-7704, USA.},
journal = {Applied Optics},
number = {12},
pages = {2085--2093},
pmid = {12716149},
title = {{Optical emission from laser-induced breakdown plasma of solid and liquid samples in the presence of a magnetic field.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12716149},
volume = {42},
year = {2003}
}
@article{Boyain-Goitia2003,
abstract = {The application of laser-induced breakdown spectroscopy to the analysis of single biological microparticles (bioaerosols) is described, exemplified here for a range of pollens. Spectra were recorded by exposure of the pollen to a single laser pulse from a Nd:YAG laser (lambda = 1064 nm, Ep approximately 30 mJ). The intensities of the single-pulse laser-induced breakdown spectra fluctuated dramatically, but an internal signal calibration procedure was applied that referenced elemental line intensities to the carbon matrix of the sample (represented by molecular bands of CN and C2). This procedure allowed us to determine relative element concentration distributions for the different types of pollen. These pollens exhibited some distinct concentration variations, for both major and minor (trace) elements in the biomatrix, through which ultimately individual pollens might be identified and classified. The same pollen samples were also analyzed by Raman microscopy, which provided molecular compositional data (even with spatial resolution). These data allowed us to distinguish between biological and nonbiological specimens and to obtain additional classification information for the various pollen families, complementing the laser-induced breakdown spectroscopy measurement data.},
author = {Boyain-Goitia, Ana R and Beddows, David C S and Griffiths, Ben C and Telle, Helmut H},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Boyain-Goitia et al. - Single-pollen analysis by laser-induced breakdown spectroscopy and Raman microscopy. - 2003.pdf:pdf},
issn = {0003-6935},
journal = {Applied optics},
keywords = {Aerosols,Aerosols: analysis,Aerosols: chemistry,Air Pollutants,Air Pollutants: analysis,Air Pollutants: chemistry,Environmental Monitoring,Environmental Monitoring: methods,Feasibility Studies,Helianthus,Helianthus: chemistry,Hot Temperature,Lasers,Lilium,Lilium: chemistry,Lilium: classification,Microspheres,Particle Size,Poaceae,Poaceae: chemistry,Pollen,Pollen: chemistry,Pollen: classification,Spectrum Analysis,Spectrum Analysis, Raman,Spectrum Analysis, Raman: methods,Spectrum Analysis: methods},
month = {oct},
number = {30},
pages = {6119--32},
pmid = {14594074},
title = {{Single-pollen analysis by laser-induced breakdown spectroscopy and Raman microscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594074},
volume = {42},
year = {2003}
}
@article{Alvey2010a,
abstract = {Laser-induced breakdown spectroscopy (LIBS) is an analytical technique real-time geochemical analysis that is being developed for portable use outside of the laboratory. In this study, statistical signal processing and classification techniques were applied to single-shot, broadband LIBS spectra, comprising measured plasma light intensities between 200 and 960 nm, for a suite of 157 garnets of different composition from 92 locations worldwide. Partial least squares discriminant analysis was applied to sets of 25 LIBS spectra for each garnet sample and used to classify the garnet samples based on composition and geographic origin. Careful consideration was given to the cross-validation procedure to ensure that the classification algorithm is robust to unseen data. The results indicate that broadband LIBS analysis can be used to discriminate garnets of different composition and has the potential to discern geographic origin.},
author = {Alvey, Daniel C and Morton, Kenneth and Harmon, Russell S and Gottfried, Jennifer L and Remus, Jeremiah J and Collins, Leslie M and Wise, Michael A},
doi = {10.1364/AO.49.00C168},
journal = {Applied Optics},
number = {13},
pages = {C168----C180},
title = {{Laser-induced breakdown spectroscopy-based geochemical fingerprinting for the rapid analysis and discrimination of minerals: the example of garnet}},
url = {http://ao.osa.org/abstract.cfm?URI=ao-49-13-C168},
volume = {49},
year = {2010}
}
@article{Cau2008,
abstract = {The boron nitride nanotubes (BNNTs) synthesis, using CO2-laser vaporization of a BN target under nitrogen gas, is investigated by UV-laser induced fluorescence (LIF) of the vapor phase and UV-Rayleigh scattering (RS) of the gas-suspended nanoparticles. The LIF signal from B atoms is mainly detected in the 1.5 mm-thick region above the BN target. It originates from a boron-rich vapor region confined near the hot boron droplet formed at the target surface. Then, recombination between hot boron and N2 gas occurs through a fast condensation process as revealed by both the depletion of B atoms from the vapor phase and the RS signal arising from the grown BN nanoparticles. Fluorescence spectra exhibit a strong peak at 250 nm due to boron fluorescence and mainly to nanoparticles Rayleigh scattering. A narrow peak is observed at 210 nm and a broader peak at 189 nm. These bands are tentatively assigned to fluorescence or photoluminescence (PL) from gaseous or solid BN species respectively since both gas and solid phases coexist in the plume due to the rapid cooling process. Two very weak bands occur at 308 nm and 350 nm. They are related to PL of defects bands from BN nanostructures on the basis of ex situ PL spectra of h-BN crystallites and multi-wall BNNTs. Detection of oxygen impurities is shown feasible through LIF from BO radical which is detected just above the BN target evaporated under vacuum pressure (approximately 1 mbar). An optical diagnostic strategy is demonstrated from these first in situ observations during BNNTs synthesis.},
author = {Cau, M and Dorval, N and Attal-Tr{\'{e}}tout, B and Cochon, J L and Cao, B and Bresson, L and Jaffrennou, P and Silly, M and Loiseau, A and Obraztsova, E D},
institution = {ONERA, Chemin de la Huni{\`{e}}re, 91761 Palaiseau Cedex, France.},
journal = {Journal of Nanoscience and Nanotechnology},
keywords = {ablation,boron,boron nitride,boron oxide,cathodoluminescence,gas phase,growth,hexagonal boron nitride,irradiation,laser induced fluorescence,laser vaporization,nanoparticle synthesis,nanoparticles,nanotubes formation,photoluminescence,rayleigh scattering,spectroscopy,wall carbon nanotubes},
number = {11},
pages = {6129--6140},
pmid = {19198355},
title = {{Laser-based diagnostics applied to the study of BN nanotubes synthesis.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19198355},
volume = {8},
year = {2008}
}
@article{Morel2003a,
abstract = {A laser-induced breakdown spectroscopy technique for analyzing biological matter for the detection of biological hazards is investigated. Eight species were considered in our experiment: six bacteria and two pollens in pellet form. The experimental setup is described, then a cumulative intensity ratio is proposed as a quantitative criterion because of its linearity and reproducibility. Time-resolved laser-induced breakdown spectroscopy (TRELIBS) exhibits a good ability to differentiate among all these species, whatever the culture medium, the species or the strain. Thus we expect that TRELIBS will be a good candidate for a sensor of hazards either on surfaces or in ambient air.},
author = {Morel, St{\'{e}}phane and Leone, Nicolas and Adam, Philippe and Amouroux, Jacques},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Morel et al. - Detection of bacteria by time-resolved laser-induced breakdown spectroscopy. - 2003.pdf:pdf},
institution = {Direction Generale de l'Armement, Direction des Centres d'expertises et d'essais, Centre d'Etudes du Bouchet, B.P. 91710 Vert-Le-Petit, France.},
journal = {Applied Optics},
keywords = {bacteria,bacteria classification,culture media,equipment design,hazardous substances,hazardous substances analysis,lasers,reproducibility results,species specificity,spectrum analysis,spectrum analysis instrumentation,spectrum analysis methods},
number = {30},
pages = {6184--6191},
pmid = {14594083},
publisher = {Optical Society of America},
title = {{Detection of bacteria by time-resolved laser-induced breakdown spectroscopy.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594083},
volume = {42},
year = {2003}
}
@article{Fahim2009,
abstract = {The present paper describes a new method utilizing rapid anodization to quickly synthesize high-quality, high aspect ratio, robust titanium dioxide nanotube powders. TiO(2) nanotube powders, With a typical nanotube outer diameter of approximately 40 nm, wall thickness of approximately 8-15 nm, and length of about 10-35 mu m, were synthesized by potentiostatic rapid breakdown anodization of titanium foils in aqueous electrolytes of 0.3 M NaCl or 0.1 M HClO(4) under an applied potential of 20 V. High reactivity and ultrahigh reaction rate are cornerstones responsible for periodic release of TiO(2) nanotubes into solution and formation of a white precipitate of TiO(2), nanotubes. The reaction yield is approximately 4-6 g in less than 3 h, and the approximate cost of the material is {\$}3.50/g, based on the laboratory-scale production. Various characterization techniques, including FESEM, HRTEM, EDX, XRD, XPS, FT-IR, UV-visible diffuse-reflectance, and NZ adsorption, have been used to probe morphology, microstructure, crystallographic, composition, bond configuration, optical properties, and surface area of the nanotubes. XPS and EDX investigations show that nanotubes formed in NaCl/phosphate electrolyte solutions contain a significant amount of phosphorus species, which strongly affects crystallization and phase transformation of TiO(2). Namely, phosphate-incorporating nanotubes stabilized the anatase phase, and initiation of the rutile phase was observed at annealing temperatures 700 degrees C. The resulting nanotube powders have a significant level of OH groups with a band gap ranging from 3.04 to 3.23 eV. Our results indicate that rapid breakdown anodization is highly efficient in the production of good-quality TiO(2) nanotube powders, which makes it an alternative to well-documented conventional methods.},
author = {Fahim, Narges F and Sekino, Tohru},
issn = {08974756},
journal = {Chemistry of Materials},
number = {9},
pages = {1967--1979},
publisher = {AMER CHEMICAL SOC},
title = {{A Novel Method for Synthesis of Titania Nanotube Powders using Rapid Breakdown Anodization}},
url = {http://pubs.acs.org/doi/abs/10.1021/cm900410x},
volume = {21},
year = {2009}
}
@article{Vestin2010,
author = {Vestin, F and Randelius, M and Bengtson, A},
doi = {10.1016/j.sab.2010.04.007},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic},
number = {8},
pages = {721--726},
publisher = {Elsevier B.V.},
title = {{Laser-induced breakdown spectroscopy applied on low-alloyed zinc samples}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854710001187},
volume = {65},
year = {2010}
}
@article{Rai2002,
abstract = {A fiber optic FO laser-induced breakdown spectroscopy LIBS sensor that measures the on-line, in situ elemental composition of a molten alloy inside the melt in a furnace is described. This sensor has applications as a process monitor and control tool for glass, aluminum, and steel melters. The sensor is based on the transmission of laser energy through a multimode optical fiber. The laser radiation from the fiber is collimated and finally focused inside the aluminum melt in the furnace by a specially designed stainless steel holder that holds the collimating and focusing lens. Atomic emission from sparks from the laser plasma is collected by the same stainless steel lens holder and transmitted back through the optical fiber and finally fed into the entrance slit of the spectrograph. The present design of the stainless steel holder is useful for obtaining a collimated LIBS signal over a long distance the distance between the focusing and collimated lenses is more than 200 cm. Parametric studies such as sample-to-lens distance and the effect of the angle of incidence of the laser beam on the sample surface were performed. Calibration curves for minor elements were obtained for solid Al alloys as well as for a molten Al alloy in the laboratory furnace by inserting the FO LIBS probe inside the molten material. The performance of the probe was also tested by inserting the stainless steel holder into the melt at a 45 angle, which is necessary for collecting LIBS data in an industrial furnace. LIBS spectra in different spectral regions were recorded in the pilot furnace during different tests where known amounts of minor elements were added to the melt. The results obtained from this sensor for different Al alloys demonstrate the usefulness of this sensor to monitor the concentration of different constituents of the molten Al alloy in an industrial furnace.},
author = {Rai, Awadhesh K and Yueh, Fang Y and Singh, Jagdish P and Zhang, Hansheng},
chapter = {100},
doi = {10.1063/1.1505101},
issn = {00346748},
journal = {Review of Scientific Instruments},
number = {10},
pages = {100--103},
publisher = {AIP},
title = {{High temperature fiber optic laser-induced breakdown spectroscopy sensor for analysis of molten alloy constituents}},
url = {http://link.aip.org/link/?RSI/73/3589/1},
volume = {73},
year = {2002}
}
@article{Bousquet2008,
abstract = {Principal Components Analysis (PCA) is successfully applied to the full laser-induced breakdown spectroscopy (LIBS) spectra of soil samples, defining classes according to the concentrations of the major elements. The large variability of the LIBS data is related to the heterogeneity of the samples and the representativeness of the data is finally discussed. Then, the development of a mobile LIBS system dedicated to the in-situ analysis of soils polluted by heavy metals is described. Based on the use of ten-meter long optical fibers, the mobile system allows deported measurements. Finally, the laser-assisted drying process studied by the use of a customized laser has not been retained to overcome the problem of moisture.},
author = {Bousquet, B and Travaill{\'{e}}, G and Isma{\"{e}}l, A and Canioni, L and {Michel-Le Pierr{\`{e}}s}, K and Brasseur, E and Roy, S and {Le Hecho}, I and Larregieu, M and Tellier, S and Potin-Gautier, M and Boriachon, T and Wazen, P and Diard, A and Belb{\`{e}}ze, S},
doi = {10.1016/j.sab.2008.09.008},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1085--1090},
publisher = {Elsevier B.V.},
title = {{Development of a mobile system based on laser-induced breakdown spectroscopy and dedicated to in situ analysis of polluted soils}},
url = {http://www.sciencedirect.com/science/article/B6THN-4TJX1SP-1/2/420785e7208b9d91377f9189b985f9f1},
volume = {63},
year = {2008}
}
@article{Samuels2003,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been used to study bacterial spores, molds, pollens, and proteins. Biosamples were prepared and deposited onto porous silver substrates. LIBS data from the individual laser shots were analyzed by principal-components analysis and were found to contain adequate information to afford discrimination among the different biomaterials. Additional discrimination within the three bacilli studied appears feasible.},
author = {Samuels, Alan C and DeLucia, Frank C and McNesby, Kevin L and Miziolek, Andrzej W},
file = {::},
issn = {0003-6935},
journal = {Applied optics},
keywords = {Bioterrorism,Fungi,Fungi: classification,Fungi: isolation {\&} purification,Hazardous Substances,Hazardous Substances: analysis,Lasers,Ovalbumin,Ovalbumin: analysis,Ovalbumin: chemistry,Pollen,Pollen: chemistry,Pollen: classification,Species Specificity,Spectrum Analysis,Spectrum Analysis: methods,Spores, Bacterial,Spores, Bacterial: chemistry,Spores, Bacterial: classification},
month = {oct},
number = {30},
pages = {6205--9},
pmid = {14594086},
title = {{Laser-induced breakdown spectroscopy of bacterial spores, molds, pollens, and protein: initial studies of discrimination potential.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14594086},
volume = {42},
year = {2003}
}
@article{Doucet2008,
abstract = {The present work describes the first quantitative molecular prediction using laser-induced molecular bands along with chemometrics. In addition, this spectroscopic procedure has demonstrated the first complete quantitative analysis utilizing traditionally insensitive elements for pharmaceutical formulations. Atomic LIBS requires certain sensitive elements, such as Cl, F, Br, S and P, in order to quantitate a specific organic compound in a complex matrix. Molecular LIBS has been demonstrated to be the first successful approach using atomic spectroscopy to evaluate a complex organic matrix. This procedure is also the first quantitative analysis using laser-induced molecular bands and chemometrics. We have successfully applied chemometrics to predict the formulation excipients and active pharmaceutical ingredient (API) in a complex pharmaceutical formulation. Using such an approach, we demonstrate that the accuracy for the API and a formulation lubricant, magnesium stearate, have less than 4{\%} relative bias. The other formulation excipients such as Avicelregistered sign and lactose have been accurately predicted to have less than a 15{\%} relative bias. Molecular LIBS and chemometrics have provided a novel approach for the quantitative analysis of several molecules that was not technically possible with the traditional atomic LIBS procedure, that required sensitive elements to be present in both API and formulation excipients.},
author = {Doucet, Fran{\c{c}}ois R and Faustino, Patrick J and Sabsabi, Mohamad and Lyon, Robbe C},
doi = {10.1039/b714219f},
issn = {02679477},
journal = {Journal Of Analytical Atomic Spectrometry},
number = {5},
pages = {694},
title = {{Quantitative molecular analysis with molecular bands emission using laser-induced breakdown spectroscopy and chemometrics}},
url = {http://xlink.rsc.org/?DOI=b714219f},
volume = {23},
year = {2008}
}
@article{Yun2002,
abstract = {The paper presents the application of laser-induced breakdown spectroscopy (LIBS) for the on-line multielement analyses of glass melts in a vitrification process of high level liquid waste (HLLW). The third harmonic pulse of an Nd:YAG laser is used for the generation of plasma on the molten glass surface and the plasma emission is monitored by an echelle spectrometer with an intensified charge-coupled device (ICCD), which simultaneously covers the wavelength range from 200 to 780 nm. Twelve different reference HLLW glass melts with a complex composition of about 27 chemical elements are simulated on a laboratory scale, varying the HLLW component concentration. By real-time analyses of the reference glasses at 1200 C, the analytical method is calibrated. A multivariate regression approach with partial least squares (PLS) is used for the data evaluation. The LIBS method thus calibrated is then applied for the multielement analysis of molten glass samples from the prototype vitrification plant under operation in our institute. The results underline that the LIBS method can be applied to a vitrification process for the on-line multielement analysis of highly radioactive glass melts.},
author = {Yun, Jong-Il and Klenze, Reinhardt and Kim, Jae-Il},
doi = {10.1366/000370202760171518},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {7},
pages = {852--858},
title = {{Laser-Induced Breakdown Spectroscopy for the On-Line Multielement Analysis of Highly Radioactive Glass Melt Simulants. Part II: Analyses of Molten Glass Samples}},
url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0003-7028{\&}volume=56{\&}issue=7{\&}spage=852},
volume = {56},
year = {2002}
}
@article{Galiova2010,
abstract = {Direct analysis of wet slurry samples with laser induced breakdown spectroscopy (LIBS) is challenging due to problems of sedimentation, splashing, and surface turbulence. Also, water can quench the laser plasma and suppress the LIBS signal, resulting in poor sensitivity. The effect of water on LIBS spectra from slurries was investigated. As the water content decreased, the LIBS signal was enhanced and the standard deviation was reduced. To improve LIBS slurry analysis, dried slurry samples prepared by applying slurry on PVC coated slides were evaluated. Univariate and multivariate calibration was performed on the LIBS spectra of the dried slurry samples for elemental analysis of Mg, Si, and Fe. Calibration results show that the dried slurry samples give a good correlation between spectral intensity and elemental concentration.},
author = {Galiov{\'{a}}, Michaela and Kaiser, Jozef and Fortes, Francisco J and Novotn{\'{y}}, Karel and Malina, Radom{\'{\i}}r and Proke{\v{s}}, Lubom{\'{\i}}r and Hrdli{\v{c}}ka, Ale{\v{s}} and Vaculovi{\v{c}}, Tom{\'{a}}{\v{s}} and {N{\'{y}}vltov{\'{a}} Fi{\v{s}}{\'{a}}kov{\'{a}}}, Miriam and Svoboda, Jiř{\'{\i}} and Kanick{\'{y}}, Viktor and Laserna, Javier J},
doi = {10.1364/AO.49.00C191},
issn = {00036935},
journal = {Applied Optics},
number = {13},
pages = {C191},
title = {{Multielemental analysis of prehistoric animal teeth by laser-induced breakdown spectroscopy and laser ablation inductively coupled plasma mass spectrometry}},
url = {http://www.opticsinfobase.org/abstract.cfm?URI=ao-49-13-C191},
volume = {49},
year = {2010}
}
@article{Apanaskevich2008,
abstract = {Two new tick species belonging to the African Haemaphysalis (Rhipistoma) leachi subgroup, namely H. (R.) colesbergensis n. sp. and H. (R.) oliveri n. sp., are described. Haemaphysalis (R.) colesbergensis adults are easily differentiated from the other species of the H. (R.) leachi subgroup, including H. (R.) oliveri, by the spur on coxa IV, which is considerably longer than that on coxa III. The adults of the 2 new species are equal in size, but the dental formula of the hypostome of H. (R.) colesbergensis is 4/4 compared to 5/5 for H. (R.) oliveri. The dental formula of H. (R.) oliveri also distinguishes it from other ticks in the subgroup, namely H. (R.) leachi, H. (R.) elliptica, H. (R.) moreli, and H. (R.) punctaleachi (4/4 in these species), but not from H. (R.) paraleachi, which has a 5/5 dental arrangement. However, the average total length and width of H. (R.) oliveri males (2.47 x 1.20 mm) are considerably shorter and narrower than those of H. (R.) paraleachi males (3.81 x 1.79 mm). Similar differences in size apply to the females. Nymphs and larvae of H. (R.) colesbergensis and H. (R.) oliveri can be distinguished from those of other members of the H. (R.) leachi subgroup, as well as from each other, by a combination of the following characters: size and measurement ratios, length of posterodorsal and posteroventral spurs on palpal segment II, and number of denticles per file on the hypostome. Haemaphysalis (R.) colesbergensis is known only from South Africa, where it has been collected from domestic cats and dogs and medium-sized wild felids. Haemaphysalis (R.) oliveri is recorded only from Sudan, where it has been collected from small- to medium-sized wild felids and canids and an antelope. The hosts of the immature stages of H. (R.) colesbergensis are unknown, while nymphs of H. (R.) oliveri have been collected from rodents.},
author = {Apanaskevich, Dmitry A and Horak, Ivan G},
institution = {United States National Tick Collection, Institute of Arthropodology and Parasitology, Georgia Southern University, Statesboro, Georgia 30460-8056, USA. dapanaskevich@georgiasouthern.edu},
journal = {The Journal of parasitology},
number = {3},
pages = {594--607},
pmid = {18605788},
title = {{Two new species of African Haemaphysalis ticks (Acari: Ixodidae), carnivore parasites of the H. (Rhipistoma) leachi group.}},
volume = {94},
year = {2008}
}
@article{Baudelet2007a,
abstract = {Ultraviolet pulses (266 nm) delivered by a quadrupled Nd:YAG laser were used to analyze organic samples with laser-induced breakdown spectroscopy (LIBS). We present characteristics of the spectra obtained from organic samples with special attentions on the emissions of organic elements, O and N, and molecular bonds CN. The choice of these atomic or molecular species is justified on one hand, by the importance of these species to specify organic or biological materials; and on the other hand by the possible interferences with ambient air when laser ablation takes place in the atmosphere. Time-resolved LIBS was used to determine the time-evolution of line intensity emitted from these species. We demonstrate different kinetic behaviors corresponding to different origins of emitters: native atomic or molecular species directly vaporized from the sample or those generated through dissociation or recombination due to interaction between laser-induced plasma and air molecules. Our results show the ability of time-resolved UV-LIBS for detection and identification of native atomic or molecular species from an organic sample.},
author = {Baudelet, Matthieu and Boueri, Myriam and Yu, Jin and Mao, Samuel S. and Piscitelli, Vincent and Mao, Xianglei and Russo, Richard E.},
doi = {10.1016/j.sab.2007.10.043},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Baudelet et al. - Time-resolved ultraviolet laser-induced breakdown spectroscopy for organic material analysis - 2007.pdf:pdf},
issn = {05848547},
journal = {Spectrochimica Acta Part B: Atomic Spectroscopy},
keywords = {organic material analysis,time-resolved libs,ultraviolet laser-induced breakdown spectroscopy},
month = {dec},
number = {12},
pages = {1329--1334},
title = {{Time-resolved ultraviolet laser-induced breakdown spectroscopy for organic material analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854707003606},
volume = {62},
year = {2007}
}
@article{Gondal2007a,
abstract = {Laser Induced Breakdown Spectroscopy (LIBS) was applied for quantitative elemental analysis of slag samples collected from a local steel plant using an Nd: YAG laser emitting radiation at 1064 nm wavelength. The concentration of different elements of environmental significance such as cadmium, calcium, sulfur, magnesium, chromium, manganese, titanium, barium, phosphorus and silicon were 44, 2193, 1724,78578, 217260, 22220, 5178, 568, 2805, 77871 were mg Kg-1, respectively. Optimal experimental conditions for analysis were investigated. The calibration curves were drawn for different elements. The concentrations determined with our Laser-Induced Breakdown Spectrometers were compared with the results obtained using Inductively Coupled Plasma (ICP) emission spectroscopy. Our study demonstrates that LIBS could be highly appropriate for rapid online analysis of iron slag waste. The relative accuracy of our LIBS system for various elements as compared with ICP method is in the range of 0.001-0.049 at 2.5{\%} error confidence. Limits of detection (LOD) of our LIBS system were also estimated for the elements noted here. The hazardous effects of some of the trace elements present in iron slag exceeding permissible safe limits are also discussed.},
author = {Gondal, M A and Hussain, T and Yamani, Z H and Bakry, A H},
institution = {Laser Research Laboratory, Physics Department, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia. magondal@kfupm.edu.sa},
journal = {Journal of environmental science and health Part A Toxichazardous substances environmental engineering},
number = {6},
pages = {767--775},
pmid = {17474003},
title = {{Study of hazardous metals in iron slag waste using laser induced breakdown spectroscopy.}},
volume = {42},
year = {2007}
}
@article{Jensen1995,
abstract = {We examine a number of factors which influence the use of laser-induced breakdown spectroscopy (LIBS) to detect the cation content of physical mixtures of Eu2O3 and K2Cr2O7 with granular, crystalline SiO2. Excitation of the powdered specimens is by focused KrF excimer laser light (248 nm, 30 ns pulse width, fluence/pulse 0.3-30 J cm-2, irradiance 10-1000 Mw cm-2) in 1 atm air. We discuss the resulting time resolved UV/vis spectra of the plasma, the parameters and physical effects which influence the detection of impurities and examine the consequences of the presence of water in the samples together with variations in the sample morphology. We also present preliminary results on spectra from mixtures of these compounds with a basaltic soil.},
author = {Jensen, L C and Langford, S C and Dickinson, J T and Addleman, R S},
doi = {10.1016/0584-8547(95)01364-4},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {12},
pages = {1501--1519},
title = {{Mechanistic studies of laser-induced breakdown spectroscopy of model environmental samples}},
url = {http://www.sciencedirect.com/science/article/B6THN-3YXBSS2-1B/2/70fe7a268df2a8c5ba90982c0ab52548},
volume = {50},
year = {1995}
}
@article{Death2009,
abstract = {In the mining industry the quality and extent of an ore body is determined on the basis of routine assays conducted on drill core and chip samples. Both the elemental composition and the mineralogical classification are important in the characterisation of an ore body for commercial exploitation. Mining industry laboratories typically analyse large numbers of samples from both exploration and mine production environments. At CSIRO we have explored the application of chemometric methods of analysis in combination with laser induced breakdown spectroscopy (LIBS) in order to produce routine quantitative analysis of several ore types including iron, nickel and lead/zinc ores. In particular, principal components regression (PCR) has been applied to perform multi-element analysis of iron ore samples from Australia and West Africa. Calibration models for iron (4.8{\%} Av. Relative Error), aluminium (2.2{\%}), silicon (3.7{\%}) and potassium (1.4{\%}) were determined for the Australian ores. In addition phosphorous measurements were made at trace level for samples from West Africa (5.5{\%} Av. Relative Error). LIBS measurements of segments of a nickel drill core were also analysed using PCR. Mineralogical classification using a combination of LIBS and principal components analysis (PCA) has also been explored. Broad discrimination of ore mineralogy was demonstrated on the basis of the PCA of LIBS spectra in selected emission wavelength bands. The combination of PCA and PCR offers potential for both broad mineralogical and elemental analysis for the minerals industry in exploration and in mine production for the on-line monitoring of ore quality.},
author = {Death, D L and Cunningham, A P and Pollard, L J},
doi = {10.1016/j.sab.2009.07.017},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
number = {10},
pages = {1048--1058},
publisher = {Elsevier B.V.},
title = {{Multi-element and mineralogical analysis of mineral ores using laser induced breakdown spectroscopy and chemometric analysis}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854709002298},
volume = {64},
year = {2009}
}
@article{Balmer1990,
abstract = {Atomic Absorption Spectrometry 3313 Flame Atomic Absorption Spectrometry 3313 Graphite Furnace Atomic Absorption Spectrometry 3314 Hydride Generation Atomic Absorption Spectrometry 3315 Atomic Fluorescence Spectrometry 3315 Atomic Emission Spectrometry 3316 Arcs and Sparks 3316 Microwave Plasmas 3316 Inductively Coupled Plasmas 3316 Laser-Induced Plasmas 3317 Microplasmas 3318 Inductively Coupled Plasma Mass Spectrometry 3318 Fundamental Studies 3318 Instrumental Developments and Applications 3322 Glow Discharge Atomic Emission and Mass Spectrometry 3328 Fundamental Studies 3328 Methodological Developments 3330 Applications of GDMS and GD-OES 3331 Literature Cited 3333 Methodological developments in atomic spectrometry are related to new techniques in optical spectrometry as well as in elemental mass spectrometry especially, as the sources used in atomic spectrometry are prominent sources of electromagnetic radiation, absorption reservoirs for atomic absorption, and ion sources for elemental mass spectrometry. Developments in the field are related to the sources themselves and their improvement and optimization as well as with the different types of spectrometers and detectors and the different ways for optimal sampling of the analytes. Improvements in the different fields have regularly been published in the journals Analytical Chemistry, Analytical and Bioanalytical Chemistry, Analytical Sciences, Analyst, Analytica Chimica Acta, Applied Spectroscopy, Journal of Analytical Atomic Spectrometry, Mikrochimica Acta, Spectrochimica Acta, Part B, and Talanta as well as to a lesser extent in a number of other journals. These progress reports published have been considered for noting the trends of development in the fields mentioned, at the hand of a selection of the papers published in the journals named in the period January 2002 to December 2003 for the case of atomic absorption and atomic emission work, whereas for inductively coupled plasma mass spectrometry and for glow discharge atomic emission and mass spectrometry, the selection of the papers considered the journals as indicated in the respective chapters. Results in the field of atomic spectrometry in the last biannual period also were reported on the following important conferences: Winter Conference on Plasma Spectrochemistry, Scottsdale, AZ (2002), the International Conference on Atomic Spectroscopy (ICAS), Tokyo (2002), the Colloquium Spectroscopicum Internationale, Granada (2003), the European Winter Conference on Plasma Spectrochemistry, Garmisch Partenkirchen (2003), and the annual Meeting of the Federation of Analytical Chemistry and Spectroscopy Societies, in Nashville, TN (2002) and Fort Lauderdale, FL (2003) as well as in many other meetings. Progress made in the field of atomic spectrometry is discussed for the following fields: optical atomic spectrometry (atomic absorption and atomic emission spectrometry with sparks, arcs, and plasma sources at atmospheric pressure including laser plasmas); plasma mass spectrometry and optical atomic and mass spectrometry with glow discharge sources.},
author = {Balmer, The},
doi = {10.1016/0584-8547(90)80097-3},
issn = {00032700},
journal = {Atomic Spectroscopy},
number = {12},
pages = {i--ii},
pmid = {15193111},
publisher = {Marcel Dekker, Inc.},
title = {{Atomic spectroscopy}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15193111},
volume = {21},
year = {1990}
}
@article{Kucheyev2003,
abstract = {Fused silica irradiated with similar to3-ns 1064-, 355-, and 266-nm laser pulses as well as with similar to120-fs 825-nm pulses is studied by a combination of photoluminescence (PL) and Raman scattering spectroscopies. Results show that, for laser fluences above the laser-induced breakdown threshold, in all the cases studied, irradiation results in the formation of four defect-related PL bands centered on similar to1.9 (655), 2.2 (565), 2.7 (460), and 4.3 eV (290 nm). Bands centered on 1.9, 2.7, and 4.3 eV are attributed to nonbridging oxygen hole centers (1.9 eV) and oxygen-deficiency defects (2.7 and 4.3 eV). However, defects giving rise to a broad band at; 2.2 eV are unknown. For all the laser-modified samples studied, Raman spectroscopy reveals a dramatic increase in the intensity of D-1 and D-2 lines, associated with in-phase breathing motions of oxygen atoms in puckered four- and planar three-membered ring structures, respectively. This indicates laser-induced material densification. Based on these results, we discuss physical processes occurring during the catastrophic laser-induced material breakdown, leading to material densification and the formation of point defects. (C) 2003 American Institute of Physics.},
author = {Kucheyev, S O and Demos, S G},
doi = {10.1063/1.1573364},
issn = {00036951},
journal = {Applied Physics Letters},
number = {19},
pages = {3230},
title = {{Optical defects produced in fused silica during laser-induced breakdown}},
url = {http://link.aip.org/link/APPLAB/v82/i19/p3230/s1{\&}Agg=doi},
volume = {82},
year = {2003}
}
@article{Yamaguchi2005,
abstract = {Laser-induced breakdown spectroscopy (LIBS) has been developed as a rapid and easy in situ technique for the analysis of inorganic elements. Qualitative and quantitative determinations of an inorganic element can be achieved by analyzing the wavelength and intensity of the light emitted from the excited atoms arising from breakdown phenomena. Because the energy threshold of breakdown phenomena increases in the order of solid{\&}lt;liquid{\&}lt;gas, preferential breakdown of solid particles in liquid is possible by adjusting the energy of laser radiation. This rapid and easy in situ technique for the selective determination of soil particles or sediments suspended in water may enhance the effectiveness of environmental monitoring systems. In the present study, we applied LIBS to selective analyses of Al particles suspended in water. In addition, particle size effects that limit the performance of LIBS for the application of suspensions in the environment were investigated. Selective quantitative analysis of Al of gibbsite and alumina particles that were suspended in water was performed when the laser pulse energy was lower than that required for the breakdown of aqueous Al ions dissolved in water. When the Al concentration in the suspension was identical, the intensity of atomic emission from an Al particle increased with the particle size. This result was ascribed to the fact that larger particles contain more Al atoms per particle. There was a linear relationship between the cross-section area of the alumina particles and the intensity of the atomic emission per particle when the particles were small enough to exceed the threshold of breakdown. This suggested that both the particle size and Al concentration could be roughly estimated when simultaneous counting of the number of particles was accomplished by the use of laser-induced breakdown detection (LIBD).},
author = {Yamaguchi, Noriko and Hotokezaka, Hiroyasu and Nagasaki, Shinya and Tanaka, Satoru},
doi = {10.1111/j.1747-0765.2005.tb00127.x},
journal = {Soil Science and Plant Nutrition},
number = {6},
pages = {911--916},
title = {{Direct Quantitative Analysis of Particulate Aluminum Suspended in Water Using Laser-Induced Breakdown Spectroscopy}},
url = {http://dx.doi.org/10.1111/j.1747-0765.2005.tb00127.x},
volume = {51},
year = {2005}
}
@article{DeLucia2011,
author = {{De Lucia}, Frank C and Gottfried, Jennifer L},
doi = {10.1016/j.sab.2010.12.007},
issn = {05848547},
journal = {Spectrochimica Acta Part B Atomic Spectroscopy},
keywords = {explosives,laser induced breakdown spectroscopy,libs,multivariate analysis,partial least squares discriminant analysis},
number = {2},
pages = {122--128},
publisher = {Elsevier B.V.},
title = {{Influence of variable selection on partial least squares discriminant analysis models for explosive residue classification}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0584854710003356},
volume = {66},
year = {2011}
}
@article{Haider2011,
author = {Haider, A F M Y and Rony, M A and Lubna, R S and Abedin, K M},
doi = {10.1016/j.optlastec.2011.04.009},
issn = {00303992},
journal = {Optics Laser Technology},
keywords = {barapukuria coal mine,laser induced breakdown spectroscopy,ytterbium},
number = {8},
pages = {1405--1410},
publisher = {Elsevier},
title = {{Optics {\&} Laser Technology Detection of multiple elements in coal samples from Bangladesh by laser-induced breakdown spectroscopy}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S003039921100096X},
volume = {43},
year = {2011}
}
@article{Cunat2008,
abstract = {This paper reports the development and field testing of a man-portable instrument based on laser-induced breakdown spectrometry (LIBS) for inspection and analysis of speleothems. The 50 mJ of a Q-switched Nd:YAG laser operating at 1064 nm was used to generate a plasma on the sample. Plasma emission was then guided using a fiber-optic cable to a 1/10 m spectrometer equipped with a charge-coupled device (CCD) array detector. Plasma light was automatically processed in order to obtain surface and in-depth information from the speleothems. A field campaign in the interior of Nerja Cave (a large karstic formation in the South of Spain) has been carried out, aimed at evaluating the analytical performance of the instrument when operating in an unfriendly environment. Identification analysis of the speleothems' alteration layers and depth profiles of Sr and Ca is carried out and reported.},
author = {Cu{\~{n}}at, J and Fortes, F J and Cabal{\'{\i}}n, L M and Carrasco, F and Sim{\'{o}}n, M D and Laserna, J J},
institution = {Department of Analytical Chemistry, University of M{\'{a}}laga, E-29071 M{\'{a}}laga, Spain.},
journal = {Applied Spectroscopy},
number = {11},
pages = {1250--1255},
pmid = {19007468},
title = {{Man-portable laser-induced breakdown spectroscopy system for in situ characterization of karstic formations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19007468},
volume = {62},
year = {2008}
}
@article{Gronlund2006,
abstract = {A mobile lidar system was used in remote imaging laser-induced breakdown spectroscopy (LIBS) and laser-induced fluorescence (LIF) experiments. Also, computer-controlled remote ablation of a chosen area was demonstrated, relevant to cleaning of cultural heritage items. Nanosecond frequency-tripled Nd:YAG laser pulses at 355 nm were employed in experiments with a stand-off distance of 60 meters using pulse energies of up to 170 mJ. By coaxial transmission and common folding of the transmission and reception optical paths using a large computer-controlled mirror, full elemental imaging capability was achieved on composite targets. Different spectral identification algorithms were compared in producing thematic data based on plasma or fluorescence light.},
author = {Gr{\"{o}}nlund, Rasmus and Lundqvist, Mats and Svanberg, Sune},
institution = {Atomic Physics Division, Lund Institute of Technology, P.O. Box 118, SE-22100 Lund, Sweden. rasmus.gronlund@fysik.lth.se},
journal = {Applied Spectroscopy},
number = {8},
pages = {853--859},
pmid = {16925920},
title = {{Remote imaging laser-induced breakdown spectroscopy and laser-induced fluorescence spectroscopy using nanosecond pulses from a mobile lidar system.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16925920},
volume = {60},
year = {2006}
}
@article{Buteau2010,
abstract = {A standoff bioaerosol sensor based on intensified range-gated spectrometric detection of Laser Induced Fluorescence was used to spectrally characterize bioaerosol simulants during in-chamber and open-air releases at Suffield, Canada, in August 2008 from a standoff position. In total, 42 in-chamber Bacillus atrophaeus (formerly Bacillus subtilis var globigii; BG) cloud and 27 open-air releases of either BG, Pantoea agglomerans (formerly Erwinia herbicola; EH), MS2 and ovalbumin (OV) were generated. The clouds were refereed by different point sensors including Aerodynamic Particle Sizer (APS) and slit or impingers samplers. The APS monitored the particle size distribution and concentration and the samplers characterized the viable portion of the cloud. The extracted spectral signatures show robustness to different degree. The correlation assessment showed good results in most cases where the LIF signal to noise ratio was significant. The sensor 4$\sigma$ sensitivity was evaluated to 1 300, 600, 100 and 30 ppl for BG, OV, MS2 and EH respectively. Correlation results are presented by plotting the SINBAHD metric versus the corresponding particle concentration, in which case, the obtained slope is proportional to the material fluorescence cross-section. The different acquired signal is hence compared in terms of their fluorescence cross-section additionally to their spectral characteristics.},
author = {Buteau, Sylvie and Simard, JR and Rowsell, Susan},
file = {:E$\backslash$:/Mina Dokument/Mendeley/Buteau, Simard, Rowsell - Bioaerosol standoff detection and correlation assessment with concentration and viability point sensors - 2010.pdf:pdf},
journal = {Society of Photo-Optical},
keywords = {acpla,aerosol,biological agent simulant,laser-induced fluorescence,lif,ppl,standoff detection},
number = {August},
title = {{Bioaerosol standoff detection and correlation assessment with concentration and viability point sensors}},
url = {http://pubs.drdc.gc.ca/PDFS/unc107/p534626{\_}A1b.pdf},
volume = {2008},
year = {2010}
}
@article{DeLucia2009,
abstract = {Recently laser-induced breakdown spectroscopy (LIBS) has been investigated as a potential technique for trace explosive detection. Typically LIBS is performed using nanosecond laser pulses. For this work, we have investigated the use of femtosecond laser pulses for explosive residue detection at two different fluences. Femtosecond laser pulses have previously been shown to provide several advantages for laser ablation and other LIBS applications. We have collected LIBS spectra of several bulk explosives and explosive residues at different pulse durations and energies. In contrast to previous femtosecond LIBS spectra of explosives, we have observed atomic emission peaks for the constituent elements of explosives - carbon, hydrogen, nitrogen, and oxygen. Preliminary results indicate that several advantages attributed to femtosecond pulses are not realized at higher laser fluences.},
author = {{De Lucia}, Frank C and Gottfried, Jennifer L and Miziolek, Andrzej W},
file = {::},
issn = {1094-4087},
journal = {Optics express},
month = {jan},
number = {2},
pages = {419--25},
pmid = {19158854},
title = {{Evaluation of femtosecond laser-induced breakdown spectroscopy for explosive residue detection.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19158854},
volume = {17},
year = {2009}
}
@article{Praher2000,
abstract = {Calibration-free laser-induced breakdown spectroscopy (CF-LIBS) method is employed for quantitative determination of oxide concentrations in multi-component materials. Industrial oxide materials from steel industry are laser ablated in air, and the optical plasma emission is collected by spectrometers and gated detectors. The temperature and electron number density of laser-induced plasma are determined from measured LIBS spectra. Emission lines of aluminium (Al), calcium (Ca), iron (Fe), manganese (Mn), magnesium (Mg), silicon (Si), titanium (Ti), and chromium (Cr) of low self-absorption are selected, and the concentration of oxides CaO, Al(2)O(3), MgO, SiO(2), FeO, MnO, TiO(2), and Cr(2)O(3) is calculated by CF-LIBS analysis. For all sample materials investigated, we find good match of calculated concentration values (C (CF)) with nominal concentration values (C (N)). The relative error in oxide concentration, e (r)=C (CF)-C (N)/C (N), decreases with increasing concentration and it is e (r)100{\%} for concentration C (N)1wt.{\%}. The CF-LIBS results are stable against fluctuations of experimental parameters. The variation of laser pulse energy over a large range changes the error by less than 10{\%} for major oxides (C (N)10wt.{\%}). The results indicate that CF-LIBS method can be employed for fast and stable quantitative compositional analysis of multi-component materials.},
author = {Praher, B and R{\"{o}}ssler, R and Arenholz, E and Heitz, J and Pedarnig, J D},
doi = {10.1007/s00216-011-5000-9},
issn = {16182650},
journal = {Analytical and Bioanalytical Chemistry},
number = {2002},
pages = {245--250},
pmid = {21523330},
title = {{A note on testing for nonlinearity with partially observed time series}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21527623},
year = {2000}
}
@article{Wormhoudt2005,
abstract = {Laser-induced breakdown spectroscopy using a microchip laser and a miniature spectrometer has been applied to the determination of carbon in steel. The goal was to investigate the capability of an apparatus, made up of commercial components, that could form the basis of a handheld device. The typical precision obtained in the range of C/Fe weight ratios of 0.001 to 0.01 was 4.3{\%}, and the limit of detection was a C/Fe ratio of 400 ppm. This is higher than values reported for conventional systems and is primarily determined by systematic variations in the spectra and not by signal intensity levels. These systematic variations are ascribed to two causes: the use of an ungated detector and the spatial variability of the emission plume.},
author = {Wormhoudt, J and Iannarilli, F J and Jones, S and Annen, K D and Freedman, A},
doi = {10.1366/0003702055012528},
issn = {00037028},
journal = {Applied Spectroscopy},
number = {9},
pages = {1098--102},
pmid = {18028607},
title = {{Determination of carbon in steel by laser-induced breakdown spectroscopy using a microchip laser and miniature spectrometer.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18028607},
volume = {59},
year = {2005}
}
@article{Cristoforetti,
author = {Cristoforetti, Gabriele and Legnaioli, Stefano and Palleschi, Vincenzo and Salvetti, A},
file = {::},
journal = {essex.ac.uk},
title = {{A new self-calibrated method for precise quantitative analysis by laser induced breakdown spectroscopy}},
url = {http://www.essex.ac.uk/bs/libs/papersLIBS/palleschi.pdf}
}
@article{Zhang2009,
abstract = {A LIBS setup was built in the Institute of Modern Physics. In our experiments, LIBS spectra produced by infrared radiation of Nd:YAG nanosecond laser with 100 and 150 mJ pulse energy, respectively, were measured by fiber optic spectrometer in the ranges of 230-430 nm and 430-1 080 nm with a delay time of 1.7 and gate width of 2 ms for potato and lily samples prepared by vacuum freeze-dried technique. The lines from different metal elements such as K, Ca, Na, Mg, Fe, Al, Mn and Ti, and nonmetal elements such as C, N, O and H, and some molecular spectra from C2, CaO, and CN were identified according to their wavelengths. The relative content of the six microelements, Ca, Na, K, Fe, Al, and Mg in the samples were analyzed according to their representative line intensities. By comparison we found that there are higher relative content of Ca and Na in lily samples and higher relative content of Mg in potato samples. The experimental results showed that LIBS technique is a fast and effective means for measuring and comparing the contents of microelements in plant samples.},
author = {Zhang, Da-Cheng and Ma, Xin-Wen and Zhu, Xiao-Long and Li, Bin and Zu, Kai-Ling},
institution = {Institute of Modern Physics, the Chinese Academy of Sciences, Lanzhou, 730000, China. dch-zhang@impcas.ac.cn},
journal = {Guang pu xue yu guang pu fen xi Guang pu},
number = {5},
pages = {1189--1192},
title = {{Microelements in potato and lily samples studied by laser-induced breakdown spectroscopy technology}},
volume = {29},
year = {2009}
}
@article{Hug2009,
abstract = {Photon Systems and JPL are continuing development of a new technology robot-mounted or hand-held sensor for reagentless, short-range, standoff detection and identification of trace levels CBE materials on surfaces. This deep ultraviolet CBE sensor is the result of ongoing Army STTR and DTRA programs. The evolving 6 lb, 15W, lantern-size sensor can discriminate CBE from background clutter materials using a combination of deep UV excited resonance Raman (RR) and laser induced native fluorescence (LINF) emissions resulting from excitation by a new technology deep UV laser. Standoff excitation of suspicious packages, vehicles, persons, and other objects that may contain hazardous materials is accomplished using wavelengths below 250nm where RR and LINF emissions occupy distinctly different wavelength regions. This enables simultaneous detection of RR and LINF emissions with no spectral overlap or interference of LINF over RR or RR over LINF.},
author = {Hug, W. F. and Reid, R. D. and Bhartia, R. and Lane, a. L.},
file = {::},
journal = {Proceedings of SPIE},
keywords = {and explosives detection and,biological,chemical,classification,deep uv raman,native fluorescence},
pages = {73040Z--73040Z--8},
publisher = {Spie},
title = {{Performance status of a small robot-mounted or hand-held, solar-blind, standoff chemical, biological, and explosives (CBE) sensor}},
url = {http://link.aip.org/link/PSISDG/v7304/i1/p73040Z/s1{\&}Agg=doi},
volume = {7304},
year = {2009}
}
@article{Kane2009,
abstract = {We present the absolute resonance Raman scattering (RRS) intensities of uracil, rhodamine 6G (R6G), and iron(II) porphyrin with imidazole and CO ligands (FePImCO) calculated using density functional theory (DFT). The spectra are calculated using both the vibronic theory and the short-time approximation. We find that the absolute RRS intensities calculated using the short-time approximation are severely overestimated, as compared with results obtained using the vibronic theory. This issue is attributed to the sensitivity of the absolute RRS intensities to the adjustable damping factor within the short-time approximation. This is illustrated for uracil, for which the relative intensities were predicted accurately using the short-time approximation, but the absolute intensities were still overestimated. Although intensities comparable to that obtained with the vibronic theory could be obtained using the short-time approximation, it requires a large damping factor, roughly twice that estimated from the absorption spectrum, to be used in the simulations. Furthermore, we find that DFT underestimates the absolute RRS intensities for R6G as compared to experiments, which is most likely due to the neglect of solvent effects in the calculations. For R6G and FePImCO, vibronic effects are shown to enhance the low-frequency modes relatively more, improving the agreement with experiments.},
author = {Kane, KA},
file = {::},
journal = {The Journal of Physical Chemistry C},
number = {12},
pages = {5540--5546},
title = {{Calculation of Absolute Resonance Raman Intensities : Vibronic Theory vs Short-Time}},
url = {http://pubs.acs.org/doi/abs/10.1021/jp906152q},
volume = {114},
year = {2009}
}
@article{Gillis2010,
abstract = {Recently, researchers at the Naval Research Laboratory have developed the SWORrD system for measuring twodimensional Raman Spectra. The device consists of a tunable 2d ultraviolet laser that illuminates the sample at various wavelengths (210-300 nm) and collects a single Raman spectrum at each laser wavelength. The single spectra are combined to form a two-dimensional spectrum (laser wavelength by scattered wavenumber). In this paper we introduce a novel method for the detection of known agents (‘targets’) within measured 2d spectra. Our method is bases on ‘linear mixed pixel’ techniques from hyperspectral imagery; in particular, we generalize the Adaptive Subspace Detector (ASD) to a form suitable for SWORrD samples. Our detector uses the individual laser runs to define a set of points within wavenumber space; the set of points corresponding to a 2d spectra defines a particular subspace that contains each material. These subspaces are then used with ASD to identify targets. We include experimental results using real-world data to illustrate our results.},
author = {Gillis, David and Grun, Jacob and Bowles, Jeffrey and Lunsford, Robert and Nikitin, Sergei and Manka, Charles},
file = {::},
journal = {Library},
keywords = {mixed samples,raman spectroscopy,target detection},
pages = {76651D--76651D--9},
title = {{Detection of chemicals in mixed, two-dimensional Raman spectra}},
url = {http://link.aip.org/link/PSISDG/v7665/i1/p76651D/s1{\&}Agg=doi},
volume = {7665},
year = {2010}
}
@article{Christesen2010,
abstract = {Raman spectroscopy is a very powerful technique for molecular identification, and small Raman instruments have been used successfully to identify toxic substances. The sensitivity of the technique, however, can be limited by fluorescence interference arising from the analyte itself or sample impurities. In the case of surface detection, the Raman signature and/or fluorescence from the surface can also interfere with identification of the target chemical. We take advantage of the polarization characteristics of the Raman scattering to reduce the broadband fluorescence background and surface Raman features. Using a custom fiber optic probe with excitation at 785 nm, we have demonstrated real-time polarization analysis. The spectrum obtained by ratioing the parallel and perpendicular polarization components of the Raman scattering, reduces the surface signature and has a better spectral correlation to the target analyte.},
author = {Christesen, Steven},
file = {::},
journal = {Proceedings of SPIE},
keywords = {depolarization ratio,polarization,raman,surface detection},
pages = {76651B--76651B--7},
title = {{Improved Raman sensitivity using polarization analysis}},
url = {http://link.aip.org/link/PSISDG/v7665/i1/p76651B/s1{\&}Agg=doi},
volume = {7665},
year = {2010}
}
@article{Ehlerding2010,
abstract = {Stand-off measurements on nitromethane (NM), 2,4-DNT and 2,4,6-TNT in vapor phase using resonance Raman spectroscopy have been performed. The Raman cross sections for NM, DNT and TNT in vapor phase have been measured in the wavelength range 210-300 nm under laboratory conditions, in order to estimate how large resonance enhancement factors can be achieved for these explosives. The measurements show that the signal is greatly enhanced, up to 250.000 times for 2,4-DNT and 60.000 times for 2,4,6-TNT compared to the non-resonant signal at 532 nm. For NM the resonance enhancement enabled realistic outdoor measurements in vapor phase at 13 m distance. This all indicate a potential for resonance Raman spectroscopy as a stand-off technique for detection of vapor phase explosives.},
author = {Ehlerding, Anneli and Johansson, Ida and Wallin, Sara and Ostmark, Henric},
file = {::},
journal = {Proceedings of SPIE},
keywords = {explosives,raman spectroscopy,resonance enhancement,resonance raman,stand-off detection},
pages = {783507--783507--9},
title = {{Stand-off detection of vapor phase explosives by resonance enhanced Raman spectroscopy}},
url = {http://link.aip.org/link/PSISDG/v7835/i1/p783507/s1{\&}Agg=doi},
volume = {7835},
year = {2010}
}
@article{Pettersson2010,
abstract = {This paper gives a brief overview on our latest progress in the area of standoff detection. Standoff Raman measurements from 200 m and 470 m distance have been performed on bulk amounts of TATP and AN respectively, the former through a double sided window, the latter under heavy rain. Resonance Raman measurements on TNT, DNT and NM vapors in the ppm concentration regime are presented, showing resonance enhancement in the range of 2 200 (NM) to 57 000 (TNT) as compared to 532 nm Raman cross sections. Finally, the application of hyper spectral Raman imaging is described, exemplified by the resolution of four different samples (sulphur, AN, DNT, and TNT) in the form of 5 mm wide discs in one single image},
author = {Pettersson, Anna and Wallin, Sara and Ostmark, Henric and Ehlerding, Anneli and Johansson, Ida and Nordberg, Markus and Ellis, Hanna and Al-Khalili, Ahmed},
file = {::},
journal = {Russell The Journal Of The Bertrand Russell Archives},
keywords = {detection,explosives,ied,imaging,raman,resonance enhanced,rrs,spectroscopy,standoff,vapors},
pages = {76641K--76641K--12},
title = {{Explosives standoff detection using Raman spectroscopy: from bulk towards trace detection}},
url = {http://link.aip.org/link/PSISDG/v7664/i1/p76641K/s1{\&}Agg=doi},
volume = {7664},
year = {2010}
}
@article{Clauson2004,
abstract = {Resonance Raman spectroscopy is an enhanced Raman technique that can be used to selectively identify a particular analyte in complex matrices. Resonance Raman requires the excitation laser to overlap with an absorption band of the analyte of interest. Since analytes have diverse absorption spectra, dilute concentrations may be detected when resonantly enhanced. A significant portion of interesting molecules absorb only in the UV; unfortunately current UV Raman instrumentation for scientifically desirable spectral resolution is large and costly. In the area of Homeland Defense, explosives, nerve agents, amino acid residues (for toxin analysis) and nucleic acids (for DNA detection and identification of bacteria) are all enhanced using UV laser sources. EIC Laboratories has developed a more user-friendly UVRRS spectrograph that is based upon the use of an echelle grating. The spectrograph has a footprint of 7” x 11” and is capable of providing 4 cm-1 resolution over a fairly wide spectral range. The spectrograph design and spectra from analytes of particular relevance will be presented.},
author = {Clauson, Susan L.},
file = {::},
issn = {0277786X},
journal = {Proceedings of SPIE},
keywords = {high resolution,raman,spectrograph,ultraviolet},
pages = {34--41},
publisher = {Spie},
title = {{High-resolution UV echelle spectrograph for environmental sensing}},
url = {http://link.aip.org/link/?PSI/5269/34/1{\&}Agg=doi},
volume = {5269},
year = {2004}
}
@article{Hagen2009,
abstract = {We have designed and constructed a coded aperture spectrometer for use in the deep UV range. The Czerny- Turner design provides sufficient spectral resolution to observe Raman scattering features, while the use of a coded aperture provides a greatly improved light collection efficiency for scattering sources. The resulting instrument is capable of analyzing Raman spectra from samples at a 1 meter viewing distance. We provide an overview of the system, its optical design, and some preliminary measurements.},
author = {Hagen, Nathan and Brady, David J.},
file = {::},
journal = {Proceedings of SPIE},
keywords = {chemical detection,coded aperture,multiplex measurement,raman spectroscopy,remote sensing},
pages = {73190D--73190D--10},
publisher = {Spie},
title = {{Coded-aperture DUV spectrometer for stand-off Raman spectroscopy}},
url = {http://link.aip.org/link/PSISDG/v7319/i1/p73190D/s1{\&}Agg=doi},
volume = {7319},
year = {2009}
}
@inproceedings{Guicheteau2011,
abstract = {We are actively investigating the use of Raman spectroscopy for proximal standoff detection of chemicals and explosive materials on surfaces. These studies include Raman Chemical Imaging of contaminated fingerprints for forensic attribution and the assessments of commercial handheld or portable Raman instruments operating with near-infrared (IR) as well as ultraviolet (UV) laser excitation specifically developed for on-the-move reconnaissance of chemical contamination. As part of these efforts, we have measured the Raman cross sections of chemical agents, toxic industrial chemicals, and explosives from the UV to NIR. We have also measured and modeled the effect interrogation angle has on the Raman return from droplets on man-made surfaces. Realistic droplet distributions have been modeled and tested against variations in surface scan patterns and laser spot size for determining the optimum scan characteristics for detection of relevant surface},
author = {Guicheteau, J.A. and Christesen, S.D. and Tripathi, A. and Emmons, E.D. and Wilcox, P.G. and Emge, D.K. and Pardoe, I.J. and {Fountain III}, A.W.},
booktitle = {Proceedings of SPIE},
file = {::},
pages = {818902},
title = {{Proximal and point detection of contaminated surfaces using Raman spectroscopy}},
url = {http://link.aip.org/link/?PSISDG/8189/818902/1},
volume = {8189},
year = {2011}
}
@article{Patel2009,
abstract = {Laser based detection of gaseous, liquid and solid residues and trace amounts has been developed ever since lasers were invented. However, the lack of availability of reasonably high power tunable lasers in the spectral regions where the relevant targets can be interrogated as well as appropriate techniques for high sensitivity, high selectivity detection has hampered the practical exploitation of techniques for the detection of targets important for homeland security and defense applications. Furthermore, emphasis has been on selectivity without particular attention being paid to the impact of interfering species on the quality of detection. Having high sensitivity is necessary but not a sufficient condition. High sensitivity assures a high probability of detection of the target species. However, it is only recently that the sensor community has come to recognize that any measure of probability of detection must be associated with a probability of false alarm, if it is to have any value as a measure of performance. This is especially true when one attempts to compare performance characteristics of different sensors based on different physical principles. In this paper, I will provide a methodology for characterizing the performance of sensors utilizing optical absorption measurement techniques. However, the underlying principles are equally application to all other sensors. While most of the current progress in high sensitivity, high selectivity detection of CWAs, TICs and explosives involve identifying and quantifying the target species in-situ, there is an urgent need for standoff detection of explosives from safe distances. I will describe our results on CO2 and quantum cascade laser (QCL) based photoacoustic sensors for the detection of CWAs, TICs and explosives as well the very new results on stand-off detection of explosives at distances up to 150 meters. The latter results are critically important for assuring safety of military personnel in battlefield environment, especially from improvised explosive devices (IEDs), and of civilian personnel from terrorist attacks in metropolitan areas.},
author = {Patel, C. Kumar N.},
file = {::},
journal = {Proceedings of SPIE},
pages = {748402--748402--14},
publisher = {Spie},
title = {{Laser based in-situ and standoff detection of chemical warfare agents and explosives}},
url = {http://link.aip.org/link/PSISDG/v7484/i1/p748402/s1{\&}Agg=doi},
volume = {7484},
year = {2009}
}
@article{Ehlerding2012,
abstract = {Resonance-enhanced Raman spectroscopy has been used to perform standoff measurements on nitromethane (NM), 2,4-DNT, and 2,4,6-TNT in vapor phase. The Raman cross sections for NM, DNT, and TNT in vapor phase have been measured in the wavelength range 210–300nm under laboratory conditions, in order to estimate how large resonance enhancement factors can be achieved for these explosives. The results show that the signal is enhanced up to 250,000 times for 2,4-DNT and up to 60,000 times for 2,4,6-TNT compared to the nonresonant signal at 532 nm. Realistic outdoor measurements on NM in vapor phase at 13m distance were also performed, which indicate a potential for resonance Raman spectroscopy as a standoff technique for detection of vapor phase explosives. In addition, the Raman spectra of acetone, ethanol, and methanol were measured at the same wavelengths, and their influence on the spectrum from NM was investigated. 1. Introduction Improvised explosive devices (IEDs) are a common and a growing threat to the civilian society as well as to peace-keeping operations. Today, detection and identification of explosive charges and IEDs in real environments (indoors or outdoors) is a very challenging task and can in many cases also be a very hazardous operation. IEDs are in a way unique compared to regular ordnances, since the IED manufacturer has to improvise the design and use whatever materials are available. For this reason, the threat varies over time and in different parts of the world; it also evolves as countermeasures are taken. The diverse and varying nature of IEDs poses great challenges to the methods for their detection since they can contain any explosive which is available; thismeans commercial, military, or homemade explosives (HMEs). An overview of HME properties is given by Menning and Ostmark [1]. From the perspective of the user of the detection equipment, much would be gained if detection and identification could be},
author = {Ehlerding, Anneli and Johansson, Ida and Wallin, Sara and {\"{O}}stmark, Henric},
file = {::},
issn = {1687-9449},
journal = {International Journal of Spectroscopy},
pages = {1--9},
title = {{Resonance-Enhanced Raman Spectroscopy on Explosives Vapor at Standoff Distances}},
url = {http://www.hindawi.com/journals/ijs/2012/158715/},
volume = {2012},
year = {2012}
}
@inproceedings{Schulze1999,
abstract = {Ultraviolet resonance Raman spectroscopy (UVRRS) is becoming a very popular spectroscopic method for bioanalytical investigations due to its high sensitivity, lack of fluorescence, and suitability for use in aqueous solutions. We have made a number of technological advances, especially the development of fiber-optic-based technologies, which pennit the performance of remote/in-situ UVRRS measurements. We will be reporting on improved optical fiber probes (OFPs) and demonstrate their benefits in perfonning UVRRSon neuroiransmitters, saliva, and ur},
author = {Schulze, H.G. and Barbosa, C.J. and Greek, L.S. and Turner, R.F.B. and Haynes, C.A. and Klein, K.F. and Blades, M.W.},
booktitle = {SPIE Conference on Biomedical Applications of Raman Spectroscopy, San Jose, California, SPIE},
file = {::},
keywords = {biological samples,ccd,deep uv resonance raman,fiber optics,iccd,spectroscopy},
number = {January 1999},
pages = {157--166},
publisher = {Citeseer},
title = {{Advances in fiber optic-based UV resonance Raman spectroscopy techniques for anatomical and physiological investigations}},
url = {http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.33.2473{\&}amp;rep=rep1{\&}amp;type=pdf},
volume = {3608},
year = {1999}
}
@article{SedlacekIII2004,
abstract = {Brookhaven National Laboratory (BNL), Edgewood Chemical and Biological Center (ECBC) and ITT Industries Advanced Engineering and Sciences Division (AES) have been collaborating on the transitioning and subsequent development of a short-range, non-contact Raman lidar system specifically designed to detect and identify chemical agents on the battlefield. [The instrument, referred to as LISA (Laser Interrogation of Surface Agents), will the subject of an accompanying paper.] As part of this collaboration, BNL has the responsibility for developing a spectral database (library) of surrogates and precursors for use with LISA’s pattern recognition algorithms. In this paper, the authors discuss the phenomenon of UV Raman and resonance-enhanced Raman spectroscopy, the development of an instrument-independent Raman spectral library, and highlight the exploitable characteristics present in the acquired spectral signatures that suggest potential utility in our country’s efforts on Homeland Security.},
author = {{Sedlacek III}, Arthur J.},
file = {::},
issn = {0277786X},
journal = {Proceedings of SPIE},
pages = {23--33},
publisher = {Spie},
title = {{Application of UV-Raman spectroscopy to the detection of chemical and biological threats}},
url = {http://link.aip.org/link/?PSI/5269/23/1{\&}Agg=doi},
volume = {5269},
year = {2004}
}
@article{Neugebauer2002b,
abstract = {In this work we demonstrate how different modern quantum chemical methods can be efficiently combined and applied for the calculation of the vibrational modes and spectra of large molecules. We are aiming at harmonic force fields, and infrared as well as Raman intensities within the double harmonic approximation, because consideration of higher order terms is only feasible for small molecules. In particular, density functional methods have evolved to a powerful quantum chemical tool for the determination of the electronic structure of molecules in the last decade. Underlying theoretical concepts for the calculation of intensities are reviewed, emphasizing necessary approximations and formal aspects of the introduced quantities, which are often not explicated in detail in elementary treatments of this topic. It is shown how complex quantum chemistry program packages can be interfaced to new programs in order to calculate IR and Raman spectra. The advantages of numerical differentiation of analytical gradients, dipole moments, and static, as well as dynamic polarizabilities, are pointed out. We carefully investigate the influence of the basis set size on polarizabilities and their spatial derivatives. This leads us to the construction of a hybrid basis set, which is equally well suited for the calculation of vibrational frequencies and Raman intensities. The efficiency is demonstrated for the highly symmetric C(60), for which we present the first all-electron density functional calculation of its Raman spectrum.},
author = {Neugebauer, Johannes and Reiher, Markus and Kind, Carsten and Hess, Bernd a},
file = {::},
issn = {0192-8651},
journal = {Journal of computational chemistry},
keywords = {computation,fullerene,infrared intensities,parallel,quantum chemistry,raman intensities,vibrational spectroscopy},
month = {jul},
number = {9},
pages = {895--910},
title = {{Quantum chemical calculation of vibrational spectra of large molecules--Raman and IR spectra for Buckminsterfullerene.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11984851},
volume = {23},
year = {2002}
}
@article{Huestis2010,
abstract = {Avoiding or minimizing potential damage from improvised explosive devices (IEDs) such as suicide, roadside, or vehicle bombs requires that the explosive device be detected and neutralized outside its effective blast radius. Only a few seconds may be available to both identify the device as hazardous and implement a response. As discussed in a study by the National Research Council, current technology is still far from capable of meeting these objectives. Conventional nitrocarbon explosive chemicals have very low vapor pressures, and any vapors are easily dispersed in air. Many pointdetection approaches rely on collecting trace solid residues from dust particles or surfaces. Practical approaches for standoff detection are yet to be developed. For the past 5 years, SRI International has been working toward development of a novel scheme for standoff detection of explosive chemicals that uses infrared (IR) laser evaporation of surfacebound explosive followed by ultraviolet (UV) laser photofragmentation of the explosive chemical vapor, and then UV laser-induced fluorescence (LIF) of nitric oxide. This method offers the potential of long standoff range (up to 100 m or more), high sensitivity (vaporized solid), simplicity (no spectrometer or library of reference spectra), and selectivity (only nitrocompounds).},
author = {Huestis, David L. and Smith, Gregory P. and Oser, Harald},
file = {::},
journal = {Nanotechnology},
keywords = {1,1 point and standoff,detection requirements and strategies,ieds,improvised explosive devices,infrared laser evaporation,introduction and background,lif,nitrocarbon explosive chemicals,photofragmentation,standoff detection,ultraviolet laser,ultraviolet laser-induced fluorescence},
pages = {76790G--76790G--10},
title = {{Laser-based standoff detection of surface-bound explosive chemicals}},
url = {http://link.aip.org/link/PSISDG/v7679/i1/p76790G/s1{\&}Agg=doi},
volume = {7679},
year = {2010}
}
@article{Jensen2006a,
abstract = {In this work, we present the first calculation of the resonance Raman scattering (RRS) spectrum of rhodamine 6G (R6G) which is a prototype molecule in surface-enhanced Raman scattering (SERS). The calculation is done using a recently developed time-dependent density functional theory (TDDFT) method, which uses a short-time approximation to evaluate the Raman scattering cross section. The normal Raman spectrum calculated with this method is in good agreement with experimental results. The calculated RRS spectrum shows qualitative agreement with SERS results at a wavelength that corresponds to excitation of the S(1) state, but there are significant differences with the measured RRS spectrum at wavelengths that correspond to excitation of the vibronic sideband of S(1). Although the agreement with the experiments is not perfect, the results provide insight into the RRS spectrum of R6G at wavelengths close to the absorption maximum where experiments are hindered due to strong fluorescence. The calculated resonance enhancements are found to be on the order of 10(5). This indicates that a surface enhancement factor of about 10(10) would be required in SERS in order to achieve single-molecule detection of R6G.},
author = {Jensen, Lasse and Schatz, George C},
file = {::},
issn = {1089-5639},
journal = {The journal of physical chemistry. A},
month = {may},
number = {18},
pages = {5973--7},
title = {{Resonance Raman scattering of rhodamine 6G as calculated using time-dependent density functional theory.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16671663},
volume = {110},
year = {2006}
}
@article{Misra2010,
abstract = {We present data on standoff detection of chemicals used in synthesis of homemade explosives (HME) using a compact portable standoff Raman system developed at the University of Hawaii. Data presented in this article show that good quality Raman spectra of various organic and inorganic chemicals, including hazardous chemicals such as ammonium nitrate, potassium nitrate, potassium perchlorate, sulfur, nitrobenzene, benzene, acetone, and gasoline, can be easily obtained from remote distances with a compact standoff Raman system utilizing only a regular 85 mm Nikon camera lens as collection optics. Raman spectra of various chemicals showing clear Raman fingerprints obtained from targets placed at 50 m distance in daylight with 1 to 10 second of integration time are presented in this article. A frequencydoubled mini Nd:YAG pulsed laser source (532 nm, 30 mJ/pulse, 20 Hz, pulse width 8 ns) is used in an oblique geometry to excite the target located at 50 m distance. The standoff Raman system uses a compact spectrograph of size 10 cm (length) x 8.2 cm (width) x 5.2 cm (height) with spectral coverage from 100 to 4500 cm-1 Stokes-Raman shifted from 532 nm laser excitation and is equipped with a gated thermo-electrically cooled ICCD detector. The system is capable of detecting both the target as well as the atmospheric gases before the target. Various chemicals could be easily identified through glass, plastic, and water media. Possible applications of the standoff Raman system for homeland security and environmental monitoring are discussed},
author = {Misra, Anupam K. and Sharma, Shiv K. and Bates, David E. and Acosta, Tayro E.},
file = {::},
journal = {Proceedings of SPIE},
keywords = {daytime raman spectroscopy,explosive detection,homemade explosives,inorganic and organic compounds,standoff raman system,time-gated remote raman},
pages = {76650U--76650U--11},
title = {{Compact standoff Raman system for detection of homemade explosives}},
url = {http://link.aip.org/link/PSISDG/v7665/i1/p76650U/s1{\&}Agg=doi},
volume = {7665},
year = {2010}
}
