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In: Proceedings of the 25th Annual International Conference of the IEEE; 17\u201321 September 2003; Cancun, Mexico. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/ieeexplore.ieee.org\/stamp\/stamp.jsp?tp=&arnumber=1279912\" xlink:type=\"simple\">http:\/\/ieeexplore.ieee.org\/stamp\/stamp.jsp?tp=&amp;arnumber=1279912<\/ext-link>. Accessed 1 February2013.","DOI":"10.1109\/IEMBS.2003.1279912"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1802","DOI":"10.1073\/pnas.1116772109","article-title":"Noninvasive inference of the molecular chemotactic response using bacterial trajectories","volume":"109","author":"JB Masson","year":"2012","journal-title":"PNAS"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1109\/TCSVT.2011.2177937","article-title":"Simplified multitarget tracking using the PHD filter for microscopic video data","volume":"22","author":"TM Wood","year":"2012","journal-title":"IEEE T Circ Syst Vid"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2238","DOI":"10.1128\/AEM.66.5.2238-2242.2000","article-title":"A new system for three-dimensional tracking of motile microorganisms","volume":"66","author":"R Thar","year":"2000","journal-title":"Appl Environ Microbiol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"4987","DOI":"10.1128\/AEM.00158-06","article-title":"Collective bacterial dynamics revealed using a three-dimensional population-scale defocused particle tracking technique","volume":"72","author":"M Wu","year":"2006","journal-title":"Appl Env Microbiol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1128\/jb.175.5.1235-1238.1993","article-title":"Inhibition of <italic>Escherichia coli<\/italic> chemotaxis by omega-conotoxin, a calcium ion channel blocker","volume":"175","author":"LS Tisa","year":"1993","journal-title":"J Bacteriol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2916","DOI":"10.1214\/10-AOS799","article-title":"Kernel density estimation via diffusion","volume":"38","author":"ZI Botev","year":"2010","journal-title":"Ann Stat"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1109\/5.18626","article-title":"A tutorial on hidden Markov models and selected applications in speech recognition","volume":"77","author":"LR Rabiner","year":"1989","journal-title":"Proc IEEE"},{"key":"ref33","unstructured":"Press WH, Teukolsky SA, Vetterling WT, Flannery BP (2007) Numerical recipes: the art of scientific computing. Cambridge University Press."},{"key":"ref34","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1088\/1478-3975\/4\/3\/007","article-title":"Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments","volume":"4","author":"JF Beausang","year":"2007","journal-title":"Phys Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e1000556+","DOI":"10.1371\/journal.pcbi.1000556","article-title":"A hidden Markov model for single particle tracks quantifies dynamic interactions between LFA-1 and the actin cytoskeleton","volume":"5","author":"R Das","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref36","unstructured":"Conn AR, Gould NIM, Toint PL (1987) Trust-Region Methods. Society for Industrial and Applied Mathematics."},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1002\/(SICI)1097-0258(20000515)19:9<1141::AID-SIM479>3.0.CO;2-F","article-title":"Bootstrap confidence intervals: when, which, what? a practical guide for medical statisticians","volume":"19","author":"J Carpenter","year":"2000","journal-title":"Stat Med"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1016\/j.bpj.2011.05.070","article-title":"Steps and bumps: precision extraction of discrete states of molecular machines","volume":"101","author":"MA Little","year":"2011","journal-title":"Biophys J"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1007\/BF00277392","article-title":"Models of dispersal in biological systems","volume":"26","author":"HG Othmer","year":"1988","journal-title":"J Math Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1128\/JB.154.1.312-323.1983","article-title":"Adaptation kinetics in bacterial chemotaxis","volume":"154","author":"SM Block","year":"1983","journal-title":"J Bacteriol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1016\/S0006-3495(00)76678-1","article-title":"Response kinetics of tethered <italic>Rhodobacter sphaeroides<\/italic> to changes in light intensity","volume":"78","author":"RM Berry","year":"2000","journal-title":"Biophys J"},{"key":"ref42","unstructured":"Brown MT (2009). Control of the unidirectional motor in <italic>Rhodobacter sphaeroides<\/italic> [PhD dissertation]. Oxford: Department of Biochemistry, University of Oxford. 141 p. [<ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/ora.ox.ac.uk\/objects\/uuid:1e9aa2bb-0e16-45df-9164-fd859a724157\" xlink:type=\"simple\">http:\/\/ora.ox.ac.uk\/objects\/uuid:1e9aa2bb-0e16-45df-9164-fd859a724157<\/ext-link>]."},{"key":"ref43","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/S0014-5793(97)00473-0","article-title":"The <italic>Rhodobacter sphaeroides<\/italic> flagellar motor is a variable-speed rotor","volume":"409","author":"HL Packer","year":"1997","journal-title":"FEBS Lett"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1093\/biomet\/48.1-2.109","article-title":"Goodness-of-fit tests on a circle","volume":"48","author":"GS Watson","year":"1961","journal-title":"Biometrika"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"6195","DOI":"10.1073\/pnas.92.13.6195","article-title":"Three-dimensional tracking of motile bacteria near a solid planar surface","volume":"92","author":"PD Frymier","year":"1995","journal-title":"PNAS"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1016\/S0006-3495(90)82436-X","article-title":"Chemotaxis of bacteria in glass capillary arrays. <italic>Rhodobacter sphaeroides<\/italic>, motility, microchannel plate, and light scattering","volume":"58","author":"HC Berg","year":"1990","journal-title":"Biophys J"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"48102+","DOI":"10.1103\/PhysRevLett.106.048102","article-title":"Enhanced diffusion due to active swimmers at a solid surface","volume":"106","author":"G Mi\u00f1o","year":"2011","journal-title":"Phys Rev Lett"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1093\/genetics\/116.4.499","article-title":"Doing behavioral genetics with bacteria","volume":"116","author":"JS Parkinson","year":"1987","journal-title":"Genetics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"3596","DOI":"10.1128\/IAI.60.9.3596-3600.1992","article-title":"Isolation of nonchemotactic mutants of <italic>Campylobacter jejuni<\/italic> and their colonization of the mouse intestinal tract","volume":"60","author":"T Takata","year":"1992","journal-title":"Infect Immun"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1093\/genetics\/114.3.717","article-title":"General nonchemotactic mutants of <italic>Caulobacter crescentus<\/italic>","volume":"114","author":"B Ely","year":"1986","journal-title":"Genetics"},{"key":"ref51","doi-asserted-by":"crossref","DOI":"10.1103\/PhysRevE.73.030901","article-title":"Reversal of bacterial locomotion at an obstacle","volume":"73","author":"L Cisneros","year":"2006","journal-title":"Phys Rev E"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1126\/science.1172667","article-title":"Chlamydomonas swims with two gears in a eukaryotic version of run-and-tumble locomotion","volume":"325","author":"M Polin","year":"2009","journal-title":"Science"},{"key":"ref53","unstructured":"Rosser G (2013). Mathematical modelling and analysis of aspects of planktonic bacterial motility [PhD dissertation]. Oxford: Mathematical Institute, University of Oxford. 258 p."},{"key":"ref54","doi-asserted-by":"crossref","first-page":"4436","DOI":"10.1128\/AEM.61.12.4436-4440.1995","article-title":"Natural assemblages of marine bacteria exhibiting high-speed motility and large accelerations","volume":"61","author":"JG Mitchell","year":"1995","journal-title":"Appl Env Microbiol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1006\/jtbi.1997.0421","article-title":"A biased random walk model for the trajectories of swimming microorganisms","volume":"186","author":"NA Hill","year":"1997","journal-title":"J Theor Biol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1073\/pnas.71.4.1388","article-title":"Temporal stimulation of chemotaxis in <italic>Escherichia coli<\/italic>","volume":"71","author":"DA Brown","year":"1974","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"3474","DOI":"10.1128\/AEM.63.9.3474-3479.1997","article-title":"Interactions between motile <italic>Rhodobacter sphaeroides<\/italic> and glass in media with various ionic strengths, as observed with a three-dimensional-tracking microscope","volume":"63","author":"MA Vigeant","year":"1997","journal-title":"Appl Environ Microbiol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"17512","DOI":"10.1073\/pnas.0704658104","article-title":"Digital holographic microscopy reveals prey-induced changes in swimming behavior of predatory dinoflagellates","volume":"104","author":"J Sheng","year":"2007","journal-title":"PNAS"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1128\/jb.169.2.514-518.1987","article-title":"Unidirectional, intermittent rotation of the flagellum of <italic>Rhodobacter sphaeroides<\/italic>","volume":"169","author":"JP Armitage","year":"1987","journal-title":"J Bacteriol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1109\/TMI.2007.904657","article-title":"A novel method for the automatic grading of retinal vessel tortuosity","volume":"27","author":"E Grisan","year":"2008","journal-title":"IEEE Trans Med Imaging"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/j.cag.2005.08.004","article-title":"Curvature and torsion estimators based on parametric curve fitting","volume":"29","author":"T Lewiner","year":"2005","journal-title":"Comput Graph"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1099\/13500872-142-3-593","article-title":"The behavioural response of anaerobic <italic>Rhodobacter sphaeroides<\/italic> to temporal stimuli","volume":"142","author":"HL Packer","year":"1996","journal-title":"Microbiol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003276","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T14:17:12Z","timestamp":1646921832000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003276"}},"subtitle":[],"editor":[{"given":"Daniel","family":"Coombs","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2013,10,24]]},"references-count":62,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2013,10,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003276","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10,24]]}}}