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Geometry of Eye Design: Biology and Technology [chapter]

Cornelia Fermüller, Yiannis Aloimonos
2001 Lecture Notes in Computer Science  
This seems intuitively evident in view of the variety of eye designs in the biological world.  ...  This result is derived from a statistical analysis of all the possible computational models that can be used for estimating 3D motion from an image sequence.  ...  Consider, then, a "negative" spherical eye like the one in Figure 6 , where video cameras are arranged on the surface of a sphere pointing toward its center.  ... 
doi:10.1007/3-540-45134-x_2 fatcat:prvw5dv77zetzfw27usdtc7dou

Intermolecular forces in biology

Deborah Leckband, Jacob Israelachvili
2001 Quarterly Reviews of Biophysics (print)  
Acknowledgements We gratefully acknowledge the very helpful comments and critiques by, as well as discussions with Pierre Bongrand, Taekjip  ...  Using the equation in Table 2 for the sphere-on-sphere geometry, with a Hamaker constant of A l 5i10 −#! J as is appropriate for hydrocarbons, and a cut-off distance of D !  ...  Thus, using the appropriate equation from Table 2 for the sphere-on-flat geometry, with a Hamaker constant of A l 1i10 −#! J and a cut-off distance of D !  ... 
doi:10.1017/s0033583501003687 fatcat:evctw4vc4je67j7lyjbzfwh4qe

Comparing Covariance Matrices by Relative Eigenanalysis, with Applications to Organismal Biology

Fred L. Bookstein, Philipp Mitteroecker
2013 Evolutionary biology  
analysis of variance as a tool for one useful description of the latter in the context of the former.  ...  Most biologists are familiar with principal component analysis as an ordination tool for questions about within-group or between-group variation in systems of quantitative traits, and with multivariate  ...  Applications This section illustrates applications of relative eigenanalysis to evolutionary and developmental biology by three examples.  ... 
doi:10.1007/s11692-013-9260-5 fatcat:tswgi2cn5zbdlalt5tc246lr4q

Perspectives In Visual Imaging For Marine Biology And Ecology: From Acquisition To Understanding

Jennifer M Durden, Timm Schoening, Franziska Althaus, Ariell Friedman, Rafael Garcia, Adrian G. Glover, Jens Greinert, Nancy Jacobsen Stout, Daniel O.B. Jones, Anne Jordt, Jeffrey Kaeli, Kevin Koser (+9 others)
2016 Zenodo  
Perspectives in visual imaging for marine biology and ecology: from acquisition to understanding  ...  also)partly)supported)by)Geoscience)Australia,)and)publishes)with)the)permission)of) the)chief)Executive)Officer)of)Geoscience)Australia.)DJL)was)partly)supported)by)JSPS) grant)KAKENHI)24248032.)Additional  ...  Southampton,) UK,) with) contributions) from) academia,) research,)industry)and)government.)We)would)like)to)thank)all)of)the)participants)for) their) contributions.)  ... 
doi:10.5281/zenodo.202685 fatcat:wp6e3ivpzffjdozxq3nmc6jhfu

Rapid, easy and reliable calibration for freehand 3D ultrasound

Po-Wei Hsu, Richard W. Prager, Andrew H. Gee, Graham M. Treece
2006 Ultrasound in Medicine and Biology  
on the reliability of the calibration using a metric based on the curvature of the calibration criterion function.  ...  In particular, we enable the calibration to be performed using water at room temperature while producing a result that is valid for average soft tissue, and we show how it is possible to provide feedback  ...  These spheres lie on a grid with known dimensions (Appendix B), and they show up as dark circles in the B-scans.  ... 
doi:10.1016/j.ultrasmedbio.2006.02.1427 pmid:16785005 fatcat:o5dtvoayerbzvdm3lx5ps53g3i

Active Vertex Model for cell-resolution description of epithelial tissue mechanics

Daniel L. Barton, Silke Henkes, Cornelis J. Weijer, Rastko Sknepnek, Stanislav Shvartsman
2017 PLoS Computational Biology  
This introduces a natural description of the cell motion and accounts for motion patterns observed on multiple scales.  ...  In addition, the AVM introduces a flexible, dynamically changing boundary of the epithelial sheet allowing for studies of phenomena such as the fingering instability or wound healing.  ...  Acknowledgments We would like to acknowledge many valuable discussions with Geoff Barton, Dapeng (Max) Bi, Luke Coburn, Amit Das, Tamal Sknepnek. Writing -review & editing: Daniel L.  ... 
doi:10.1371/journal.pcbi.1005569 pmid:28665934 pmcid:PMC5493290 fatcat:vx6224xf4fcwrbvjwfdv7wg5xa

Online detector response calculations for high-resolution PET image reconstruction

Guillem Pratx, Craig Levin
2011 Physics in Medicine and Biology  
In addition, the spatial resolution was more uniform across the field-of-view: for an array of 1.75 mm hot spheres in air, the variation in reconstructed sphere size was 0.5 mm RMS for the shift-invariant  ...  We investigated a shift-varying model of the geometrical system response based on an analytical formulation.  ...  Acknowledgments This work was supported in part by the National Institutes of Health (NIH) under grants R01-CA119056, R01-CA120474, and R01-CA119056-S1 (ARRA), and by a fellowship from the Stanford Bio-X  ... 
doi:10.1088/0031-9155/56/13/018 pmid:21677367 pmcid:PMC3147176 fatcat:5gjvmvuhzfc4rakfqp6rqda3sq

Hydrodynamic forces and band formation in swimming magnetotactic bacteria

D.C. Guell, H. Brenner, R.B. Frankel, H. Hartman
1988 Journal of Theoretical Biology  
A mechanism for this phenomenon is proposed in which the hydrodynamic coupling between two swimming cells is described in terms of an approximate, far-field solution for the flow around one swimming cell  ...  Dense suspensions of magnetotactic bacteria form long, thin, stable bands perpen dicutar to the common, net direction of motion of the cells in a magnetic field.  ...  We thank A. M. Spormann for discussions and for providing a video tape of magnetotactic bacterial bands as well as the photograph shown in Fig  ... 
doi:10.1016/s0022-5193(88)80274-1 fatcat:55cxnloixne7pcb2fxjdmkg7sq

Stereotypic leg searching movements in the stick insect: kinematic analysis, behavioural context and simulation

V Dürr
2001 Journal of Experimental Biology  
Insects are capable of efficient locomotion in a spatially complex environment, such as walking on a forest floor or climbing in a bush.  ...  Accordingly, the stereotyped loop structure of searching differs between front-, middle- and hindlegs, with leg-specific patterns being caused by differing protraction/retraction movements in the thorax-coxa  ...  For spatial analysis, video sequences were either displayed on a NEXT computer or captured as non-compressed AVI files (Microsoft video format) to an IBM-compatible computer via a graphics card (Elsa Victory  ... 
pmid:11398748 fatcat:xnree5narjax5ha5536ugtgg3y

Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures

Xian Hao, Jyotsana J. Parmar, Benoît Lelandais, Andrey Aristov, Wei Ouyang, Christian Weber, Christophe Zimmer
2021 Genome Biology  
We image chromosomes in G1 and M phase and examine the effect of cohesin on interphase chromatin structure.  ...  Background The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression.  ...  Lelek for initial help with imaging and E. Rensen, M. Woringer, F. Mueller, T. Sabaté, and all other members of the lab for helpful suggestions. We thank S. Fournier and S.  ... 
doi:10.1186/s13059-021-02343-w pmid:33975635 pmcid:PMC8111965 fatcat:5xdunxfm6fa3bo4xmilpmhp6gm

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Eitan Lerner, Anders Barth, Jelle Hendrix, Benjamin Ambrose, Victoria Birkedal, Scott C Blanchard, Richard Börner, Hoi Sung Jung, Thorben Cordes, Timothy D Craggs, Ashok A Deniz, Jiajia Diao (+34 others)
2021 eLife  
This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations  ...  The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and  ...  This position paper was supported by the National Institutes of Health (NIH, grant R01 GM130942 to SW, and to EL as a subaward; grant R01 GM095904 to XM; grants R01 GM079238 and 7R01GM098859-09 to SCB;  ... 
doi:10.7554/elife.60416 pmid:33779550 pmcid:PMC8007216 fatcat:rhklli2olbeljckxzo7f7gwf3y

Measuring fish and their physical habitats: versatile 2D and 3D video techniques with user-friendly software

Jason R. Neuswanger, Mark S. Wipfli, Amanda E. Rosenberger, Nicholas F. Hughes
2016 Canadian Journal of Fisheries and Aquatic Sciences  
Arrows on the bottom right indicate the direction of water flow. The radius of 724 the orange circle is the mean fork length of the fish.  ...  These 229 cameras recorded video in 1080i resolution on internal hard drives in AVCHD format, which 230 was transcoded to Apple Intermediate Codec upon downloading to a computer, deinterlaced by 231 interpolation  ...  This technique is usable whenever 6 cameras are placed in a stationary position to observe behavior, with the surface of the water 7 visible and the current flowing in an approximately steady direction  ... 
doi:10.1139/cjfas-2016-0010 fatcat:jsp5sjmzhvbbbesgegvytpvh4u

Modeling human intuitions about liquid flow with particle-based simulation

Christopher J. Bates, Ilker Yildirim, Joshua B. Tenenbaum, Peter Battaglia, Jean Daunizeau
2019 PLoS Computational Biology  
Our model is analogous to a "game engine in the head", drawing on techniques for interactive simulations (as in video games) that optimize for efficiency and natural appearance rather than physical accuracy  ...  Here we propose and test a computational model of how people perceive and predict these liquid dynamics, based on coarse approximate simulations of fluids as collections of interacting particles.  ...  Physics, engineering, and graphics applications may use on the order of 10 5 up to 10 7 particles to achieve sufficiently realistic simulations [10, 11] , depending on the specific application.  ... 
doi:10.1371/journal.pcbi.1007210 pmid:31329579 pmcid:PMC6675131 fatcat:wpqajqthlne73d4lncwddrihyi

High throughput automated detection of axial malformations in Medaka embryo

Diane Genest, Elodie Puybareau, Marc Léonard, Jean Cousty, Noémie De Crozé, Hugues Talbot
2019 Computers in Biology and Medicine  
We built and validated our learning model on 1459 images with a 10-fold cross-validation by comparison with the gold standard of 3D observations performed under a microscope by a trained operator.  ...  Our pipeline results in correct classification in 85% of the cases included in the database. This percentage is similar to the percentage of success of a trained human operator working on 2D images.  ...  "An automated assay for the assessment of cardiac arrests in fish embryo", in Computer in Biology and Medicine, pp 32-44, 2017.  ... 
doi:10.1016/j.compbiomed.2018.12.016 pmid:30654166 fatcat:nen2k7fv7fhbfkfbb52zk7bgca

Decentralized control of insect walking: A simple neural network explains a wide range of behavioral and neurophysiological results

Malte Schilling, Holk Cruse, Samuel J. Gershman
2020 PLoS Computational Biology  
of neural computation.  ...  Furthermore, negotiation of curves and walking on a treadmill with various treatments of individual legs is possible as well as backward walking and performing short steps.  ...  Acknowledgments The authors thank Thierry Hoinville, Josef Schmitz, Axel Schneider, and Volker Dürr for discussions and helpful comments on the manuscript.  ... 
doi:10.1371/journal.pcbi.1007804 pmid:32339162 fatcat:7rwllijixzhd7emkd5dwczrrdi
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