@inproceedings{3557, abstract = {A challenging problem in computer-aided geometric design is the decomposition of a surface into four-sided regions that are then represented by NURBS patches. There are various approaches published in the literature and implemented as commercially available software, but all fall short in either automation or quality of the result. At Raindrop Geomagic, we have recently taken a fresh approach based on concepts from Morse theory. This by itself is not a new idea, but we have some novel ingredients that make this work, one being a rational notion of hierarchy that guides the construction of a simplified decomposition sensitive to only the major critical points.}, author = {Herbert Edelsbrunner}, pages = {9 -- 11}, publisher = {ACM}, title = {{Surface tiling with differential topology}}, doi = {http://dx.doi.org/10.2312/SGP/SGP05/009-011}, year = {2005}, } @inproceedings{3558, abstract = {The tandem algorithm combines the marching cube algorithm for surface extraction and the edge contraction algorithm for surface simplification in lock-step to avoid the costly intermediate step of storing the entire extracted surface triangulation. Beyond this basic strategy, we introduce refinements to prevent artifacts in the resulting triangulation, first, by carefully monitoring the amount of simplification during the process and, second, by driving the simplification toward a compromise between shape approximation and mesh quality. We have implemented the algorithm and used extensive computational experiments to document the effects of various design options and to further fine-tune the algorithm.}, author = {Attali, Dominique and Cohen-Steiner, David and Herbert Edelsbrunner}, pages = {139 -- 148}, publisher = {ACM}, title = {{Extraction and simplification of iso-surfaces in tandem}}, year = {2005}, } @inbook{3576, abstract = {ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes. Here we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics. In parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation.}, author = {Herbert Edelsbrunner and Koehl, Patrice}, booktitle = {Combinatorial and Computational Geometry}, pages = {243 -- 275}, publisher = {Cambridge University Press}, title = {{The geometry of biomolecular solvation}}, volume = {52}, year = {2005}, } @inbook{3588, author = {Castanon Ortega, Irinka and Heisenberg, Carl-Philipp J}, booktitle = {Cell Migration in Development and Disease}, editor = {Wedlich, Doris}, pages = {71 -- 105}, publisher = {Wiley-VCH}, title = {{Cell migration during zebrafish gastrulation}}, doi = {10.1002/3527604669}, year = {2005}, } @inbook{3589, abstract = {During zebrafish gastrulation, the interplay between patterning events and morphogenesis creates an embryo out of a seemingly unstructured blastula stage embryo, an embryo with distinct polarities along its anterior–posterior, dorsoventral and left–right axes at the end of gastrulation.}, author = {Köppen, Mathias and Heisenberg, Carl-Philipp J}, booktitle = {Encyclopedia of Life Sciences}, publisher = {Wiley-Blackwell}, title = {{Cleavage and gastrulation in zebrafish embryos}}, doi = {10.1038/npg.els.0001072}, year = {2005}, } @misc{3590, author = {Castanon Ortega, Irinka and Heisenberg, Carl-Philipp J}, booktitle = {Nature Cell Biology}, number = {1}, pages = {19 -- 19}, publisher = {Nature Publishing Group}, title = {{A stern view of gastrulation}}, doi = {10.1038/ncb0105-19}, volume = {7}, year = {2005}, } @article{3611, abstract = {We present two novel methods to infer mating patterns from genetic data. They differ from existing statistical methods of parentage inference in that they apply to populations that deviate from Hardy–Weinberg and linkage equilibrium, and so are suited for the study of assortative mating in hybrid zones. The core data set consists of genotypes at several loci for a number of full-sib clutches of unknown parentage. Our inference is based throughout on estimates of allelic associations within and across loci, such as heterozygote deficit and pairwise linkage disequilibrium. In the first method, the most likely parents of a given clutch are determined from the genotypic distribution of the associated adult population, given an explicit model of nonrandom mating. This leads to estimates of the strength of assortment. The second approach is based solely on the offspring genotypes and relies on the fact that a linear relation exists between associations among the offspring and those in the population of breeding pairs. We apply both methods to a sample from the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both approaches provide no evidence for a departure from random mating, despite adequate statistical power. Instead, B. variegata-like individuals among the adults contributed disproportionately to the offspring cohort, consistent with their preference for the type of breeding habitat in which this study was conducted.}, author = {Nürnberger, Beate and Nicholas Barton and Kruuk, Loeske E and Vines, Timothy H}, journal = {Heredity}, number = {2}, pages = {247 -- 257}, publisher = {Nature Publishing Group}, title = {{Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes}}, doi = {10.1038/sj.hdy.6800607}, volume = {94}, year = {2005}, } @article{3612, abstract = {Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent “single-gene speciation” or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be necessary to investigate populations in which both chiral morphs coexist.}, author = {Davison, Angus and Chiba, Satoshi and Nicholas Barton and Clarke, Bernard}, journal = {PLoS Biology}, number = {9}, publisher = {Public Library of Science}, title = {{Speciation and gene flow between snails of opposing chirality}}, doi = {10.1371/journal.pbio.0030282}, volume = {3}, year = {2005}, } @article{3613, abstract = {The extent of genetic variation in fitness is a crucial issue in evolutionary biology and yet remains largely unresolved. In Drosophila melanogaster, we have devised a method that allows the net effects on fitness of heterozygous wild-type chromosomes to be measured, by competing them against two different “balancer” chromosomes. We have applied the method to a large sample of 40 wild-type third chromosomes and have measured fitnesses of nonlethal chromosomes as well as chromosomes bearing recessive lethals. The measurements were made in the environment to which the population was adapted and did not involve inbreeding. The results show an extraordinary similarity in the behavior of replicates of the same chromosome, indicating consistent genetic effects on total fitness. Some invading chromosomes increased rapidly and some slowly, and some rose to appreciable frequency after several months, but then declined again: in every case, the same pattern was seen in each replicate. We estimated relative fitnesses, rates of change of fitness, and relative viabilities, for each chromosome. There were significant fluctuations around the fitted model, which were also highly replicable. Wild-type chromosomes varied substantially in their effects on heterozygous fitness, and these effects vary through time, most likely as a result of genotype × environment interactions.}, author = {Gardner, Michael P and Fowler, Kevin and Nicholas Barton and Patridge, Linda}, journal = {Genetics}, number = {3}, pages = {1553 -- 1571}, publisher = {Genetics Society of America}, title = {{Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns}}, doi = {10.1534/genetics.104.032367}, volume = {169}, year = {2005}, } @inproceedings{3684, abstract = {Ever since text processors became popular, users have dreamt of handling documents printed on paper as comfortably as electronic ones, with full text search typically appearing very close to the top of the wish list. This paper presents the design of a prototype system that takes a step into this direction. The user’s desktop is continuously monitored and of each detected document a high resolution snapshot is taken using a digital camera. The resulting image is processed using specially designed dewarping and OCR algorithms, making a digital and fully searchable version of the document available to the user in real-time. These steps are performed without any user interaction. This enables the system to run as a background task without disturbing the user in her work, while at the same time offering electronic access to all paper documents that have been present on the desktop during the uptime of the system.}, author = {Christoph Lampert and Braun,Tim and Ulges, Adrian and Keysers,Daniel and Breuel,Thomas M}, pages = {79 -- 86}, publisher = {CBDAR}, title = {{Oblivious document capture and real-time retrieval}}, year = {2005}, } @inproceedings{3689, abstract = {Digital cameras have become almost ubiquitous and their use for fast and casual capturing of natural images is unchallenged. For making images of documents, however, they have not caught up to flatbed scanners yet, mainly because camera images tend to suffer from distortion due to the perspective and are therefore limited in their further use for archival or OCR. For images of non-planar paper surfaces like books, page curl causes additional distortion, which poses an even greater problem due to its nonlinearity. This paper presents a new algorithm for removing both perspective and page curl distortion. It requires only a single camera image as input and relies on a priori layout information instead of additional hardware. Therefore, it is much more user friendly than most previous approaches, and allows for flexible ad hoc document capture. Results are presented showing that the algorithm produces visually pleasing output and increases OCR accuracy, thus having the potential to become a general purpose preprocessing tool for camera based document capture.}, author = {Ulges, Adrian and Christoph Lampert and Breuel,Thomas M}, pages = {1001 -- 1005}, publisher = {IEEE}, title = {{Document image dewarping using robust estimation of curled text lines}}, doi = { 10.1109/ICDAR.2005.90}, volume = {2}, year = {2005}, } @article{3691, abstract = {In strictly pseudoconvex domains with smooth boundary, we prove a commutator relationship between admissible integral operators, as introduced by Lieb and Range, and smooth vector fields which are tangential at boundary points. This makes it possible to gain estimates for admissible operators in function spaces which involve tangential derivatives. Examples are given under with circumstances these can be transformed into genuine Sobolev- and C k-estimates.}, author = {Christoph Lampert}, journal = {Publicacions Matemàtiques}, number = {1}, pages = {179 -- 195}, publisher = {Universitat Autònoma de Barcelona, Departament de Matemàtique}, title = {{Boundary regularity of admissible operators}}, doi = {10.5565/PUBLMAT_49105_08}, volume = {49}, year = {2005}, } @article{3720, author = {Guzmán, José and Gerevich, Zoltan and Hengstler, Jan and Illes, Peter and Kleemann, Werner}, journal = {Synapse}, number = {4}, pages = {235 -- 238}, publisher = {Wiley}, title = {{P2Y1 receptors inhibit both strength and plasticity of glutamatergic synaptic neurotransmission in the rat prefrontal cortex.}}, doi = {10.1002/syn.20177}, volume = {57}, year = {2005}, } @article{3721, abstract = {Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6–9nm) were supplied to the vertical displacement of the cantilever at a frequency of 3kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1μNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins.}, author = {Harald Janovjak and Mueller, Daniel J and Humphris, Andrew D}, journal = {Biophysical Journal}, number = {2}, pages = {1423 -- 1431}, publisher = {Biophysical Society}, title = {{Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins}}, doi = {10.1529/biophysj.104.052746}, volume = {88}, year = {2005}, } @article{3741, abstract = {In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster "prototype," does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures.}, author = {Slonim,N. and Atwal,G. and Gasper Tkacik and Bialek, William S}, journal = {PNAS}, number = {51}, pages = {18297 -- 18302}, publisher = {National Academy of Sciences}, title = {{Information-based clustering}}, doi = {10.1073/pnas.0507432102}, volume = {102}, year = {2005}, } @unpublished{3746, abstract = {We address the practical problems of estimating the information relations that characterize large networks. Building on methods developed for analysis of the neural code, we show that reliable estimates of mutual information can be obtained with manageable computational effort. The same methods allow estimation of higher order, multi-information terms. These ideas are illustrated by analyses of gene expression, financial markets, and consumer preferences. In each case, information theoretic measures correlate with independent, intuitive measures of the underlying structures in the system.}, author = {Slonim,Noam and Atwal,Gurinder S and Gasper Tkacik and Bialek, William S}, booktitle = {ArXiv}, pages = {1 -- 11}, publisher = {ArXiv}, title = {{Estimating mutual information and multi-information in large networks}}, year = {2005}, } @article{3753, abstract = {Characterizing the dynamics of specific RNA levels requires real-time RNA profiling in a single cell. We show that the combination of a synthetic modular genetic system with fluorescence correlation spectroscopy allows us to directly measure in real time the activity of any specific promoter in prokaryotes. Using a simple inducible gene expression system, we found that induced RNA levels within a single bacterium of Escherichia coli exhibited a pulsating profile in response to a steady input of inducer. The genetic deletion of an efflux pump system, a key determinant of antibiotic resistance, altered the pulsating transcriptional dynamics and caused overexpression of induced RNA. In contrast with population measurements, real-time RNA profiling permits identifying relationships between genotypes and transcriptional dynamics that are accessible only at the level of the single cell.}, author = {Le,Thuc T. and Harlepp, Sébastien and Calin Guet and Dittmar,Kimberly and Emonet,Thierry and Pan,Tao and Cluzel,Philippe}, journal = {PNAS}, number = {26}, pages = {9160 -- 9164}, publisher = {National Academy of Sciences}, title = {{Real-time RNA profiling within a single bacterium}}, doi = {10.1073/pnas.0503311102}, volume = {102}, year = {2005}, } @article{3763, abstract = {The generation of realistic motion satisfying user-defined requirements is one of the most important goals of computer animation. Our aim in this paper is the synthesis of realistic, controllable motion for lightweight natural objects in a gaseous medium. We formulate this problem as a large-scale spacetime optimization with user controls and fluid motion equations as constraints. We have devised novel and effective methods to make this large optimization tractable. Initial trajectories are generated with data-driven synthesis based on stylistic motion planning. Smoothed particle hydrodynamics (SPH) is used during optimization to produce fluid simulations at a reasonable computational cost, while interesting vortex-based fluid motion is generated by recording the presence of vortices in the initial trajectories and maintaining them through optimization. Object rotations are refined as a postprocess to enhance the visual quality of the results. We demonstrate our techniques on a number of animations involving single or multiple objects.}, author = {Shi, Lin and Yu, Yizhou and Wojtan, Christopher J and Chenney, Stephen}, journal = {The Visual Computer}, number = {7}, pages = {474 -- 487}, publisher = {Springer}, title = {{Controllable motion synthesis in a gaseous medium}}, doi = {10.1007/s00371-005-0296-0}, volume = {21}, year = {2005}, } @article{3808, abstract = {Action potentials in central neurons are initiated near the axon initial segment, propagate into the axon, and finally invade the presynaptic terminals, where they trigger transmitter release. Voltage-gated Na(+) channels are key determinants of excitability, but Na(+) channel density and properties in axons and presynaptic terminals of cortical neurons have not been examined yet. In hippocampal mossy fiber boutons, which emerge from parent axons en passant, Na(+) channels are very abundant, with an estimated number of approximately 2000 channels per bouton. Presynaptic Na(+) channels show faster inactivation kinetics than somatic channels, suggesting differences between subcellular compartments of the same cell. Computational analysis of action potential propagation in axon-multibouton structures reveals that Na(+) channels in boutons preferentially amplify the presynaptic action potential and enhance Ca(2+) inflow, whereas Na(+) channels in axons control the reliability and speed of propagation. Thus, presynaptic and axonal Na(+) channels contribute differentially to mossy fiber synaptic transmission.}, author = {Engel, Dominique and Peter Jonas}, journal = {Neuron}, number = {3}, pages = {405 -- 17}, publisher = {Elsevier}, title = {{Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons}}, doi = {10.1016/j.neuron.2004.12.048 }, volume = {45}, year = {2005}, } @misc{3812, abstract = {Hippocampal GABAergic interneurons show diverse molecular and morphological properties. The functional significance of this diversity for information processing is poorly understood. Here we show that cholecystokinin (CCK)-expressing interneurons in rat dentate gyrus release GABA in a highly asynchronous manner, in contrast to parvalbumin (PV) interneurons. With a gamma-frequency burst of ten action potentials, the ratio of asynchronous to synchronous release is 3:1 in CCK interneurons but is 1:5 in parvalbumin interneurons. N-type channels trigger synchronous and asynchronous release in CCK interneuron synapses, whereas P/Q-type Ca(2+) channels mediate release at PV interneuron synapses. Effects of Ca(2+) chelators suggest that both a long-lasting presynaptic Ca(2+) transient and a large distance between Ca(2+) source and sensor of exocytosis contribute to the higher ratio of asynchronous to synchronous release in CCK interneuron synapses. Asynchronous release occurs at physiological temperature and with behaviorally relevant stimulation patterns, thus generating long-lasting inhibition in the brain.}, author = {Hefft, Stefan and Peter Jonas}, booktitle = {Nature Neuroscience}, number = {10}, pages = {1319 -- 28}, publisher = {Nature Publishing Group}, title = {{Asynchronous GABA release generates long-lasting inhibition at a hippocampal interneuron-principal neuron synapse (Review)}}, doi = {10.1038/nn1542}, volume = {8}, year = {2005}, }