@article{6153, abstract = {A current challenge in neuroscience is to bridge the gaps between genes, proteins, neurons, neural circuits, and behavior in a single animal model. The nematode Caenorhabditis elegans has unique features that facilitate this synthesis. Its nervous system includes exactly 302 neurons, and their pattern of synaptic connectivity is known. With only five olfactory neurons, C. elegans can dynamically respond to dozens of attractive and repellant odors. Thermosensory neurons enable the nematode to remember its cultivation temperature and to track narrow isotherms. Polymodal sensory neurons detect a wide range of nociceptive cues and signal robust escape responses. Pairing of sensory stimuli leads to long-lived changes in behavior consistent with associative learning. Worms exhibit social behaviors and complex ultradian rhythms driven by Ca2+ oscillators with clock-like properties. Genetic analysis has identified gene products required for nervous system function and elucidated the molecular and neural bases of behaviors.}, author = {de Bono, Mario and Villu Maricq, Andres}, issn = {1545-4126}, journal = {Annual Review of Neuroscience}, pages = {451--501}, publisher = {Annual Reviews}, title = {{Neuronal substrates of complex behaviors in C. elegans}}, doi = {10.1146/annurev.neuro.27.070203.144259}, volume = {28}, year = {2005}, } @article{6154, author = {Cheung, Benny H.H. and Cohen, Merav and Rogers, Candida and Albayram, Onder and de Bono, Mario}, issn = {0960-9822}, journal = {Current Biology}, number = {10}, pages = {905--917}, publisher = {Elsevier}, title = {{Experience-dependent modulation of C. elegans behavior by ambient oxygen}}, doi = {10.1016/j.cub.2005.04.017}, volume = {15}, year = {2005}, } @article{3426, abstract = {We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from the binding of ligands to receptors on the cell surface, incorporation into the cell, and subsequent externalization. Starting from a microscopic model, we derive effective transport equations. We show that, in contrast to morphogen transport by extracellular diffusion, transcytosis leads to robust ligand profiles which are insensitive to the rate of ligand production.}, author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and González Gaitán, Marcos and Jülicher, Frank}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Robust formation of morphogen gradients}}, doi = {10.1103/PhysRevLett.94.018103}, volume = {94}, year = {2005}, } @inbook{3433, author = {Jonathan Bollback}, booktitle = {Statistical methods in Molecular Evolution}, editor = {Nielsen, Rasmus}, pages = {439 -- 462}, publisher = {Springer}, title = {{Posterior mapping and posterior predictive distributions}}, doi = {10.1007/0-387-27733-1}, year = {2005}, } @article{3443, abstract = {In the hippocampal CA1 area, a relatively homogenous population of pyramidal cells is accompanied by a diversity of GABAergic interneurons. Previously, we found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum moleculare cells, innervating different domains of pyramidal cells, have distinct firing patterns during network oscillations in vivo. A second family of interneurons, expressing cholecystokinin but not parvalbumin, is known to target the same domains of pyramidal cells as do the parvalbumin cells. To test the temporal activity of these independent and parallel GABAergic inputs, we recorded the precise spike timing of identified cholecystokinin interneurons during hippocampal network oscillations in anesthetized rats and determined their molecular expression profiles and synaptic targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing basket and dendrite-innervating cells discharge, on average, with 1.7 ± 2.0 Hz during high-frequency ripple oscillations in an episode-dependent manner. During theta oscillations, cholecystokinin- expressing interneurons fire with 8.8 ± 3.3 Hz at a characteristic time on the ascending phase of theta waves (155 ± 81°), when place cells start firing in freely moving animals. The firing patterns of some interneurons recorded in drug-free behaving rats were similar to cholecystokinin cells in anesthetized animals. Our results demonstrate that cholecystokinin- and parvalbumin-expressing interneurons make different contributions to network oscillations and play distinct roles in different brain states. We suggest that the specific spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids might contribute to differentiate subgroups of pyramidal cells forming neuronal assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire network. Copyright © 2005 Society for Neuroscience.}, author = {Klausberger,Thomas and Marton,Laszlo F and Joseph O'Neill and Huck, Jojanneke H and Dalezios, Yannis and Fuentealba,Pablo and Suen, Wai Yee and Papp, Edit Cs and Kaneko, Takeshi and Watanabe, Masahiko and Jozsef Csicsvari and Somogyi, Péter}, journal = {Journal of Neuroscience}, number = {42}, pages = {9782 -- 9793}, publisher = {Society for Neuroscience}, title = {{Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations}}, doi = {10.1523/JNEUROSCI.3269-05.2005}, volume = {25}, year = {2005}, } @misc{3509, abstract = {Methods, apparatus and computer program products can generate light weight but highly realistic and accurate colored models of three-dimensional colored objects. The colored model may be generated from a second plurality of points that define a coarse digital representation of the surface and at least one texture map containing information derived from a first plurality of colored points that define a fine digital representation of the surface. This derivation is achieved by mapping points within the texture map to the fine digital representation of the three-dimensional surface. Colored scan data may be used to construct the fine digital representation as a triangulated surface (i.e., triangulation) using a wrapping operation.}, author = {Williams, Steven and Edelsbrunner, Herbert and Fu, Ping}, title = {{Methods, apparatus and computer program products for modeling three-dimensional colored objects}}, year = {2005}, } @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}, }