@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}, } @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}, } @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}, } @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}, } @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}, } @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{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}, } @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}, } @inproceedings{3896, abstract = {Temporal Logic Model Checking is one of the most potent tools for the verification of finite state systems. Computation Tree Logic (CTL) has gained popularity because unlike most other logics, CTL model checking of a single transition system can be achieved in polynomial time. However, in most real-life problems, specially in distributed and parallel systems, the system consist of a set of concurrent processes and the verification problem translates to model check the composition of the component processes. Since explicit composition leads to state explosion, verifying the system without actually composing the components is attractive, even for possibly restrictive class of systems. We show that the problem of compositional CTL model checking is PSPACE complete for the class of systems composed of components that are tree-like transition structure and do not interact among themselves. For the simplest forms of existential and universal CTL formulas model checking turns out to be NP complete and coNP complete, respectively. The results hold for both synchronous and asynchronous composition.}, author = {Krishnendu Chatterjee and Dasgupta, Pallab and Chakrabarti, Partha P}, pages = {89 -- 102}, publisher = {Springer}, title = {{Complexity of compositional model checking of computation tree logic on simple structures}}, doi = {10.1007/978-3-540-30536-1_13}, volume = {3326}, year = {2005}, } @inproceedings{3893, abstract = {We study infinite stochastic games played by two-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players' goals are not necessarily conflicting), and undiscounted. We show that if each player has an W-regular objective expressed as a paxity objective, then there exists an epsilon-Nash equilibrium, for every epsilon > 0. However, exact Nash equilibria need not exist. We study the complexity of finding values (payoff profile) of an epsilon-Nash equilibrium. We show that the values of an epsilon-Nash equilibrium in nonzero-sum concurrent parity games can be computed by solving the following two simpler problems: computing the values of zero-sum (the goals of the players axe strictly conflicting) concurrent parity games and computing epsilon-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives. As a consequence we establish that values of an epsilon-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME.}, author = {Krishnendu Chatterjee}, pages = {413 -- 427}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Two-player nonzero-sum ω-regular games}}, doi = {10.1007/11539452_32}, volume = {3653}, year = {2005}, } @article{3916, abstract = {Divergent reproductive interests of males and females often cause sexual conflict [1] and [2]. Males of many species manipulate females by transferring seminal fluids that boost female short-term fecundity while decreasing their life expectancy and future reproductivity [3] and [4]. The life history of ants, however, is expected to reduce sexual conflict; whereas most insect females show repeated phases of mating and reproduction, antqueens mate only during a short period early in life and undergo a lifelong commitment to their mates by storing sperm [5]. Furthermore, sexual offspring can only be reared after a sterile worker force has been built up [5]. Therefore, the males should also profit from a long female lifespan. In the antCardiocondyla obscurior, mating indeed has a positive effect on the lifetime reproductive success of queens. Queens that mated to either one fertile or one sterilized male lived considerably longer and started laying eggs earlier than virgin queens. Only queens that received viable sperm from fertile males showed increased fecundity. The lack of a trade-off between fecundity and longevity is unexpected, given evolutionary theories of aging [6]. Our data instead reveal the existence of sexual cooperation in ants.}, author = {Schrempf, Alexandra and Heinze, Jürgen and Cremer, Sylvia}, journal = {Current Biology}, number = {3}, pages = {267 -- 270}, publisher = {Cell Press}, title = {{Sexual cooperation: mating increases longevity in ant queens}}, doi = {10.1016/j.cub.2005.01.036}, volume = {15}, year = {2005}, } @article{3915, abstract = {In the ant Cardiocondyla obscurior, wingless males compete with nestmate males for access to female mating partners, leading to local mate competition (LMC). Queen number varies between colonies, resulting in variation in the strength of LMC. Cremer & Heinze (2002, Proceedings of the Royal Society of London, Series B, 269, 417–422) showed that colonies responded to increasing queen number by producing a less femalebiased sex ratio, as predicted by LMC theory. However, the proximate mechanisms responsible for this variation in the sex ratio could not be determined because the study was restricted to adult sex ratios.With LMC, the primary sex ratio (proportion of haploid eggs laid by the queen) is expected to be female biased, which lowers the conflict between queens and workers over sex allocation. We compared the primary sex ratios laid by queens in monogynous and in polygynous experimental colonies of C. obscurior. The proportion of haploid eggs laid by queens was significantly lower in single-queen than in multiple-queen colonies. Furthermore, queens rapidly adjusted their primary sex ratios to changes in colony queen number. This is the first report of an adaptive adjustment of the primary sex ratio in response to LMC by ant queens.}, author = {De Menten, Ludivine and Cremer, Sylvia and Heinze, Jürgen and Aron, Serge}, journal = {Animal Behaviour}, number = {5}, pages = {1031 -- 1035}, publisher = {Elsevier}, title = {{Primary sex ratio adjustment by ant queens in response to local mate competition}}, doi = {10.1016/j.anbehav.2004.09.005}, volume = {69}, year = {2005}, } @article{4167, abstract = {In this study, we elucidate the roles of the winged-helix transcription factor Foxa2 in ventral CNS development in zebrafish. Through cloning of monorail (mol), which we find encodes the transcription factor Foxa2, and phenotypic analysis of mol(-/-) embryos, we show that floorplate is induced in the absence of Foxa2 function but fails to further differentiate. In mol(-/-) mutants, expression of Foxa and Hh family genes is not maintained in floorplate cells and lateral expansion of the floorplate fails to occur. Our results suggest that this is due to defects both in the regulation of Hh activity in medial floorplate cells as well as cell-autonomous requirements for Foxa2 in the prospective laterally positioned floorplate cells themselves. Foxa2 is also required for induction and/or patterning of several distinct cell types in the ventral CNS. Serotonergic neurones of the raphe nucleus and the trochlear motor nucleus are absent in mol(-/-) embryos, and oculomotor and facial motoneurones ectopically occupy ventral CNS midline positions in the midbrain and hindbrain. There is also a severe reduction of prospective oligodendrocytes in the midbrain and hindbrain. Finally, in the absence of Foxa2, at least two likely Hh pathway target genes are ectopically expressed in more dorsal regions of the midbrain and hindbrain ventricular neuroepithelium, raising the possibility that Foxa2 activity may normally be required to limit the range of action of secreted Hh proteins.}, author = {Norton, Will and Mangoli, Maryam and Lele, Zsolt and Pogoda, Hans and Diamond, Brianne and Mercurio, Sara and Russell, Claire and Teraoka, Hiroki and Stickney, Heather and Rauch, Gerd and Heisenberg, Carl-Philipp J and Houart, Corinne and Schilling, Thomas and Frohnhoefer, Hans and Rastegar, Sepand and Neumann, Carl and Gardiner, R Mark and Strähle, Uwe and Geisler, Robert and Rees, Michelle and Talbot, William and Wilson, Stephen}, journal = {Development}, number = {4}, pages = {645 -- 658}, publisher = {Company of Biologists}, title = {{Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones}}, doi = {10.1242/dev.01611}, volume = {132}, year = {2005}, } @article{4183, abstract = {The spreading of an epithelial cell sheet over a substrate is a common process during embryogenesis. Typical examples include epiboly during zebrafish gastrulation and Drosophila dorsal closure. We provide evidence that in both cases, actin-based contraction of the leading edge of the epithelium is of critical importance.}, author = {Köppen, Mathias and Fernández, Beatriz and Carvalho, Lara and Jacinto, António and Heisenberg, Carl-Philipp J}, journal = {Mechanisms of Development}, number = {Supplement 1}, pages = {S112 -- S113}, publisher = {Elsevier}, title = {{Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure}}, doi = {10.1016/j.mod.2005.06.010}, volume = {122}, year = {2005}, } @inproceedings{4367, author = {Podelski,Andreas and Thomas Wies}, pages = {267 -- 282}, publisher = {Springer}, title = {{Boolean Heaps}}, doi = {1550}, year = {2005}, } @article{3143, abstract = {Two ETS transcription factors of the Pea3 subfamily are induced in subpopulations of dorsal root ganglion (DRG) sensory and spinal motor neurons by target-derived factors. Their expression controls late aspects of neuronal differentiation such as target invasion and branching. Here, we show that the late onset of ETS gene expression is an essential requirement for normal sensory neuron differentiation. We provide genetic evidence in the mouse that precocious ETS expression in DRG sensory neurons perturbs axonal projections, the acquisition of terminal differentiation markers, and their dependence on neurotrophic support. Together, our findings indicate that DRG sensory neurons exhibit a temporal developmental switch that can be revealed by distinct responses to ETS transcription factor signaling at sequential steps of neuronal maturation.}, author = {Simon Hippenmeyer and Vrieseling, Eline and Sigrist, Markus and Portmann, Thomas and Laengle, Celia and Ladle, David R and Arber, Silvia}, journal = {PLoS Biology}, number = {5}, pages = {0878 -- 0890}, publisher = {Public Library of Science}, title = {{A developmental switch in the response of DRG neurons to ETS transcription factor signaling}}, doi = {10.1371/journal.pbio.0030159}, volume = {3}, year = {2005}, } @article{3141, abstract = {The two actin-related subunits of the Arp2/3 complex, Arp2 and Arp3, are proposed to form a pseudo actin dimer that nucleates actin polymerization. However, in the crystal structure of the inactive complex, they are too far apart to form such a nucleus. Here, we show using EM that yeast and bovine Arp2/3 complexes exist in a distribution among open, intermediate and closed conformations. The crystal structure docks well into the open conformation. The activator WASp binds at the cleft between Arp2 and Arp3, and all WASp-bound complexes are closed. The inhibitor coronin binds near the p35 subunit, and all coronin-bound complexes are open. Activating and loss-of-function mutations in the p35 subunit skew conformational distribution in opposite directions, closed and open, respectively. We conclude that WASp stabilizes p35-dependent closure of the complex, holding Arp2 and Arp3 closer together to nucleate an actin filament.}, author = {Rodal, Avital A and Sokolova, Olga and Robins, Deborah B and Daugherty, Karen M and Simon Hippenmeyer and Riezman, Howard and Grigorieff, Nikolaus and Goode, Bruce L}, journal = {Nature Structural and Molecular Biology}, number = {1}, pages = {26 -- 31}, publisher = {Nature Publishing Group}, title = {{Conformational changes in the Arp2 3 complex leading to actin nucleation}}, doi = {10.1038/nsmb870}, volume = {12}, year = {2005}, } @inproceedings{3175, abstract = {This paper addresses the novel problem of automatically synthesizing an output image from a large collection of different input images. The synthesized image, called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail' of all the images in the input collection. The problem of creating the tapestry is cast as a multi-class labeling problem such that each region in the tapestry is constructed from input image blocks that are salient and such that neighboring blocks satisfy spatial compatibility. This is formulated using a Markov Random Field and optimized via the graph cut based expansion move algorithm. The standard expansion move algorithm can only handle energies with metric terms, while our energy contains non-metric (soft and hard) constraints. Therefore we propose two novel contributions. First, we extend the expansion move algorithm for energy functions with non-metric hard constraints. Secondly, we modify it for functions with "almost" metric soft terms, and show that it gives good results in practice. The proposed framework was tested on several consumer photograph collections, and the results are presented.}, author = {Rother, Carsten and Kumar, Sanjiv and Vladimir Kolmogorov and Blake, Andrew}, pages = {589 -- 596}, publisher = {IEEE}, title = {{Digital tapestry}}, doi = {10.1109/CVPR.2005.130}, volume = {1}, year = {2005}, } @inproceedings{3176, abstract = {This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, layered dynamic programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, layered graph cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output. }, author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten}, pages = {1186 -- 1186}, publisher = {IEEE}, title = {{Bi-layer segmentation of binocular stereo video}}, doi = {10.1109/CVPR.2005.90}, year = {2005}, }