TY - CONF AU - Bollenbach, Mark Tobias AU - Strother, T. AU - Bauer, Wolfgang ID - 3425 TI - 3D supernova collapse calculations VL - 166 ER - TY - CHAP AU - Peter Jonas AU - Unsicker, Klaus ED - Schmidt, R. F. ID - 3458 T2 - Lehrbuch Vorklinik TI - Molekulare und zelluläre Grundlagen des Nervensystems. VL - B ER - TY - JOUR AB - Genetic engineering of the mouse brain allows investigators to address novel hypotheses in vivo. Because of the paucity of information on the network patterns of the mouse hippocampus, we investigated the electrical patterns in the behaving animal using multisite silicon probes and wire tetrodes. Theta (6-9 Hz) and gamma (40-100 Hz) oscillations were present during exploration and rapid eye movement sleep. Gamma power and theta power were comodulated and gamma power varied as a function of the theta cycle. Pyramidal cells and putative interneurons were phase-locked to theta oscillations. During immobility, consummatory behaviors and slow-wave sleep, sharp waves were present in cornu ammonis region CA1 of the hippocampus stratum radiatum associated with 140-200-Hz “ripples” in the pyramidal cell layer and population burst of CA1 neurons. In the hilus, large-amplitude “dentate spikes” occurred in association with increased discharge of hilar neurons. The amplitude of field patterns was larger in the mouse than in the rat, likely reflecting the higher neuron density in a smaller brain. We suggest that the main hippocampal network patterns are mediated by similar pathways and mechanisms in mouse and rat. AU - Buzsáki, György AU - Buhl, Derek L AU - Harris, Kenneth D AU - Jozsef Csicsvari AU - Czéh, Boldizsár AU - Morozov, Alexei ID - 3536 IS - 1 JF - Neuroscience TI - Hippocampal network patterns of activity in the mouse VL - 116 ER - TY - CONF AB - We define the Morse-Smale complex of a Morse function over a 3-manifold as the overlay of the descending and as- cending manifolds of all critical points. In the generic case, its 3-dimensional cells are shaped like crystals and are sepa- rated by quadrangular faces. In this paper, we give a combi- natorial algorithm for constructing such complexes for piece- wise linear data. AU - Herbert Edelsbrunner AU - Harer, John AU - Natarajan, Vijay AU - Pascucci, Valerio ID - 3556 TI - Morse-Smale complexes for piecewise linear 3-manifolds ER - TY - CHAP AB - Given a finite point set in R, the surface reconstruction problem asks for a surface that passes through many but not necessarily all points. We describe an unambigu- ous definition of such a surface in geometric and topological terms, and sketch a fast algorithm for constructing it. Our solution overcomes past limitations to special point distributions and heuristic design decisions. AU - Herbert Edelsbrunner ID - 3573 T2 - Discrete & Computational Geometry TI - Surface reconstruction by wrapping finite sets in space ER - TY - JOUR AB - We develop fast algorithms for computing the linking number of a simplicial complex within a filtration.We give experimental results in applying our work toward the detection of non-trivial tangling in biomolecules, modeled as alpha complexes. AU - Edelsbrunner, Herbert AU - Zomorodian, Afra ID - 3584 IS - 2 JF - Homology, Homotopy and Applications TI - Computing linking numbers of a filtration VL - 5 ER - TY - JOUR AB - Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5′ end of the repeats. AU - Nürnberger, Beate AU - Hofman, Sebastian AU - Förg-Brey, Bqruni AU - Praetzel, Gabriele AU - Maclean, Alan W AU - Szymura, Jacek M AU - Abbott, Catherine M AU - Nicholas Barton ID - 3620 IS - 2 JF - Heredity TI - A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae) VL - 91 ER - TY - JOUR AB - What is the chance that some part of a stretch of genome will survive? In a population of constant size, and with no selection, the probability of survival of some part of a stretch of map length y<1 approaches View the MathML source for View the MathML source. Thus, the whole genome is certain to be lost, but the rate of loss is extremely slow. This solution extends to give the whole distribution of surviving block sizes as a function of time. We show that the expected number of blocks at time t is 1+yt and give expressions for the moments of the number of blocks and the total amount of genome that survives for a given time. The solution is based on a branching process and assumes complete interference between crossovers, so that each descendant carries only a single block of ancestral material. We consider cases where most individuals carry multiple blocks, either because there are multiple crossovers in a long genetic map, or because enough time has passed that most individuals in the population are related to each other. For species such as ours, which have a long genetic map, the genome of any individual which leaves descendants (∼80% of the population for a Poisson offspring number with mean two) is likely to persist for an extremely long time, in the form of a few short blocks of genome. AU - Baird, Stuart J AU - Nicholas Barton AU - Etheridge, Alison M ID - 3619 IS - 4 JF - Theoretical Population Biology TI - The distribution of surviving blocks of an ancestral genome VL - 64 ER - TY - JOUR AB - There are several analyses in evolutionary ecology which assume that a family of offspring has come from only two parents. Here, we present a simple test for detecting when a batch involves two or more subfamilies. It is based on the fact that the mixing of families generates associations amongst unlinked marker loci. We also present simulations illustrating the power of our method for varying numbers of loci, alleles per locus and genotyped individuals. AU - Vines, Timothy H AU - Nicholas Barton ID - 3618 IS - 7 JF - Molecular Ecology TI - A new approach to detecting mixed families VL - 12 ER - TY - JOUR AB - We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description (molecular, cellular, and that of cell population) into a single model, which seems to capture many experimental aspects of the system. AU - Vilar,Jose M AU - Calin Guet AU - Leibler, Stanislas ID - 3752 IS - 3 JF - Journal of Cell Biology TI - Modeling network dynamics: the lac operon, a case study VL - 161 ER - TY - JOUR AU - Bauer, Wolfgang AU - Kleine Berkenbusch, Marco AU - Bollenbach, Mark Tobias ID - 3797 IS - 4 JF - Revista Mexicana De Fisica TI - Breaking atomic nuclei into little pieces: evidence for a phase transition VL - 49 ER - TY - CONF AB - Many verification, planning, and control problems can be modeled as games played on state-transition graphs by one or two players whose conflicting goals are to form a path in the graph. The focus here is on simple stochastic parity games, that is, two-player games with turn-based probabilistic transitions and omega-regular objectives formalized as parity (Rabin chain) winning conditions. An efficient translation from simple stochastic parity games to nonstochastic parity games is given. As many algorithms are known for solving the latter, the translation yields efficient algorithms for computing the states of a simple stochastic parity game from which a player can win with probability 1. An important special case of simple stochastic parity games are the Markov decision processes with Buchi objectives. For this special case a first provably subquadratic algorithm is given for computing the states from which the single player has a strategy to achieve a Buchi objective with probability 1. For game graphs with m edges the algorithm works in time O(mrootm). Interestingly, a similar technique sheds light on the question of the computational complexity of solving simple Buchi games and yields the first provably subquadratic algorithm, with a running time of O(n(2)/log n) for game graphs with n vertices and O(n) edges. AU - Krishnendu Chatterjee AU - Jurdziński, Marcin AU - Thomas Henzinger ID - 3897 TI - Simple stochastic parity games VL - 2803 ER - TY - CONF AB - We study the problem of determining stack boundedness and the exact maximum stack size for three classes of interrupt-driven programs. Interrupt-driven programs axe used in many real-time applications that require responsive interrupt handling. In order to ensure responsiveness, programmers often enable interrupt processing in the body of lower-priority interrupt handlers. In such programs a programming error can allow interrupt handlers to be interrupted in cyclic fashion to lead to an unbounded stack, causing the system to crash. For a restricted class of interrupt-driven programs, we show that there is a polynomial-time procedure to check stack boundedness, while determining the exact maximum stack size is PSPACE-complete. For a larger class of programs, the two problems are both PSPACE-complete, and for the largest class of programs we consider, the two problems are PSPACE-hard and can be solved in exponential time. AU - Krishnendu Chatterjee AU - Ma, Di AU - Majumdar, Ritankar S AU - Zhao, Tian AU - Thomas Henzinger AU - Palsberg, Jens ID - 3898 TI - Stack size analysis for interrupt-driven programs VL - 2694 ER - TY - JOUR AB - We present algorithms for constructing a hierarchy of increasingly coarse Morse-Smale complexes that decompose a piecewise linear 2-manifold. While these complexes are defined only in the smooth category, we extend the construction to the piecewise linearcategory by ensuring structural integrity and simulating differentiability. We then simplify Morse-Smale complexes by canceling pairs of critical points in order of increasing persistence. AU - Herbert Edelsbrunner AU - Harer, John AU - Zomorodian, Afra ID - 3993 IS - 1 JF - Discrete & Computational Geometry TI - Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds VL - 30 ER - TY - JOUR AB - The body defined by a finite collection of disks is a subset of the plane bounded by a tangent continuous curve, which we call the skin. We give analytic formulas for the area, the perimeter, the area derivative, and the perimeter derivative of the body. Given the filtrations of the Delaunay triangulation and the Voronoi diagram of the disks, all formulas can be evaluated in time proportional to the number of disks. AU - Cheng, Ho-Lun AU - Herbert Edelsbrunner ID - 3994 IS - 2 JF - Computational Geometry: Theory and Applications TI - Area, perimeter and derivatives of a skin curve VL - 26 ER - TY - GEN AB - Significant advances have been made during the past few years in our understanding of how the spinal monosynaptic reflex develops. Transcription factors in the Neurogenin, Runt, ETS, and LIM families control sequential steps of the specification of various subtypes of dorsal root ganglia sensory neurons. The initiation of muscle spindle differentiation requires neuregulin 1, derived from Ia afferent sensory neurons, and signaling through ErbB receptors in intrafusal muscle fibers. Several retrograde signals from the periphery are important for the establishment of late connectivity in the reflex circuit. Finally, neurotrophin 3 released from muscle spindles regulates the strength of sensory-motor connections within the spinal cord postnatally. AU - Chen, Hsiao Huei AU - Simon Hippenmeyer AU - Arber, Silvia AU - Frank, Eric ID - 3139 IS - 1 T2 - Current Opinion in Neurobiology TI - Development of the monosynaptic stretch reflex circuit VL - 13 ER - TY - CONF AB - Reconstructing a 3-D scene from more than one camera is a classical problem in computer vision. One of the major sources of difficulty is the fact that not all scene elements are visible from all cameras. In the last few years, two promising approaches have been developed 11,12 that formulate the scene reconstruction problem in terms of energy minimization, and minimize the energy using graph cuts. These energy minimization approaches treat the input images symmetrically, handle visibility constraints correctly, and allow spatial smoothness to be enforced. However, these algorithm propose different problem formulations, and handle a limited class of smoothness terms. One algorithm 11 uses a problem formulation that is restricted to two-camera stereo, and imposes smoothness between a pair of cameras. The other algorithm 12 can handle an arbitrary number of cameras, but imposes smoothness only with respect to a single camera. In this paper we give a more general energy minimization formulation for the problem, which allows a larger class of spatial smoothness constraints. We show that our formulation includes both of the previous approaches as special cases, as well as permitting new energy functions. Experimental results on real data with ground truth are also included. AU - Vladimir Kolmogorov AU - Zabih, Ramin AU - Gortler, Steven ID - 3171 TI - Generalized multi camera scene reconstruction using graph cuts VL - 2683 ER - TY - CONF AB - We address visual correspondence problems without assuming that scene points have similar intensities in different views. This situation is common, usually due to non-lambertian scenes or to differences between cameras. We use maximization of mutual information, a powerful technique for registering images that requires no a priori model of the relationship between scene intensities in different views. However, it has proven difficult to use mutual information to compute dense visual correspondence. Comparing fixed-size windows via mutual information suffers from the well-known problems of fixed windows, namely poor performance at discontinuities and in low-texture regions. In this paper, we show how to compute visual correspondence using mutual information without suffering from these problems. Using 'a simple approximation, mutual information can be incorporated into the standard energy minimization framework used in early vision. The energy can then be efficiently minimized using graph cuts, which preserve discontinuities and handle low-texture regions. The resulting algorithm combines the accurate disparity maps that come from graph cuts with the tolerance for intensity changes that comes from mutual information. AU - Kim, Junhwan AU - Vladimir Kolmogorov AU - Zabih, Ramin ID - 3174 TI - Visual correspondence using energy minimization and mutual information VL - 2 ER - TY - CONF AB - Geodesic active contours and graph cuts are two standard image segmentation techniques. We introduce a new segmentation method combining some of their benefits. Our main intuition is that any cut on a graph embedded in some continuous space can be interpreted as a contour (in 2D) or a surface (in 3D). We show how to build a grid graph and set its edge weights so that the cost of cuts is arbitrarily close to the length (area) of the corresponding contours (surfaces) for any anisotropic Riemannian metric. There are two interesting consequences of this technical result. First, graph cut algorithms can be used to find globally minimum geodesic contours (minimal surfaces in 3D) under arbitrary Riemannian metric for a given set of boundary conditions. Second, we show how to minimize metrication artifacts in existing graph-cut based methods in vision. Theoretically speaking, our work provides an interesting link between several branches of mathematics -differential geometry, integral geometry, and combinatorial optimization. The main technical problem is solved using Cauchy-Crofton formula from integral geometry. AU - Boykov, Yuri AU - Vladimir Kolmogorov ID - 3170 TI - Computing geodesics and minimal surfaces via graph cuts VL - 1 ER - TY - JOUR AB - Neurons can produce action potentials with high temporal precision(1). A fundamental issue is whether, and how, this capability is used in information processing. According to the `cell assembly' hypothesis, transient synchrony of anatomically distributed groups of neurons underlies processing of both external sensory input and internal cognitive mechanisms(2-4). Accordingly, neuron populations should be arranged into groups whose synchrony exceeds that predicted by common modulation by sensory input. Here we find that the spike times of hippocampal pyramidal cells can be predicted more accurately by using the spike times of simultaneously recorded neurons in addition to the animals location in space. This improvement remained when the spatial prediction was refined with a spatially dependent theta phase modulation(5-8). The time window in which spike times are best predicted from simultaneous peer activity is 10-30 ms, suggesting that cell assemblies are synchronized at this timescale. Because this temporal window matches the membrane time constant of pyramidal neurons(9), the period of the hippocampal gamma oscillation(10) and the time window for synaptic plasticity(11), we propose that cooperative activity at this timescale is optimal for information transmission and storage in cortical circuits. AU - Harris, Kenneth D AU - Jozsef Csicsvari AU - Hirase, Hajima AU - Dragoi, George AU - Buzsáki, György ID - 3526 IS - 6948 JF - Nature TI - Organization of cell assemblies in the hippocampus VL - 424 ER -