@article{3584, abstract = {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.}, author = {Edelsbrunner, Herbert and Zomorodian, Afra}, journal = {Homology, Homotopy and Applications}, number = {2}, pages = {19 -- 37}, publisher = {International Press}, title = {{Computing linking numbers of a filtration}}, volume = {5}, year = {2003}, } @article{3620, abstract = {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.}, author = {Nürnberger, Beate and Hofman, Sebastian and Förg-Brey, Bqruni and Praetzel, Gabriele and Maclean, Alan W and Szymura, Jacek M and Abbott, Catherine M and Nicholas Barton}, journal = {Heredity}, number = {2}, pages = {136 -- 142}, publisher = {Nature Publishing Group}, title = {{A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)}}, doi = {10.1038/sj.hdy.6800291}, volume = {91}, year = {2003}, } @article{3619, abstract = {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.}, author = {Baird, Stuart J and Nicholas Barton and Etheridge, Alison M}, journal = {Theoretical Population Biology}, number = {4}, pages = {451 -- 471}, publisher = {Academic Press}, title = {{The distribution of surviving blocks of an ancestral genome}}, doi = {10.1016/S0040-5809(03)00098-4}, volume = {64}, year = {2003}, } @article{3618, abstract = {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.}, author = {Vines, Timothy H and Nicholas Barton}, journal = {Molecular Ecology}, number = {7}, pages = {1999 -- 2002}, publisher = {Wiley-Blackwell}, title = {{A new approach to detecting mixed families}}, doi = {10.1046/j.1365-294X.2003.01867.x}, volume = {12}, year = {2003}, } @article{3752, abstract = {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.}, author = {Vilar,Jose M and Calin Guet and Leibler, Stanislas}, journal = {Journal of Cell Biology}, number = {3}, pages = {471 -- 476}, publisher = {Rockefeller University Press}, title = {{Modeling network dynamics: the lac operon, a case study}}, doi = {10.1083/jcb.200301125}, volume = {161}, year = {2003}, } @article{3797, author = {Bauer, Wolfgang and Kleine Berkenbusch, Marco and Bollenbach, Mark Tobias}, journal = {Revista Mexicana De Fisica}, number = {4}, pages = {1 -- 6}, publisher = {Sociedad Mexicana de Física}, title = {{Breaking atomic nuclei into little pieces: evidence for a phase transition}}, volume = {49}, year = {2003}, } @inproceedings{3897, abstract = {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.}, author = {Krishnendu Chatterjee and Jurdziński, Marcin and Thomas Henzinger}, pages = {100 -- 113}, publisher = {Springer}, title = {{Simple stochastic parity games}}, doi = {10.1007/978-3-540-45220-1_11}, volume = {2803}, year = {2003}, } @inproceedings{3898, abstract = {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.}, author = {Krishnendu Chatterjee and Ma, Di and Majumdar, Ritankar S and Zhao, Tian and Thomas Henzinger and Palsberg, Jens}, pages = {109 -- 126}, publisher = {Springer}, title = {{Stack size analysis for interrupt-driven programs}}, doi = {10.1007/3-540-44898-5_7}, volume = {2694}, year = {2003}, } @article{3993, abstract = {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.}, author = {Herbert Edelsbrunner and Harer, John and Zomorodian, Afra}, journal = {Discrete & Computational Geometry}, number = {1}, pages = {87 -- 107}, publisher = {Springer}, title = {{Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds}}, doi = {10.1007/s00454-003-2926-5}, volume = {30}, year = {2003}, } @article{3994, abstract = {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.}, author = {Cheng, Ho-Lun and Herbert Edelsbrunner}, journal = {Computational Geometry: Theory and Applications}, number = {2}, pages = {173 -- 192}, publisher = {Elsevier}, title = {{Area, perimeter and derivatives of a skin curve}}, doi = {10.1016/S0925-7721(02)00124-4}, volume = {26}, year = {2003}, } @misc{3139, abstract = {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.}, author = {Chen, Hsiao Huei and Simon Hippenmeyer and Arber, Silvia and Frank, Eric}, booktitle = {Current Opinion in Neurobiology}, number = {1}, pages = {96 -- 102}, publisher = {Elsevier}, title = {{Development of the monosynaptic stretch reflex circuit}}, doi = {10.1016/S0959-4388(03)00006-0}, volume = {13}, year = {2003}, } @inproceedings{3171, abstract = {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. }, author = {Vladimir Kolmogorov and Zabih, Ramin and Gortler, Steven}, pages = {501 -- 516}, publisher = {Springer}, title = {{Generalized multi camera scene reconstruction using graph cuts}}, doi = {10.1007/978-3-540-45063-4_32}, volume = {2683}, year = {2003}, } @inproceedings{3174, abstract = {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.}, author = {Kim, Junhwan and Vladimir Kolmogorov and Zabih, Ramin}, pages = {1033 -- 1040}, publisher = {IEEE}, title = {{Visual correspondence using energy minimization and mutual information}}, doi = {10.1109/ICCV.2003.1238463}, volume = {2}, year = {2003}, } @inproceedings{3170, abstract = {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.}, author = {Boykov, Yuri and Vladimir Kolmogorov}, pages = {26 -- 33}, publisher = {IEEE}, title = {{Computing geodesics and minimal surfaces via graph cuts}}, doi = {10.1109/ICCV.2003.1238310}, volume = {1}, year = {2003}, } @article{3526, abstract = {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.}, author = {Harris, Kenneth D and Jozsef Csicsvari and Hirase, Hajima and Dragoi, George and Buzsáki, György}, journal = {Nature}, number = {6948}, pages = {552 -- 556}, publisher = {Nature Publishing Group}, title = {{Organization of cell assemblies in the hippocampus}}, doi = {0.1038/nature01834}, volume = {424}, year = {2003}, } @article{3529, abstract = {Parallel recording of neuronal activity in the behaving animal is a prerequisite for our understanding of neuronal representation and storage of information. Here we describe the development of micro-machined silicon microelectrode arrays for unit and local field recordings. The two-dimensional probes with 96 or 64 recording sites provided high-density recording of unit and field activity with minimal tissue displacement or damage. The on-chip active circuit eliminated movement and other artifacts and greatly reduced the weight of the headgear. The precise geometry of the recording tips allowed for the estimation of the spatial location of the recorded neurons and for high-resolution estimation of extracellular current source density. Action potentials could be simultaneously recorded from the soma and dendrites of the same neurons. Silicon technology is a promising approach for high-density, high-resolution sampling of neuronal activity in both basic research and prosthetic devices.}, author = {Jozsef Csicsvari and Henze, Darrell A and Jamieson, Brian G and Harris, Kenneth D and Sirota, Anton M and Bartho, Peter and Wise, Kensall D and Buzsáki, György}, journal = {Journal of Neurophysiology}, number = {2}, pages = {1314 -- 1323}, publisher = {American Physiological Society}, title = {{Massively parallel recording of unit and local field potentials with silicon-based electrodes}}, doi = {10.1152/jn.00116.2003}, volume = {90}, year = {2003}, } @article{3528, abstract = {Gamma frequency oscillations (30-100 Hz) have been suggested to underlie various cognitive and motor functions. Here, we examine the generation of gamma oscillation currents in the hippocampus, using two-dimensional, 96-site silicon probes. Two gamma generators were identified, one in the dentate gyrus and another in the CA3-CA1 regions. The coupling strength between the two oscillators varied during both theta and nontheta states. Both pyramidal cells and interneurons were phase-locked to gamma waves. Anatomical connectivity, rather than physical distance, determined the coupling strength of the oscillating neurons. CA3 pyramidal neurons discharged CA3 and CA1 interneurons at latencies indicative of monosynaptic connections. Intrahippocampal gamma oscillation emerges in the CA3 recurrent system, which entrains the CA1 region via its interneurons.}, author = {Jozsef Csicsvari and Jamieson, Brian G and Wise, Kensall D and Buzsáki, György}, journal = {Neuron}, number = {2}, pages = {311 -- 322}, publisher = {Elsevier}, title = {{Mechanisms of gamma oscillations in the hippocampus of the behaving rat}}, doi = {10.1016/S0896-6273(02)01169-8}, volume = {37}, year = {2003}, } @article{3543, abstract = {Both neocortical and hippocampal networks organize the firing patterns of their neurons by prominent oscillations during sleep, but the functional role of these rhythms is not well understood. Here, we show a robust correlation of neuronal discharges between the somatosensory cortex and hippocampus on both slow and fine time scales in the mouse and rat. Neuronal bursts in deep cortical layers, associated with sleep spindles and delta waves/slow rhythm, effectively triggered hippocampal discharges related to fast (ripple) oscillations. We hypothesize that oscillation-mediated temporal links coordinate specific information transfer between neocortical and hippocampal cell assemblies. Such a neocortical-hippocampal interplay may be important for memory consolidation.}, author = {Sirota, Anton M and Jozsef Csicsvari and Buhl, Derek L and Buzsáki, György}, journal = {PNAS}, number = {4}, pages = {2065 -- 2069}, publisher = {National Academy of Sciences}, title = {{Communication between neocortex and hippocampus during sleep in rodents}}, doi = {10.1073/pnas.0437938100}, volume = {100}, year = {2003}, } @article{3593, abstract = {Temporal logics such as Computation Tree Logic (CTL) and Linear Temporal Logic (LTL) have become popular for specifying temporal properties over a wide variety of planning and verification problems. In this paper we work towards building a generalized framework for automated reasoning based on temporal logics. We present a powerful extension of CTL with first-order quantification over the set of reachable states for reasoning about extremal properties of weighted labeled transition systems in general. The proposed logic, which we call Weighted Quantified Computation Tree Logic (WQCTL), captures the essential elements common to the domain of planning and verification problems and can thereby be used as an effective specification language in both domains. We show that in spite of the rich, expressive power of the logic, we are able to evaluate WQCTL formulas in time polynomial in the size of the state space times the length of the formula. Wepresent experimental results on the WQCTL verifier.}, author = {Krishnendu Chatterjee and Dasgupta, Pallab and Chakrabarti, Partha P}, journal = {Journal of Automated Reasoning}, number = {2}, pages = {205 -- 232}, publisher = {Springer}, title = {{A branching time temporal framework for quantitative reasoning}}, doi = {10.1023/A:1023217515688}, volume = {30}, year = {2003}, } @phdthesis{3678, author = {Christoph Lampert}, booktitle = {Bonner Mathematische Schriften}, pages = {1 -- 165}, publisher = {Universität Bonn, Fachbibliothek Mathematik}, title = {{The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric }}, volume = {356}, year = {2003}, }