@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}, } @article{3804, abstract = {Kv3 channels are thought to be essential for the fast-spiking (FS) phenotype in GABAergic interneurons, but how these channels confer the ability to generate action potentials (APs) at high frequency is unknown. To address this question, we developed a fast dynamic-clamp system (approximately 50 kHz) that allowed us to add a Kv3 model conductance to CA1 oriens alveus (OA) interneurons in hippocampal slices. Selective pharmacological block of Kv3 channels by 0.3 mm 4-aminopyridine or 1 mm tetraethylammonium ions led to a marked broadening of APs during trains of short stimuli and a reduction in AP frequency during 1 sec stimuli. The addition of artificial Kv3 conductance restored the original AP pattern. Subtraction of Kv3 conductance by dynamic clamp mimicked the effects of the blockers. Application of artificial Kv3 conductance also led to FS in OA interneurons after complete K+ channel block and even induced FS in hippocampal pyramidal neurons in the absence of blockers. Adding artificial Kv3 conductance with altered deactivation kinetics revealed a nonmonotonic relationship between mean AP frequency and deactivation rate, with a maximum slightly above the original value. Insertion of artificial Kv3 conductance with either lowered activation threshold or inactivation also led to a reduction in the mean AP frequency. However, the mechanisms were distinct. Shifting the activation threshold induced adaptation, whereas adding inactivation caused frequency-dependent AP broadening. In conclusion, Kv3 channels are necessary for the FS phenotype of OA interneurons, and several of their gating properties appear to be optimized for high-frequency repetitive activity.}, author = {Lien, Cheng-Chang and Peter Jonas}, journal = {Journal of Neuroscience}, number = {6}, pages = {2058 -- 68}, publisher = {Society for Neuroscience}, title = {{Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons}}, volume = {23}, year = {2003}, } @article{3806, abstract = {To probe exocytosis at a cortical glutamatergic synapse, we made capacitance measurements in whole-cell recorded hippocampal mossy fiber terminals. Evaluation of different methods by using a morphology-based equivalent electrical model revealed that quantitative capacitance measurements are possible in this presynaptic structure. Voltage pulses leading to presynaptic Ca2+ inflow evoked large capacitance signals that showed saturation with increasing pulse duration. The mean peak capacitance increase was 100 fF, corresponding to a pool of approximately 1,400 releasable vesicles. Thus hippocampal mossy fiber synapses have a vesicular "maxipool." Large pool size and rapid vesicle recycling may underlie the uniquely large extent of activity-dependent plasticity in this synapse.}, author = {Hallermann, Stefan and Pawlu, Christian and Peter Jonas and Heckmann, Manfred}, journal = {PNAS}, number = {15}, pages = {8975 -- 80}, publisher = {National Academy of Sciences}, title = {{A large pool of releasable vesicles in a cortical glutamatergic synapse}}, doi = {10.1073/pnas.1432836100}, volume = {100}, 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{3917, abstract = {Male dimorphism is not genetically determined, but is induced by environmental conditions particularly decreasing temperature and density.}, author = {Cremer, Sylvia and Heinze, Jürgen}, journal = {Blick in die Wissenschaft}, number = {15}, pages = {32 -- 36}, publisher = {Schnell und Steiner}, title = {{Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen}}, volume = {12}, year = {2003}, } @article{3921, abstract = {Unlike most social insects, many Cardiocondyla ant species have two male morphs: wingless (ergatoid) males, who remain in the natal nest, and winged males who disperse but, strangely, before leaving may also mate within the nest. Whereas ergatoid males are highly intolerant of each other and fight among themselves, they tend to tolerate their winged counterparts. This is despite the fact that these winged males, like ergatoid males, represent mating competition. Why should ergatoid males tolerate their winged rivals? We developed a mathematical model to address this question. Our model focuses on a number of factors likely toinfluence whether ergatoid males are tolerant of winged males: ergatoid male–winged male relatedness, number of virgin queens, number of winged males, and the number of ejaculates a winged male has (winged males are sperm limited, whereas ergatoid males have lifelong spermatogenesis). Surprisingly, we found that increasing the number of virgin queens favors a kill strategy, whereas an increase in the other factors favors a let-live strategy; these predictions appear true for C. obscurior and for a number of other Cardiocondyla species. Two further aspects, unequal insemination success and multiple mating in queens, were also incorporated into the model and predictions made about their effects on toleration of winged males. The model is applicable more generally in species that have dimorphic males, such as some other ants, bees, and fig wasps.}, author = {Anderson, Carl and Cremer, Sylvia and Heinze, Jürgen}, journal = {Behavioral Ecology}, number = {1}, pages = {54 -- 62}, publisher = {Oxford University Press}, title = {{Live and let die: Why fighter males of the ant Cardiocondyla kill each other but tolerate their winged rivals}}, doi = {10.1093/beheco/14.1.54}, volume = {14}, year = {2003}, } @article{3922, abstract = {Dispersal is advantageous, but, at the same time, it implies high costs and risks. Due to these counteracting selection pressures, many species evolved dispersal polymorphisms, which, in ants, are typically restricted to the female sex (queens). Male polymorphism is presently only known from a few genera, such as Cardiocondyla, in which winged dispersing males coexist with wingless fighter males that mate exclusively inside their maternal nests. We studied the developmental mechanisms underlying these alternative male morphs and found that, first, male dimorphism is not genetically determined, but is induced by environmental conditions (decreasing temperature and density). Second, male morph is not yet fixed at the egg stage, but it differentiates during larval development. This flexible developmental pattern of male morphs allows Cardiocondyla ant colonies to react quickly to changes in their environment. Under good conditions, they invest exclusively in philopatric wingless males. But, when environmental conditions turn bad, colonies start to produce winged dispersal males, even though these males require a many times higher investment by the colony than their much smaller wingless counterparts. Cardiocondyla ants share this potential of optimal resource allocation with other colonial animals and some seed dimorphic plants.}, author = {Cremer, Sylvia and Heinze, Jürgen}, journal = {Current Biology}, number = {3}, pages = {219 -- 223}, publisher = {Cell Press}, title = {{Stress grows wings: Environmental induction of winged dispersal males in Cardiocondyla ants}}, doi = {10.1016/S0960-9822(03)00012-5}, volume = {13}, year = {2003}, } @inbook{3991, abstract = {We give analytic inclusion-exclusion formulas for the area and perimeter derivatives of a union of finitely many disks in the plane.}, author = {Cheng, Ho and Edelsbrunner, Herbert}, booktitle = {Computer Science in Perspective: Essays Dedicated to Thomas Ottmann}, isbn = {9783540005797}, pages = {88 -- 97}, publisher = {Springer}, title = {{Area and perimeter derivatives of a union of disks}}, doi = {10.1007/3-540-36477-3_7}, volume = {2598}, year = {2003}, } @article{3992, abstract = {Computing the volume occupied by individual atoms in macromolecular structures has been the subject of research for several decades. This interest has grown in the recent years, because weighted volumes are widely used in implicit solvent models. Applications of the latter in molecular mechanics simulations require that the derivatives of these weighted volumes be known. In this article, we give a formula for the volume derivative of a molecule modeled as a space-filling diagram made up of balls in motion. The formula is given in terms of the weights, radii, and distances between the centers as well as the sizes of the facets of the power diagram restricted to the space-filling diagram. Special attention is given to the detection and treatment of singularities as well as discontinuities of the derivative.}, author = {Edelsbrunner, Herbert and Koehl, Patrice}, issn = {0027-8424}, journal = {PNAS}, number = {5}, pages = {2203 -- 2208}, publisher = {National Academy of Sciences}, title = {{The weighted-volume derivative of a space-filling diagram}}, doi = {10.1073/pnas.0537830100}, volume = {100}, 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}, } @inproceedings{3997, abstract = {We combine topological and geometric methods to construct a multi-resolution data structure for functions over two-dimensional domains. Starting with the Morse-Smale complex, we construct a topological hierarchy by progressively canceling critical points in pairs. Concurrently, we create a geometric hierarchy by adapting the geometry to the changes in topology. The data structure supports mesh traversal operations similarly to traditional multi-resolution representations.}, author = {Bremer, Peer and Edelsbrunner, Herbert and Hamann, Bernd and Pascucci, Valerio}, booktitle = {Proceedings of the 14th IEEE Conference on Visualization }, isbn = {0780381203}, location = {Seattle, WA, USA }, pages = {139 -- 146}, publisher = {IEEE}, title = {{A multi-resolution data structure for two-dimensional Morse-Smale functions}}, doi = {10.1109/VISUAL.2003.1250365}, year = {2003}, } @inproceedings{3999, abstract = {We introduce relaxed scheduling as a paradigm for mesh maintenance and demonstrate its applicability to triangulating a skin surface in R-3.}, author = {Edelsbrunner, Herbert and Üngör, Alper}, booktitle = {Proceedings of the Japanese Conference on Discrete and Computational Geometry }, isbn = {9783540207764}, location = {Tokyo, Japan}, pages = {135 -- 151}, publisher = {Springer}, title = {{Relaxed scheduling in dynamic skin triangulation}}, doi = {10.1007/978-3-540-44400-8_14}, volume = {2866}, year = {2003}, } @article{4146, abstract = {During vertebrate gastrulation, highly coordinated cellular rearrangements lead to the formation of the three germ layers, ectoderm, mesoderm and endoderm. In zebrafish, silberblick (slb)/wnt11 regulates normal gastrulation movements by activating a signalling pathway similar to the Frizzled-signalling pathway, which establishes epithelial planar cell polarity (PCP) in Drosophila. However, the cellular mechanisms by which slb/wnt11 functions during zebrafish gastrulation are still unclear. Using high-resolution two-photon confocal imaging followed by computer-assisted reconstruction and motion analysis, we have analysed the movement and morphology of individual cells in three dimensions during the course of gastrulation. We show that in slb-mutant embryos, hypoblast cells within the forming germ ring have slower, less directed migratory movements at the onset of gastrulation. These aberrant cell movements are accompanied by defects in the orientation of cellular processes along the individual movement directions of these cells. We conclude that slb/wnt11-mediated orientation of cellular processes plays a role in facilitating and stabilising movements of hypoblast cells in the germ ring, thereby pointing at a novel function of the slb/wnt11 signalling pathway for the regulation of migratory cell movements at early stages of gastrulation.}, author = {Ulrich, Florian and Concha, Miguel and Heid, Paul and Voss, Ed and Witzel, Sabine and Roehl, Henry and Tada, Masazumi and Wilson, Stephen and Adams, Richard and Soll, David and Heisenberg, Carl-Philipp J}, issn = {1011-6370}, journal = {Development}, number = {22}, pages = {5375 -- 5384}, publisher = {Company of Biologists}, title = {{Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation}}, doi = {10.1242/dev.00758}, volume = {130}, year = {2003}, } @article{4168, abstract = {Recent studies show that signaling through integrin receptors is required for normal cell movements during Xenopus gastrulation. Integrins function in this process by modulating the activity of cadherin adhesion molecules within tissues undergoing convergence and extension movements.}, author = {Montero, Juan and Heisenberg, Carl-Philipp J}, issn = {1878-1551}, journal = {Developmental Cell}, number = {2}, pages = {190 -- 191}, publisher = {Cell Press}, title = {{Adhesive crosstalk in gastrulation}}, doi = {10.1016/S1534-5807(03)00235-1}, volume = {5}, year = {2003}, } @article{4169, abstract = {Background: During vertebrate gastrulation, cell polarization and migration are core components in the cellular rearrangements that lead to the formation of the three germ layers, ectoderm, mesoderm, and endoderm. Previous studies have implicated the Wnt/planar cell polarity (PCP) signaling pathway in controlling cell morphology and movement during gastrulation. However, cell polarization and directed cell migration are reduced but not completely abolished in the absence of Wnt/PCP signals; this observation indicates that other signaling pathways must be involved. Results: We show that Phosphoinositide 3-Kinases (PI3Ks) are required at the onset of zebrafish gastrulation in mesendodermal cells for process formation and cell polarization. Platelet Derived Growth Factor (PDGF) functions upstream of PI3K, while Protein Kinase B (PKB), a downstream effector of PI3K activity, localizes to the leading edge of migrating mesendodermal cells. In the absence of PI3K activity, PKB localization and cell polarization are strongly reduced in mesendodermal cells and are followed by slower but still highly coordinated and directed movements of these cells. Conclusions: We have identified a novel role of a signaling pathway comprised of PDGF, PI3K, and PKB in the control of morphogenetic cell movements during gastrulation. Furthermore, our findings provide insight into the relationship between cell polarization and directed cell migration at the onset of zebrafish gastrulation.}, author = {Montero, Juan and Kilian, Beate and Chan, Joanne and Bayliss, Peter and Heisenberg, Carl-Philipp J}, issn = {1879-0445}, journal = {Current Biology}, number = {15}, pages = {1279 -- 1289}, publisher = {Cell Press}, title = {{Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells}}, doi = {10.1016/S0960-9822(03)00505-0}, volume = {13}, year = {2003}, } @article{4185, abstract = {Wnt genes play important roles in regulating patterning and morphogenesis during vertebrate gastrulation. In zebrafish, slb/wnt11 is required for convergence and extension movements, but not cell fate specification during gastrulation. To determine if other Wnt genes functionally interact with slb/wnt11, we analysed the role of ppt/wnt5 during zebrafish gastrulation. ppt/wnt5 is maternally provided and zygotically expressed at all stages during gastrulation. The analysis of ppt mutant embryos reveals that Ppt/Wnt5 regulates cell elongation and convergent extension movements in posterior regions of the gastrula, while its function in more anterior regions is largely redundant to that of Slb/Wnt11. Frizzled-2 functions downstream of ppt/wnt5, indicating that it might act as a receptor for Ppt/Wnt5 in this process. The characterisation of the role of Ppt/Wnt5 provides insight into the functional diversity of Wnt genes in regulating vertebrate gastrulation movements. (C) 2003 Elsevier Science Ireland Ltd. All rights reserved.}, author = {Kilian, Beate and Mansukoski, Hannu and Barbosa, Filipa and Ulrich, Florian and Tada, Masazumi and Heisenberg, Carl-Philipp J}, issn = {0925-4773}, journal = {Mechanisms of Development}, number = {4}, pages = {467 -- 476}, publisher = {Elsevier}, title = {{The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation}}, doi = {10.1016/S0925-4773(03)00004-2}, volume = {120}, year = {2003}, } @article{4254, abstract = {Chromosomal rearrangements can promote reproductive isolation by reducing recombination along a large section of the genome. We model the effects of the genetic barrier to gene flow caused by a chromosomal rearrangement on the rate of accumulation of postzygotic isolation genes in parapatry. We find that, if reproductive isolation is produced by the accumulation in parapatry of sets of alleles compatible within but incompatible across species, chromosomal rearrangements are far more likely to favor it than classical genetic barriers without chromosomal changes. New evidence of the role of chromosomal rearrangements in parapatric speciation suggests that postzygotic isolation is often due to the accumulation of such incompatibilities. The model makes testable qualitative predictions about the genetic signature of speciation.}, author = {Navarro, Arcadio and Barton, Nicholas H}, issn = {0014-3820}, journal = {Evolution; International Journal of Organic Evolution}, number = {3}, pages = {447 -- 459}, publisher = {Wiley-Blackwell}, title = {{Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation}}, doi = {10.1111/j.0014-3820.2003.tb01537.x}, volume = {57}, year = {2003}, }