@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}, } @article{3725, abstract = {The combination of high-resolution atomic force microscopy (AFM) imaging and single-molecule force-spectroscopy was employed to unfold single bacteriorhodopsins (BR) from native purple membrane patches at various physiologically relevant temperatures. The unfolding spectra reveal detailed insight into the stability of individual structural elements of BR against mechanical unfolding. Intermittent states in the unfolding process are associated with the stepwise unfolding of alpha-helices, whereas other states are associated with the unfolding of polypeptide loops connecting the alpha-helices. It was found that the unfolding forces of the secondary structures considerably decreased upon increasing the temperature from 8 to 52°C. Associated with this effect, the probability of individual unfolding pathways of BR was significantly influenced by the temperature. At lower temperatures, transmembrane alpha-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, whereas they predominantly unfolded collectively at elevated temperatures. This suggests that increasing the temperature decreases the mechanical stability of secondary structural elements and changes molecular interactions between secondary structures, thereby forcing them to act as grouped structures.}, author = {Harald Janovjak and Kessler, Max and Oesterhelt, Dieter and Gaub, Hermann and Mueller, Daniel J}, journal = {EMBO Journal}, number = {19}, pages = {5220 -- 5229}, publisher = {Wiley-Blackwell}, title = {{Unfolding pathways of native bacteriorhodopsin depend on temperature}}, doi = {10.1093/emboj/cdg509}, volume = {22}, 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}, } @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}, } @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}, } @phdthesis{4416, abstract = {Methods for the formal specification and verification of systems are indispensible for the development of complex yet correct systems. In formal verification, the designer describes the system in a modeling language with a well-defined semantics, and this system description is analyzed against a set of correctness requirements. Model checking is an algorithmic technique to check that a system description indeed satisfies correctness requirements given as logical specifications. While successful in hardware verification, the potential for model checking for software and embedded systems has not yet been realized. This is because traditional model checking focuses on systems modeled as finite state-transition graphs. While a natural model for hardware (especially synchronous hardware), state-transition graphs often do not capture software and embedded systems at an appropriate level of granularity. This dissertation considers two orthogonal extensions to finite state-transition graphs making model checking techniques applicable to both a wider class of systems and a wider class of properties. The first direction is an extension to infinite-state structures finitely represented using constraints and operations on constraints. Infinite state arises when we wish to model variables with unbounded range (e.g., integers), or data structures, or real time. We provide a uniform framework of symbolic region algebras to study model checking of infinite-state systems. We also provide sufficient language-independent termination conditions for symbolic model checking algorithms on infinite state systems. The second direction supplements verification with game theoretic reasoning. Games are natural models for interactions between components. We study game theoretic behavior with winning conditions given by temporal logic objectives both in the deterministic and in the probabilistic context. For deterministic games, we provide an extremal model characterization of fixpoint algorithms that link solutions of verification problems to solutions for games. For probabilistic games we study fixpoint characterization of winning probabilities for games with omega-regular winning objectives, and construct (epsilon-)optimal winning strategies.}, author = {Majumdar, Ritankar}, pages = {1 -- 201}, publisher = {University of California, Berkeley}, title = {{Symbolic algorithms for verification and control}}, year = {2003}, } @phdthesis{4425, abstract = {Giotto provides a time-triggered programmer’s model for the implementation of embedded control systems with hard real-time constraints. Giotto’s precise semantics and predictabil- ity make it suitable for safety-critical applications. Giotto is based around the idea that time-triggered task invocation together with time-triggered mode switching can form a useful programming model for real-time systems. To substantiate this claim, we describe the use of Giotto to refactor the software of a small, autonomous helicopter. The ease with which Giotto expresses the existing software provides evidence that Giotto is an appropriate programming language for control systems. Since Giotto is a real-time programming language, ensuring that Giotto programs meet their deadlines is crucial. To study precedence-constrained Giotto scheduling, we first examine single-mode, single-processor scheduling. We extend to an infinite, periodic setting the classical problem of meeting deadlines for a set of tasks with release times, deadlines, precedence constraints, and preemption. We then develop an algorithm for scheduling Giotto programs on a single processor by representing Giotto programs as instances of the extended scheduling problem. Next, we study multi-mode, single-processor Giotto scheduling. This problem is different from classical scheduling problems, since in our precedence-constrained approach, the deadlines of tasks may vary depending on the mode switching behavior of the program. We present conditional scheduling models which capture this varying-deadline behavior. We develop polynomial-time algorithms for some conditional scheduling models, and prove oth- ers to be computationally hard. We show how to represent multi-mode Giotto programs as instances of the model, resulting in an algorithm for scheduling multi-mode Giotto programs on a single processor. Finally, we show that the problem of scheduling Giotto programs for multiple net- worked processors is strongly NP-hard.}, author = {Horowitz, Benjamin}, pages = {1 -- 237}, publisher = {University of California, Berkeley}, title = {{Giotto: A time-triggered language for embedded programming}}, year = {2003}, } @article{576, abstract = {We study the free expansion of a pancake-shaped Bose-condensed gas, which is initially trapped under harmonic confinement and containing a vortex at its centre. In the case of a radial expansion holding the axial confinement fixed we consider various models for the interactions, depending on the thickness of the condensate relative to the value of the scattering length. We are thus able to evaluate different scattering regimes ranging from quasi-three-dimensional (Q3D) to strictly two-dimensional (2D). We find that as the system goes from Q3D to 2D the expansion rate of the condensate increases whereas that of the vortex core decreases. In the Q3D scattering regime we also examine a fully free expansion in 3D and find oscillatory behaviour for the vortex core radius: an initial fast expansion of the vortex core is followed by a slowing down. Such a nonuniform expansion rate of the vortex core implies that the timing of its observation should be chosen appropriately.}, author = {Onur Hosten and Vignolo, Patrizia and Minguzzi, Anna and Tanatar, Bilal and Tosi, Mario P}, journal = {Journal of Physics B: Atomic, Molecular and Optical Physics}, number = {12}, pages = {2455 -- 2463}, publisher = {IOP Publishing Ltd.}, title = {{Free expansion of two-dimensional condensates with a vortex}}, doi = {10.1088/0953-4075/36/12/306}, volume = {36}, year = {2003}, } @article{6156, abstract = {Social and solitary feeding in natural Caenorhabditis elegans isolates are associated with two alleles of the orphan G-protein-coupled receptor (GPCR) NPR-1: social feeders contain NPR-1 215F, whereas solitary feeders contain NPR-1 215V. Here we identify FMRFamide-related neuropeptides (FaRPs) encoded by the flp-18 and flp-21 genes as NPR-1 ligands and show that these peptides can differentially activate the NPR-1 215F and NPR-1 215V receptors. Multicopy overexpression of flp-21 transformed wild social animals into solitary feeders. Conversely, a flp-21 deletion partially phenocopied the npr-1(null) phenotype, which is consistent with NPR-1 activation by FLP-21 in vivo but also implicates other ligands for NPR-1. Phylogenetic studies indicate that the dominant npr-1 215V allele likely arose from an ancestral npr-1 215F gene in C. elegans. Our data suggest a model in which solitary feeding evolved in an ancestral social strain of C. elegans by a gain-of-function mutation that modified the response of NPR-1 to FLP-18 and FLP-21 ligands.}, author = {Rogers, Candida and Reale, Vincenzina and Kim, Kyuhyung and Chatwin, Heather and Li, Chris and Evans, Peter and de Bono, Mario}, issn = {1097-6256}, journal = {Nature Neuroscience}, number = {11}, pages = {1178--1185}, publisher = {Springer Nature}, title = {{Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation of NPR-1}}, doi = {10.1038/nn1140}, volume = {6}, year = {2003}, } @article{6157, abstract = {In many animal species individuals aggregate to live in groups. A range of experimental approaches in different animals, including studies of social feeding in nematodes, maternal behavior in rats and sheep, and pair-bonding in voles, are providing insights into the neural bases for these behaviors. These studies are delineating multiple neural circuits and gene networks in the brain that interact in ways that are as yet poorly understood to coordinate social behavior.}, author = {de Bono, Mario}, issn = {0022-3034}, journal = {Journal of Neurobiology}, number = {1}, pages = {78--92}, publisher = {Wiley}, title = {{Molecular approaches to aggregation behavior and social attachment}}, doi = {10.1002/neu.10162}, volume = {54}, year = {2003}, } @article{847, abstract = {The accumulation of genome-wide information on single nucleotide polymorphisms in humans provides an unprecedented opportunity to detect the evolutionary forces responsible for heterogeneity of the level of genetic variability across loci. Previous studies have shown that history of recombination events has produced long haplotype blocks in the human genome, which contribute to this heterogeneity. Other factors, however, such as natural selection or the heterogeneity of mutation rates across loci, may also lead to heterogeneity of genetic variability. We compared synonymous and non-synonymous variability within human genes with their divergence from murine orthologs. We separately analyzed the non-synonymous variants predicted to damage protein structure or function and the variants predicted to be functionally benign. The predictions were based on comparative sequence analysis and, in some cases, on the analysis of protein structure. A strong correlation between non-synonymous, benign variability and non-synonymous human-mouse divergence suggests that selection played an important role in shaping the pattern of variability in coding regions of human genes. However, the lack of correlation between deleterious variability and evolutionary divergence shows that a substantial proportion of the observed non-synonymous single-nucleotide polymorphisms reduces fitness and never reaches fixation. Evolutionary and medical implications of the impact of selection on human polymorphisms are discussed.}, author = {Sunyaev, Shamil R and Fyodor Kondrashov and Bork, Peer and Ramensky, Vasily}, journal = {Human Molecular Genetics}, number = {24}, pages = {3325 -- 3330}, publisher = {Oxford University Press}, title = {{Impact of selection, mutation rate and genetic drift on human genetic variation}}, doi = {10.1093/hmg/ddg359}, volume = {12}, year = {2003}, } @article{876, abstract = {Alternative splicing is thought to be a major source of functional diversity in animal proteins. We analyzed the evolutionary conservation of proteins encoded by alternatively spliced genes and predicted the ancestral state for 73 cases of alternative splicing (25 insertions and 48 deletions). The amino acid sequences of most of the inserts in proteins produced by alternative splicing are as conserved as the surrounding sequences. Thus, alternative splicing often creates novel isoforms by the insertion of new, functional protein sequences that probably originated from noncoding sequences of introns.}, author = {Fyodor Kondrashov and Koonin, Eugene V}, journal = {Trends in Genetics}, number = {3}, pages = {115 -- 119}, publisher = {Elsevier}, title = {{Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences}}, doi = {10.1016/S0168-9525(02)00029-X}, volume = {19}, year = {2003}, } @article{9495, abstract = {RNA interference is a conserved process in which double-stranded RNA is processed into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing. In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM) in which DNA with sequence identity to silenced RNA is de novo methylated at its cytosine residues. This methylation is not only at canonical CpG sites but also at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly complete loss of asymmetric methylation and a partial loss of CpNpG methylation. The remaining asymmetric and CpNpG methylation was dependent on the activity of CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation. These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2 cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of siRNAs. Finally, we demonstrate that DRM activity is required for the initial establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric sites.}, author = {Cao, Xiaofeng and Aufsatz, Werner and Zilberman, Daniel and Mette, M.Florian and Huang, Michael S. and Matzke, Marjori and Jacobsen, Steven E.}, issn = {1879-0445}, journal = {Current Biology}, number = {24}, pages = {2212--2217}, publisher = {Elsevier}, title = {{Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation}}, doi = {10.1016/j.cub.2003.11.052}, volume = {13}, year = {2003}, } @article{8519, author = {Kaloshin, Vadim}, issn = {0020-9910}, journal = {Inventiones mathematicae}, keywords = {General Mathematics}, number = {3}, pages = {451--512}, publisher = {Springer Nature}, title = {{The existential Hilbert 16-th problem and an estimate for cyclicity of elementary polycycles}}, doi = {10.1007/s00222-002-0244-9}, volume = {151}, year = {2003}, } @article{9455, abstract = {Proteins of the ARGONAUTE family are important in diverse posttranscriptional RNA-mediated gene-silencing systems as well as in transcriptional gene silencing in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena. We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing of the Arabidopsis SUPERMAN(SUP) gene. The ago4-1 mutant reactivated silentSUP alleles and decreased CpNpG and asymmetric DNA methylation as well as histone H3 lysine-9 methylation. In addition,ago4-1 blocked histone and DNA methylation and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct chromatin modifications, including histone methylation and non-CpG DNA methylation.}, author = {Zilberman, Daniel and Cao, Xiaofeng and Jacobsen, Steven E.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5607}, pages = {716--719}, publisher = {American Association for the Advancement of Science}, title = {{ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation}}, doi = {10.1126/science.1079695}, volume = {299}, year = {2003}, } @inproceedings{4628, abstract = {Discounting the future means that the value, today, of a unit payoffis 1 if the payoffo ccurs today, a if it occurs tomorrow, a 2 if it occurs the day after tomorrow, and so on, for some real-valued discount factor 0 < a < 1. Discounting (or inflation) is a key paradigm in economics and has been studied in Markov decision processes as well as game theory. We submit that discounting also has a natural place in systems engineering: for nonterminating systems, a potential bug in the far-away future is less troubling than a potential bug today. We therefore develop a systems theory with discounting. Our theory includes several basic elements: discounted versions of system properties that correspond to the ω-regular properties, fixpoint-based algorithms for checking discounted properties, and a quantitative notion of bisimilarity for capturing the difference between two states with respect to discounted properties. We present the theory in a general form that applies to probabilistic systems as well as multicomponent systems (games), but it readily specializes to classical transition systems. We show that discounting, besides its natural practical appeal, has also several mathematical benefits. First, the resulting theory is robust, in that small perturbations of a system can cause only small changes in the properties of the system. Second, the theory is computational, in that the values of discounted properties, as well as the discounted bisimilarity distance between states, can be computed to any desired degree of precision.}, author = {De Alfaro, Luca and Henzinger, Thomas A and Majumdar, Ritankar}, booktitle = {Proceedings of the 30th International Colloquium on Automata, Languages and Programming}, isbn = {9783540404934}, location = {Eindhoven, The Netherlands}, pages = {1022 -- 1037}, publisher = {Springer}, title = {{Discounting the future in systems theory}}, doi = {10.1007/3-540-45061-0_79}, volume = {2719}, year = {2003}, } @article{13436, abstract = {Cross-metathesis reactions of α,β-unsaturated sulfones and sulfoxides in the presence of molybdenum and ruthenium pre-catalysts were tested. A selective metahesis reaction was achieved between functionalized terminal olefins and vinyl sulfones by using the ‘second generation’ ruthenium catalysts 1c–h while the highly active Schrock catalyst 1b was found to be functional group incompatible with vinyl sulfones. The cross-metathesis products were isolated in good yields with an excellent (E)-selectivity. Both the molybdenum and ruthenium-based complexes were, however, incompatible with α,β- and β,γ-unsaturated sulfoxides.}, author = {Michrowska, Anna and Bieniek, Michał and Kim, Mikhail and Klajn, Rafal and Grela, Karol}, issn = {1464-5416}, journal = {Tetrahedron}, keywords = {Organic Chemistry, Drug Discovery, Biochemistry}, number = {25}, pages = {4525--4531}, publisher = {Elsevier}, title = {{Cross-metathesis reaction of vinyl sulfones and sulfoxides}}, doi = {10.1016/s0040-4020(03)00682-3}, volume = {59}, year = {2003}, } @inproceedings{4561, abstract = {We present a formalism for specifying component interfaces that expose component requirements on limited resources. The formalism permits an algorithmic check if two or more components, when put together, exceed the available resources. Moreover, the formalism can be used to compute the quantity of resources necessary for satisfying the requirements of a collection of components. The formalism can be instantiated in several ways. For example, several components may draw power from the same source. Then, the formalism supports compatibility checks such as: can two components, when put together, achieve their tasks without ever exceeding the available amount of peak power? or, can they achieve their tasks by using no more than the initially available amount of energy (i.e., power accumulated over time)? The corresponding quantitative questions that our algorithms answer are the following: what is the amount of peak power needed for two components to be put together? what is the corresponding amount of initial energy? To solve these questions, we model interfaces with resource requirements as games with quantitative objectives. The games are played on state spaces where each state is labeled by a number (representing, e.g., power consumption), and a play produces an infinite path of labels. The objective may be, for example, to minimize the largest label that occurs during a play. We illustrate our approach by modeling compatibility questions for the components of robot control software, and of wireless sensor networks.}, author = {Chakrabarti, Arindam and De Alfaro, Luca and Henzinger, Thomas A and Stoelinga, Mariëlle}, booktitle = {Third International Conference on Embedded Software}, isbn = {9783540202233}, location = {Philadelphia, PA, USA}, pages = {117 -- 133}, publisher = {ACM}, title = {{Resource interfaces}}, doi = {10.1007/978-3-540-45212-6_9}, volume = {2855}, year = {2003}, } @inproceedings{4630, abstract = {We consider concurrent two-person games played in real time, in which the players decide both which action to play, and when to play it. Such timed games differ from untimed games in two essential ways. First, players can take each other by surprise, because actions are played with delays that cannot be anticipated by the opponent. Second, a player should not be able to win the game by preventing time from diverging. We present a model of timed games that preserves the element of surprise and accounts for time divergence in a way that treats both players symmetrically and applies to all ω-regular winning conditions. We prove that the ability to take each other by surprise adds extra power to the players. For the case that the games are specified in the style of timed automata, we provide symbolic algorithms for their solution with respect to all ω-regular winning conditions. We also show that for these timed games, memory strategies are more powerful than memoryless strategies already in the case of reachability objectives.}, author = {De Alfaro, Luca and Faella, Marco and Henzinger, Thomas A and Majumdar, Ritankar and Stoelinga, Mariëlle}, booktitle = {Proceedings of the 14th International Conference on Concurrency Theory}, isbn = {9783540407539}, location = {Marseille, France}, pages = {144 -- 158}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The element of surprise in timed games}}, doi = {10.1007/978-3-540-45187-7_9}, volume = {2761}, year = {2003}, } @article{4468, abstract = {Giotto is a high-level programming language for time-triggered control applications. The authors begin with a conceptual overview of its methodology, discuss the Giotto helicopter project, and summarize available Giotto implementations.}, author = {Henzinger, Thomas A and Kirsch, Christoph and Sanvido, Marco and Pree, Wolfgang}, issn = {1066-033X }, journal = {IEEE Control Systems Magazine}, number = {1}, pages = {50 -- 64}, publisher = {IEEE}, title = {{From control models to real-time code using Giotto}}, doi = {10.1109/MCS.2003.1172829}, volume = {23}, year = {2003}, } @inbook{4465, abstract = {Giotto is a principled, tool-supported design methodology for implementing embedded control systems on platforms of possibly distributed sensors, actuators, CPUs, and networks. Giotto is based on the principle that time-triggered task invocations plus time-triggered mode switches can form the abstract essence of programming real-time control systems. Giotto consists of a programming language with a formal semantics, and a retargetable compiler and runtime library. Giotto supports the automation of control system design by strictly separating platform-independent functionality and timing concerns from platform-dependent scheduling and communication issues. The time-triggered predictability of Giotto makes it particularly suitable for safety-critical applications with hard real-time constraints. We illustrate the platform independence and time-triggered execution of Giotto by coordinating a heterogeneous flock of Intel x86 robots and Lego Mindstorms robots.}, author = {Henzinger, Thomas A and Horowitz, Benjamin and Kirsch, Christoph}, booktitle = {Software-Enabled Control: Information Technology for Dynamical Systems}, isbn = {9780471234364 }, pages = {123 -- 146}, publisher = {Wiley-Blackwell}, title = {{Embedded control systems development with Giotto}}, doi = {10.1002/047172288X.ch8}, year = {2003}, } @inproceedings{4466, abstract = {One source of complexity in the μ-calculus is its ability to specify an unbounded number of switches between universal (AX) and existential (EX) branching modes. We therefore study the problems of satisfiability, validity, model checking, and implication for the universal and existential fragments of the μ-calculus, in which only one branching mode is allowed. The universal fragment is rich enough to express most specifications of interest, and therefore improved algorithms are of practical importance. We show that while the satisfiability and validity problems become indeed simpler for the existential and universal fragments, this is, unfortunately, not the case for model checking and implication. We also show the corresponding results for the alternationfree fragment of the μ-calculus, where no alternations between least and greatest fixed points are allowed. Our results imply that efforts to find a polynomial-time model-checking algorithm for the μ-calculus can be replaced by efforts to find such an algorithm for the universal or existential fragment.}, author = {Henzinger, Thomas A and Kupferman, Orna and Majumdar, Ritankar}, booktitle = {Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems }, isbn = {9783540008989}, location = {Warsaw, Poland}, pages = {49 -- 64}, publisher = {Springer}, title = {{On the universal and existential fragments of the mu-calculus}}, doi = {10.1007/3-540-36577-X_5}, volume = {2619}, year = {2003}, } @inproceedings{4467, abstract = {BLAST (the Berkeley Lazy Abstraction Software verification Tool) is a verification system for checking safety properties of C programs using automatic property-driven construction and model checking of software abstractions. Blast implements an abstract-model check-refine loop to check for reachability of a specified label in the program. The abstract model is built on the fly using predicate abstraction. This model is then checked for reachability. If there is no (abstract) path to the specified error label, Blast reports that the system is safe and produces a succinct proof. Otherwise, it checks if the path is feasible using symbolic execution of the program. If the path is feasible, Blast outputs the path as an error trace, otherwise, it uses the infeasibility of the path to refine the abstract model. Blast short-circuits the loop from abstraction to verification to refinement, integrating the three steps tightly through “lazy abstraction” [5]. This integration can offer significant advantages in performance by avoiding the repetition of work from one iteration of the loop to the next. }, author = {Henzinger, Thomas A and Jhala, Ranjit and Majumdar, Ritankar and Sutre, Grégoire}, booktitle = {Proceedings of the 10th International SPIN Workshop }, isbn = {9783540401179}, location = {Portland, OR, USA}, pages = {235 -- 239}, publisher = {Springer}, title = {{Software verification with BLAST}}, doi = {10.1007/3-540-44829-2_17}, volume = {2648}, year = {2003}, } @inproceedings{4463, abstract = {We present an algorithm called TAR (“Thread-modular Abstraction Refinement”) for model checking safety properties of concurrent software. The TAR algorithm uses thread-modular assume-guarantee reasoning to overcome the exponential complexity in the control state of multithreaded programs. Thread modularity means that TAR explores the state space of one thread at a time, making assumptions about how the environment can interfere. The TAR algorithm uses counterexample-guided predicate-abstraction refinement to overcome the usually infinite complexity in the data state of C programs. A successive approximation scheme automatically infers the necessary precision on data variables as well as suitable environment assumptions. The scheme is novel in that transition relations are approximated from above, while at the same time environment assumptions are approximated from below. In our software verification tool BLAST we have implemented a fully automatic race checker for multithreaded C programs which is based on the TAR algorithm. This tool has verified a wide variety of commonly used locking idioms, including locking schemes that are not amenable to existing dynamic and static race checkers such as ERASER or WARLOCK.}, author = {Henzinger, Thomas A and Jhala, Ranjit and Majumdar, Ritankar and Qadeer, Shaz}, booktitle = {Proceedings of the 15th International Conference on Computer Aided Verification}, isbn = {9783540405245}, location = {Boulder, CO, USA}, pages = {262 -- 274}, publisher = {Springer}, title = {{Thread-modular abstraction refinement}}, doi = {10.1007/978-3-540-45069-6_27}, volume = {2725}, year = {2003}, } @inproceedings{4462, abstract = {A major hurdle in the algorithmic verification and control of systems is the need to find suitable abstract models, which omit enough details to overcome the state-explosion problem, but retain enough details to exhibit satisfaction or controllability with respect to the specification. The paradigm of counterexample-guided abstraction refinement suggests a fully automatic way of finding suitable abstract models: one starts with a coarse abstraction, attempts to verify or control the abstract model, and if this attempt fails and the abstract counterexample does not correspond to a concrete counterexample, then one uses the spurious counterexample to guide the refinement of the abstract model. We present a counterexample-guided refinement algorithm for solving ω-regular control objectives. The main difficulty is that in control, unlike in verification, counterexamples are strategies in a game between system and controller. In the case that the controller has no choices, our scheme subsumes known counterexample-guided refinement algorithms for the verification of ω-regular specifications. Our algorithm is useful in all situations where ω-regular games need to be solved, such as supervisory control, sequential and program synthesis, and modular verification. The algorithm is fully symbolic, and therefore applicable also to infinite-state systems.}, author = {Henzinger, Thomas A and Jhala, Ranjit and Majumdar, Ritankar}, booktitle = {Proceedings of the 30th International Colloquium on Automata, Languages and Programming}, isbn = {9783540404934}, location = {Eindhoven, The Netherlands}, pages = {886 -- 902}, publisher = {Springer}, title = {{Counterexample-guided control}}, doi = {10.1007/3-540-45061-0_69}, volume = {2719}, year = {2003}, } @inproceedings{4464, abstract = {We introduce the paradigm of schedule-carrying code (SCC). A hard real-time program can be executed on a given platform only if there exists a feasible schedule for the real-time tasks of the program. Traditionally, a scheduler determines the existence of a feasible schedule according to some scheduling strategy. With SCC, a compiler proves the existence of a feasible schedule by generating executable code that is attached to the program and represents its schedule. An SCC executable is a real-time program that carries its schedule as code, which is produced once and can be revalidated and executed with each use. We evaluate SCC both in theory and practice. In theory, we give two scenarios, of nonpreemptive and distributed scheduling for Giotto programs, where the generation of a feasible schedule is hard, while the validation of scheduling instructions that are attached to the programs is easy. In practice, we implement SCC and show that explicit scheduling instructions can reduce the scheduling overhead up to 35% and can provide an efficient, flexible, and verifiable means for compiling Giotto programs on complex architectures, such as the TTA.}, author = {Henzinger, Thomas A and Kirsch, Christoph and Matic, Slobodan}, booktitle = {Proceedings of the 3rd International Conference on Embedded Software}, isbn = {9783540202233}, location = {Philadelphia, PA, USA}, pages = {241 -- 256}, publisher = {ACM}, title = {{Schedule-carrying code}}, doi = {10.1007/978-3-540-45212-6_16}, volume = {2855}, year = {2003}, } @article{4460, abstract = {Symbolic model checking, which enables the automatic verification of large systems, proceeds by calculating expressions that represent state sets. Traditionally, symbolic model-checking tools are based on back- ward state traversal; their basic operation is the function pre, which, given a set of states, returns the set of all predecessor states. This is because specifiers usually employ formalisms with future-time modalities, which are naturally evaluated by iterating applications of pre. It has been shown experimentally that symbolic model checking can perform significantly better if it is based, instead, on forward state traversal; in this case, the basic operation is the function post, which, given a set of states, returns the set of all successor states. This is because forward state traversal can ensure that only parts of the state space that are reachable from an initial state and relevant for the satisfaction or violation of the specification are explored; that is, errors can be detected as soon as possible. In this paper, we investigate which specifications can be checked by symbolic forward state traversal. We formulate the problems of symbolic backward and forward model checking by means of two μ-calculi. The pre-μ calculus is based on the pre operation, and the post-μ calculus is based on the post operation. These two μ-calculi induce query logics, which augment fixpoint expressions with a boolean emptiness query. Using query logics, we are able to relate and compare the symbolic backward and forward approaches. In particular, we prove that all ω-regular (linear-time) specifications can be expressed as post-μ queries, and therefore checked using symbolic forward state traversal. On the other hand, we show that there are simple branching-time specifications that cannot be checked in this way.}, author = {Henzinger, Thomas A and Kupferman, Orna and Qadeer, Shaz}, issn = {0925-9856}, journal = {Formal Methods in System Design}, number = {3}, pages = {303 -- 327}, publisher = {Springer}, title = {{From pre-historic to post-modern symbolic model checking}}, doi = {10.1023/A:1026228213080}, volume = {23}, year = {2003}, } @article{4469, abstract = {Giotto provides an abstract programmer's model for the implementation of embedded control systems with hard real-time constraints. A typical control application consists of periodic software tasks together with a mode-switching logic for enabling and disabling tasks. Giotto specifies time-triggered sensor readings, task invocations, actuator updates, and mode switches independent of any implementation platform. Giotto can be annotated with platform constraints such as task-to-host mappings, and task and communication schedules. The annotations are directives for the Giotto compiler, but they do not alter the functionality and timing of a Giotto program. By separating the platform-independent from the platform-dependent concerns, Giotto enables a great deal of flexibility in choosing control platforms as well as a great deal of automation in the validation and synthesis of control software. The time-triggered nature of Giotto achieves timing predictability, which makes Giotto particularly suitable for safety-critical applications.}, author = {Henzinger, Thomas A and Horowitz, Benjamin and Kirsch, Christoph}, issn = {0018-9219 }, journal = {Proceedings of the IEEE}, number = {1}, pages = {84 -- 99}, publisher = {IEEE}, title = {{Giotto: A time-triggered language for embedded programming}}, doi = {10.1109/JPROC.2002.805825}, volume = {91}, year = {2003}, } @article{4338, abstract = {Mosaic hybrid zones arise when ecologically differentiated taxa hybridize across a network of habitat patches. Frequent interbreeding across a small-scale patchwork can erode species differences that might have been preserved in a clinal hybrid zone. In particular, the rapid breakdown of neutral divergence sets an upper limit to the time for which differences at marker loci can persist. We present here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our 20 × 20 km study area, we detected no evidence of a clinal transition but found a strong association between aquatic habitat and mean allele frequencies at four molecular markers. In particular, pure populations of B. bombina in ponds appear to cause massive introgression into the surrounding B. variegata gene pool found in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid populations was remarkably similar to those of a previously studied transect near Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote deficit and linkage disequilibrium in each country are similar. In Apahida, the observed strong linkage disequilibria should stem from an imperfect habitat preference that guides most (but not all) adults into the habitats to which they are adapted. In the absence of a clinal structure, the inferred migration rate between habitats implies that associations between selected loci and neutral markers should break down rapidly. Although plausible selection strengths can maintain differentiation at those loci adapting the toads to either permanent or temporary breeding sites, the divergence at neutral markers must be transient. The hybrid zone may be approaching a state in which the gene pools are homogenized at all but the selected loci, not dissimilar from an early stage of sympatric divergence.}, author = {Vines, Timothy and Kohler, S C and Thiel, M and Ghira, Ioan and Sands, T R and Maccallum, Catriona and Barton, Nicholas H and Nürnberger, Beate}, issn = {0014-3820}, journal = {Evolution}, number = {8}, pages = {1876 -- 1888}, publisher = {Wiley-Blackwell}, title = {{On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata}}, doi = {10.1111/j.0014-3820.2003.tb00595.x}, volume = {57}, year = {2003}, } @article{4350, abstract = {The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, have appeared in all cladistic morphological analyses as distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have shown them to be sister taxa. We present the first phylogenetic study of Crocodylia using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator mississippiensis to facilitate primer design and then sequenced an 1,100-base pair fragment that includes both coding and noncoding regions and informative indels for one species in each extant crocodylian genus and six avian outgroups. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference all strongly agreed on the same tree, which is identical to the tree found in previous molecular analyses: Gavialis and Tomistoma are sister taxa and together are the sister group of Crocodylidae. Kishino-Hasegawa tests rejected the morphological tree in favor of the molecular tree. We excluded long-branch attraction and variation in base composition among taxa as explanations for this topology. To explore the causes of discrepancy between molecular and morphological estimates of crocodylian phylogeny, we examined puzzling features of the morphological data using a priori partitions of the data based on anatomical regions and investigated the effects of different coding schemes for two obvious morphological similarities of the two gharials.}, author = {Harshman, John and Huddleston, Christopher and Bollback, Jonathan P and Parsons, Thomas and Braun, Michael}, issn = {0039-7989 }, journal = {Systematic Biology}, number = {3}, pages = {386 -- 402}, publisher = {Oxford University Press}, title = {{True and false gharials: A nuclear gene phylogeny of crocodylia}}, doi = {10.1080/10635150390197028}, volume = {52}, year = {2003}, } @article{4348, abstract = {Many questions in evolutionary biology are best addressed by comparing traits in different species. Often such studies involve mapping characters on phylogenetic trees. Mapping characters on trees allows the nature, number, and timing of the transformations to be identified. The parsimony method is the only method available for mapping morphological characters on phylogenies. Although the parsimony method often makes reasonable reconstructions of the history of a character, it has a number of limitations. These limitations include the inability to consider more than a single change along a branch on a tree and the uncoupling of evolutionary time from amount of character change. We extended a method described by Nielsen (2002, Syst. Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation.}, author = {Huelsenbeck, John and Nielsen, Rasmus and Bollback, Jonathan P}, issn = {0039-7989 }, journal = {Systematic Biology}, number = {2}, pages = {131 -- 158}, publisher = {Oxford University Press}, title = {{Stochastic mapping of morphological characters}}, doi = {10.1080/10635150390192780}, volume = {52}, 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}, } @article{4257, abstract = {Variation within a species may be structured both geographically and by genetic background. We review the effects of such structuring on neutral variants, using a framework based on the coalescent process. Short-term effects of sex differences and age structure can be averaged out using fast timescale approximations, allowing a simple general treatment of effective population size and migration. We consider the effects of geographic structure on variation within and between local populations, first in general terms, and then for specific migration models. We discuss the close parallels between geographic structure and stable types of genetic structure caused by selection, including balancing selection and background selection. The effects of departures from stability, such as selective sweeps and population bottlenecks, are also described. Methods for distinguishing population history from the effects of ongoing gene flow are discussed. We relate the theoretical results to observed patterns of variation in natural populations.}, author = {Charlesworth, Brian and Charlesworth, Deborah and Barton, Nicholas H}, issn = {1543-592X}, journal = {Annual Review of Ecology and Systematics}, pages = {99 -- 125}, publisher = {Annual Reviews}, title = {{The effects of genetic and geographic structure on neutral variation}}, doi = {10.1146/annurev.ecolsys.34.011802.132359}, volume = {34}, year = {2003}, } @article{4256, abstract = {Artificial Life models may shed new light on the long-standing challenge for evolutionary biology of explaining the origins of complex organs. Real progress on this issue, however, requires Artificial Life researchers to take seriously the tools and insights from population genetics.}, author = {Barton, Nicholas H and Zuidema, Willem}, issn = {0960-9822}, journal = {Current Biology}, number = {16}, pages = {R649 -- R651}, publisher = {Cell Press}, title = {{The erratic path towards complexity}}, doi = {10.1016/S0960-9822(03)00573-6}, volume = {13}, year = {2003}, }