TY - CONF
AB - Geodesic active contours and graph cuts are two standard image segmentation techniques. We introduce a new segmentation method combining some of their benefits. Our main intuition is that any cut on a graph embedded in some continuous space can be interpreted as a contour (in 2D) or a surface (in 3D). We show how to build a grid graph and set its edge weights so that the cost of cuts is arbitrarily close to the length (area) of the corresponding contours (surfaces) for any anisotropic Riemannian metric. There are two interesting consequences of this technical result. First, graph cut algorithms can be used to find globally minimum geodesic contours (minimal surfaces in 3D) under arbitrary Riemannian metric for a given set of boundary conditions. Second, we show how to minimize metrication artifacts in existing graph-cut based methods in vision. Theoretically speaking, our work provides an interesting link between several branches of mathematics -differential geometry, integral geometry, and combinatorial optimization. The main technical problem is solved using Cauchy-Crofton formula from integral geometry.
AU - Boykov, Yuri
AU - Vladimir Kolmogorov
ID - 3170
TI - Computing geodesics and minimal surfaces via graph cuts
VL - 1
ER -
TY - CONF
AB - Reconstructing a 3-D scene from more than one camera is a classical problem in computer vision. One of the major sources of difficulty is the fact that not all scene elements are visible from all cameras. In the last few years, two promising approaches have been developed 11,12 that formulate the scene reconstruction problem in terms of energy minimization, and minimize the energy using graph cuts. These energy minimization approaches treat the input images symmetrically, handle visibility constraints correctly, and allow spatial smoothness to be enforced. However, these algorithm propose different problem formulations, and handle a limited class of smoothness terms. One algorithm 11 uses a problem formulation that is restricted to two-camera stereo, and imposes smoothness between a pair of cameras. The other algorithm 12 can handle an arbitrary number of cameras, but imposes smoothness only with respect to a single camera. In this paper we give a more general energy minimization formulation for the problem, which allows a larger class of spatial smoothness constraints. We show that our formulation includes both of the previous approaches as special cases, as well as permitting new energy functions. Experimental results on real data with ground truth are also included.
AU - Vladimir Kolmogorov
AU - Zabih, Ramin
AU - Gortler, Steven
ID - 3171
TI - Generalized multi camera scene reconstruction using graph cuts
VL - 2683
ER -
TY - CONF
AB - We address visual correspondence problems without assuming that scene points have similar intensities in different views. This situation is common, usually due to non-lambertian scenes or to differences between cameras. We use maximization of mutual information, a powerful technique for registering images that requires no a priori model of the relationship between scene intensities in different views. However, it has proven difficult to use mutual information to compute dense visual correspondence. Comparing fixed-size windows via mutual information suffers from the well-known problems of fixed windows, namely poor performance at discontinuities and in low-texture regions. In this paper, we show how to compute visual correspondence using mutual information without suffering from these problems. Using 'a simple approximation, mutual information can be incorporated into the standard energy minimization framework used in early vision. The energy can then be efficiently minimized using graph cuts, which preserve discontinuities and handle low-texture regions. The resulting algorithm combines the accurate disparity maps that come from graph cuts with the tolerance for intensity changes that comes from mutual information.
AU - Kim, Junhwan
AU - Vladimir Kolmogorov
AU - Zabih, Ramin
ID - 3174
TI - Visual correspondence using energy minimization and mutual information
VL - 2
ER -
TY - JOUR
AB - We show that the fixed alphabet shortest common supersequence (SCS) and the fixed alphabet longest common subsequence (LCS) problems parameterized in the number of strings are W[1]-hard. Unless W[1]=FPT, this rules out the existence of algorithms with time complexity of O(f(k)nα) for those problems. Here n is the size of the problem instance, α is constant, k is the number of strings and f is any function of k. The fixed alphabet version of the LCS problem is of particular interest considering the importance of sequence comparison (e.g. multiple sequence alignment) in the fixed length alphabet world of DNA and protein sequences.
AU - Krzysztof Pietrzak
ID - 3209
IS - 4
JF - Journal of Computer and System Sciences
TI - On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems
VL - 67
ER -
TY - CONF
AB - Luby and Rackoff showed how to construct a (super-)pseudo-random permutation {0,1}2n→ {0,1}2n from some number r of pseudo-random functions {0,1}n → {0,1}n. Their construction, motivated by DES, consists of a cascade of r Feistel permutations. A Feistel permutation 1for a pseudo-random function f is defined as (L, R) → (R,L ⊕ f (R)), where L and R are the left and right part of the input and ⊕ denotes bitwise XOR or, in this paper, any other group operation on {0,1}n. The only non-trivial step of the security proof consists of proving that the cascade of r Feistel permutations with independent uniform random functions {0,1}n → {0,1}n, denoted Ψ2nr is indistinguishable from a uniform random permutation {0,1}2n → {0,1}2n by any computationally unbounded adaptive distinguisher making at most O(2cn) combined chosen plaintext/ciphertext queries for any c < α, where a is a security parameter. Luby and Rackoff proved α = 1/2 for r = 4. A natural problem, proposed by Pieprzyk is to improve on α for larger r. The best known result, α = 3/4 for r = 6, is due to Patarin. In this paper we prove a = 1 -O(1/r), i.e., the trivial upper bound α = 1 can be approached. The proof uses some new techniques that can be of independent interest.
AU - Maurer, Ueli M
AU - Krzysztof Pietrzak
ID - 3210
TI - The security of many round Luby Rackoff pseudo random permutations
VL - 2656
ER -
TY - CONF
AU - Bollenbach, Tobias
AU - Strother, T.
AU - Bauer, Wolfgang
ID - 3425
TI - 3D supernova collapse calculations
VL - 166
ER -
TY - CHAP
AU - Peter Jonas
AU - Unsicker, Klaus
ED - Schmidt, R. F.
ID - 3458
T2 - Lehrbuch Vorklinik
TI - Molekulare und zelluläre Grundlagen des Nervensystems.
VL - B
ER -
TY - JOUR
AB - Neurons can produce action potentials with high temporal precision(1). A fundamental issue is whether, and how, this capability is used in information processing. According to the `cell assembly' hypothesis, transient synchrony of anatomically distributed groups of neurons underlies processing of both external sensory input and internal cognitive mechanisms(2-4). Accordingly, neuron populations should be arranged into groups whose synchrony exceeds that predicted by common modulation by sensory input. Here we find that the spike times of hippocampal pyramidal cells can be predicted more accurately by using the spike times of simultaneously recorded neurons in addition to the animals location in space. This improvement remained when the spatial prediction was refined with a spatially dependent theta phase modulation(5-8). The time window in which spike times are best predicted from simultaneous peer activity is 10-30 ms, suggesting that cell assemblies are synchronized at this timescale. Because this temporal window matches the membrane time constant of pyramidal neurons(9), the period of the hippocampal gamma oscillation(10) and the time window for synaptic plasticity(11), we propose that cooperative activity at this timescale is optimal for information transmission and storage in cortical circuits.
AU - Harris, Kenneth D
AU - Jozsef Csicsvari
AU - Hirase, Hajima
AU - Dragoi, George
AU - Buzsáki, György
ID - 3526
IS - 6948
JF - Nature
TI - Organization of cell assemblies in the hippocampus
VL - 424
ER -
TY - JOUR
AB - 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.
AU - Jozsef Csicsvari
AU - Jamieson, Brian G
AU - Wise, Kensall D
AU - Buzsáki, György
ID - 3528
IS - 2
JF - Neuron
TI - Mechanisms of gamma oscillations in the hippocampus of the behaving rat
VL - 37
ER -
TY - JOUR
AB - 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.
AU - Jozsef Csicsvari
AU - Henze, Darrell A
AU - Jamieson, Brian G
AU - Harris, Kenneth D
AU - Sirota, Anton M
AU - Bartho, Peter
AU - Wise, Kensall D
AU - Buzsáki, György
ID - 3529
IS - 2
JF - Journal of Neurophysiology
TI - Massively parallel recording of unit and local field potentials with silicon-based electrodes
VL - 90
ER -
TY - JOUR
AB - Genetic engineering of the mouse brain allows investigators to address novel hypotheses in vivo. Because of the paucity of information on the network patterns of the mouse hippocampus, we investigated the electrical patterns in the behaving animal using multisite silicon probes and wire tetrodes. Theta (6-9 Hz) and gamma (40-100 Hz) oscillations were present during exploration and rapid eye movement sleep. Gamma power and theta power were comodulated and gamma power varied as a function of the theta cycle. Pyramidal cells and putative interneurons were phase-locked to theta oscillations. During immobility, consummatory behaviors and slow-wave sleep, sharp waves were present in cornu ammonis region CA1 of the hippocampus stratum radiatum associated with 140-200-Hz “ripples” in the pyramidal cell layer and population burst of CA1 neurons. In the hilus, large-amplitude “dentate spikes” occurred in association with increased discharge of hilar neurons. The amplitude of field patterns was larger in the mouse than in the rat, likely reflecting the higher neuron density in a smaller brain. We suggest that the main hippocampal network patterns are mediated by similar pathways and mechanisms in mouse and rat.
AU - Buzsáki, György
AU - Buhl, Derek L
AU - Harris, Kenneth D
AU - Jozsef Csicsvari
AU - Czéh, Boldizsár
AU - Morozov, Alexei
ID - 3536
IS - 1
JF - Neuroscience
TI - Hippocampal network patterns of activity in the mouse
VL - 116
ER -
TY - JOUR
AB - 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.
AU - Sirota, Anton M
AU - Jozsef Csicsvari
AU - Buhl, Derek L
AU - Buzsáki, György
ID - 3543
IS - 4
JF - PNAS
TI - Communication between neocortex and hippocampus during sleep in rodents
VL - 100
ER -
TY - CONF
AB - We define the Morse-Smale complex of a Morse function over a 3-manifold as the overlay of the descending and as- cending manifolds of all critical points. In the generic case, its 3-dimensional cells are shaped like crystals and are sepa- rated by quadrangular faces. In this paper, we give a combi- natorial algorithm for constructing such complexes for piece- wise linear data.
AU - Herbert Edelsbrunner
AU - Harer, John
AU - Natarajan, Vijay
AU - Pascucci, Valerio
ID - 3556
TI - Morse-Smale complexes for piecewise linear 3-manifolds
ER -
TY - CHAP
AB - Given a finite point set in R, the surface reconstruction problem asks for a surface that passes through many but not necessarily all points. We describe an unambigu- ous definition of such a surface in geometric and topological terms, and sketch a fast algorithm for constructing it. Our solution overcomes past limitations to special point distributions and heuristic design decisions.
AU - Herbert Edelsbrunner
ID - 3573
T2 - Discrete & Computational Geometry
TI - Surface reconstruction by wrapping finite sets in space
ER -
TY - JOUR
AB - We develop fast algorithms for computing the linking number of a simplicial complex within a filtration.We give experimental results in applying our work toward the detection of non-trivial tangling in biomolecules, modeled as alpha complexes.
AU - Edelsbrunner, Herbert
AU - Zomorodian, Afra
ID - 3584
IS - 2
JF - Homology, Homotopy and Applications
TI - Computing linking numbers of a filtration
VL - 5
ER -
TY - JOUR
AB - 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.
AU - Krishnendu Chatterjee
AU - Dasgupta, Pallab
AU - Chakrabarti, Partha P
ID - 3593
IS - 2
JF - Journal of Automated Reasoning
TI - A branching time temporal framework for quantitative reasoning
VL - 30
ER -
TY - JOUR
AB - There are several analyses in evolutionary ecology which assume that a family of offspring has come from only two parents. Here, we present a simple test for detecting when a batch involves two or more subfamilies. It is based on the fact that the mixing of families generates associations amongst unlinked marker loci. We also present simulations illustrating the power of our method for varying numbers of loci, alleles per locus and genotyped individuals.
AU - Vines, Timothy H
AU - Nicholas Barton
ID - 3618
IS - 7
JF - Molecular Ecology
TI - A new approach to detecting mixed families
VL - 12
ER -
TY - JOUR
AB - What is the chance that some part of a stretch of genome will survive? In a population of constant size, and with no selection, the probability of survival of some part of a stretch of map length y<1 approaches View the MathML source for View the MathML source. Thus, the whole genome is certain to be lost, but the rate of loss is extremely slow. This solution extends to give the whole distribution of surviving block sizes as a function of time. We show that the expected number of blocks at time t is 1+yt and give expressions for the moments of the number of blocks and the total amount of genome that survives for a given time. The solution is based on a branching process and assumes complete interference between crossovers, so that each descendant carries only a single block of ancestral material. We consider cases where most individuals carry multiple blocks, either because there are multiple crossovers in a long genetic map, or because enough time has passed that most individuals in the population are related to each other. For species such as ours, which have a long genetic map, the genome of any individual which leaves descendants (∼80% of the population for a Poisson offspring number with mean two) is likely to persist for an extremely long time, in the form of a few short blocks of genome.
AU - Baird, Stuart J
AU - Nicholas Barton
AU - Etheridge, Alison M
ID - 3619
IS - 4
JF - Theoretical Population Biology
TI - The distribution of surviving blocks of an ancestral genome
VL - 64
ER -
TY - JOUR
AB - Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5′ end of the repeats.
AU - Nürnberger, Beate
AU - Hofman, Sebastian
AU - Förg-Brey, Bqruni
AU - Praetzel, Gabriele
AU - Maclean, Alan W
AU - Szymura, Jacek M
AU - Abbott, Catherine M
AU - Nicholas Barton
ID - 3620
IS - 2
JF - Heredity
TI - A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)
VL - 91
ER -
TY - THES
AU - Christoph Lampert
ID - 3678
T2 - Bonner Mathematische Schriften
TI - The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric
VL - 356
ER -
TY - JOUR
AB - 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.
AU - Harald Janovjak
AU - Kessler, Max
AU - Oesterhelt, Dieter
AU - Gaub, Hermann
AU - Mueller, Daniel J
ID - 3725
IS - 19
JF - EMBO Journal
TI - Unfolding pathways of native bacteriorhodopsin depend on temperature
VL - 22
ER -
TY - JOUR
AB - We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description (molecular, cellular, and that of cell population) into a single model, which seems to capture many experimental aspects of the system.
AU - Vilar,Jose M
AU - Calin Guet
AU - Leibler, Stanislas
ID - 3752
IS - 3
JF - Journal of Cell Biology
TI - Modeling network dynamics: the lac operon, a case study
VL - 161
ER -
TY - JOUR
AU - Bauer, Wolfgang
AU - Kleine-Berkenbusch, Marco
AU - Bollenbach, Tobias
ID - 3797
IS - 4
JF - Revista Mexicana De Fisica
TI - Breaking atomic nuclei into little pieces: evidence for a phase transition
VL - 49
ER -
TY - JOUR
AB - 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.
AU - Lien, Cheng-Chang
AU - Peter Jonas
ID - 3804
IS - 6
JF - Journal of Neuroscience
TI - Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons
VL - 23
ER -
TY - JOUR
AB - 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.
AU - Hallermann, Stefan
AU - Pawlu, Christian
AU - Peter Jonas
AU - Heckmann, Manfred
ID - 3806
IS - 15
JF - PNAS
TI - A large pool of releasable vesicles in a cortical glutamatergic synapse
VL - 100
ER -
TY - CONF
AB - Many verification, planning, and control problems can be modeled as games played on state-transition graphs by one or two players whose conflicting goals are to form a path in the graph. The focus here is on simple stochastic parity games, that is, two-player games with turn-based probabilistic transitions and omega-regular objectives formalized as parity (Rabin chain) winning conditions. An efficient translation from simple stochastic parity games to nonstochastic parity games is given. As many algorithms are known for solving the latter, the translation yields efficient algorithms for computing the states of a simple stochastic parity game from which a player can win with probability 1. An important special case of simple stochastic parity games are the Markov decision processes with Buchi objectives. For this special case a first provably subquadratic algorithm is given for computing the states from which the single player has a strategy to achieve a Buchi objective with probability 1. For game graphs with m edges the algorithm works in time O(mrootm). Interestingly, a similar technique sheds light on the question of the computational complexity of solving simple Buchi games and yields the first provably subquadratic algorithm, with a running time of O(n(2)/log n) for game graphs with n vertices and O(n) edges.
AU - Krishnendu Chatterjee
AU - Jurdziński, Marcin
AU - Thomas Henzinger
ID - 3897
TI - Simple stochastic parity games
VL - 2803
ER -
TY - CONF
AB - We study the problem of determining stack boundedness and the exact maximum stack size for three classes of interrupt-driven programs. Interrupt-driven programs axe used in many real-time applications that require responsive interrupt handling. In order to ensure responsiveness, programmers often enable interrupt processing in the body of lower-priority interrupt handlers. In such programs a programming error can allow interrupt handlers to be interrupted in cyclic fashion to lead to an unbounded stack, causing the system to crash. For a restricted class of interrupt-driven programs, we show that there is a polynomial-time procedure to check stack boundedness, while determining the exact maximum stack size is PSPACE-complete. For a larger class of programs, the two problems are both PSPACE-complete, and for the largest class of programs we consider, the two problems are PSPACE-hard and can be solved in exponential time.
AU - Krishnendu Chatterjee
AU - Ma, Di
AU - Majumdar, Ritankar S
AU - Zhao, Tian
AU - Thomas Henzinger
AU - Palsberg, Jens
ID - 3898
TI - Stack size analysis for interrupt-driven programs
VL - 2694
ER -
TY - JOUR
AB - Let k⩾5 be an integer, and let x⩾1 be an arbitrary real number. We derive a bound[Formula presented] for the number of positive integers less than or equal to x which can be represented as a sum of two non-negative coprime kth powers, in essentially more than one way.
AU - Timothy Browning
ID - 204
IS - 2
JF - Journal of Number Theory
TI - Equal Sums of Two kth Powers
VL - 96
ER -
TY - CHAP
AU - Lieb, Élliott H
AU - Solovej, Jan P
AU - Robert Seiringer
AU - Yngvason, Jakob
ID - 2338
T2 - Current Developments in Mathematics, 2001
TI - The ground state of the Bose gas
ER -
TY - CONF
AU - Robert Seiringer
ED - Weder, Richardo
ED - Exner, Pavel
ED - Grébert, Benoit
ID - 2339
TI - Symmetry breaking in a model of a rotating Bose gas
VL - 307
ER -
TY - JOUR
AB - The Bose-Einstein condensation (BEC) of the ground state of bosonic atoms in a trap was discussed. The BEC was proved for bosons with two-body repulsive interaction potentials in the dilute limit, starting from the basic Schrodinger equation. The BEC was 100% into the state which minimized the Gross-Pitaevskii energy functional. The analysis also included rigorous proof of BEC in a physically realistic, continuum model.
AU - Lieb, Élliott H
AU - Robert Seiringer
ID - 2349
IS - 17
JF - Physical Review Letters
TI - Proof of Bose-Einstein condensation for dilute trapped gases
VL - 88
ER -
TY - JOUR
AB - Using the Pauli-Fierz model of non-relativistic quantum electrodynamics, we calculate the binding energy of an electron in the field of a nucleus of charge Z and in presence of the quantized radiation field. We consider the case of small coupling constant α, but fixed Zα and ultraviolet cut-off Λ. We prove that after renormalizing the mass the binding energy has, to leading order in α, a finite limit as Λ goes to infinity; i.e., the cut-off can be removed. The expression for the ground state energy shift thus obtained agrees with Bethe's formula for small values of Zα, but shows a different behavior for bigger values.
AU - Hainzl, Christian
AU - Robert Seiringer
ID - 2350
IS - 5
JF - Advances in Theoretical and Mathematical Physics
TI - Mass renormalization and energy level shift in non-relativistic QED
VL - 6
ER -
TY - JOUR
AB - We study the Gross-Pitaevskii functional for a rotating two-dimensional Bose gas in a trap. We prove that there is a breaking of the rotational symmetry in the ground state; more precisely, for any value of the angular velocity and for large enough values of the interaction strength, the ground state of the functional is not an eigenfunction of the angular momentum. This has interesting consequences on the Bose gas with spin; in particular, the ground state energy depends non-trivially on the number of spin components, and the different components do not have the same wave function. For the special case of a harmonic trap potential, we give explicit upper and lower bounds on the critical coupling constant for symmetry breaking.
AU - Robert Seiringer
ID - 2351
IS - 3
JF - Communications in Mathematical Physics
TI - Gross-Pitaevskii theory of the rotating Bose gas
VL - 229
ER -
TY - JOUR
AB - We present a generalization of the Fefferman-de la Llave decomposition of the Coulomb potential to quite arbitrary radial functions V on ℝn going to zero at infinity. This generalized decomposition can be used to extend previous results on N-body quantum systems with Coulomb interaction to a more general class of interactions. As an example of such an application, we derive the high density asymptotics of the ground state energy of jellium with Yukawa interaction in the thermodynamic limit, using a correlation estimate by Graf and Solovej.
AU - Hainzl, Christian
AU - Robert Seiringer
ID - 2352
IS - 1
JF - Letters in Mathematical Physics
TI - General decomposition of radial functions on ℝn and applications to N-body quantum systems
VL - 61
ER -
TY - JOUR
AB - A commonly used theoretical definition of superfluidity in the ground state of a Bose gas is based on the response of the system to an imposed velocity field or, equivalently, to twisted boundary conditions in a box. We are able to carry out this program in the case of a dilute interacting Bose gas in a trap, and we prove that a gas with repulsive interactions is 100% superfluid in the dilute limit in which the Gross-Pitaevskii equation is exact. This is the first example in an experimentally realistic continuum model in which superfluidity is rigorously verified.
AU - Lieb, Élliott H
AU - Robert Seiringer
AU - Yngvason, Jakob
ID - 2353
IS - 13
JF - Physical Review B - Condensed Matter and Materials Physics
TI - Superfluidity in dilute trapped Bose gases
VL - 66
ER -
TY - JOUR
AB - A corner cut in dimension d is a finite subset of N0d that can be separated from its complement in N0d by an affine hyperplane disjoint from N0d. Corner cuts were first investigated by Onn and Sturmfels [Adv. Appl. Math. 23 (1999) 29-48], their original motivation stemmed from computational commutative algebra. Let us write (Nd0k)cut for the set of corner cuts of cardinality k; in the computational geometer's terminology, these are the k-sets of N0d. Among other things, Onn and Sturmfels give an upper bound of O(k2d(d-1)/(d+1)) for the size of (Nd0k)cut when the dimension is fixed. In two dimensions, it is known (see [Corteel et al., Adv. Appl. Math. 23 (1) (1999) 49-53]) that #(Nd0k)cut = Θ(k log k). We will see that in general, for any fixed dimension d, the order of magnitude of #(Nd0k)cut is between kd-1 log k and (k log k)d-1. (It has been communicated to me that the same bounds have been found independently by G. Rémond.) In fact, the elements of (Nd0k)cut correspond to the vertices of a certain polytope, and what our proof shows is that the above upper bound holds for the total number of flags of that polytope.
AU - Uli Wagner
ID - 2420
IS - 2
JF - Advances in Applied Mathematics
TI - On the number of corner cuts
VL - 29
ER -
TY - CONF
AB - Intersection graphs of disks and of line segments, respectively, have been well studied, because of both, practical applications and theoretically interesting properties of these graphs. Despite partial results, the complexity status of the Clique problem for these two graph classes is still open. Here, we consider the Clique problem for intersection graphs of ellipses which in a sense, interpolate between disc and ellipses, and show that it is APX-hard in that case. Moreover, this holds even if for all ellipses, the ratio of the larger over the smaller radius is some prescribed number. To our knowledge, this is the first hardness result for the Clique problem in intersection graphs of objects with finite description complexity. We also describe a simple approximation algorithm for the case of ellipses for which the ratio of radii is bounded.
AU - Ambühl, Christoph
AU - Uli Wagner
ID - 2421
TI - On the Clique problem in intersection graphs of ellipses
VL - 2518
ER -
TY - JOUR
AB - In this investigation, we report identification and characterization of a 95 kDa postsynaptic density protein (PSD-95)/discs-large/ ZO-1 (PDZ) domain-containing protein termed tamalin, also recently named GRP1-associated scaffold protein (GRASP), that interacts with group 1 metabotropic glutamate receptors (mGluRs). The yeast two-hybrid system and in vitro pull-down assays indicated that the PDZ domain-containing, amino-terminal half of tamalin directly binds to the class I PDZ-binding motif of group 1 mGluRs. The C-terminal half of tamalin also bound to cytohesins, the members of guanine nucleotide exchange factors (GEFs) specific for the ADP-ribosylation factor (ARF) family of small GTP-binding proteins. Tamalin mRNA is expressed predominantly in the telencephalic region and highly overlaps with the expression of group 1 mGluR mRNAs. Both tamalin and cytohesin-2 were enriched and codistributed with mGluR1a in postsynaptic membrane fractions. Importantly, recombinant and native mGluR1a/tamalin/cytohesin-2 complexes were coimmunoprecipitated from transfected COS-7 cells and rat brain tissue, respectively. Transfection of tamalin and mutant tamalin lacking a cytohesin-binding domain caused an increase and decrease in cell-surface expression of mGluR1a in COS-7 cells, respectively. Furthermore, adenovirus-mediated expression of tamalin and dominant-negative tamalin facilitated and reduced the neuritic distribution of endogenous mGluR5 in cultured hippocampal neurons, respectively. The results indicate that tamalin plays a key role in the association of group 1 mGluRs with the ARF-specific GEF proteins and contributes to intracellular trafficking and the macromolecular organization of group 1 mGluRs at synapses.
AU - Kitano, Jun
AU - Kimura, Kouji
AU - Yamazaki, Yoshimitsu
AU - Soda, Takeshi
AU - Ryuichi Shigemoto
AU - Nakajima, Yoshiaki
AU - Nakanishi, Shigetada
ID - 2613
IS - 4
JF - Journal of Neuroscience
TI - Tamalin, a PDZ domain-containing protein, links a protein complex formation of group 1 metabotropic glutamate receptors and the guanine nucleotide exchange factor cytohesins
VL - 22
ER -
TY - JOUR
AB - Metabotropic glutamate receptors (mGluRs) from group III reduce glutamate release. Because these receptors reduce cAMP levels, we explored whether this signaling pathway contributes to release inhibition caused by mGluRs with low affinity for L-2-amino-4-phosphonobutyrate (L-AP4). In biochemical experiments with the population of cerebrocortical nerve terminals we find that L-AP4 (1 mM) inhibited the Ca2+dependent-evoked release of glutamate by 25%. This inhibitory effect was largely prevented by the pertussis toxin but was insensitive to inhibitors of protein kinase C bisindolylmaleimide and protein kinase A H-89. Furthermore, this inhibition was associated with reduction in N-type Ca2+ channel activity in the absence of any detectable change in cAMP levels. In the presence of forskolin, however, L-AP4 decreased the levels of cAMP. The activation of this additional signaling pathway was very efficient in counteracting the facilitation of glutamate release induced either by forskolin or the β-adrenergic receptor agonist isoproterenol. Imaging experiments to measure Ca2+ dynamics in single nerve terminals showed that L-AP4 strongly reduced the Ca2+ response in 28% of the nerve terminals. Moreover, immunochemical experiments showed that 25-35% of the nerve terminals that were immunopositive to synaptophysin were also immunoreactive to the low affinity L-AP4-sensitive mGluR7. Then, mGluR7 mediates the inhibition of glutamate release caused by 1 mM L-AP4, primarily by a strong inhibition of Ca2+ channels, although high cAMP uncovers the receptor ability to decrease cAMP.
AU - Millán, Carmelo
AU - Luján, Rafael
AU - Ryuichi Shigemoto
AU - Sánchez-Prieto, José
ID - 2614
IS - 16
JF - Journal of Biological Chemistry
TI - The inhibition of glutamate release by metabotropic glutamate receptor 7 affects both [Ca2+]c and cAMP. Evidence for a strong reduction of Ca2+ entry in single nerve terminals
VL - 277
ER -
TY - JOUR
AB - Taste-mGluR4, cloned from taste tissues, is a truncated variant of brain-expressed mGluR4a (brain-mGluR4), and is known to be a candidate for the receptor involved in the umami taste sense. Although the expression patterns of taste- and brain-mGluR4 mRNAs have been demonstrated, no mention has so far been made of the expression of these two mGluR4 proteins in taste tissues. The present study examined the expression of taste-mGluR4 and brain-mGluR4 proteins in rat taste tissues by using a specific antibody for mGluR4a which shared a C-terminus of both taste- and brain-mGluR4, for immunoblot analysis and immunohistochemistry. Immunoblot analysis showed that both brain-mGluR4 and taste-mGluR4 were expressed in the taste tissues. Taste-mGluR4 was not detected in the cerebellum. The immunoreactive band for brain-mGluR4 protein was much stronger than that for taste-mGluR4 protein. In the cryosections of fungiform, foliate and circumvallate papillae, the antibody against taste-mGluR4 exhibited intense labeling of the taste pores and taste hairs in all the taste buds of gustatory papillae examined; the immunoreaction to the antibody against brain-mGluR4 was more intense at the same sites of the taste buds. The portions of the taste bud cells below the taste pore and surrounding keratinocytes did not show any immunoreactivities. The results of the present study strongly suggest that, in addition to taste-mGluR4, brain-mGluR4 may function even more importantly than the former as a receptor for glutamate, i.e. the umami taste sensation.
AU - Toyono, Takashi
AU - Seta, Yuji
AU - Sataoka, Shinji
AU - Harumi Harada
AU - Morotomi, Takahiko
AU - Kawano, Shintaro
AU - Ryuichi Shigemoto
AU - Toyoshima, Kuniaki
ID - 2615
IS - 1
JF - Archives of Histology and Cytology
TI - Expression of the metabotropic glutamate receptor, mGluR4a, in the taste hairs of taste buds in rat gustatory papillae
VL - 65
ER -
TY - JOUR
AB - Neurons in the rat cerebral cortex are enriched in group I metabotropic glutamate receptor (mGluR) subtypes and respond to their activation during development. To understand better the mechanisms by which mGluR1 and mGluR5 mediate these effects, the goal of this study was to elucidate the expression pattern and to determine the cellular and the precise subcellular localization of these two receptor subtypes in the rat neocortex and hippocampus during late prenatal and postnatal development. At the light microscopic level, mGluR1 α and mGluR5 were first detected in the cerebral cortex with different expression levels at embryonic day E18. Thus, mGluR5 had a moderate expression, whereas mGluR1 α was detected as a diffuse and weak labeling. mGluR5 was localized in some Cajal-Retzius cells as well as in other cell types, such as pioneer neurons of the marginal zone. During postnatal development, the distribution of the receptors dramatically changed. From P0 to around P10, mGluR1α was localized in identified, transient Cajal-Retzius cells of neocortex and hippocampus, until these cells disappear. In addition, a population of interneurons localized the receptor from the second/third postnatal week. In contrast, mGluR5 was localized mainly in pyramidal cells and in some interneurons, with a neuropilar staining throughout the cerebral cortex. At the electron microscopic level, the immunoreactivity for both group I mGluR subtypes was expressed postsynaptically. Using immunogold methods, mGluR1α and mGluR5 immunoreactivities were found throughout postnatal development at the edge of postsynaptic specialization of asymmetrical synapses. These results show that the two group I mGluRs have a differential expression pattern in neocortex and hippocampus that may suggest roles for the receptors in the early processing of cortical information and in the control of cortical developmental events.
AU - López-Bendito, Guillermina
AU - Ryuichi Shigemoto
AU - Fairén, Alfonso
AU - Luján, Rafael
ID - 2616
IS - 6
JF - Cerebral Cortex
TI - Differential distribution of group I metabotropic glutamate receptors during rat cortical development
VL - 12
ER -
TY - JOUR
AB - Synapses exhibit different short-term plasticity patterns and this behaviour influences information processing in neuronal networks. We tested how the short-term plasticity of excitatory postsynaptic currents (EPSCs) depends on the postsynaptic cell type, identified by axonal arborizations and molecular markers in the hippocampal CA1 area. Three distinct types of short-term synaptic behaviour (facilitating, depressing and combined facilitating-depressing) were defined by fitting a dynamic neurotransmission model to the data. Approximately 75 % of the oriens-lacunosum-moleculare (O-LM) interneurones received facilitating EPSCs, but in three of 12 O-LM cells EPSCs also showed significant depression. Over 90 % of the O-LM cells were immunopositive for somatostatin and mGluR1α and all tested cells were decorated by strongly mGluR7a positive axon terminals. Responses in eight of 12 basket cells were described well with a model involving only depression, but the other cells displayed combined facilitating-depressing EPSCs. No apparent difference was found between the plasticity of EPSCs in cholecystokinin- or parvalbumin-containing basket cells. In oriens-bistratified cells (O-Bi), two of nine cells showed facilitating EPSCs, another two depressing, and the remaining five cells combined facilitating-depressing EPSCs. Seven of 10 cells tested for somatostatin were immunopositive, but mGluR1α was detectable only in two of 11 tested cells. Furthermore, most O-Bi cells projected to the CA3 area and the subiculum, as well as outside the hippocampal formation. Postsynaptic responses to action potentials recorded in vivo from a CA1 place cell were modelled, and revealed great differences between and within cell types. Our results demonstrate that the short-term plasticity of EPSCs is cell type dependent, but with significant heterogeneity within all three interneurone populations.
AU - Losonczy, Attila
AU - Zhang, Limei
AU - Ryuichi Shigemoto
AU - Somogyi, Péter
AU - Nusser, Zoltán
ID - 2617
IS - 1
JF - Journal of Physiology
TI - Cell type dependence and variability in the short-term plasticity of EPSCs in identified mouse hippocampal interneurones
VL - 542
ER -
TY - JOUR
AB - The unipolar brush cell (UBC) is a type of glutamatergic interneuron in the granular layer of the cerebellum. The UBC brush and a single mossy fiber (MF) terminal contact each other within a cerebellar glomerulus, forming a giant synapse. Many UBCs receive input from extrinsic MFs, whereas others are innervated by intrinsic mossy terminals formed by the axons of other UBCs. In all mammalian species so far examined, the vestibulocerebellum is enriched of UBCs that are strongly immunoreactive for the calcium binding protein calretinin (CR) in both the somatodendritic and axonal compartment. UBCs have postsynaptic ionotropic glutamate receptors and extrasynaptic metabotropic glutamate receptors that immunocytochemically highlight their somatodendritic compartment and brush, respectively. In this study on the mouse cerebellum, we present evidence that immunoreactivities to CR and mGluR1α define two distinct UBC subsets with partly overlapping distributions in lobule X (the nodulus). In sections double-labeled for CR and mGluR1α, the patterns of distributions of CR+/mGluR1α- UBCs and CR-/mGluR1α+ UBCs differed along the mediolateral and dorsoventral axes of the folium. Moreover, mGluR1α+ UBCs outnumbered CR+ UBCs. Both UBC subsets were mGluR2/3, GluR2/3, and NMDAR1 immunoreactive. The different distribution patterns of the two UBC subsets within lobule X suggest that expression of CR or mGluR1α by UBCs may be afferent-specific and related to the terminal fields of different vestibular MF afferents.
AU - Nunzi, Maria G
AU - Ryuichi Shigemoto
AU - Mugnaini, Enrico
ID - 2618
IS - 2
JF - Journal of Comparative Neurology
TI - Differential expression of calretinin and metabotropic glutamate receptor mGluR1α defines subsets of unipolar brush cells in mouse cerebellum
VL - 451
ER -
TY - JOUR
AB - The release of glutamate and GABA is modulated by presynaptic metabotropic glutamate receptors (mGluRs). We used immunocytochemical methods to define the location of the group III receptor mGluR7a in glutamatergic and GABAergic terminals innervating GABAergic interneurons and pyramidal cells. Immunoreactivity for mGluR7a was localized in the presynaptic active zone of both identified GABAergic and presumed glutamatergic terminals. Terminals innervating dendritic spines showed a variable level of receptor immunoreactivity, ranging from immunonegative to strongly immunopositive. The frequency of strongly mGluR7a positive terminals innervating the soma and dendrites of mGluR1α/somatostatin-expressing interneurons was very high relative to other neurons. On dendrites that received mGluR7a-enriched glutamatergic innervation, at least 80% of GABAergic terminals were immunopositive for mGluR7a. On such dendrites virtually all (95%) vasoactive intestinal polypeptide (VIP) positive (GABAergic) terminals were enriched in mGluR7a. The targets of VIP/mGluR7a-expressing terminals were mainly (88%) mGluR1α-expressing interneurons, which were mostly somatostatin immunopositive. Parvalbumin positive terminals were immunonegative for mGluR7a. Some parvalbumin immunoreactive dendrites received strongly mGluR7a positive terminals. The subcellular location, as well as the cell type and synapse-specific distribution of mGluR7a in isocortical neuronal circuits, is homologous to its distribution in the hippocampus. The specific location of mGluR7a in the presynaptic active zone of both glutamatergic and GABAergic synapses may be related to the proximity of calcium channels and the vesicle fusion machinery. The enrichment of mGluR7a in the main GABAergic, as well as in the glutamatergic, innervation of mGluR1α/somatostatin-expressing interneurons suggests that their activation is under unique regulation by extracellular glutamate.
AU - Dalezios, Yannis
AU - Luján, Rafael
AU - Ryuichi Shigemoto
AU - Roberts, John D
AU - Somogyi, Péter
ID - 2619
IS - 9
JF - Cerebral Cortex
TI - Enrichment of mGluR7a in the presynaptic active zones of GABAergic and non-GABAergic terminals on interneurons in the rat somatosensory cortex
VL - 12
ER -
TY - JOUR
AB - Hamilton's concept of local mate competition (LMC) is the standard model to explain female-biased sex ratios in solitary Hymenoptera. In social Hymenoptera, however, LMC has remained controversial, mainly because manipulation of sex allocation by workers in response to relatedness asymmetries is an additional powerful mechanism of female bias. Furthermore, the predominant mating systems in the social insects are thought to make LMC unlikely. Nevertheless, several species exist in which dispersal of males is limited and mating occurs in the nest. Some of these species, such as the ant Cardiocondyla obscurior, have evolved dimorphic males, with one morph being specialized for dispersal and the other for fighting with nest-mate males over access to females. Such life history, combining sociality and alternative reproductive tactics in males, provides a unique opportunity to test the power of LMC as a selective force leading to female-biased sex ratios in social Hymenoptera. We show that, in concordance with LMC predictions, an experimental increase in queen number leads to a shift in sex allocation in favour of non-dispersing males, but does not influence the proportion of disperser males. Furthermore, we can assign this change in sex allocation at the colony level to the queens and rule out worker manipulation.
AU - Cremer, Sylvia
AU - Heinze, Jürgen
ID - 3919
IS - 1489
JF - Proceedings of the Royal Society of London Series B Biological Sciences
TI - Adaptive production of fighter males: queens of the ant Cardiocondyla adjust the sex ratio under local mate competition
VL - 269
ER -
TY - JOUR
AB - A particular Solid Injector needle, suitable for GC-MS analyses of small specimens, is described together with its application in a study on ants.
AU - Turillazzi, Stefano
AU - Sledge, Matthew
AU - Cremer, Sylvia
AU - Heinze, Jürgen
ID - 3920
JF - Insect Social Life
TI - A method for analysing small-size specimens in GC-MS
VL - 4
ER -
TY - JOUR
AB - Males of the ant Cardiocondyla show a dispersal dimorphism of a winged and wingless morph. The loss of flight has lead to morphological reductions in the wingless (ergatoid) males and also affected body size, eye size and pigmentation. As ergatoid males mate exclusively inside the maternal nest, they underlie increased male-male competition and therefore have also evolved additional changes in behaviour and physiology: in contrast to winged males, ergatoid males are highly aggressive towards each other and their spermatogenesis is prolonged compared to all other hymenopteran males. In addition to these two male morphs, we found males with an intermediate appearance. These "intermorphic" males provide a transitional stage between normal males in most investigated morphological and physiological parameters. As they are produced extremely rarely and only in colonies that switch between pure ergatoid to mixed male production, we argue that they likely represent a developmental mistake. Parallels between the determination of male morphs and female castes (queen-worker dimorphism and worker polymorphism) might help to understand how the large potential of phenotypic plasticity in both sexes of social insects is realised during development.
AU - Cremer, Sylvia
AU - Lautenschläger, Birgit
AU - Heinze, Jürgen
ID - 3924
IS - 3
JF - Insectes Sociaux
TI - A transitional stage between the ergatoid and winged male morph in the ant Cardiocondyla obscurior
VL - 49
ER -
TY - JOUR
AB - Males of the tropical ant Cardiocondyla obscurior are either wingless and aggressive or winged and docile, and both compete for access to virgin queens in the nest1, 2. Although the fighter males (ergatoids) attack and kill other ergatoids, they tolerate and even attempt to mate with their winged rivals. Here we show that the winged males avoid the aggression of wingless males by mimicking the chemical bouquet of virgin queens, but that their mating success is not reduced as a result. This example of female mimicry by vigorous males is surprising, as in other species it is typically used as a protective strategy by weaker males, and may explain the coexistence and equal mating success of two male morphs.
AU - Cremer, Sylvia
AU - Sledge, Matthew
AU - Heinze, Jürgen
ID - 3925
JF - Nature
TI - Chemical mimicry: Male ants disguised by the queen's bouquet
VL - 419
ER -
TY - JOUR
AB - This article is a survey of research areas in which motion plays a pivotal role. The aim of the article is to review current approaches to modeling motion together with related data structures and algorithms, and to summarize the challenges that lie ahead in producing a more unified theory of motion representation that would be useful across several disciplines.
AU - Agarwal, Pankaj K
AU - Guibas, Leonidas J
AU - Herbert Edelsbrunner
AU - Erickson, Jeff
AU - Isard, Michael
AU - Har-Peled, Sariel
AU - Hershberger, John
AU - Jensen, Christian
AU - Kavraki, Lydia
AU - Koehl, Patrice
AU - Lin, Ming
AU - Manocha, Dinesh
AU - Metaxas, Dimitris
AU - Mirtich, Brian
AU - Mount, David
AU - Muthukrishnan, Sankara
AU - Pai, Dinesh
AU - Sacks, Elisha
AU - Snoeyink, Jack
AU - Suri, Subhash
AU - Wolefson, Ouri
ID - 3995
IS - 4
JF - ACM Computing Surveys
TI - Algorithmic issues in modeling motion
VL - 34
ER -
TY - JOUR
AB - We formalize a notion of topological simplification within the framework of a filtration, which is the history of a growing complex. We classify a topological change that happens during growth as either a feature or noise depending on its lifetime or persistence within the filtration. We give fast algorithms for computing persistence and experimental evidence for their speed and utility.
AU - Herbert Edelsbrunner
AU - Letscher, David
AU - Zomorodian, Afra
ID - 3996
IS - 4
JF - Discrete & Computational Geometry
TI - Topological persistence and simplification
VL - 28
ER -
TY - JOUR
AB - We present results on a two-step improvement of mesh quality in three-dimensional Delaunay triangulations. The first step refines the triangulation by inserting sinks and eliminates tetrahedra with large circumradius over shortest edge length ratio. The second step assigns weights to the vertices to eliminate slivers. Our experimental findings provide evidence for the practical effectiveness of sliver exudation.
AU - Herbert Edelsbrunner
AU - Guoy, Damrong
ID - 3998
IS - 3
JF - Engineering with Computers
TI - An experimental study of sliver exudation
VL - 18
ER -
TY - JOUR
AB - We present fast implementations of a hybrid algorithm for reporting box and cube intersections. Our algorithm initially takes a divide-and-conquer approach and switches to simpler algorithms for low numbers of boxes. We use our implementations as engines to solve problems about geometric primitives. We look at two such problems in the category of quality analysis of surface triangulations.
AU - Zomorodian, Afra
AU - Herbert Edelsbrunner
ID - 4000
IS - 1-2
JF - International Journal of Computational Geometry and Applications
TI - Fast software for box intersections
VL - 12
ER -
TY - CONF
AB - The writhing number measures the global geometry of a closed space curve or knot. We show that this measure is related to the average winding number of its Gauss map. Using this relationship, we give an algorithm for computing the writhing number for a polygonal knot with n edges in time roughly proportional to n(1.6). We also implement a different, simple algorithm and provide experimental evidence for its practical efficiency.
AU - Agarwal, Pankaj K
AU - Herbert Edelsbrunner
AU - Wang, Yusu
ID - 4003
TI - Computing the writhing number of a polygonal knot
ER -
TY - JOUR
AU - Jitka Polechova
AU - Stopka,P.
ID - 4139
IS - 8
JF - Canadian Journal of Zoology
TI - Geometry of social relationships in the Old World wood mouse, Apodemus sylvaticus
VL - 80
ER -
TY - JOUR
AB - Members of the Wnt family have been implicated in a variety of developmental processes including axis formation, Patterning of the central nervous system and tissue morphogenesis. Recent studies have shown that a Wnt signalling pathway similar to that involved in the establishment of planar cell polarity in Drosophila regulates convergent extension movements during zebrafish and Xenopus gastrulation. This finding provides a good starting point to dissect the complex cell biology and genetic regulation of vertebrate gastrulation movements.
AU - Tada, Masazumi
AU - Concha, Miguel L
AU - Heisenberg, Carl-Philipp
ID - 4148
IS - 3
JF - Seminars in Cell & Developmental Biology
TI - Non-canonical Wnt signalling and regulation of gastrulation movements
VL - 13
ER -
TY - JOUR
AB - Cells at the anterior boundary of the neural plate (ANB) can induce telencephalic gene expression when transplanted to more posterior regions. Here, we identify a secreted Frizzled-related Wnt antagonist, Tic, that is expressed in ANB cells and can cell nonautonomously promote telencephalic gene expression in a concentration-dependent manner. Moreover, abrogation of Tlc function compromises telencephalic development. We also identify Wnt8b as a locally acting modulator of regional fate in the anterior neural plate and a likely target for antagonism by Tic. Finally, we show that tlc expression is regulated by signals that establish early antero-posterior and dorso-ventral ectodermal pattern. From these studies, we propose that local antagonism of Wnt activity within the anterior ectoderm is required to establish the telencephalon.
AU - Houart, Corinne
AU - Caneparo, Luca
AU - Heisenberg, Carl-Philipp
AU - Barth, K Anukampa
AU - Take-uchi, Masaya
AU - Wilson, Stephen W
ID - 4194
IS - 2
JF - Neuron
TI - Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling
VL - 35
ER -
TY - JOUR
AB - During vertebrate gastrulation, large cellular rearrangements lead to the formation of the three germ layers, ectoderm, mesoderm and endoderm. Zebrafish offer many genetic and experimental advantages for studying vertebrate gastrulation movements. For instance, several mutants, including silberblick, knypek and trilobite, exhibit defects in morphogenesis during gastrulation. The identification of the genes mutated in these lines together with the analysis of the mutant phenotypes has provided new insights into the molecular and cellular mechanisms that underlie vertebrate gastrulation movements.
AU - Heisenberg, Carl-Philipp
AU - Tada, Masazumi
ID - 4196
IS - 6
JF - Seminars in Cell & Developmental Biology
TI - Zebrafish gastrulation movements: bridging cell and developmental biology
VL - 13
ER -
TY - JOUR
AB - Recent studies on vertebrate homologues of the van gogh/strabismus (vang/stbm) gene, a key player in planar cell polarity signalling in Drosophila, show that vang/stbm is involved in patterning and morphogenesis during vertebrate gastrulation where it modulates two distinct Wnt signals.
AU - Heisenberg, Carl-Philipp
AU - Tada, Masazumi
ID - 4199
IS - 4
JF - Current Biology
TI - Wnt signalling: A moving picture emerges from van gogh
VL - 12
ER -
TY - JOUR
AB - Vertebrate homologues of the Strabismus/van Gogh (stbm/vang) gene have been implicated in patterning and morphogenesis during gastrulation. Recent work shows that stbm/vang is mutated in zebrafish trilobite mutants and that stbm/vang is required for morphogenesis but not patterning during zebrafish gastrulation.
AU - Heisenberg, Carl-Philipp
ID - 4207
IS - 19
JF - Current Biology
TI - Wnt signalling: Refocusing on Strabismus
VL - 12
ER -
TY - JOUR
AB - We have identified widerborst (wdb), a B' regulatory subunit of PP2A, as a conserved component of planar cell polarization mechanisms in both Drosophila and in zebrafish. In Drosophila, wdb acts at two steps during planar polarization of wing epithelial cells. It is required to organize tissue polarity proteins into proximal and distal cortical domains, thus determining wing hair orientation. It is also needed to generate the polarized membrane outgrowth that becomes the wing hair. Widerborst activates the catalytic subunit of PP2A and localizes to the distal side of a planar microtubule web that lies at the level of apical cell junctions. This suggests that polarized PP2A activation along the planar microtubule web is important for planar polarization. In zebrafish, two wdb homologs are required for convergent extension during gastrulation, supporting the conjecture that Drosophila planar cell polarization and vertebrate gastrulation movements are regulated by similar mechanisms.
AU - Hannus, Michael
AU - Feiguin, Fabian
AU - Heisenberg, Carl-Philipp
AU - Eaton, Suzanne
ID - 4209
IS - 14
JF - Development
TI - Planar cell polarization requires Widerborst, a B ' regulatory subunit of protein phosphatase 2A
VL - 129
ER -
TY - JOUR
AB - We studied the effect of multilocus balancing selection on neutral nucleotide variability at linked sites by simulating a model where diallelic polymorphisms are maintained at an arbitrary number of selected loci by means of symmetric overdominance. Different combinations of alleles define different genetic backgrounds that subdivide the population and strongly affect variability. Several multilocus fitness regimes with different degrees of epistasis and gametic disequilibrium are allowed. Analytical results based on a multilocus extension of the structured coalescent predict that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. Our simulation results show that although variability increases with the number of genetic backgrounds that are maintained in the population, it is reduced by random fluctuations in the frequencies of those backgrounds and does not reach high levels even in very large populations. We also show that previous results on balancing selection in single-locus systems do not extend to the multilocus scenario in a straightforward way. Different patterns of linkage disequilibrium and of the frequency spectrum of neutral mutations are expected under different degrees of epistasis. Interestingly, the power to detect balancing selection using deviations from a neutral distribution of allele frequencies seems to be diminished under the fitness regime that leads to the largest increase of variability over the neutral case. This and other results are discussed in the light of data from the Mhc.
AU - Navarro, Arcadio
AU - Nicholas Barton
ID - 4258
IS - 2
JF - Genetics
TI - The effects of multilocus balancing selection on neutral variability
VL - 161
ER -
TY - JOUR
AB - We extend current multilocus models to describe the effects of migration, recombination, selection, and nonrandom mating on sets of genes in diploids with varied modes of inheritance, allowing us to consider the patterns of nuclear and cytonuclear associations (disequilibria) under various models of migration. We show the relationship between the multilocus notation recently presented by Kirkpatrick, Johnson, and Barton (developed from previous work by Barton and Turelli) and the cytonuclear parameterization of Asmussen, Arnold, and Avise and extend this notation to describe associations between cytoplasmic elements and multiple nuclear genes. Under models with sexual symmetry, both nuclear-nuclear and cytonuclear disequilibria are equivalent. They differ, however, in cases involving some type of sexual asymmetry, which is then reflected in the asymmetric inheritance of cytoplasmic markers. An example given is the case of different migration rates in males and females; simulations using 2, 3, 4, or 5 unlinked autosomal markers with a maternally inherited cytoplasmic marker illustrate how nuclear-nuclear and cytonuclear associations can be used to separately estimate female and male migration rates. The general framework developed here allows us to investigate conditions where associations between loci with different modes of inheritance are not equivalent and to use this nonequivalence to test for deviations from simple models of admixture.
AU - Orive, Maria E
AU - Nicholas Barton
ID - 4259
IS - 3
JF - Genetics
TI - Associations between cytoplasmic and nuclear loci in hybridizing populations
VL - 162
ER -
TY - JOUR
AB - We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.
AU - Johnson, Toby
AU - Nicholas Barton
ID - 4260
IS - 1
JF - Genetics
TI - The effect of deleterious alleles on adaptation in asexual populations
VL - 162
ER -
TY - JOUR
AB - Until recently, it was impracticable to identify the genes that are responsible for variation in continuous traits, or to directly observe the effects of their different alleles. Now, the abundance of genetic markers has made it possible to identify quantitative trait loci (QTL) — the regions of a chromosome or, ideally, individual sequence variants that are responsible for trait variation. What kind of QTL do we expect to find and what can our observations of QTL tell us about how organisms evolve? The key to understanding the evolutionary significance of QTL is to understand the nature of inherited variation, not in the immediate mechanistic sense of how genes influence phenotype, but, rather, to know what evolutionary forces maintain genetic variability.
AU - Nicholas Barton
AU - Keightley, Peter D
ID - 4261
JF - Nature Reviews Genetics
TI - Understanding quantitative genetic variation
VL - 3
ER -
TY - JOUR
AB - Natural populations are structured spatially into local populations and genetically into diverse ‘genetic backgrounds’ defined by different combinations of selected alleles. If selection maintains genetic backgrounds at constant frequency then neutral diversity is enhanced. By contrast, if background frequencies fluctuate then diversity is reduced. Provided that the population size of each background is large enough, these effects can be described by the structured coalescent process. Almost all the extant results based on the coalescent deal with a single selected locus. Yet we know that very large numbers of genes are under selection and that any substantial effects are likely to be due to the cumulative effects of many loci. Here, we set up a general framework for the extension of the coalescent to multilocus scenarios and we use it to study the simplest model, where strong balancing selection acting on a set of n loci maintains 2n backgrounds at constant frequencies and at linkage equilibrium. Analytical results show that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. However, simulation results reveal that the structured coalescent approach breaks down when the number of backgrounds approaches the population size, because of stochastic fluctuations in background frequencies. A new method is needed to extend the structured coalescent to cases with large numbers of backgrounds.
AU - Nicholas Barton
AU - Navarro, Arcadio
ID - 4262
IS - 2
JF - Genetical Research
TI - Extending the coalescent to multilocus systems: the case of balancing selection
VL - 79
ER -
TY - JOUR
AB - We introduce a general recursion for the probability of identity in state of two individuals sampled from a population subject to mutation, migration, and random drift in a two-dimensional continuum. The recursion allows for the interactions induced by density-dependent regulation of the population, which are inevitable in a continuous population. We give explicit series expansions for large neighbourhood size and for low mutation rates respectively and investigate the accuracy of the classical Malécot formula for these general models. When neighbourhood size is small, this formula does not give the identity even over large scales. However, for large neighbourhood size, it is an accurate approximation which summarises the local population structure in terms of three quantities: the effective dispersal rate, σe; the effective population density, ρe; and a local scale, κ, at which local interactions become significant. The results are illustrated by simulations.
AU - Nicholas Barton
AU - Depaulis, Frantz
AU - Etheridge, Alison M
ID - 4263
IS - 1
JF - Theoretical Population Biology
TI - Neutral evolution in spatially continuous populations
VL - 61
ER -
TY - JOUR
AB - Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.
AU - Huelsenbeck, John P
AU - Jonathan Bollback
AU - Levine, Amy M
ID - 4347
IS - 1
JF - Systematic Biology
TI - Inferring the root of a phylogenetic tree
VL - 51
ER -
TY - JOUR
AB - Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.
AU - Jonathan Bollback
ID - 4349
IS - 7
JF - Molecular Biology and Evolution
TI - Bayesian model adequacy and choice in phylogenetics
VL - 19
ER -
TY - JOUR
AB - This paper presents a complete axiomatization of two decidable propositional real-time linear temporal logics: Event Clock Logic (EventClockTL) and Metric Interval Temporal Logic with past (MetricIntervalTL). The completeness proof consists of an effective proof building procedure for EventClockTL. From this result we obtain a complete axiomatization of MetricIntervalTL by providing axioms translating MetricIntervalTL formulae into EventClockTL formulae, the two logics being equally expressive. Our proof is structured to yield axiomatizations also for interesting fragments of these logics, such as the linear temporal logic of the real numbers (TLR).
AU - Raskin, Jean-François
AU - Schobbens, Pierre Y
AU - Thomas Henzinger
ID - 4407
IS - 1-2
JF - Theoretical Computer Science
TI - Axioms for real-time logics
VL - 274
ER -
TY - CONF
AB - An essential problem in component-based design is how to compose components designed in isolation. Several approaches have been proposed for specifying component interfaces that capture behavioral aspects such as interaction protocols, and for verifying interface compatibility. Likewise, several approaches have been developed for synthesizing converters between incompatible protocols. In this paper, we introduce the notion of adaptability as the property that two interfaces have when they can be made compatible by communicating through a converter that meets specified requirements. We show that verifying adaptability and synthesizing an appropriate converter are two faces of the same coin: adaptability can be formalized and solved using a game-theoretic framework, and then the converter can be synthesized as a strategy that always wins the game. Finally we show that this framework can be related to the rectification problem in trace theory.
AU - Passerone, Roberto
AU - de Alfaro, Luca
AU - Thomas Henzinger
AU - Sangiovanni-Vincentelli, Alberto
ID - 4413
TI - Convertibility verification and converter synthesis: Two faces of the same coin
ER -
TY - THES
AB - This dissertation investigates game-theoretic approaches to the algorithmic analysis of concurrent, reactive systems. A concurrent system comprises a number of components working concurrently; a reactive system maintains an ongoing interaction with its environment. Traditional approaches to the formal analysis of concurrent reactive systems usually view the system as an unstructured state-transition graphs; instead, we view them as collections of interacting components, where each one is an open system which accepts inputs from the other components. The interactions among the components are naturally modeled as games.
Adopting this game-theoretic view, we study three related problems pertaining to the verification and synthesis of systems. Firstly, we propose two novel game-theoretic techniques for the model-checking of concurrent reactive systems, and improve the performance of model-checking. The first technique discovers an error as soon as it cannot be prevented, which can be long before it actually occurs. This technique is based on the key observation that "unpreventability" is a local property to a module: an error is unpreventable in a module state if no environment can prevent it. The second technique attempts to decompose a model-checking proof into smaller proof obligations by constructing abstract modules automatically, using reachability and "unpreventability" information about the concrete modules. Three increasingly powerful proof decomposition rules are proposed and we show that in practice, the resulting abstract modules are often significantly smaller than the concrete modules and can drastically reduce the space and time requirements for verification. Both techniques fall into the category of compositional reasoning.
Secondly, we investigate the composition and control of synchronous systems. An essential property of synchronous systems for compositional reasoning is non-blocking. In the composition of synchronous systems, however, due to circular causal dependency of input and output signals, non-blocking is not always guaranteed. Blocking compositions of systems can be ruled out semantically, by insisting on the existence of certain fixed points, or syntactically, by equipping systems with types, which make the dependencies between input and output signals transparent. We characterize various typing mechanisms in game-theoretic terms, and study their effects on the controller synthesis problem. We show that our typing systems are general enough to capture interesting real-life synchronous systems such as all delay-insensitive digital circuits. We then study their corresponding single-step control problems --a restricted form of controller synthesis problem whose solutions can be iterated in appropriate manners to solve all LTL controller synthesis problems. We also consider versions of the controller synthesis problem in which the type of the controller is given. We show that the solution of these fixed-type control problems requires the evaluation of partially ordered (Henkin) quantifiers on boolean formulas, and is therefore harder (nondeterministic exponential time) than more traditional control questions.
Thirdly, we study the synthesis of a class of open systems, namely, uninitialized state machines. The sequential synthesis problem, which is closely related to Church's solvability problem, asks, given a specification in the form of a binary relation between input and output streams, for the construction of a finite-state stream transducer that converts inputs to appropriate outputs. For efficiency reasons, practical sequential hardware is often designed to operate without prior initialization. Such hardware designs can be modeled by uninitialized state machines, which are required to satisfy their specification if started from any state. We solve the sequential synthesis problem for uninitialized systems, that is, we construct uninitialized finite-state stream transducers. We consider specifications given by LTL formulas, deterministic, nondeterministic, universal, and alternating Buechi automata. We solve this uninitialized synthesis problem by reducing it to the well-understood initialized synthesis problem. While our solution is straightforward, it leads, for some specification formalisms, to upper bounds that are exponentially worse than the complexity of the corresponding initialized problems. However, we prove lower bounds to show that our simple solutions are optimal for all considered specification formalisms. The lower bound proofs require nontrivial generic reductions.
AU - Mang, Freddy Y
ID - 4414
TI - Games in open systems verification and synthesis
ER -
TY - CONF
AB - We demonstrate the feasibility and benefits of Giotto-based control software development by reimplementing the autopilot system of an autonomously flying model helicopter. Giotto offers a clean separation between the platform-independent concerns of software functionality and I/O timing, and the platform-dependent concerns of software scheduling and execution. Functionality code such as code computing control laws can be generated automatically from Simulink models or, as in the case of this project, inherited from a legacy system. I/O timing code is generated automatically from Giotto models that specify real-time requirements such as task frequencies and actuator update rates. We extend Simulink to support the design of Giotto models, and from these models, the automatic generation of Giotto code that supervises the interaction of the functionality code with the physical environment. The Giotto compiler performs a schedulability analysis on the Giotto code, and generates timing code for the helicopter platform. The Giotto methodology guarantees the stringent hard real-time requirements of the autopilot system, and at the same time supports the automation of the software development process in a way that produces a transparent software architecture with predictable behavior and reusable components.
AU - Kirsch, Christoph M
AU - Sanvido, Marco A
AU - Thomas Henzinger
AU - Pree, Wolfgang
ID - 4421
TI - A Giotto-based helicopter control system
VL - 2491
ER -
TY - CONF
AB - Behavioral properties of open systems can be formalized as objectives in two-player games. Turn-based games model asynchronous interaction between the players (the system and its environment) by interleaving their moves. Concurrent games model synchronous interaction: the players always move simultaneously. Infinitary winning criteria are considered: Büchi, co-Büchi, and more general parity conditions. A generalization of determinacy for parity games to concurrent parity games demands probabilistic (mixed) strategies: either player 1 has a mixed strategy to win with probability 1 (almost-sure winning), or player 2 has a mixed strategy to win with positive probability.
This work provides efficient reductions of concurrent probabilistic Büchi and co-Büchi games to turn-based games with Büchi condition and parity winning condition with three priorities, respectively. From a theoretical point of view, the latter reduction shows that one can trade the probabilistic nature of almost-sure winning for a more general parity (fairness) condition. The reductions improve understanding of concurrent games and provide an alternative simple proof of determinacy of concurrent Büchi and co-Büchi games. From a practical point of view, the reductions turn solvers of turn-based games into solvers of concurrent probabilistic games. Thus improvements in the well-studied algorithms for the former carry over immediately to the latter. In particular, a recent improvement in the complexity of solving turn-based parity games yields an improvement in time complexity of solving concurrent probabilistic co-Büchi games from cubic to quadratic.
AU - Jurdziński, Marcin
AU - Kupferman, Orna
AU - Thomas Henzinger
ID - 4422
TI - Trading probability for fairness
VL - 2471
ER -
TY - CONF
AB - Automation control systems typically incorporate legacy code and components that were originally designed to operate independently. Furthermore, they operate under stringent safety and timing constraints. Current design strategies deal with these requirements and characteristics with ad hoc approaches. In particular, when designing control laws, implementation constraints are often ignored or cursorily estimated. Indeed, costly redesigns are needed after a prototype of the control system is built due to missed timing constraints and subtle transient errors. In this paper, we use the concepts of platform-based design, and the Giotto programming language, to develop a methodology for the design of automation control systems that builds in modularity and correct-by-construction procedures. We illustrate our strategy by describing the (successful) application of the methodology to the design of a time-based control system for a rotorcraft Uninhabited Aerial Vehicle (UAV).
AU - Horowitz, Benjamin
AU - Liebman, Judith
AU - Ma, Cedric
AU - Koo, T John
AU - Thomas Henzinger
AU - Sangiovanni-Vincentelli, Alberto
AU - Sastry, Shankar
ID - 4423
IS - 1
TI - Embedded software design and system integration for rotorcraft UAV using platforms
VL - 15
ER -
TY - CONF
AB - The Embedded Machine is a virtual machine that mediates in real time the interaction between software processes and physical processes. It separates the compilation of embedded programs into two phases. The first, platform-independent compiler phase generates E code (code executed by the Embedded Machine), which supervises the timing ---not the scheduling--- of application tasks relative to external events, such as clock ticks and sensor interrupts. E~code is portable and exhibits, given an input behavior, predictable (i.e., deterministic) timing and output behavior. The second, platform-dependent compiler phase checks the time safety of the E code, that is, whether platform performance (determined by the hardware) and platform utilization (determined by the scheduler of the operating system) enable its timely execution. We have used the Embedded Machine to compile and execute high-performance control applications written in Giotto, such as the flight control system of an autonomous model helicopter.
AU - Thomas Henzinger
AU - Kirsch, Christoph M
ID - 4444
TI - The embedded machine: predictable, portable real-time code
ER -
TY - CONF
AB - Giotto is a platform-independent language for specifying software for high-performance control applications. In this paper we present a new approach to the compilation of Giotto. Following this approach, the Giotto compiler generates code for a virtual machine, called the E machine, which can be ported to different platforms. The Giotto compiler also checks if the generated E code is time safe for a given platform, that is, if the platform offers sufficient performance to ensure that the E code is executed in a timely fashion that conforms with the Giotto semantics. Time-safety checking requires a schedulability analysis. We show that while for arbitrary E code, the analysis is exponential, for E code generated from typical Giotto programs, the analysis is polynomial. This supports our claim that Giotto identifies a useful fragment of embedded programs.
AU - Thomas Henzinger
AU - Kirsch, Christoph M
AU - Majumdar, Ritankar S
AU - Matic, Slobodan
ID - 4470
TI - Time-safety checking for embedded programs
VL - 2491
ER -
TY - CONF
AB - The sequential synthesis problem, which is closely related to Church’s solvability problem, asks, given a specification in the form of a binary relation between input and output streams, for the construction of a finite-state stream transducer that converts inputs to appropriate outputs. For efficiency reasons, practical sequential hardware is often designed to operate without prior initialization. Such hardware designs can be modeled by uninitialized state machines, which are required to satisfy their specification if started from any state. In this paper we solve the sequential synthesis problem for uninitialized systems, that is, we construct uninitialized finite-state stream transducers. We consider specifications given by LTL formulas, deterministic, nondeterministic, universal, and alternating Büchi automata. We solve this uninitialized synthesis problem by reducing it to the well-understood initialized synthesis problem. While our solution is straightforward, it leads, for some specification formalisms, to upper bounds that are exponentially worse than the complexity of the corresponding initialized problems. However, we prove lower bounds to show that our simple solutions are optimal for all considered specification formalisms. We also study the problem of deciding whether a given specification is uninitialized, that is, if its uninitialized and initialized synthesis problems coincide. We show that this problem has, for each specification formalism, the same complexity as the equivalence problem.
AU - Thomas Henzinger
AU - Krishnan, Sriram C
AU - Kupferman, Orna
AU - Mang, Freddy Y
ID - 4471
TI - Synthesis of uninitialized systems
VL - 2380
ER -
TY - CONF
AB - We present a methodology and tool for verifying and certifying systems code. The verification is based on the lazy-abstraction paradigm for intertwining the following three logical steps: construct a predicate abstraction from the code, model check the abstraction, and automatically refine the abstraction based on counterexample analysis. The certification is based on the proof-carrying code paradigm. Lazy abstraction enables the automatic construction of small proof certificates. The methodology is implemented in Blast, the Berkeley Lazy Abstraction Software verification Tool. We describe our experience applying Blast to Linux and Windows device drivers. Given the C code for a driver and for a temporal-safety monitor, Blast automatically generates an easily checkable correctness certificate if the driver satisfies the specification, and an error trace otherwise.
AU - Thomas Henzinger
AU - Necula, George C
AU - Jhala, Ranjit
AU - Sutre, Grégoire
AU - Majumdar, Ritankar S
AU - Weimer, Westley
ID - 4472
TI - Temporal safety proofs for systems code
VL - 2404
ER -
TY - JOUR
AB - The simulation preorder on state transition systems is widely accepted as a useful notion of refinement, both in its own right and as an efficiently checkable sufficient condition for trace containment. For composite systems, due to the exponential explosion of the state space, there is a need for decomposing a simulation check of the form P ≤s Q, denoting "P is simulated by Q," into simpler simulation checks on the components of P and Q. We present an assume-guarantee rule that enables such a decomposition. To the best of our knowledge, this is the first assume-guarantee rule that applies to a refinement relation different from trace containment. Our rule is circular, and its soundness proof requires induction on trace trees. The proof is constructive: given simulation relations that witness the simulation preorder between corresponding components of P and Q, we provide a procedure for constructing a witness relation for P ≤s Q. We also extend our assume-guarantee rule to account for fairness constraints on transition systems.
AU - Thomas Henzinger
AU - Qadeer,Shaz
AU - Rajamani, Sriram K
AU - Tasiran, Serdar
ID - 4473
IS - 1
JF - ACM Transactions on Programming Languages and Systems (TOPLAS)
TI - An assume-guarantee rule for checking simulation
VL - 24
ER -
TY - JOUR
AB - The simulation preorder for labeled transition systems is defined locally, and operationally, as a game that relates states with their immediate successor states. Simulation enjoys many appealing properties. First, simulation has a denotational characterization: system S simulates system I iff every computation tree embedded in the unrolling of I can be embedded also in the unrolling of S. Second, simulation has a logical characterization: S simulates I iff every universal branching-time formula satisfied by S is satisfied also by I. It follows that simulation is a suitable notion of implementation, and it is the coarsest abstraction of a system that preserves universal branching-time properties. Third, based on its local definition, simulation between finite-state systems can be checked in polynomial time. Finally, simulation implies trace containment, which cannot be defined locally and requires polynomial space for verification. Hence simulation is widely used both in manual and in automatic verification. Liveness assumptions about transition systems are typically modeled using fairness constraints. Existing notions of simulation for fair transition systems, however, are not local, and as a result, many appealing properties of the simulation preorder are lost. We propose a new view of fair simulation by extending the local definition of simulation to account for fairness: system View the MathML sourcefairly simulates system View the MathML source iff in the simulation game, there is a strategy that matches with each fair computation of View the MathML source a fair computation of View the MathML source. Our definition enjoys a denotational characterization and has a logical characterization: View the MathML source fairly simulates View the MathML source iff every fair computation tree (whose infinite paths are fair) embedded in the unrolling of View the MathML source can be embedded also in the unrolling of View the MathML source or, equivalently, iff every Fair-∀AFMC formula satisfied by View the MathML source is satisfied also by View the MathML source (∀AFMC is the universal fragment of the alternation-free μ-calculus). The locality of the definition leads us to a polynomial-time algorithm for checking fair simulation for finite-state systems with weak and strong fairness constraints. Finally, fair simulation implies fair trace containment and is therefore useful as an efficiently computable local criterion for proving linear-time abstraction hierarchies of fair systems.
AU - Thomas Henzinger
AU - Kupferman, Orna
AU - Rajamani, Sriram K
ID - 4474
IS - 1
JF - Information and Computation
TI - Fair simulation
VL - 173
ER -
TY - CONF
AB - One approach to model checking software is based on the abstract-check-refine paradigm: build an abstract model, then check the desired property, and if the check fails, refine the model and start over. We introduce the concept of lazy abstraction to integrate and optimize the three phases of the abstract-check-refine loop. Lazy abstraction continuously builds and refines a single abstract model on demand, driven by the model checker, so that different parts of the model may exhibit different degrees of precision, namely just enough to verify the desired property. We present an algorithm for model checking safety properties using lazy abstraction and describe an implementation of the algorithm applied to C programs. We also provide sufficient conditions for the termination of the method.
AU - Thomas Henzinger
AU - Jhala, Ranjit
AU - Majumdar, Ritankar S
AU - Sutre, Grégoire
ID - 4476
TI - Lazy abstraction
ER -
TY - CONF
AB - We present interface models that describe both the input assumptions of a component, and its output behavior. By enabling us to check that the input assumptions of a component are met in a design, interface models provide a compatibility check for component-based design. When refining a design into an implementation, interface models require that the output behavior of a component satisfies the design specification only when the input assumptions of the specification are satisfied, yielding greater flexibility in the choice of implementations. Technically, our interface models are games between two players, Input and Output; the duality of the players accounts for the dual roles of inputs and outputs in composition and refinement. We present two interface models in detail, one for a simple synchronous form of interaction between components typical in hardware, and the other for more complex synchronous interactions on bidirectional connections. As an example, we specify the interface of a bidirectional bus, with the input assumption that at any time at most one component has write access to the bus. For these interface models, we present algorithms for compatibility and refinement checking, and we describe efficient symbolic implementations.
AU - Chakrabarti, Arindam
AU - de Alfaro, Luca
AU - Thomas Henzinger
AU - Mang, Freddy Y
ID - 4562
TI - Synchronous and bidirectional component interfaces
VL - 2404
ER -
TY - CONF
AB - We present a formal methodology and tool for uncovering errors in the interaction of software modules. Our methodology consists of a suite of languages for defining software interfaces, and algorithms for checking interface compatibility. We focus on interfaces that explain the method-call dependencies between software modules. Such an interface makes assumptions about the environment in the form of call and availability constraints. A call constraint restricts the accessibility of local methods to certain external methods. An availability constraint restricts the accessibility of local methods to certain states of the module. For example, the interface for a file server with local methods open and read may assert that a file cannot be read without having been opened. Checking interface compatibility requires the solution of games, and in the presence of availability constraints, of pushdown games. Based on this methodology, we have implemented a tool that has uncovered incompatibilities in TinyOS, a small operating system for sensor nodes in adhoc networks.
AU - Chakrabarti, Arindam
AU - de Alfaro, Luca
AU - Thomas Henzinger
AU - Jurdziński, Marcin
AU - Mang, Freddy Y
ID - 4563
TI - Interface compatibility checking for software modules
VL - 2404
ER -
TY - CONF
AB - In the literature, we find several formulations of the control
problem for timed and hybrid systems. We argue that formulations where
a controller can cause an action at any point in dense (rational or real)
time are problematic, by presenting an example where the controller
must act faster and faster, yet causes no Zeno effects (say, the control
actions are at times 0, 1/2, 1, 1 1/4, 2, 2 1/8, 3, 3 1/16 ,...). Such a controller is,
of course, not implementable in software. Such controllers are avoided by formulations where the controller can cause actions only at discrete (integer) points in time. While the resulting control problem is well- understood if the time unit, or “sampling rate” of the controller, is fixed a priori, we define a novel, stronger formulation: the discrete-time control problem with unknown sampling rate asks if a sampling controller exists for some sampling rate. We prove that this problem is undecidable even in the special case of timed automata.
AU - Cassez, Franck
AU - Thomas Henzinger
AU - Raskin, Jean-François
ID - 4565
TI - A comparison of control problems for timed and hybrid systems
VL - 2289
ER -
TY - JOUR
AB - Temporal logic comes in two varieties: linear-time temporal logic assumes implicit universal quantification over all paths that are generated by the execution of a system; branching-time temporal logic allows explicit existential and universal quantification over all paths. We introduce a third, more general variety of temporal logic: alternating-time temporal logic offers selective quantification over those paths that are possible outcomes of games, such as the game in which the system and the environment alternate moves. While linear-time and branching-time logics are natural specification languages for closed systems, alternating-time logics are natural specification languages for open systems. For example, by preceding the temporal operator "eventually" with a selective path quantifier, we can specify that in the game between the system and the environment, the system has a strategy to reach a certain state. The problems of receptiveness, realizability, and controllability can be formulated as model-checking problems for alternating-time formulas. Depending on whether or not we admit arbitrary nesting of selective path quantifiers and temporal operators, we obtain the two alternating-time temporal logics ATL and ATL*.ATL and ATL* are interpreted over concurrent game structures. Every state transition of a concurrent game structure results from a choice of moves, one for each player. The players represent individual components and the environment of an open system. Concurrent game structures can capture various forms of synchronous composition for open systems, and if augmented with fairness constraints, also asynchronous composition. Over structures without fairness constraints, the model-checking complexity of ATL is linear in the size of the game structure and length of the formula, and the symbolic model-checking algorithm for CTL extends with few modifications to ATL. Over structures with weak-fairness constraints, ATL model checking requires the solution of 1-pair Rabin games, and can be done in polynomial time. Over structures with strong-fairness constraints, ATL model checking requires the solution of games with Boolean combinations of Büchi conditions, and can be done in PSPACE. In the case of ATL*, the model-checking problem is closely related to the synthesis problem for linear-time formulas, and requires doubly exponential time.
AU - Alur, Rajeev
AU - Thomas Henzinger
AU - Kupferman, Orna
ID - 4595
IS - 5
JF - Journal of the ACM
TI - Alternating-time temporal logic
VL - 49
ER -
TY - CONF
AB - We present a theory of timed interfaces, which is capable of specifying both the timing of the inputs a component expects from the environment, and the timing of the outputs it can produce. Two timed interfaces are compatible if there is a way to use them together such that their timing expectations are met. Our theory provides algorithms for checking the compatibility between two interfaces and for deriving the composite interface; the theory can thus be viewed as a type system for real-time interaction. Technically, a timed interface is encoded as a timed game between two players, representing the inputs and outputs of the component. The algorithms for compatibility checking and interface composition are thus derived from algorithms for solving timed games.
AU - de Alfaro, Luca
AU - Thomas Henzinger
AU - Stoelinga, Mariëlle
ID - 4631
TI - Timed interfaces
VL - 2491
ER -
TY - JOUR
AB - Wild isolates of Caenorhabditis elegans can feed either alone or in groups1,2. This natural variation in behaviour is associated with a single residue difference in NPR-1, a predicted G-protein-coupled neuropeptide receptor related to Neuropeptide Y receptors2. Here we show that the NPR-1 isoform associated with solitary feeding acts in neurons exposed to the body fluid to inhibit social feeding. Furthermore, suppressing the activity of these neurons, called AQR, PQR and URX, using an activated K+ channel, inhibits social feeding. NPR-1 activity in AQR, PQR and URX neurons seems to suppress social feeding by antagonizing signalling through a cyclic GMP-gated ion channel encoded by tax-2 and tax-4. We show that mutations in tax-2 or tax-4 disrupt social feeding, and that tax-4 is required in several neurons for social feeding, including one or more of AQR, PQR and URX. The AQR, PQR and URX neurons are unusual in C. elegans because they are directly exposed to the pseudocoelomic body fluid3. Our data suggest a model in which these neurons integrate antagonistic signals to control the choice between social and solitary feeding behaviour.
AU - Coates, Juliet C.
AU - de Bono, Mario
ID - 6158
IS - 6910
JF - Nature
SN - 0028-0836
TI - Antagonistic pathways in neurons exposed to body fluid regulate social feeding in Caenorhabditis elegans
VL - 419
ER -
TY - JOUR
AB - Natural Caenorhabditis elegans isolates exhibit either social or solitary feeding on bacteria. We show here that social feeding is induced by nociceptive neurons that detect adverse or stressful conditions. Ablation of the nociceptive neurons ASH and ADL transforms social animals into solitary feeders. Social feeding is probably due to the sensation of noxious chemicals by ASH and ADL neurons; it requires the genes ocr-2 and osm-9, which encode TRP-related transduction channels, and odr-4 and odr-8, which are required to localize sensory chemoreceptors to cilia. Other sensory neurons may suppress social feeding, as social feeding in ocr-2 and odr-4 mutants is restored by mutations in osm-3, a gene required for the development of 26 ciliated sensory neurons. Our data suggest a model for regulation of social feeding by opposing sensory inputs: aversive inputs to nociceptive neurons promote social feeding, whereas antagonistic inputs from neurons that express osm-3 inhibit aggregation.
AU - de Bono, Mario
AU - Tobin, David M.
AU - Davis, M. Wayne
AU - Avery, Leon
AU - Bargmann, Cornelia I.
ID - 6159
IS - 6910
JF - Nature
SN - 0028-0836
TI - Social feeding in Caenorhabditis elegans is induced by neurons that detect aversive stimuli
VL - 419
ER -
TY - JOUR
AB - An ion channel's function depends largely on its location and density on neurons. Here we used high-resolution immunolocalization to determine the subcellular distribution of the hyperpolarization-activated and cyclic-nucleotide-gated channel subunit 1 (HCN1) in rat brain. Light microscopy revealed graded HCN1 immunoreactivity in apical dendrites of hippocampal, subicular and neocortical layer-5 pyramidal cells. Quantitative comparison of immunogold densities showed a 60-fold increase from somatic to distal apical dendritic membranes. Distal dendritic shafts had 16 times more HCN1 labeling than proximal dendrites of similar diameters. At the same distance from the soma, the density of HCN1 was significantly higher in dendritic shafts than in spines. Our results reveal the complex cell surface distribution of voltage-gated ion-channels, and predict its role in increasing the computational power of single neurons via subcellular domain and input-specific mechanisms.
AU - Lörincz, Andrea
AU - Notomi, Takuya
AU - Tamás, Gábor
AU - Ryuichi Shigemoto
AU - Nusser, Zoltán
ID - 2620
IS - 11
JF - Nature Neuroscience
TI - Polarized and compartment-dependent distribution of HCN1 in pyramidal cell dendrites
VL - 5
ER -
TY - JOUR
AB - The release properties of glutamatergic nerve terminals are influenced by a number of factors, including the subtype of voltage-dependent calcium channel and the presence of presynaptic autoreceptors. Group III metabotropic glutamate receptors (mGluRs) mediate feedback inhibition of glutamate release by inhibiting Ca2+ channel activity. By imaging Ca2+ in preparations of cerebrocortical nerve terminals, we show that voltage-dependent Ca2+ channels are distributed in a heterogeneous manner in individual nerve terminals. Presynaptic terminals contained only N-type (47.5%; conotoxin GVIA-sensitive), P/Q-type (3.9%; agatoxin IVA-sensitive), or both N- and P/Q-type (42.6%) Ca2+ channels, although the remainder of the terminals (6.1%) were insensitive to these two toxins. In this preparation, two mGluRs with high and low affinity for L(+)-2-amino-4-phosphonobutyrate were identified by immunocytochemistry as mGluR4 and mGluR7, respectively. These receptors were responsible for 22.2 and 24.1% reduction of glutamate release, and they reduced the Ca2+ response in 24.4 and 30.3% of the nerve terminals, respectively. Interestingly, mGluR4 was largely (73.7%) located in nerve terminals expressing both N- and P/Q-type Ca2+ channels, whereas mGluR7 was predominantly (69.9%) located in N-type Ca2+ channel-expressing terminals. This specific coexpression of different group III mGluRs and Ca2+ channels may endow synaptic terminals with distinct release properties and reveals the existence of a high degree of presynaptic heterogeneity.
AU - Millán, Carmelo
AU - Luján, Rafael
AU - Ryuichi Shigemoto
AU - Sánchez-Prieto, José
ID - 2621
IS - 49
JF - Journal of Biological Chemistry
TI - Subtype-specific expression of Group III metabotropic glutamate receptors and Ca2+ channels in single nerve terminals
VL - 277
ER -
TY - JOUR
AB - To understand the possible contribution of metabotropic γ-aminobutyric acid receptors (GABABR) in cortical development, we investigated the expression pattern and the cellular and subcellular localization of the GABABR1 and GABABR2 subtypes in the rat neocortex from embryonic day 14 (E14) to adulthood. At the light microscopic level, both GABABR1 and GABABR2 were detected as early as E14. During prenatal development, both subtypes were expressed highly in the cortical plate. Using double immunofluorescence, GABABR1 colocalized with GABABR2 in neurons of the marginal zone and subplate, indicating that these proteins are coexpressed and could be forming functional GABABRs during prenatal development in vivo. In contrast, only GABABR1 but not GABABR2 was detected in the tangentially migratory cells in the lower intermediate zone. During postnatal development, immunoreactivity for GABABR1 and GABABR2 was distributed mainly in pyramidal cells. Discrete GABABR1-immunopositive cell bodies of interneurons were present throughout the neocortex. In addition, GABABR1 but not GABABR2 was found in identified Cajal-Retzius cells in layer I. At the electron microscopic level, immunoreactivity for GABABR1 and GABABR2 was found in dendritic spines and dendritic shafts at extrasynaptic and perisynaptic sites throughout postnatal development. We further demonstrated the presynaptic localization of GABABR1 and GABABR2, as well as the association of the receptors with asymmetrical synaptic junctions. These results indicate potentially important roles for the GABABRs in the regulation of migratory processes during corticogenesis and in the modulation of synaptic transmission during early development of cortical circuitry.
AU - López-Bendito, Guillermina
AU - Ryuichi Shigemoto
AU - Kulik, Ákos
AU - Paulsen, Ole
AU - Fairén, Alfonso
AU - Luján, Rafael
ID - 2622
IS - 11
JF - European Journal of Neuroscience
TI - Expression and distribution of metabotropic GABA receptor subtypes GABABR1 and GABABR2 during rat neocortical development
VL - 15
ER -
TY - JOUR
AB - Metabotropic γ-aminobutyric acid receptors (GABABRs) are involved in modulation of synaptic transmission and activity of cerebellar and thalamic neurons. We used subtype-specific antibodies in pre- and postembedding immunohistochemistry combined with three-dimensional reconstruction of labelled profiles and quantification of immunoparticles to reveal the subcellular distribution of pre- and postsynaptic GABABR1a/b and GABABR2 in the rat cerebellum and ventrobasal thalamus. GABABR1a/b and R2 were extensively colocalized in most brain regions including the cerebellum and thalamus. In the cerebellum, immunoreactivity for both subtypes was prevalent in the molecular layer. The most intense immunoreactivity was found in Purkinje cell spines with a high density of immunoparticles at extrasynaptic sites peaking at around 240 nm from glutamatergic synapses between spines and parallel fibre varicosities. This is in contrast to dendrites at sites around GABAergic synapses where sparse and random distribution was found for both subtypes. In addition, more than one-tenth of the synaptic membrane specialization of spine-parallel fibre synapses were labelled at pre- or postsynaptic sites. Weak immunolabelling for both subtypes was also seen in parallel fibres but only rarely in GABAergic axons. In the ventrobasal thalamus, immunolabelling for both receptor subtypes was intense over the dendritic field of thalamocortical cells. Electron microscopy demonstrated an extrasynaptic localization of GABABR1a/b and R2 exclusively in postsynaptic elements. Quantitative analysis further revealed the density of GABABR1a/b around GABAergic synapses was higher than glutamatergic synapses on thalamocortical cell dendrites. The distinct localization of GABABRs relative to synaptic sites in the cerebellum and ventrobasal thalamus suggests that GABABRs differentially regulate activity of different neuronal populations.
AU - Kulik, Ákos
AU - Nakadate, Kazuhiko
AU - Nyíri, Gábor
AU - Notomi, Takuya
AU - Malitschek, Barbara
AU - Bettler, Bernhard
AU - Ryuichi Shigemoto
ID - 2624
IS - 2
JF - European Journal of Neuroscience
TI - Distinct localization of GABAB receptors relative to synaptic sites in the rat cerebellum and ventrobasal thalamus
VL - 15
ER -
TY - CONF
AB - We outline the status of rigorous derivations of certain classical evolution equations as limits of Schrödinger dynamics. We explain two recent results jointly with H.T. Yau in more details. The first one is the derivation of the linear Boltzmann equation as the long time limit of the one-body Schrödinger equation with a random potential. The second one is the mean field limit of high density bosons with Coulomb interaction that leads to the nonlinear Hartree equation.
AU - László Erdös
ID - 2694
TI - Scaling limits of Schrödinger quantum mechanics
VL - 597
ER -
TY - CONF
AU - László Erdös
ID - 2708
TI - Two dimensional Pauli operator via scalar potential
VL - 307
ER -
TY - JOUR
AB - We derive the time-dependent Schrödinger–Poisson equation as the weak coupling limit of the N-body linear Schrödinger equation with Coulomb potential.
AU - Bardos, Claude
AU - László Erdös
AU - Golse, François
AU - Mauser, Norbert J
AU - Yau, Horng-Tzer
ID - 2737
IS - 6
JF - Comptes Rendus Mathematique
TI - Derivation of the Schrödinger-Poisson equation from the quantum N-body problem
VL - 334
ER -
TY - JOUR
AB - We consider the long time evolution of a quantum particle weakly interacting with a phonon field. We show that in the weak coupling limit the Wigner distribution of the electron density matrix converges to the solution of the linear Boltzmann equation globally in time. The collision kernel is identified as the sum of an emission and an absorption term that depend on the equilibrium distribution of the free phonon modes.
AU - László Erdös
ID - 2738
IS - 5-6
JF - Journal of Statistical Physics
TI - Linear Boltzmann equation as the long time dynamics of an electron weakly coupled to a phonon field
VL - 107
ER -
TY - JOUR
AB - We define the two dimensional Pauli operator and identify its core for magnetic fields that are regular Borel measures. The magnetic field is generated by a scalar potential hence we bypass the usual A L 2loc condition on the vector potential, which does not allow to consider such singular fields. We extend the Aharonov-Casher theorem for magnetic fields that are measures with finite total variation and we present a counterexample in case of infinite total variation. One of the key technical tools is a weighted L 2 estimate on a singular integral operator.
AU - László Erdös
AU - Vougalter, Vitali
ID - 2739
IS - 2
JF - Communications in Mathematical Physics
TI - Pauli operator and Aharonov-Casher theorem for measure valued magnetic fields
VL - 225
ER -
TY - JOUR
AB - We show that the lowest eigenvalue of the magnetic Schrödinger operator on a line bundle over a compact Riemann surface M is bounded by the L1-norm of the magnetic field B. This implies a similar bound on the multiplicity of the ground state. An example shows that this degeneracy can indeed be comparable with ∫M |B| even in case of the trivial bundle.
AU - László Erdös
ID - 2740
IS - 6
JF - Annales de l'Institut Fourier
TI - Spectral shift and multiplicity of the first eigenvalue of the magnetic Schrödinger operator in two dimensions
VL - 52
ER -
TY - JOUR
AB - Developmental responses to the plant hormone auxin are thought to be mediated by interacting pairs from two protein families: short-lived inhibitory IAA proteins and ARF transcription factors binding to auxin-response elements. Monopteros mutants lacking activating ARF5 and the auxin-insensitive mutant bodenlos fail to initiate the root meristem during early embryogenesis. Here we show that the bodenlos phenotype results from an amino-acid exchange in the conserved degradation domain of IAA12. BODENLOS and MONOPTEROS interact in the yeast two-hybrid assay and the two genes are coexpressed in early embryogenesis, suggesting that BODENLOS inhibits MONOPTEROS action in root meristem initiation.
AU - Hamann, Thorsten
AU - Eva Benková
AU - Bäurle, Isabel
AU - Kientz, Marika
AU - Jürgens, Gerd
ID - 2866
IS - 13
JF - Genes and Development
TI - The Arabidopsis BODENLOS gene encodes an auxin response protein inhibiting MONOPTEROS-mediated embryo patterning
VL - 16
ER -
TY - CONF
AB - In the last few years, several new algorithms based on graph cuts have been developed to solve energy minimization problems in computer vision. Each of these techniques constructs a graph such that the minimum cut on the graph also minimizes the energy. Yet because these graph constructions are complex and highly specific to a particular energy function, graph cuts have seen limited application to date. In this paper we characterize the energy functions that can be minimized by graph cuts. Our results are restricted to energy functions with binary variables. However, our work generalizes many previous constructions, and is easily applicable to vision problems that involve large numbers of labels, such as stereo, motion, image restoration and scene reconstruction. We present three main results: a necessary condition for any energy function that can be minimized by graph cuts; a sufficient condition for energy functions that can be written as a sum of functions of up to three variables at a time; and a general-purpose construction to minimize such an energy function. Researchers who are considering the use of graph cuts to optimize a particular energy function can use our results to determine if this is possible, and then follow our construction to create the appropriate graph.
AU - Vladimir Kolmogorov
AU - Zabih, Ramin
ID - 2927
TI - Multi-camera scene reconstruction via graph cuts
ER -