@inproceedings{2298, abstract = {We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. We have implemented this analysis in a prototype tool and applied it on several interesting case studies that manipulate overlaid and nested linked lists. }, author = {Dragoi, Cezara and Enea, Constantin and Sighireanu, Mihaela}, location = {Seattle, WA, United States}, pages = {150 -- 171}, publisher = {Springer}, title = {{Local shape analysis for overlaid data structures}}, doi = {10.1007/978-3-642-38856-9_10}, volume = {7935}, year = {2013}, } @article{2299, abstract = {The standard hardware design flow involves: (a) design of an integrated circuit using a hardware description language, (b) extensive functional and formal verification, and (c) logical synthesis. However, the above-mentioned processes consume significant effort and time. An alternative approach is to use a formal specification language as a high-level hardware description language and synthesize hardware from formal specifications. Our work is a case study of the synthesis of the widely and industrially used AMBA AHB protocol from formal specifications. Bloem et al. presented the first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter circuit. However, in the first formal specification some important assumptions were missing. Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. Thus with systematic description we are able to automatically and completely synthesize an important and widely used industrial protocol.}, author = {Godhal, Yashdeep and Chatterjee, Krishnendu and Henzinger, Thomas A}, journal = {International Journal on Software Tools for Technology Transfer}, number = {5-6}, pages = {585 -- 601}, publisher = {Springer}, title = {{Synthesis of AMBA AHB from formal specification: A case study}}, doi = {10.1007/s10009-011-0207-9}, volume = {15}, year = {2013}, } @article{2300, abstract = {We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability.}, author = {Giuliani, Alessandro and Lieb, Élliott and Seiringer, Robert}, journal = {Physical Review B}, number = {6}, publisher = {American Physical Society}, title = {{Realization of stripes and slabs in two and three dimensions}}, doi = {10.1103/PhysRevB.88.064401}, volume = {88}, year = {2013}, } @inproceedings{2305, abstract = {We study the complexity of central controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize both the expected mean-payoff performance of the system and its stability. e argue that the basic theoretical notion of expressing the stability in terms of the variance of the mean-payoff (called global variance in our paper) is not always sufficient, since it ignores possible instabilities on respective runs. For this reason we propose alernative definitions of stability, which we call local and hybrid variance, and which express how rewards on each run deviate from the run's own mean-payoff and from the expected mean-payoff, respectively. We show that a strategy ensuring both the expected mean-payoff and the variance below given bounds requires randomization and memory, under all the above semantics of variance. We then look at the problem of determining whether there is a such a strategy. For the global variance, we show that the problem is in PSPACE, and that the answer can be approximated in pseudo-polynomial time. For the hybrid variance, the analogous decision problem is in NP, and a polynomial-time approximating algorithm also exists. For local variance, we show that the decision problem is in NP. Since the overall performance can be traded for stability (and vice versa), we also present algorithms for approximating the associated Pareto curve in all the three cases. Finally, we study a special case of the decision problems, where we require a given expected mean-payoff together with zero variance. Here we show that the problems can be all solved in polynomial time.}, author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín}, booktitle = {28th Annual ACM/IEEE Symposium}, location = {New Orleans, LA, United States}, pages = {331 -- 340}, publisher = {IEEE}, title = {{Trading performance for stability in Markov decision processes}}, doi = {10.1109/LICS.2013.39}, year = {2013}, } @book{2306, abstract = {Das Buch ist sowohl eine Einführung in die Themen Linked Data, Open Data und Open Linked Data als es auch den konkreten Bezug auf Bibliotheken behandelt. Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut sind.}, author = {Danowski, Patrick and Pohl, Adrian}, isbn = { 978-3-11-027634-3}, issn = {2191-3587}, publisher = {De Gruyter}, title = {{(Open) Linked Data in Bibliotheken}}, doi = {10.1515/9783110278736}, volume = {50}, year = {2013}, } @inproceedings{2315, abstract = { We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the interval. }, author = {Seiringer, Robert and Yngvason, Jakob and Zagrebnov, Valentin}, pages = {610--619}, publisher = {World Scientific Publishing}, title = {{Disordered Bose-Einstein condensates with interaction}}, doi = {10.1142/9789814449243_0063}, year = {2013}, } @inproceedings{2319, abstract = {In a recent paper [7] we give the first rigorous derivation of the celebrated Ginzburg-Landau (GL)theory, starting from the microscopic Bardeen- Cooper-Schrieffer (BCS)model. Here we present our results in the simplified case of a one-dimensional system of particles interacting via a δ-potential.}, author = {Frank, Rupert L and Hainzl, Christian and Robert Seiringer and Solovej, Jan P}, pages = {57 -- 88}, publisher = {Springer}, title = {{ Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction}}, doi = {10.1007/978-3-0348-0531-5_3}, year = {2013}, } @inproceedings{2327, abstract = {We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M′ within distance ρ from M satisfy (or violate) φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.}, author = {Henzinger, Thomas A and Otop, Jan}, location = {Buenos Aires, Argentina}, pages = {273 -- 287}, publisher = {Springer}, title = {{From model checking to model measuring}}, doi = {10.1007/978-3-642-40184-8_20}, volume = {8052}, year = {2013}, } @inproceedings{2328, abstract = {Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates. In response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof.}, author = {Henzinger, Thomas A and Sezgin, Ali and Vafeiadis, Viktor}, location = {Buenos Aires, Argentina}, pages = {242 -- 256}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Aspect-oriented linearizability proofs}}, doi = {10.1007/978-3-642-40184-8_18}, volume = {8052}, year = {2013}, } @inproceedings{2329, abstract = {Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games.}, author = {Chatterjee, Krishnendu and Velner, Yaron}, location = {Buenos Aires, Argentinia}, pages = {500 -- 515}, publisher = {Springer}, title = {{Hyperplane separation technique for multidimensional mean-payoff games}}, doi = {10.1007/978-3-642-40184-8_35}, volume = {8052}, year = {2013}, } @article{2404, abstract = {The Lieb-Thirring inequalities give a bound on the negative eigenvalues of a Schrödinger operator in terms of an Lp-norm of the potential. These are dual to bounds on the H1-norms of a system of orthonormal functions. Here we extend these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting particles (i.e., for perturbations of the continuous spectrum of the Laplacian by local potentials).}, author = {Frank, Rupert L and Lewin, Mathieu and Lieb, Élliott H and Robert Seiringer}, journal = {Duke Mathematical Journal}, number = {3}, pages = {435 -- 495}, publisher = {Duke University Press}, title = {{A positive density analogue of the Lieb-Thirring inequality}}, doi = {10.1215/00127094-2019477}, volume = {162}, year = {2013}, } @article{2405, abstract = {We consider the bipolaron in the Pekar-Tomasevich approximation and address the question whether the ground state is spherically symmetric or not. Numerical analysis has, so far, not completely settled the question. Our contribution is to prove rigorously that the ground state remains spherical for small values of the electron-electron Coulomb repulsion.}, author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {557 -- 573}, publisher = {Springer}, title = {{Symmetry of bipolaron bound states for small Coulomb repulsion}}, doi = {10.1007/s00220-012-1604-y}, volume = {319}, year = {2013}, } @article{2408, abstract = {We investigate the low-energy excitation spectrum of a Bose gas confined in a trap, with weak long-range repulsive interactions. In particular, we prove that the spectrum can be described in terms of the eigenvalues of an effective one-particle operator, as predicted by the Bogoliubov approximation.}, author = {Grech, Philip and Robert Seiringer}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {559 -- 591}, publisher = {Springer}, title = {{The excitation spectrum for weakly interacting Bosons in a trap}}, doi = {10.1007/s00220-013-1736-8}, volume = {322}, year = {2013}, } @article{2410, abstract = {Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. }, author = {Fernandes Redondo, Rodrigo A and Kupczok, Anne and Stift, Gertraud and Bollback, Jonathan P}, journal = {Genome Announcements}, number = {3}, publisher = {American Society for Microbiology}, title = {{Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis}}, doi = {10.1128/genomeA.00216-13}, volume = {1}, year = {2013}, } @article{2412, abstract = {Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.}, author = {Kupczok, Anne and Bollback, Jonathan P}, journal = {BMC Evolutionary Biology}, number = {1}, pages = {54 -- 54}, publisher = {BioMed Central}, title = {{Probabilistic models for CRISPR spacer content evolution }}, doi = {10.1186/1471-2148-13-54}, volume = {13}, year = {2013}, } @article{6768, abstract = {The paper presents an algorithm that applies a stack filter simulating the Mean Curvature Motion equation via a finite difference scheme.}, author = {Mondelli, Marco}, issn = {2105-1232}, journal = {Image Processing On Line}, pages = {68--111}, publisher = {Image Processing On Line}, title = {{A finite difference scheme for the stack filter simulating the MCM}}, doi = {10.5201/ipol.2013.53}, volume = {3}, year = {2013}, } @article{476, abstract = {Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. }, author = {Dickerson, Desiree and Bilkey, David}, journal = {Frontiers in Behavioral Neuroscience}, number = {DEC}, publisher = {Frontiers Research Foundation}, title = {{Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions}}, doi = {10.3389/fnbeh.2013.00217}, volume = {7}, year = {2013}, } @article{500, abstract = {Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.}, author = {Ward, Melissa and Lycett, Samantha and Avila, Dorita and Bollback, Jonathan P and Leigh Brown, Andrew}, journal = {BMC Evolutionary Biology}, number = {1}, publisher = {BioMed Central}, title = {{Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza}}, doi = {10.1186/1471-2148-13-222}, volume = {13}, year = {2013}, } @article{501, abstract = {All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.}, author = {Cozzuol, Mario and Clozato, Camila and Holanda, Elizete and Rodrigues, Flávio and Nienow, Samuel and De Thoisy, Benoit and Fernandes Redondo, Rodrigo A and Santos, Fabrício}, journal = {Journal of Mammalogy}, number = {6}, pages = {1331 -- 1345}, publisher = {Oxford University Press}, title = {{A new species of tapir from the Amazon}}, doi = {10.1644/12-MAMM-A-169.1}, volume = {94}, year = {2013}, } @article{507, abstract = {Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs.}, author = {Kim, Soo and Xu, Zheng and Song, Kyungyoung and Kim, Dae and Kang, Hyangju and Reichardt, Ilka and Sohn, Eun and Friml, Jirí and Juergens, Gerd and Hwang, Inhwan}, journal = {Plant Cell}, number = {8}, pages = {2970 -- 2985}, publisher = {American Society of Plant Biologists}, title = {{Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis}}, doi = {10.1105/tpc.113.114264}, volume = {25}, year = {2013}, }