@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},
}
@article{508,
abstract = {The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.},
author = {Tarazona Santos, Eduardo and Machado, Moara and Magalhães, Wagner and Chen, Renee and Lyon, Fernanda and Burdett, Laurie and Crenshaw, Andrew and Fabbri, Cristina and Pereira, Latife and Pinto, Laelia and Fernandes Redondo, Rodrigo A and Sestanovich, Ben and Yeager, Meredith and Chanock, Stephen},
journal = {Molecular Biology and Evolution},
number = {9},
pages = {2157 -- 2167},
publisher = {Oxford University Press},
title = {{Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications}},
doi = {10.1093/molbev/mst119},
volume = {30},
year = {2013},
}
@article{509,
abstract = {Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. },
author = {Di Rubbo, Simone and Irani, Niloufer and Kim, Soo and Xu, Zheng and Gadeyne, Astrid and Dejonghe, Wim and Vanhoutte, Isabelle and Persiau, Geert and Eeckhout, Dominique and Simon, Sibu and Song, Kyungyoung and Kleine Vehn, Jürgen and Friml, Jirí and De Jaeger, Geert and Van Damme, Daniël and Hwang, Inhwan and Russinova, Eugenia},
journal = {Plant Cell},
number = {8},
pages = {2986 -- 2997},
publisher = {American Society of Plant Biologists},
title = {{The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis}},
doi = {10.1105/tpc.113.114058},
volume = {25},
year = {2013},
}
@article{511,
abstract = {The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.},
author = {Pěnčík, Aleš and Simonovik, Biljana and Petersson, Sara and Henyková, Eva and Simon, Sibu and Greenham, Kathleen and Zhang, Yi and Kowalczyk, Mariusz and Estelle, Mark and Zažímalová, Eva and Novák, Ondřej and Sandberg, Göran and Ljung, Karin},
journal = {Plant Cell},
number = {10},
pages = {3858 -- 3870},
publisher = {American Society of Plant Biologists},
title = {{Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid}},
doi = {10.1105/tpc.113.114421},
volume = {25},
year = {2013},
}
@article{516,
abstract = {In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.},
author = {Bargmann, Bastiaan and Vanneste, Steffen and Krouk, Gabriel and Nawy, Tal and Efroni, Idan and Shani, Eilon and Choe, Goh and Friml, Jirí and Bergmann, Dominique and Estelle, Mark and Birnbaum, Kenneth},
journal = {Molecular Systems Biology},
number = {1},
publisher = {Nature Publishing Group},
title = {{A map of cell type‐specific auxin responses}},
doi = {10.1038/msb.2013.40},
volume = {9},
year = {2013},
}
@misc{5399,
abstract = {In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.},
author = {Reiter, Johannes and Bozic, Ivana and Chatterjee, Krishnendu and Nowak, Martin},
issn = {2664-1690},
pages = {17},
publisher = {IST Austria},
title = {{TTP: Tool for Tumor Progression}},
doi = {10.15479/AT:IST-2013-104-v1-1},
year = {2013},
}
@misc{5400,
abstract = {We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages extends regular languages to infinite strings and provides a robust specification language to express all properties used in verification, and parity objectives are canonical forms to express ω-regular conditions. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satis- fied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite- memory strategies. We establish asymptotically optimal (exponential) memory bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives.},
author = {Chatterjee, Krishnendu and Chmelik, Martin and Tracol, Mathieu},
issn = {2664-1690},
pages = {41},
publisher = {IST Austria},
title = {{What is decidable about partially observable Markov decision processes with ω-regular objectives}},
doi = {10.15479/AT:IST-2013-109-v1-1},
year = {2013},
}
@techreport{5401,
abstract = {This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the actual initiatives, projects and standards related to the project. It supports the preparation of standards and specifications for the project, which should be considered and followed to ensure interoperability and visibility of the uploaded data.},
author = {Porsche, Jana},
publisher = {IST Austria},
title = {{Initiatives and projects related to RD}},
year = {2013},
}
@misc{5402,
abstract = {Linearizability requires that the outcome of calls by competing threads to a concurrent data structure is the same as some sequential execution where each thread has exclusive access to the data structure. In an ordered data structure, such as a queue or a stack, linearizability is ensured by requiring threads commit in the order dictated by the sequential semantics of the data structure; e.g., in a concurrent queue implementation a dequeue can only remove the oldest element.
In this paper, we investigate the impact of this strict ordering, by comparing what linearizability allows to what existing implementations do. We first give an operational definition for linearizability which allows us to build the most general linearizable implementation as a transition system for any given sequential specification. We then use this operational definition to categorize linearizable implementations based on whether they are bound or free. In a bound implementation, whenever all threads observe the same logical state, the updates to the logical state and the temporal order of commits coincide. All existing queue implementations we know of are bound. We then proceed to present, to the best of our knowledge, the first ever free queue implementation. Our experiments show that free implementations have the potential for better performance by suffering less from contention.},
author = {Henzinger, Thomas A and Sezgin, Ali},
issn = {2664-1690},
pages = {16},
publisher = {IST Austria},
title = {{How free is your linearizable concurrent data structure?}},
doi = {10.15479/AT:IST-2013-123-v1-1},
year = {2013},
}
@misc{5403,
abstract = {We consider concurrent games played by two-players on a finite state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to every transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of mean-payoff games) that is not known to be in polynomial time.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus},
issn = {2664-1690},
pages = {33},
publisher = {IST Austria},
title = {{Qualitative analysis of concurrent mean-payoff games}},
doi = {10.15479/AT:IST-2013-126-v1-1},
year = {2013},
}
@misc{5404,
abstract = {We study finite-state two-player (zero-sum) concurrent mean-payoff games played on a graph. We focus on the important sub-class of ergodic games where all states are visited infinitely often with probability 1. The algorithmic study of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic complexity questions have remained unresolved. Our main results for ergodic games are as follows: We establish (1) an optimal exponential bound on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy); (2) the approximation problem lie in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP and coNP is the long-standing best known bound). We show that the exact value can be expressed in the existential theory of the reals, and also establish square-root sum hardness for a related class of games.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus},
issn = {2664-1690},
pages = {29},
publisher = {IST Austria},
title = {{The complexity of ergodic games}},
doi = {10.15479/AT:IST-2013-127-v1-1},
year = {2013},
}
@misc{5405,
abstract = {The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2-1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2-1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic) with only parity objectives, or with only mean-payoff objectives. We present an algorithm running
in time O(d · n^{2d}·MeanGame) to compute the set of almost-sure winning states from which the objective
can be ensured with probability 1, where n is the number of states of the game, d the number of priorities
of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states
in 2-1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems
with both functional requirement (given as a qualitative objective) and performance requirement (given
as a quantitative objective).},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Gimbert, Hugo and Oualhadj, Youssouf},
issn = {2664-1690},
pages = {22},
publisher = {IST Austria},
title = {{Perfect-information stochastic mean-payoff parity games}},
doi = {10.15479/AT:IST-2013-128-v1-1},
year = {2013},
}
@misc{5406,
abstract = {We consider the distributed synthesis problem fortemporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTLand our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3)Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan and Pavlogiannis, Andreas},
issn = {2664-1690},
pages = {11},
publisher = {IST Austria},
title = {{Distributed synthesis for LTL Fragments}},
doi = {10.15479/AT:IST-2013-130-v1-1},
year = {2013},
}
@techreport{5407,
abstract = {This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the mandatory features, which need to be fulfilled to provide an institutional repository as a platform and also a service to the scientists at the institute. It also includes optional features, which would be of strong benefit for the scientists and would increase the usage of the repository, and hence the visibility of research at IST Austria.},
author = {Porsche, Jana},
publisher = {IST Austria},
title = {{Technical requirements and features}},
year = {2013},
}
@misc{5408,
abstract = {We consider two-player partial-observation stochastic games where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are omega-regular conditions specified as parity objectives. The qualitative analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, they were shown to be decidable in 2EXPTIME under finite-memory strategies. We improve the complexity and show that the qualitative analysis problems for partial-observation stochastic parity games under finite-memory strategies are
EXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis. },
author = {Chatterjee, Krishnendu and Doyen, Laurent and Nain, Sumit and Vardi, Moshe},
issn = {2664-1690},
pages = {17},
publisher = {IST Austria},
title = {{The complexity of partial-observation stochastic parity games with finite-memory strategies}},
doi = {10.15479/AT:IST-2013-141-v1-1},
year = {2013},
}
@misc{5409,
abstract = {The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition.
In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in timestamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than delta away from the parameter, for delta>0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and we show analogous decidability results for rectangular automata.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Majumdar, Rupak},
issn = {2664-1690},
pages = {12},
publisher = {IST Austria},
title = {{Edit distance for timed automata}},
doi = {10.15479/AT:IST-2013-144-v1-1},
year = {2013},
}
@misc{5410,
abstract = {Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in development of mathematical and logical skills, but also in emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants.
Our approach generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. Also, the presence of such states for standard game variants like Tic-Tac-Toe on board size 4x4 opens up new games to be played that have not been played for ages since the default start state is heavily biased. },
author = {Ahmed, Umair and Chatterjee, Krishnendu and Gulwani, Sumit},
issn = {2664-1690},
pages = {13},
publisher = {IST Austria},
title = {{Automatic generation of alternative starting positions for traditional board games}},
doi = {10.15479/AT:IST-2013-146-v1-1},
year = {2013},
}
@inbook{5747,
author = {Dragoi, Cezara and Gupta, Ashutosh and Henzinger, Thomas A},
booktitle = {Computer Aided Verification},
isbn = {9783642397981},
issn = {0302-9743},
location = {Saint Petersburg, Russia},
pages = {174--190},
publisher = {Springer Berlin Heidelberg},
title = {{Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates}},
doi = {10.1007/978-3-642-39799-8_11},
volume = {8044},
year = {2013},
}
@misc{6440,
abstract = {In order to guarantee that each method of a data structure updates the logical state exactly once, al-most all non-blocking implementations employ Compare-And-Swap (CAS) based synchronization. For FIFO queue implementations this translates into concurrent enqueue or dequeue methods competing among themselves to update the same variable, the tail or the head, respectively, leading to high contention and poor scalability. Recent non-blocking queue implementations try to alleviate high contentionby increasing the number of contention points, all the while using CAS-based synchronization. Furthermore, obtaining a wait-free implementation with competition is achieved by additional synchronization which leads to further degradation of performance.In this paper we formalize the notion of competitiveness of a synchronizing statement which can beused as a measure for the scalability of concurrent implementations. We present a new queue implementation, the Speculative Pairing (SP) queue, which, as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead of CAS. We prove that the SP queue is linearizable and lock-free.We also show that replacing CAS with FAI leads to wait-freedom for dequeue methods without an adverse effect on performance. In fact, our experiments suggest that the SP queue can perform and scale better than the state-of-the-art queue implementations.},
author = {Henzinger, Thomas A and Payer, Hannes and Sezgin, Ali},
issn = {2664-1690},
pages = {23},
publisher = {IST Austria},
title = {{Replacing competition with cooperation to achieve scalable lock-free FIFO queues }},
doi = {10.15479/AT:IST-2013-124-v1-1},
year = {2013},
}
@inproceedings{1374,
abstract = {We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.},
author = {Chatterjee, Krishnendu and Fijalkow, Nathanaël},
booktitle = {22nd EACSL Annual Conference on Computer Science Logic},
location = {Torino, Italy},
pages = {181 -- 196},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Infinite-state games with finitary conditions}},
doi = {10.4230/LIPIcs.CSL.2013.181},
volume = {23},
year = {2013},
}
@inproceedings{1385,
abstract = {It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results.},
author = {Hofferek, Georg and Gupta, Ashutosh and Könighofer, Bettina and Jiang, Jie and Bloem, Roderick},
booktitle = {2013 Formal Methods in Computer-Aided Design},
location = {Portland, OR, United States},
pages = {77 -- 84},
publisher = {IEEE},
title = {{Synthesizing multiple boolean functions using interpolation on a single proof}},
doi = {10.1109/FMCAD.2013.6679394},
year = {2013},
}
@inproceedings{1387,
abstract = {Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata.},
author = {Boker, Udi and Kuperberg, Denis and Kupferman, Orna and Skrzypczak, Michał},
location = {Riga, Latvia},
number = {PART 2},
pages = {89 -- 100},
publisher = {Springer},
title = {{Nondeterminism in the presence of a diverse or unknown future}},
doi = {10.1007/978-3-642-39212-2_11},
volume = {7966},
year = {2013},
}
@article{450,
abstract = {Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.},
author = {Pickup, Melinda and Field, David and Rowell, David and Young, Andrew},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1750},
publisher = {Royal Society, The},
title = {{Source population characteristics affect heterosis following genetic rescue of fragmented plant populations}},
doi = {10.1098/rspb.2012.2058},
volume = {280},
year = {2013},
}
@article{3261,
abstract = {Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.},
author = {Dubuis, Julien and Tkacik, Gasper and Wieschaus, Eric and Gregor, Thomas and Bialek, William},
journal = {PNAS},
number = {41},
pages = {16301 -- 16308},
publisher = {National Academy of Sciences},
title = {{Positional information, in bits}},
doi = {10.1073/pnas.1315642110},
volume = {110},
year = {2013},
}
@phdthesis{1405,
abstract = {Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.
First, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point.},
author = {Zufferey, Damien},
pages = {134},
publisher = {IST Austria},
title = {{Analysis of dynamic message passing programs}},
year = {2013},
}
@inproceedings{2847,
abstract = {Depth-Bounded Systems form an expressive class of well-structured transition systems. They can model a wide range of concurrent infinite-state systems including those with dynamic thread creation, dynamically changing communication topology, and complex shared heap structures. We present the first method to automatically prove fair termination of depth-bounded systems. Our method uses a numerical abstraction of the system, which we obtain by systematically augmenting an over-approximation of the system’s reachable states with a finite set of counters. This numerical abstraction can be analyzed with existing termination provers. What makes our approach unique is the way in which it exploits the well-structuredness of the analyzed system. We have implemented our work in a prototype tool and used it to automatically prove liveness properties of complex concurrent systems, including nonblocking algorithms such as Treiber’s stack and several distributed processes. Many of these examples are beyond the scope of termination analyses that are based on traditional counter abstractions.},
author = {Bansal, Kshitij and Koskinen, Eric and Wies, Thomas and Zufferey, Damien},
editor = {Piterman, Nir and Smolka, Scott},
location = {Rome, Italy},
pages = {62 -- 77},
publisher = {Springer},
title = {{Structural Counter Abstraction}},
doi = {10.1007/978-3-642-36742-7_5},
volume = {7795},
year = {2013},
}
@inproceedings{2445,
abstract = {We develop program synthesis techniques that can help programmers fix concurrency-related bugs. We make two new contributions to synthesis for concurrency, the first improving the efficiency of the synthesized code, and the second improving the efficiency of the synthesis procedure itself. The first contribution is to have the synthesis procedure explore a variety of (sequential) semantics-preserving program transformations. Classically, only one such transformation has been considered, namely, the insertion of synchronization primitives (such as locks). Based on common manual bug-fixing techniques used by Linux device-driver developers, we explore additional, more efficient transformations, such as the reordering of independent instructions. The second contribution is to speed up the counterexample-guided removal of concurrency bugs within the synthesis procedure by considering partial-order traces (instead of linear traces) as counterexamples. A partial-order error trace represents a set of linear (interleaved) traces of a concurrent program all of which lead to the same error. By eliminating a partial-order error trace, we eliminate in a single iteration of the synthesis procedure all linearizations of the partial-order trace. We evaluated our techniques on several simplified examples of real concurrency bugs that occurred in Linux device drivers.},
author = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun and Ryzhyk, Leonid and Tarrach, Thorsten},
location = {St. Petersburg, Russia},
pages = {951 -- 967},
publisher = {Springer},
title = {{Efficient synthesis for concurrency by semantics-preserving transformations}},
doi = {10.1007/978-3-642-39799-8_68},
volume = {8044},
year = {2013},
}
@article{2247,
abstract = {Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise.},
author = {Zagorsky, Benjamin and Reiter, Johannes and Chatterjee, Krishnendu and Nowak, Martin},
journal = {PLoS One},
number = {12},
publisher = {Public Library of Science},
title = {{Forgiver triumphs in alternating prisoner's dilemma }},
doi = {10.1371/journal.pone.0080814},
volume = {8},
year = {2013},
}
@article{2263,
abstract = {Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.},
author = {Liang, Huixuan and Hippenmeyer, Simon and Ghashghaei, H.},
journal = {Biology open},
number = {12},
pages = {1200 -- 1203},
publisher = {The Company of Biologists},
title = {{A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors}},
doi = {10.1242/bio.20122287},
volume = {1},
year = {2012},
}
@article{2318,
abstract = {We show that bosons interacting via pair potentials with negative scattering length form bound states for a suitable number of particles. In other words, the absence of many-particle bound states of any kind implies the non-negativity of the scattering length of the interaction potential. },
author = {Seiringer, Robert},
journal = {Journal of Spectral Theory},
number = {3},
pages = {321--328},
publisher = {European Mathematical Society},
title = {{Absence of bound states implies non-negativity of the scattering length}},
doi = {10.4171/JST/31},
volume = {2},
year = {2012},
}
@article{2411,
abstract = {The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.},
author = {Ebersberger, Ingo and De Matos Simoes, Ricardo and Kupczok, Anne and Gube, Matthias and Kothe, Erika and Voigt, Kerstin and Von Haeseler, Arndt},
journal = {Molecular Biology and Evolution},
number = {5},
pages = {1319 -- 1334},
publisher = {Oxford University Press},
title = {{A consistent phylogenetic backbone for the fungi}},
doi = {10.1093/molbev/msr285},
volume = {29},
year = {2012},
}
@inproceedings{2715,
abstract = {We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning vertices from where the objective can be ensured with probability 1. We study for the first time the average case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average case running time is linear (as compared to the worst case linear number of iterations and quadratic time complexity). Second, for the average case analysis over all MDPs we show that the expected number of iterations is constant and the average case running time is linear (again as compared to the worst case linear number of iterations and quadratic time complexity). Finally we also show that given that all MDPs are equally likely, the probability that the classical algorithm requires more than constant number of iterations is exponentially small.},
author = {Chatterjee, Krishnendu and Joglekar, Manas and Shah, Nisarg},
location = {Hyderabad, India},
pages = {461 -- 473},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives}},
doi = {10.4230/LIPIcs.FSTTCS.2012.461},
volume = {18},
year = {2012},
}
@article{2848,
abstract = {We study evolutionary game theory in a setting where individuals learn from each other. We extend the traditional approach by assuming that a population contains individuals with different learning abilities. In particular, we explore the situation where individuals have different search spaces, when attempting to learn the strategies of others. The search space of an individual specifies the set of strategies learnable by that individual. The search space is genetically given and does not change under social evolutionary dynamics. We introduce a general framework and study a specific example in the context of direct reciprocity. For this example, we obtain the counter intuitive result that cooperation can only evolve for intermediate benefit-to-cost ratios, while small and large benefit-to-cost ratios favor defection. Our paper is a step toward making a connection between computational learning theory and evolutionary game dynamics.},
author = {Chatterjee, Krishnendu and Zufferey, Damien and Nowak, Martin},
journal = {Journal of Theoretical Biology},
pages = {161 -- 173},
publisher = {Elsevier},
title = {{Evolutionary game dynamics in populations with different learners}},
doi = {10.1016/j.jtbi.2012.02.021},
volume = {301},
year = {2012},
}
@article{2849,
author = {Edelsbrunner, Herbert and Strelkova, Nataliya},
journal = {Russian Mathematical Surveys},
number = {6},
pages = {1167 -- 1168},
publisher = {IOP Publishing Ltd.},
title = {{On the configuration space of Steiner minimal trees}},
doi = {10.1070/RM2012v067n06ABEH004820},
volume = {67},
year = {2012},
}
@inproceedings{2891,
abstract = {Quantitative automata are nondeterministic finite automata with edge weights. They value a
run by some function from the sequence of visited weights to the reals, and value a word by its
minimal/maximal run. They generalize boolean automata, and have gained much attention in
recent years. Unfortunately, important automaton classes, such as sum, discounted-sum, and
limit-average automata, cannot be determinized. Yet, the quantitative setting provides the potential
of approximate determinization. We define approximate determinization with respect to
a distance function, and investigate this potential.
We show that sum automata cannot be determinized approximately with respect to any
distance function. However, restricting to nonnegative weights allows for approximate determinization
with respect to some distance functions.
Discounted-sum automata allow for approximate determinization, as the influence of a word’s
suffix is decaying. However, the naive approach, of unfolding the automaton computations up
to a sufficient level, is shown to be doubly exponential in the discount factor. We provide an
alternative construction that is singly exponential in the discount factor, in the precision, and
in the number of states. We prove matching lower bounds, showing exponential dependency on
each of these three parameters.
Average and limit-average automata are shown to prohibit approximate determinization with
respect to any distance function, and this is the case even for two weights, 0 and 1.},
author = {Boker, Udi and Henzinger, Thomas A},
booktitle = {Leibniz International Proceedings in Informatics},
location = {Hyderabad, India},
pages = {362 -- 373},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Approximate determinization of quantitative automata}},
doi = {10.4230/LIPIcs.FSTTCS.2012.362},
volume = {18},
year = {2012},
}
@inproceedings{2903,
abstract = {In order to enjoy a digital version of the Jordan Curve Theorem, it is common to use the closed topology for the foreground and the open topology for the background of a 2-dimensional binary image. In this paper, we introduce a single topology that enjoys this theorem for all thresholds decomposing a real-valued image into foreground and background. This topology is easy to construct and it generalizes to n-dimensional images.},
author = {Edelsbrunner, Herbert and Symonova, Olga},
location = {New Brunswick, NJ, USA },
pages = {41 -- 48},
publisher = {IEEE},
title = {{The adaptive topology of a digital image}},
doi = {10.1109/ISVD.2012.11},
year = {2012},
}
@article{2904,
abstract = {Generalized van der Corput sequences are onedimensional, infinite sequences in the unit interval. They are generated from permutations in integer base b and are the building blocks of the multi-dimensional Halton sequences. Motivated by recent progress of Atanassov on the uniform distribution behavior of Halton sequences, we study, among others, permutations of the form P(i) = ai (mod b) for coprime integers a and b. We show that multipliers a that either divide b - 1 or b + 1 generate van der Corput sequences with weak distribution properties. We give explicit lower bounds for the asymptotic distribution behavior of these sequences and relate them to sequences generated from the identity permutation in smaller bases, which are, due to Faure, the weakest distributed generalized van der Corput sequences.},
author = {Pausinger, Florian},
issn = {2118-8572},
journal = {Journal de Theorie des Nombres des Bordeaux},
number = {3},
pages = {729 -- 749},
publisher = {Universite de Bordeaux},
title = {{Weak multipliers for generalized van der Corput sequences}},
doi = {10.5802/jtnb.819},
volume = {24},
year = {2012},
}
@inproceedings{2916,
abstract = {The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a quantitative measure for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intu- itively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, and that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies.},
author = {Cerny, Pavol and Chmelik, Martin and Henzinger, Thomas A and Radhakrishna, Arjun},
booktitle = {Electronic Proceedings in Theoretical Computer Science},
location = {Napoli, Italy},
pages = {29 -- 42},
publisher = {EPTCS},
title = {{Interface Simulation Distances}},
doi = {10.4204/EPTCS.96.3},
volume = {96},
year = {2012},
}
@unpublished{2928,
abstract = { This paper addresses the problem of approximate MAP-MRF inference in general graphical models. Following [36], we consider a family of linear programming relaxations of the problem where each relaxation is specified by a set of nested pairs of factors for which the marginalization constraint needs to be enforced. We develop a generalization of the TRW-S algorithm [9] for this problem, where we use a decomposition into junction chains, monotonic w.r.t. some ordering on the nodes. This generalizes the monotonic chains in [9] in a natural way. We also show how to deal with nested factors in an efficient way. Experiments show an improvement over min-sum diffusion, MPLP and subgradient ascent algorithms on a number of computer vision and natural language processing problems. },
author = {Kolmogorov, Vladimir and Schoenemann, Thomas},
booktitle = {arXiv},
pages = {16},
publisher = {ArXiv},
title = {{Generalized sequential tree-reweighted message passing}},
year = {2012},
}
@inproceedings{2930,
abstract = {In this paper we investigate k-submodular functions. This natural family of discrete functions includes submodular and bisubmodular functions as the special cases k = 1 and k = 2 respectively.
In particular we generalize the known Min-Max-Theorem for submodular and bisubmodular functions. This theorem asserts that the minimum of the (bi)submodular function can be found by solving a maximization problem over a (bi)submodular polyhedron. We define a k-submodular polyhedron, prove a Min-Max-Theorem for k-submodular functions, and give a greedy algorithm to construct the vertices of the polyhedron.
},
author = {Huber, Anna and Kolmogorov, Vladimir},
location = {Athens, Greece},
pages = {451 -- 462},
publisher = {Springer},
title = {{Towards minimizing k-submodular functions}},
doi = {10.1007/978-3-642-32147-4_40},
volume = {7422},
year = {2012},
}
@inproceedings{2936,
abstract = {The notion of delays arises naturally in many computational models, such as, in the design of circuits, control systems, and dataflow languages. In this work, we introduce automata with delay blocks (ADBs), extending finite state automata with variable time delay blocks, for deferring individual transition output symbols, in a discrete-time setting. We show that the ADB languages strictly subsume the regular languages, and are incomparable in expressive power to the context-free languages. We show that ADBs are closed under union, concatenation and Kleene star, and under intersection with regular languages, but not closed under complementation and intersection with other ADB languages. We show that the emptiness and the membership problems are decidable in polynomial time for ADBs, whereas the universality problem is undecidable. Finally we consider the linear-time model checking problem, i.e., whether the language of an ADB is contained in a regular language, and show that the model checking problem is PSPACE-complete. Copyright 2012 ACM.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Prabhu, Vinayak},
booktitle = {roceedings of the tenth ACM international conference on Embedded software},
location = {Tampere, Finland},
pages = {43 -- 52},
publisher = {ACM},
title = {{Finite automata with time delay blocks}},
doi = {10.1145/2380356.2380370},
year = {2012},
}
@inproceedings{2937,
abstract = {Developers building cryptography into security-sensitive applications face a daunting task. Not only must they understand the security guarantees delivered by the constructions they choose, they must also implement and combine them correctly and efficiently. Cryptographic compilers free developers from this task by turning high-level specifications of security goals into efficient implementations. Yet, trusting such tools is hard as they rely on complex mathematical machinery and claim security properties that are subtle and difficult to verify. In this paper we present ZKCrypt, an optimizing cryptographic compiler achieving an unprecedented level of assurance without sacrificing practicality for a comprehensive class of cryptographic protocols, known as Zero-Knowledge Proofs of Knowledge. The pipeline of ZKCrypt integrates purpose-built verified compilers and verifying compilers producing formal proofs in the CertiCrypt framework. By combining the guarantees delivered by each stage, ZKCrypt provides assurance that the output implementation securely realizes the abstract proof goal given as input. We report on the main characteristics of ZKCrypt, highlight new definitions and concepts at its foundations, and illustrate its applicability through a representative example of an anonymous credential system.},
author = {Almeida, José and Barbosa, Manuel and Bangerter, Endre and Barthe, Gilles and Krenn, Stephan and Béguelin, Santiago},
booktitle = {Proceedings of the 2012 ACM conference on Computer and communications security},
location = {Raleigh, NC, USA},
pages = {488 -- 500},
publisher = {ACM},
title = {{Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols}},
doi = {10.1145/2382196.2382249},
year = {2012},
}
@article{2941,
author = {Dolbilin, Nikolai and Edelsbrunner, Herbert and Musin, Oleg},
journal = {Russian Mathematical Surveys},
number = {4},
pages = {781 -- 783},
publisher = {IOP Publishing},
title = {{On the optimality of functionals over triangulations of Delaunay sets}},
doi = {10.1070/RM2012v067n04ABEH004807},
volume = {67},
year = {2012},
}
@article{2943,
abstract = {We examine whether the Escherichia coli chromosome is folded into a self-adherent nucleoprotein complex, or alternately is a confined but otherwise unconstrained self-avoiding polymer. We address this through in vivo visualization, using an inducible GFP fusion to the nucleoid-associated protein Fis to non-specifically decorate the entire chromosome. For a range of different growth conditions, the chromosome is a compact structure that does not fill the volume of the cell, and which moves from the new pole to the cell centre. During rapid growth, chromosome segregation occurs well before cell division, with daughter chromosomes coupled by a thin inter-daughter filament before complete segregation, whereas during slow growth chromosomes stay adjacent until cell division occurs. Image correlation analysis indicates that sub-nucleoid structure is stable on a 1min timescale, comparable to the timescale for redistribution time measured for GFP-Fis after photobleaching. Optical deconvolution and writhe calculation analysis indicate that the nucleoid has a large-scale coiled organization rather than being an amorphous mass. Our observations are consistent with the chromosome having a self-adherent filament organization.},
author = {Hadizadeh Yazdi, Nastaran and Guet, Calin C and Johnson, Reid and Marko, John},
journal = {Molecular Microbiology},
number = {6},
pages = {1318 -- 1333},
publisher = {Wiley-Blackwell},
title = {{Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions}},
doi = {10.1111/mmi.12071},
volume = {86},
year = {2012},
}
@article{2946,
abstract = {MicroRNAs (miRNAs) are small noncoding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3′-untranslated region (3′-UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected.},
author = {Dueck, Anne and Ziegler, Christian and Eichner, Alexander and Berezikov, Eugène and Meister, Gunter},
journal = {Nucleic Acids Research},
number = {19},
pages = {9850 -- 9862},
publisher = {Oxford University Press},
title = {{MicroRNAs associated with the different human Argonaute proteins}},
doi = {10.1093/nar/gks705},
volume = {40},
year = {2012},
}
@inproceedings{2947,
abstract = {We introduce games with probabilistic uncertainty, a model for controller synthesis in which the controller observes the state through imprecise sensors that provide correct information about the current state with a fixed probability. That is, in each step, the sensors return an observed state, and given the observed state, there is a probability distribution (due to the estimation error) over the actual current state. The controller must base its decision on the observed state (rather than the actual current state, which it does not know). On the other hand, we assume that the environment can perfectly observe the current state. We show that controller synthesis for qualitative ω-regular objectives in our model can be reduced in polynomial time to standard partial-observation stochastic games, and vice-versa. As a consequence we establish the precise decidability frontier for the new class of games, and establish optimal complexity results for all the decidable problems.},
author = {Chatterjee, Krishnendu and Chmelik, Martin and Majumdar, Ritankar},
location = {Thiruvananthapuram, India},
pages = {385 -- 399},
publisher = {Springer},
title = {{Equivalence of games with probabilistic uncertainty and partial observation games}},
doi = {10.1007/978-3-642-33386-6_30},
volume = {7561},
year = {2012},
}
@article{2954,
abstract = {Spontaneous postsynaptic currents (PSCs) provide key information about the mechanisms of synaptic transmission and the activity modes of neuronal networks. However, detecting spontaneous PSCs in vitro and in vivo has been challenging, because of the small amplitude, the variable kinetics, and the undefined time of generation of these events. Here, we describe a, to our knowledge, new method for detecting spontaneous synaptic events by deconvolution, using a template that approximates the average time course of spontaneous PSCs. A recorded PSC trace is deconvolved from the template, resulting in a series of delta-like functions. The maxima of these delta-like events are reliably detected, revealing the precise onset times of the spontaneous PSCs. Among all detection methods, the deconvolution-based method has a unique temporal resolution, allowing the detection of individual events in high-frequency bursts. Furthermore, the deconvolution-based method has a high amplitude resolution, because deconvolution can substantially increase the signal/noise ratio. When tested against previously published methods using experimental data, the deconvolution-based method was superior for spontaneous PSCs recorded in vivo. Using the high-resolution deconvolution-based detection algorithm, we show that the frequency of spontaneous excitatory postsynaptic currents in dentate gyrus granule cells is 4.5 times higher in vivo than in vitro.},
author = {Pernia-Andrade, Alejandro and Goswami, Sarit and Stickler, Yvonne and Fröbe, Ulrich and Schlögl, Alois and Jonas, Peter M},
journal = {Biophysical Journal},
number = {7},
pages = {1429 -- 1439},
publisher = {Biophysical},
title = {{A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo}},
doi = {10.1016/j.bpj.2012.08.039},
volume = {103},
year = {2012},
}
@inproceedings{2955,
abstract = {We consider two-player stochastic games played on finite graphs with reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1), or positively (i.e., with positive probability), no matter the strategy of the second player. We classify such games according to the information and the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two-sided with (c) both players having partial observation. On the basis of randomization, the players (a) may not be allowed to use randomization (pure strategies), or (b) may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) may use full randomization. Our main results for pure strategies are as follows. (1) For one-sided games with player 1 having partial observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strategies are not sufficient, and we present an exponential upper bound on memory both for almostsure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete. (2) For one-sided games with player 2 having partial observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and positive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence result exhibits serious flaws in previous results of the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
booktitle = {Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science},
location = {Dubrovnik, Croatia},
publisher = {IEEE},
title = {{Partial-observation stochastic games: How to win when belief fails}},
doi = {10.1109/LICS.2012.28},
year = {2012},
}
@inproceedings{2957,
abstract = {We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether words are accepted with probability arbitrarily close to 1. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape (regular) words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions. For most decidable problems we show an optimal PSPACE-complete complexity bound.},
author = {Chatterjee, Krishnendu and Tracol, Mathieu},
booktitle = {Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science},
location = {Dubrovnik, Croatia },
publisher = {IEEE},
title = {{Decidable problems for probabilistic automata on infinite words}},
doi = {10.1109/LICS.2012.29},
year = {2012},
}
@article{2958,
abstract = {The activity of hippocampal pyramidal cells reflects both the current position of the animal and information related to its current behavior. Here we investigated whether single hippocampal neurons can encode several independent features defining trials during a memory task. We also tested whether task-related information is represented by partial remapping of the place cell population or, instead, via firing rate modulation of spatially stable place cells. To address these two questions, the activity of hippocampal neurons was recorded in rats performing a conditional discrimination task on a modified T-maze in which the identity of a food reward guided behavior. When the rat was on the central arm of the maze, the firing rate of pyramidal cells changed depending on two independent factors: (1) the identity of the food reward given to the animal and (2) the previous location of the animal on the maze. Importantly, some pyramidal cells encoded information relative to both factors. This trial-type specific and retrospective coding did not interfere with the spatial representation of the maze: hippocampal cells had stable place fields and their theta-phase precession profiles were unaltered during the task, indicating that trial-related information was encoded via rate remapping. During error trials, encoding of both trial-related information and spatial location was impaired. Finally, we found that pyramidal cells also encode trial-related information via rate remapping during the continuous version of the rewarded alternation task without delays. These results suggest that hippocampal neurons can encode several task-related cognitive aspects via rate remapping.},
author = {Allen, Kevin and Rawlins, J Nick and Bannerman, David and Csicsvari, Jozsef L},
journal = {Journal of Neuroscience},
number = {42},
pages = {14752 -- 14766},
publisher = {Society for Neuroscience},
title = {{Hippocampal place cells can encode multiple trial-dependent features through rate remapping}},
doi = {10.1523/JNEUROSCI.6175-11.2012},
volume = {32},
year = {2012},
}
@article{2959,
abstract = {We study maximum likelihood estimation in Gaussian graphical models from a geometric point of view. An algebraic elimination criterion allows us to find exact lower bounds on the number of observations needed to ensure that the maximum likelihood estimator (MLE) exists with probability one. This is applied to bipartite graphs, grids and colored graphs. We also study the ML degree, and we present the first instance of a graph for which the MLE exists with probability one, even when the number of observations equals the treewidth.},
author = {Uhler, Caroline},
journal = {Annals of Statistics},
number = {1},
pages = {238 -- 261},
publisher = {Institute of Mathematical Statistics},
title = {{Geometry of maximum likelihood estimation in Gaussian graphical models}},
doi = {10.1214/11-AOS957},
volume = {40},
year = {2012},
}
@article{2962,
abstract = {The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates.},
author = {Aeschbacher, Simon and Beaumont, Mark and Futschik, Andreas},
journal = {Genetics},
number = {3},
pages = {1027 -- 1047},
publisher = {Genetics Society of America},
title = {{A novel approach for choosing summary statistics in approximate Bayesian computation}},
doi = {10.1534/genetics.112.143164},
volume = {192},
year = {2012},
}
@article{2965,
abstract = {Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).},
author = {Danowski, Patrick},
journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare},
number = {2},
pages = {200 -- 212},
publisher = {VÖB},
title = {{Kontext Open Access: Creative Commons}},
volume = {65},
year = {2012},
}
@article{2966,
abstract = {Background: The outcome of male-male competition can be predicted from the relative fighting qualities of the opponents, which often depend on their age. In insects, freshly emerged and still sexually inactive males are morphologically indistinct from older, sexually active males. These young inactive males may thus be easy targets for older males if they cannot conceal themselves from their attacks. The ant Cardiocondyla obscurior is characterised by lethal fighting between wingless (" ergatoid" ) males. Here, we analyse for how long young males are defenceless after eclosion, and how early adult males can detect the presence of rival males.Results: We found that old ergatoid males consistently won fights against ergatoid males younger than two days. Old males did not differentiate between different types of unpigmented pupae several days before emergence, but had more frequent contact to ready-to-eclose pupae of female sexuals and winged males than of workers and ergatoid males. In rare cases, old ergatoid males displayed alleviated biting of pigmented ergatoid male pupae shortly before adult eclosion, as well as copulation attempts to dark pupae of female sexuals and winged males. Ergatoid male behaviour may be promoted by a closer similarity of the chemical profile of ready-to-eclose pupae to the profile of adults than that of young pupae several days prior to emergence.Conclusion: Young ergatoid males of C. obscurior would benefit greatly by hiding their identity from older, resident males, as they are highly vulnerable during the first two days of their adult lives. In contrast to the winged males of the same species, which are able to prevent ergatoid male attacks by chemical female mimicry, young ergatoids do not seem to be able to produce a protective chemical profile. Conflicts in male-male competition between ergatoid males of different age thus seem to be resolved in favour of the older males. This might represent selection at the colony level rather than the individual level. © 2012 Cremer et al.; licensee BioMed Central Ltd.},
author = {Cremer, Sylvia and Suefuji, Masaki and Schrempf, Alexandra and Heinze, Jürgen},
journal = {BMC Ecology},
publisher = {BioMed Central},
title = {{The dynamics of male-male competition in Cardiocondyla obscurior ants}},
doi = {10.1186/1472-6785-12-7},
volume = {12},
year = {2012},
}
@article{2968,
abstract = {Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and-using triplet alignments of intronic loci-quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times. © 2012 Blackwell Publishing Ltd.},
author = {Lohse, Konrad and Barton, Nicholas H and Melika, George and Stone, Graham},
journal = {Molecular Ecology},
number = {18},
pages = {4605 -- 4617},
publisher = {Wiley-Blackwell},
title = {{A likelihood based comparison of population histories in a parasitoid guild}},
doi = {10.1111/j.1365-294X.2012.05700.x},
volume = {21},
year = {2012},
}
@article{2969,
abstract = {The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of exocytosis is a key determinant of synaptic transmission. Evoked release from parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing interneurons is generated by microdomain coupling of N-type channels. Nanodomain coupling has several functional advantages, including speed and efficacy of transmission. One potential disadvantage is that stochastic
opening of presynaptic Ca^(2+) channels may trigger spontaneous transmitter release. We addressed this possibility in rat hippocampal
granule cells, which receive converging inputs from different inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic Ca^(2+) channels contributes to spontaneous release. Application of the selective P/Q-type Ca^(2+) channel blocker
ω-agatoxin IVa had no detectable effects, whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine reduced
mIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM and the slow chelator EGTA-AM reduced the mIPSC frequency,
suggesting that Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than nanodomain coupling. The CB_(1) receptor
agonist WIN 55212-2 also decreased spontaneous release; this effect was occluded by prior application of ω-conotoxin GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release was generated at the terminals of CCK-expressing interneurons. Tonic inhibition generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels may be important for hippocampal information processing.
},
author = {Goswami, Sarit and Bucurenciu, Iancu and Jonas, Peter M},
journal = {Journal of Neuroscience},
number = {41},
pages = {14294 -- 14304},
publisher = {Society for Neuroscience},
title = {{Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling}},
doi = {10.1523/JNEUROSCI.6104-11.2012},
volume = {32},
year = {2012},
}
@article{2972,
abstract = {Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objectives. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is logspace-equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
journal = {Theoretical Computer Science},
pages = {49 -- 60},
publisher = {Elsevier},
title = {{Energy parity games}},
doi = {10.1016/j.tcs.2012.07.038},
volume = {458},
year = {2012},
}
@inproceedings{2974,
abstract = {We construct a perfectly binding string commitment scheme whose security is based on the learning parity with noise (LPN) assumption, or equivalently, the hardness of decoding random linear codes. Our scheme not only allows for a simple and efficient zero-knowledge proof of knowledge for committed values (essentially a Σ-protocol), but also for such proofs showing any kind of relation amongst committed values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u) for any circuit C.
To get soundness which is exponentially small in a security parameter t, and when the zero-knowledge property relies on the LPN problem with secrets of length l, our 3 round protocol has communication complexity O(t|C|l log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants are small, and the computation consists mostly of computing inner products of bit-vectors.},
author = {Jain, Abhishek and Krenn, Stephan and Pietrzak, Krzysztof Z and Tentes, Aris},
editor = {Wang, Xiaoyun and Sako, Kazue},
location = {Beijing, China},
pages = {663 -- 680},
publisher = {Springer},
title = {{Commitments and efficient zero knowledge proofs from learning parity with noise}},
doi = {10.1007/978-3-642-34961-4_40},
volume = {7658},
year = {2012},
}
@inproceedings{2048,
abstract = {Leakage resilient cryptography attempts to incorporate side-channel leakage into the black-box security model and designs cryptographic schemes that are provably secure within it. Informally, a scheme is leakage-resilient if it remains secure even if an adversary learns a bounded amount of arbitrary information about the schemes internal state. Unfortunately, most leakage resilient schemes are unnecessarily complicated in order to achieve strong provable security guarantees. As advocated by Yu et al. [CCS’10], this mostly is an artefact of the security proof and in practice much simpler construction may already suffice to protect against realistic side-channel attacks. In this paper, we show that indeed for simpler constructions leakage-resilience can be obtained when we aim for relaxed security notions where the leakage-functions and/or the inputs to the primitive are chosen non-adaptively. For example, we show that a three round Feistel network instantiated with a leakage resilient PRF yields a leakage resilient PRP if the inputs are chosen non-adaptively (This complements the result of Dodis and Pietrzak [CRYPTO’10] who show that if a adaptive queries are allowed, a superlogarithmic number of rounds is necessary.) We also show that a minor variation of the classical GGM construction gives a leakage resilient PRF if both, the leakage-function and the inputs, are chosen non-adaptively.},
author = {Faust, Sebastian and Pietrzak, Krzysztof Z and Schipper, Joachim},
booktitle = { Conference proceedings CHES 2012},
location = {Leuven, Belgium},
pages = {213 -- 232},
publisher = {Springer},
title = {{Practical leakage-resilient symmetric cryptography}},
doi = {10.1007/978-3-642-33027-8_13},
volume = {7428},
year = {2012},
}
@inproceedings{2049,
abstract = {We propose a new authentication protocol that is provably secure based on a ring variant of the learning parity with noise (LPN) problem. The protocol follows the design principle of the LPN-based protocol from Eurocrypt’11 (Kiltz et al.), and like it, is a two round protocol secure against active attacks. Moreover, our protocol has small communication complexity and a very small footprint which makes it applicable in scenarios that involve low-cost, resource-constrained devices.
Performance-wise, our protocol is more efficient than previous LPN-based schemes, such as the many variants of the Hopper-Blum (HB) protocol and the aforementioned protocol from Eurocrypt’11. Our implementation results show that it is even comparable to the standard challenge-and-response protocols based on the AES block-cipher. Our basic protocol is roughly 20 times slower than AES, but with the advantage of having 10 times smaller code size. Furthermore, if a few hundred bytes of non-volatile memory are available to allow the storage of some off-line pre-computations, then the online phase of our protocols is only twice as slow as AES.
},
author = {Heyse, Stefan and Kiltz, Eike and Lyubashevsky, Vadim and Paar, Christof and Pietrzak, Krzysztof Z},
booktitle = { Conference proceedings FSE 2012},
location = {Washington, DC, USA},
pages = {346 -- 365},
publisher = {Springer},
title = {{Lapin: An efficient authentication protocol based on ring-LPN}},
doi = {10.1007/978-3-642-34047-5_20},
volume = {7549},
year = {2012},
}
@article{492,
abstract = {Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis.},
author = {Galkovskyi, Taras and Mileyko, Yuriy and Bucksch, Alexander and Moore, Brad and Symonova, Olga and Price, Charles and Topp, Chrostopher and Iyer Pascuzzi, Anjali and Zurek, Paul and Fang, Suqin and Harer, John and Benfey, Philip and Weitz, Joshua},
journal = {BMC Plant Biology},
publisher = {BioMed Central},
title = {{GiA Roots: Software for the high throughput analysis of plant root system architecture}},
doi = {10.1186/1471-2229-12-116},
volume = {12},
year = {2012},
}
@article{493,
abstract = {The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.},
author = {Tangermann, Michael and Müller, Klaus and Aertsen, Ad and Birbaumer, Niels and Braun, Christoph and Brunner, Clemens and Leeb, Robert and Mehring, Carsten and Miller, Kai and Müller Putz, Gernot and Nolte, Guido and Pfurtscheller, Gert and Preissl, Hubert and Schalk, Gerwin and Schlögl, Alois and Vidaurre, Carmen and Waldert, Stephan and Blankertz, Benjamin},
journal = {Frontiers in Neuroscience},
publisher = {Frontiers Research Foundation},
title = {{Review of the BCI competition IV}},
doi = {10.3389/fnins.2012.00055},
volume = {6},
year = {2012},
}
@inproceedings{495,
abstract = {An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice.},
author = {Kruckman, Alex and Rubin, Sasha and Sheridan, John and Zax, Ben},
booktitle = {Proceedings GandALF 2012},
location = {Napoli, Italy},
pages = {238 -- 246},
publisher = {Open Publishing Association},
title = {{A Myhill Nerode theorem for automata with advice}},
doi = {10.4204/EPTCS.96.18},
volume = {96},
year = {2012},
}
@inproceedings{496,
abstract = {We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations.},
author = {Rabinovich, Alexander and Rubin, Sasha},
location = {Dubrovnik, Croatia},
publisher = {IEEE},
title = {{Interpretations in trees with countably many branches}},
doi = {10.1109/LICS.2012.65},
year = {2012},
}
@inproceedings{497,
abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.},
author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish},
location = {Fontainebleau, France},
pages = {167 -- 182},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Faster algorithms for alternating refinement relations}},
doi = {10.4230/LIPIcs.CSL.2012.167},
volume = {16},
year = {2012},
}
@article{498,
abstract = {Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.},
author = {Pickup, Melinda and Field, David and Rowell, David and Young, Andrew},
journal = {Evolutionary Applications},
number = {8},
pages = {913 -- 924},
publisher = {Wiley-Blackwell},
title = {{Predicting local adaptation in fragmented plant populations: Implications for restoration genetics}},
doi = {10.1111/j.1752-4571.2012.00284.x},
volume = {5},
year = {2012},
}
@article{506,
author = {Sixt, Michael K},
journal = {Journal of Cell Biology},
number = {3},
pages = {347 -- 349},
publisher = {Rockefeller University Press},
title = {{Cell migration: Fibroblasts find a new way to get ahead}},
doi = {10.1083/jcb.201204039},
volume = {197},
year = {2012},
}
@misc{5377,
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 solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. 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, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.},
author = {Chatterjee, Krishnendu and Velner, Yaron},
issn = {2664-1690},
pages = {33},
publisher = {IST Austria},
title = {{Mean-payoff pushdown games}},
doi = {10.15479/AT:IST-2012-0002},
year = {2012},
}
@misc{5378,
abstract = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.},
author = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish},
issn = {2664-1690},
pages = {21},
publisher = {IST Austria},
title = {{Faster algorithms for alternating refinement relations}},
doi = {10.15479/AT:IST-2012-0001},
year = {2012},
}
@misc{5396,
abstract = {We consider the problem of inference in agraphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pair-wise terms over a discretized domain. This allows the use of techniques originally devel-oped for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can out-perform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.},
author = {Korc, Filip and Kolmogorov, Vladimir and Lampert, Christoph},
issn = {2664-1690},
pages = {13},
publisher = {IST Austria},
title = {{Approximating marginals using discrete energy minimization}},
doi = {10.15479/AT:IST-2012-0003},
year = {2012},
}
@techreport{5398,
abstract = {This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers.},
author = {Porsche, Jana},
publisher = {IST Austria},
title = {{Actual state of research data @ ISTAustria}},
year = {2012},
}
@inbook{5745,
author = {Gupta, Ashutosh},
booktitle = {Automated Technology for Verification and Analysis},
isbn = {9783642333859},
issn = {0302-9743},
location = {Thiruvananthapuram, Kerala, India},
pages = {107--121},
publisher = {Springer Berlin Heidelberg},
title = {{Improved Single Pass Algorithms for Resolution Proof Reduction}},
doi = {10.1007/978-3-642-33386-6_10},
volume = {7561},
year = {2012},
}
@article{6588,
abstract = {First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions.},
author = {Pausinger, Florian},
issn = {1812-9471},
journal = {Journal of Mathematical Physics, Analysis, Geometry},
number = {1},
pages = {63--78},
publisher = {B. Verkin Institute for Low Temperature Physics and Engineering},
title = {{Elementary solutions of the Bernstein problem on two intervals}},
volume = {8},
year = {2012},
}
@inproceedings{1384,
abstract = {Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before.},
author = {Beyer, Dirk and Henzinger, Thomas A and Keremoglu, Mehmet and Wendler, Philipp},
booktitle = {Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering},
location = {Cary, NC, USA},
publisher = {ACM},
title = {{Conditional model checking: A technique to pass information between verifiers}},
doi = {10.1145/2393596.2393664},
year = {2012},
}
@article{3846,
abstract = {We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A},
journal = {Journal of Computer and System Sciences},
number = {2},
pages = {394 -- 413},
publisher = {Elsevier},
title = {{A survey of stochastic ω regular games}},
doi = {10.1016/j.jcss.2011.05.002},
volume = {78},
year = {2012},
}
@article{3115,
abstract = {We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P's offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one.},
author = {Berberich, Eric and Halperin, Dan and Kerber, Michael and Pogalnikova, Roza},
journal = {Discrete & Computational Geometry},
number = {4},
pages = {964 -- 989},
publisher = {Springer},
title = {{Deconstructing approximate offsets}},
doi = {10.1007/s00454-012-9441-5},
volume = {48},
year = {2012},
}
@article{3117,
abstract = {We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms.},
author = {Kolmogorov, Vladimir},
journal = {Discrete Applied Mathematics},
number = {15},
pages = {2246 -- 2258},
publisher = {Elsevier},
title = {{Minimizing a sum of submodular functions}},
doi = {10.1016/j.dam.2012.05.025},
volume = {160},
year = {2012},
}
@article{3118,
abstract = {We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.},
author = {Bojsen-Hansen, Morten and Li, Hao and Wojtan, Christopher J},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Tracking surfaces with evolving topology}},
doi = {10.1145/2185520.2185549},
volume = {31},
year = {2012},
}
@inproceedings{3119,
abstract = {We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.
},
author = {Raveendran, Karthik and Thuerey, Nils and Wojtan, Christopher J and Turk, Greg},
booktitle = {Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation},
location = {Aire-la-Ville, Switzerland},
pages = {255 -- 264},
publisher = {ACM},
title = {{Controlling liquids using meshes}},
year = {2012},
}
@article{3120,
abstract = {We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica.},
author = {Brown, Gavin and Kerber, Michael and Reid, Miles},
journal = {Compositio Mathematica},
number = {4},
pages = {1171 -- 1194},
publisher = {Cambridge University Press},
title = {{Fano 3 folds in codimension 4 Tom and Jerry Part I}},
doi = {10.1112/S0010437X11007226},
volume = {148},
year = {2012},
}
@article{3121,
abstract = {Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type.},
author = {Williams, Courtney and Chen, Wenyan and Lee, Chia and Yaeger, Daniel and Vyleta, Nicholas and Smith, Stephen},
journal = {Nature Neuroscience},
number = {9},
pages = {1195 -- 1197},
publisher = {Nature Publishing Group},
title = {{Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA}},
doi = {10.1038/nn.3162},
volume = {15},
year = {2012},
}
@inproceedings{3123,
abstract = {We introduce the idea of using an explicit triangle mesh to track the air/fluid interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial surface mesh is created, this mesh is carried forward in time using nearby particle velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged across time-steps; it is only modified locally for topology change events or for the improvement of triangle quality. In order to ensure that the surface mesh does not diverge from the underlying particle simulation, we periodically project the mesh surface onto an implicit surface defined by the physics simulation. The mesh surface gives us several advantages over previous SPH surface tracking techniques. We demonstrate a new method for surface tension calculations that clearly outperforms the state of the art in SPH surface tension for computer graphics. We also demonstrate a method for tracking detailed surface information (like colors) that is less susceptible to numerical diffusion than competing techniques. Finally, our temporally-coherent surface mesh allows us to simulate high-resolution surface wave dynamics without being limited by the particle resolution of the SPH simulation.},
author = {Yu, Jihun and Wojtan, Christopher J and Turk, Greg and Yap, Chee},
booktitle = {Computer Graphics Forum},
location = {Cagliari, Sardinia, Italy},
number = {2},
pages = {815 -- 824},
publisher = {Blackwell Publishing},
title = {{Explicit mesh surfaces for particle based fluids}},
doi = {10.1111/j.1467-8659.2012.03062.x},
volume = {31},
year = {2012},
}
@inproceedings{3124,
abstract = {We consider the problem of inference in a graphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pairwise terms over a discretized domain. This allows the use of techniques originally developed for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can outperform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.
},
author = {Korc, Filip and Kolmogorov, Vladimir and Lampert, Christoph},
location = {Edinburgh, Scotland},
publisher = {ICML},
title = {{Approximating marginals using discrete energy minimization}},
year = {2012},
}
@inproceedings{3125,
abstract = {We propose a new learning method to infer a mid-level feature representation that combines the advantage of semantic attribute representations with the higher expressive power of non-semantic features. The idea lies in augmenting an existing attribute-based representation with additional dimensions for which an autoencoder model is coupled with a large-margin principle. This construction allows a smooth transition between the zero-shot regime with no training example, the unsupervised regime with training examples but without class labels, and the supervised regime with training examples and with class labels. The resulting optimization problem can be solved efficiently, because several of the necessity steps have closed-form solutions. Through extensive experiments we show that the augmented representation achieves better results in terms of object categorization accuracy than the semantic representation alone.},
author = {Sharmanska, Viktoriia and Quadrianto, Novi and Lampert, Christoph},
location = {Florence, Italy},
number = {PART 5},
pages = {242 -- 255},
publisher = {Springer},
title = {{Augmented attribute representations}},
doi = {10.1007/978-3-642-33715-4_18},
volume = {7576},
year = {2012},
}
@inproceedings{3127,
abstract = {When searching for characteristic subpatterns in potentially noisy graph data, it appears self-evident that having multiple observations would be better than having just one. However, it turns out that the inconsistencies introduced when different graph instances have different edge sets pose a serious challenge. In this work we address this challenge for the problem of finding maximum weighted cliques.
We introduce the concept of most persistent soft-clique. This is subset of vertices, that 1) is almost fully or at least densely connected, 2) occurs in all or almost all graph instances, and 3) has the maximum weight. We present a measure of clique-ness, that essentially counts the number of edge missing to make a subset of vertices into a clique. With this measure, we show that the problem of finding the most persistent soft-clique problem can be cast either as: a) a max-min two person game optimization problem, or b) a min-min soft margin optimization problem. Both formulations lead to the same solution when using a partial Lagrangian method to solve the optimization problems. By experiments on synthetic data and on real social network data, we show that the proposed method is able to reliably find soft cliques in graph data, even if that is distorted by random noise or unreliable observations.},
author = {Quadrianto, Novi and Lampert, Christoph and Chen, Chao},
booktitle = {Proceedings of the 29th International Conference on Machine Learning},
location = {Edinburgh, United Kingdom},
pages = {211--218},
publisher = {Omnipress},
title = {{The most persistent soft-clique in a set of sampled graphs}},
year = {2012},
}
@article{3128,
abstract = {We consider two-player zero-sum stochastic games on graphs with ω-regular winning conditions specified as parity objectives. These games have applications in the design and control of reactive systems. We survey the complexity results for the problem of deciding the winner in such games, and in classes of interest obtained as special cases, based on the information and the power of randomization available to the players, on the class of objectives and on the winning mode. On the basis of information, these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have complete view of the game). The one-sided partial-observation games have two important subclasses: the one-player games, known as partial-observation Markov decision processes (POMDPs), and the blind one-player games, known as probabilistic automata. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Finally, various classes of games are obtained by restricting the parity objective to a reachability, safety, Büchi, or coBüchi condition. We also consider several winning modes, such as sure-winning (i.e., all outcomes of a strategy have to satisfy the winning condition), almost-sure winning (i.e., winning with probability 1), limit-sure winning (i.e., winning with probability arbitrarily close to 1), and value-threshold winning (i.e., winning with probability at least ν, where ν is a given rational). },
author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A},
journal = {Formal Methods in System Design},
number = {2},
pages = {268 -- 284},
publisher = {Springer},
title = {{A survey of partial-observation stochastic parity games}},
doi = {10.1007/s10703-012-0164-2},
volume = {43},
year = {2012},
}
@inproceedings{3129,
abstract = {Let K be a simplicial complex and g the rank of its p-th homology group Hp(K) defined with ℤ2 coefficients. We show that we can compute a basis H of Hp(K) and annotate each p-simplex of K with a binary vector of length g with the following property: the annotations, summed over all p-simplices in any p-cycle z, provide the coordinate vector of the homology class [z] in the basis H. The basis and the annotations for all simplices can be computed in O(n ω ) time, where n is the size of K and ω < 2.376 is a quantity so that two n×n matrices can be multiplied in O(n ω ) time. The precomputed annotations permit answering queries about the independence or the triviality of p-cycles efficiently.
Using annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1 - dimensional homology. Specifically, for computing an optimal basis of H1(K) , we improve the previously known time complexity from O(n 4) to O(n ω + n 2 g ω − 1). Here n denotes the size of the 2-skeleton of K and g the rank of H1(K) . Computing an optimal cycle homologous to a given 1-cycle is NP-hard even for surfaces and an algorithm taking 2 O(g) nlogn time is known for surfaces. We extend this algorithm to work with arbitrary 2-complexes in O(n ω ) + 2 O(g) n 2logn time using annotations.
},
author = {Busaryev, Oleksiy and Cabello, Sergio and Chen, Chao and Dey, Tamal and Wang, Yusu},
location = {Helsinki, Finland},
pages = {189 -- 200},
publisher = {Springer},
title = {{Annotating simplices with a homology basis and its applications}},
doi = {10.1007/978-3-642-31155-0_17},
volume = {7357},
year = {2012},
}
@article{3130,
abstract = {Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.},
author = {Bergmiller, Tobias and Ackermann, Martin and Silander, Olin},
journal = {PLoS Genetics},
number = {6},
publisher = {Public Library of Science},
title = {{Patterns of evolutionary conservation of essential genes correlate with their compensability}},
doi = {10.1371/journal.pgen.1002803},
volume = {8},
year = {2012},
}
@article{3131,
abstract = {In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.},
author = {Weissman, Daniel and Barton, Nicholas H},
journal = {PLoS Genetics},
number = {6},
publisher = {Public Library of Science},
title = {{Limits to the rate of adaptive substitution in sexual populations}},
doi = {10.1371/journal.pgen.1002740},
volume = {8},
year = {2012},
}
@inproceedings{3133,
abstract = {This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. },
author = {Edelsbrunner, Herbert and Kerber, Michael},
booktitle = {Proceedings of the twenty-eighth annual symposium on Computational geometry },
location = {Chapel Hill, NC, USA},
pages = {249 -- 258},
publisher = {ACM},
title = {{Alexander duality for functions: The persistent behavior of land and water and shore}},
doi = {10.1145/2261250.2261287},
year = {2012},
}
@inproceedings{3135,
abstract = {We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. },
author = {Brázdil, Brázdil and Chatterjee, Krishnendu and Kučera, Antonín and Novotny, Petr},
location = {Berkeley, CA, USA},
pages = {23 -- 38},
publisher = {Springer},
title = {{Efficient controller synthesis for consumption games with multiple resource types}},
doi = {10.1007/978-3-642-31424-7_8},
volume = {7358},
year = {2012},
}
@inproceedings{3155,
abstract = {We propose synchronous interfaces, a new interface theory for discrete-time systems. We use an application to time-triggered scheduling to drive the design choices for our formalism; in particular, additionally to deriving useful mathematical properties, we focus on providing a syntax which is adapted to natural high-level system modeling. As a result, we develop an interface model that relies on a guarded-command based language and is equipped with shared variables and explicit discrete-time clocks. We define all standard interface operations: compatibility checking, composition, refinement, and shared refinement. Apart from the synchronous interface model, the contribution of this paper is the establishment of a formal relation between interface theories and real-time scheduling, where we demonstrate a fully automatic framework for the incremental computation of time-triggered schedules.},
author = {Delahaye, Benoît and Fahrenberg, Uli and Henzinger, Thomas A and Legay, Axel and Nickovic, Dejan},
location = {Stockholm, Sweden},
pages = {203 -- 218},
publisher = {Springer},
title = {{Synchronous interface theories and time triggered scheduling}},
doi = {10.1007/978-3-642-30793-5_13},
volume = {7273},
year = {2012},
}
@article{3157,
abstract = {Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion.},
author = {Diaz Jr, Luis and Williams, Richard and Wu, Jian and Kinde, Isaac and Hecht, Joel and Berlin, Jordan and Allen, Benjamin and Božić, Ivana and Reiter, Johannes and Nowak, Martin and Kinzler, Kenneth and Oliner, Kelly and Vogelstein, Bert},
journal = {Nature},
number = {7404},
pages = {537 -- 540},
publisher = {Nature Publishing Group},
title = {{The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers}},
doi = {10.1038/nature11219},
volume = {486},
year = {2012},
}
@article{3158,
abstract = {We describe here the development and characterization of a conditionally inducible mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous actin. We have used this model to study platelets, megakaryocytes and melanoblasts and we provide evidence that Lifeact-GFP is a useful reporter in these cell types ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable by traditional methods, so conditional activation of Lifeact allows the study of actin dynamics in these cells live. We studied melanoblasts in native skin explants from embryos, allowing the visualization of live actin dynamics during cytokinesis and migration. Our study revealed that melanoblasts lacking the small GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis that accounts for the previously reported cytokinesis delay in these cells. Thus, through use of this mouse model, we were able to gain insights into the actin dynamics of cells that could only previously be studied using fixed specimens or following isolation from their native tissue environment.},
author = {Schachtner, Hannah and Li, Ang and Stevenson, David and Calaminus, Simon and Thomas, Steven and Watson, Steve and Sixt, Michael K and Wedlich Söldner, Roland and Strathdee, Douglas and Machesky, Laura},
journal = {European Journal of Cell Biology},
number = {11-12},
pages = {923 -- 929},
publisher = {Elsevier},
title = {{Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo}},
doi = {10.1016/j.ejcb.2012.04.002},
volume = {91},
year = {2012},
}
@article{3159,
abstract = {The structure of hierarchical networks in biological and physical systems has long been characterized using the Horton-Strahler ordering scheme. The scheme assigns an integer order to each edge in the network based on the topology of branching such that the order increases from distal parts of the network (e.g., mountain streams or capillaries) to the "root" of the network (e.g., the river outlet or the aorta). However, Horton-Strahler ordering cannot be applied to networks with loops because they they create a contradiction in the edge ordering in terms of which edge precedes another in the hierarchy. Here, we present a generalization of the Horton-Strahler order to weighted planar reticular networks, where weights are assumed to correlate with the importance of network edges, e.g., weights estimated from edge widths may correlate to flow capacity. Our method assigns hierarchical levels not only to edges of the network, but also to its loops, and classifies the edges into reticular edges, which are responsible for loop formation, and tree edges. In addition, we perform a detailed and rigorous theoretical analysis of the sensitivity of the hierarchical levels to weight perturbations. In doing so, we show that the ordering of the reticular edges is more robust to noise in weight estimation than is the ordering of the tree edges. We discuss applications of this generalized Horton-Strahler ordering to the study of leaf venation and other biological networks.},
author = {Mileyko, Yuriy and Edelsbrunner, Herbert and Price, Charles and Weitz, Joshua},
journal = {PLoS One},
number = {6},
publisher = {Public Library of Science},
title = {{Hierarchical ordering of reticular networks}},
doi = {10.1371/journal.pone.0036715},
volume = {7},
year = {2012},
}
@article{3161,
abstract = {Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by inducing efflux of cellular potassium. Loss of cellular potassium is known to potently suppress protein synthesis, leading us to test whether the inhibition of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome. Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide, puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin, ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of IL-1ß from cells in response to these agents was detected by immunoblotting and ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition of translation by each of the tested translation inhibitors led to processing of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger efflux of intracellular potassium, the addition of high extracellular potassium suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA, which are known to activate the NLRP3 inflammasome, also substantially inhibited protein translation, supporting a close association between inhibition of translation and inflammasome activation. These data demonstrate that translational inhibition itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent inflammatory signaling and that other physical, chemical, or pathogen-associated agents that impair translation may lead to IL-1ß-dependent inflammation through activation of the NLRP3 inflammasome. For agents that inhibit translation through decreased cellular potassium, the application of high extracellular potassium restores protein translation and suppresses activation of the NLRP inflammasome. For agents that inhibit translation through mechanisms that do not involve loss of potassium, high extracellular potassium suppresses IL-1ß processing through a mechanism that remains undefined.},
author = {Vyleta, Meghan and Wong, John and Magun, Bruce},
journal = {PLoS One},
number = {5},
publisher = {Public Library of Science},
title = {{Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome}},
doi = {10.1371/journal.pone.0036044},
volume = {7},
year = {2012},
}
@inproceedings{3162,
abstract = {Given a dense-time real-valued signal and a parameterized temporal logic formula with both magnitude and timing parameters, we compute the subset of the parameter space that renders the formula satisfied by the trace. We provide two preliminary implementations, one which follows the exact semantics and attempts to compute the validity domain by quantifier elimination in linear arithmetics and one which conducts adaptive search in the parameter space.},
author = {Asarin, Eugene and Donzé, Alexandre and Maler, Oded and Nickovic, Dejan},
location = {San Francisco, CA, United States},
pages = {147 -- 160},
publisher = {Springer},
title = {{Parametric identification of temporal properties}},
doi = {10.1007/978-3-642-29860-8_12},
volume = {7186},
year = {2012},
}