@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{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{3126,
abstract = {In this work we propose a new information-theoretic clustering algorithm that infers cluster memberships by direct optimization of a non-parametric mutual information estimate between data distribution and cluster assignment. Although the optimization objective has a solid theoretical foundation it is hard to optimize. We propose an approximate optimization formulation that leads to an efficient algorithm with low runtime complexity. The algorithm has a single free parameter, the number of clusters to find. We demonstrate superior performance on several synthetic and real datasets.
},
author = {Müller, Andreas and Nowozin, Sebastian and Lampert, Christoph},
location = {Graz, Austria},
pages = {205 -- 215},
publisher = {Springer},
title = {{Information theoretic clustering using minimal spanning trees}},
doi = {10.1007/978-3-642-32717-9_21},
volume = {7476},
year = {2012},
}
@article{3164,
abstract = {Overview of the Special Issue on structured prediction and inference.},
author = {Blaschko, Matthew and Lampert, Christoph},
journal = {International Journal of Computer Vision},
number = {3},
pages = {257 -- 258},
publisher = {Springer},
title = {{Guest editorial: Special issue on structured prediction and inference}},
doi = {10.1007/s11263-012-0530-y},
volume = {99},
year = {2012},
}
@inproceedings{3265,
abstract = {We propose a mid-level statistical model for image segmentation that composes multiple figure-ground hypotheses (FG) obtained by applying constraints at different locations and scales, into larger interpretations (tilings) of the entire image. Inference is cast as optimization over sets of maximal cliques sampled from a graph connecting all non-overlapping figure-ground segment hypotheses. Potential functions over cliques combine unary, Gestalt-based figure qualities, and pairwise compatibilities among spatially neighboring segments, constrained by T-junctions and the boundary interface statistics of real scenes. Learning the model parameters is based on maximum likelihood, alternating between sampling image tilings and optimizing their potential function parameters. State of the art results are reported on the Berkeley and Stanford segmentation datasets, as well as VOC2009, where a 28% improvement was achieved.},
author = {Ion, Adrian and Carreira, Joao and Sminchisescu, Cristian},
location = {Barcelona, Spain},
publisher = {IEEE},
title = {{Image segmentation by figure-ground composition into maximal cliques}},
doi = {10.1109/ICCV.2011.6126486},
year = {2012},
}
@inbook{3277,
abstract = {The problem of the origin of metazoa is becoming more urgent in the context of astrobiology. By now it is clear that clues to the understanding of this crucial transition in the evolution of life can arise in a fourth pathway besides the three possibilities in the quest for simplicity outlined by Bonner in his classical book. In other words, solar system exploration seems to be one way in the long-term to elucidate the simplicity of evolutionary development. We place these ideas in the context of different inheritance systems, namely the genotypic and phenotypic replicators with limited or unlimited heredity, and ask which of these can support multicellular development, and to which degree of complexity. However, the quest for evidence on the evolution of biotas from planets around other stars does not seem to be feasible with present technology with direct visualization of living organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter where there is a possibility of detecting reliable biomarkers in the next decade with the Europa Jupiter System Mission, in view of recent progress by landing micropenetrators on planetary, or satellite surfaces. Mars is a second possibility in the inner Solar System, in spite of the multiple difficulties faced by the fleet of past, present and future missions. We discuss a series of preliminary ideas for elucidating the origin of metazoan analogues with available instrumentation in potential payloads of feasible space missions to the Galilean moons.},
author = {de Vladar, Harold and Chela Flores, Julian},
booktitle = {Life on Earth and other planetary bodies},
pages = {387 -- 405},
publisher = {Springer},
title = {{Can the evolution of multicellularity be anticipated in the exploration of the solar system?}},
doi = {10.1007/978-94-007-4966-5_22},
volume = {24},
year = {2012},
}
@article{3289,
abstract = {Viral manipulation of transduction pathways associated with key cellular functions such as survival, response to microbial infection, and cytoskeleton reorganization can provide the supportive milieu for a productive infection. Here, we demonstrate that vaccinia virus (VACV) infection leads to activation of the stress-activated protein kinase (SAPK)/extracellular signal-regulated kinase (ERK) 4/7 (MKK4/7)-c-Jun N-terminal protein kinase 1/2 (JNK1/2) pathway; further, the stimulation of this pathway requires postpenetration, prereplicative events in the viral replication cycle. Although the formation of intracellular mature virus (IMV) was not affected in MKK4/7- or JNK1/2-knockout (KO) cells, we did note an accentuated deregulation of microtubule and actin network organization in infected JNK1/2-KO cells. This was followed by deregulated viral trafficking to the periphery and enhanced enveloped particle release. Furthermore, VACV infection induced alterations in the cell contractility and morphology, and cell migration was reduced in the JNK-KO cells. In addition, phosphorylation of proteins implicated with early cell contractility and cell migration, such as microtubule-associated protein 1B and paxillin, respectively, was not detected in the VACV-infected KO cells. In sum, our findings uncover a regulatory role played by the MKK4/7-JNK1/2 pathway in cytoskeleton reorganization during VACV infection.
},
author = {Pereira, Anna and Leite, Flávia and Brasil, Bruno and Soares Martins, Jamaria and Torres, Alice and Pimenta, Paulo and Souto Padrón, Thais and Tranktman, Paula and Ferreira, Paulo and Kroon, Erna and Bonjardim, Cláudio},
journal = {Journal of Virology},
number = {1},
pages = {172 -- 184},
publisher = {ASM},
title = {{A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization}},
doi = {10.1128/JVI.05638-11},
volume = {86},
year = {2012},
}
@article{3258,
abstract = {CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. It is generally thought that proximal synapses from the mossy fibers activate these neurons most efficiently, whereas distal inputs from the perforant path have a weaker modulatory influence. We used confocally targeted patch-clamp recording from dendrites and axons to map the activation of rat CA3 pyramidal neurons at the subcellular level. Our results reveal two distinct dendritic domains. In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+ channel–mediated dendritic spikes are efficiently initiated by waveforms mimicking synaptic events. CA3 pyramidal neuron dendrites showed a high Na+-to-K+ conductance density ratio, providing ideal conditions for active backpropagation and dendritic spike initiation. Dendritic spikes may enhance the computational power of CA3 pyramidal neurons in the hippocampal network.},
author = {Kim, Sooyun and Guzmán, José and Hu, Hua and Jonas, Peter M},
journal = {Nature Neuroscience},
number = {4},
pages = {600 -- 606},
publisher = {Nature Publishing Group},
title = {{Active dendrites support efficient initiation of dendritic spikes in hippocampal CA3 pyramidal neurons}},
doi = {10.1038/nn.3060},
volume = {15},
year = {2012},
}
@inproceedings{3253,
abstract = {We describe a framework for reasoning about programs with lists carrying integer numerical data. We use abstract domains to describe and manipulate complex constraints on configurations of these programs mixing constraints on the shape of the heap, sizes of the lists, on the multisets of data stored in these lists, and on the data at their different positions. Moreover, we provide powerful techniques for automatic validation of Hoare-triples and invariant checking, as well as for automatic synthesis of invariants and procedure summaries using modular inter-procedural analysis. The approach has been implemented in a tool called Celia and experimented successfully on a large benchmark of programs.},
author = {Bouajjani, Ahmed and Dragoi, Cezara and Enea, Constantin and Sighireanu, Mihaela},
location = {Philadelphia, PA, USA},
pages = {1 -- 22},
publisher = {Springer},
title = {{Abstract domains for automated reasoning about list manipulating programs with infinite data}},
doi = {10.1007/978-3-642-27940-9_1},
volume = {7148},
year = {2012},
}
@phdthesis{2964,
abstract = {CA3 pyramidal neurons are important for memory formation and pattern completion in the hippocampal network. These neurons receive multiple excitatory inputs from numerous sources. Therefore, the rules of spatiotemporal integration of multiple synaptic inputs and propagation of action potentials are important to understand how CA3 neurons contribute to higher brain functions at cellular level. By using confocally targeted patch-clamp recording techniques, we investigated the biophysical properties of rat CA3 pyramidal neuron dendrites. We found two distinct dendritic domains critical for action potential initiation and propagation: In the proximal domain, action potentials initiated in the axon backpropagate actively with large amplitude and fast time course. In the distal domain, Na+-channel mediated dendritic spikes are efficiently evoked by local dendritic depolarization or waveforms mimicking synaptic events. These findings can be explained by a high Na+-to-K+ conductance density ratio of CA3 pyramidal neuron dendrites. The results challenge the prevailing view that proximal mossy fiber inputs activate CA3 pyramidal neurons more efficiently than distal perforant inputs by showing that the distal synapses trigger a different form of activity represented by dendritic spikes. The high probability of dendritic spike initiation in the distal area may enhance the computational power of CA3 pyramidal neurons in the hippocampal network. },
author = {Kim, Sooyun},
pages = {65},
publisher = {IST Austria},
title = {{Active properties of hippocampal CA3 pyramidal neuron dendrites}},
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},
}
@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},
}
@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},
}
@article{3246,
abstract = {Visualizing and analyzing shape changes at various scales, ranging from single molecules to whole organisms, are essential for understanding complex morphogenetic processes, such as early embryonic development. Embryo morphogenesis relies on the interplay between different tissues, the properties of which are again determined by the interaction between their constituent cells. Cell interactions, on the other hand, are controlled by various molecules, such as signaling and adhesion molecules, which in order to exert their functions need to be spatiotemporally organized within and between the interacting cells. In this review, we will focus on the role of cell adhesion functioning at different scales to organize cell, tissue and embryo morphogenesis. We will specifically ask how the subcellular distribution of adhesion molecules controls the formation of cell-cell contacts, how cell-cell contacts determine tissue shape, and how tissue interactions regulate embryo morphogenesis.},
author = {Barone, Vanessa and Heisenberg, Carl-Philipp J},
journal = {Current Opinion in Cell Biology},
number = {1},
pages = {148 -- 153},
publisher = {Elsevier},
title = {{Cell adhesion in embryo morphogenesis}},
doi = {10.1016/j.ceb.2011.11.006},
volume = {24},
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{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},
}
@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{3260,
abstract = {Many scenarios in the living world, where individual organisms compete for winning positions (or resources), have properties of auctions. Here we study the evolution of bids in biological auctions. For each auction, n individuals are drawn at random from a population of size N. Each individual makes a bid which entails a cost. The winner obtains a benefit of a certain value. Costs and benefits are translated into reproductive success (fitness). Therefore, successful bidding strategies spread in the population. We compare two types of auctions. In “biological all-pay auctions”, the costs are the bid for every participating individual. In “biological second price all-pay auctions”, the cost for everyone other than the winner is the bid, but the cost for the winner is the second highest bid. Second price all-pay auctions are generalizations of the “war of attrition” introduced by Maynard Smith. We study evolutionary dynamics in both types of auctions. We calculate pairwise invasion plots and evolutionarily stable distributions over the continuous strategy space. We find that the average bid in second price all-pay auctions is higher than in all-pay auctions, but the average cost for the winner is similar in both auctions. In both cases, the average bid is a declining function of the number of participants, n. The more individuals participate in an auction the smaller is the chance of winning, and thus expensive bids must be avoided.
},
author = {Chatterjee, Krishnendu and Reiter, Johannes and Nowak, Martin},
journal = {Theoretical Population Biology},
number = {1},
pages = {69 -- 80},
publisher = {Academic Press},
title = {{Evolutionary dynamics of biological auctions}},
doi = {10.1016/j.tpb.2011.11.003},
volume = {81},
year = {2012},
}
@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{2302,
abstract = {We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.},
author = {Henzinger, Thomas A and Mateescu, Maria},
journal = {IEEE ACM Transactions on Computational Biology and Bioinformatics},
number = {2},
pages = {310 -- 322},
publisher = {IEEE},
title = {{The propagation approach for computing biochemical reaction networks}},
doi = {10.1109/TCBB.2012.91},
volume = {10},
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},
}
@inproceedings{2915,
author = {Kroemer, Oliver and Lampert, Christoph and Peters, Jan},
publisher = {Deutsches Zentrum für Luft und Raumfahrt},
title = {{Multi-modal learning for dynamic tactile sensing}},
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{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{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},
}
@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{2953,
author = {Heisenberg, Carl-Philipp J and Fässler, Reinhard},
journal = {Current Opinion in Cell Biology},
number = {5},
pages = {559 -- 561},
publisher = {Elsevier},
title = {{Cell-cell adhesion and extracellular matrix diversity counts}},
doi = {10.1016/j.ceb.2012.09.002},
volume = {24},
year = {2012},
}
@article{3122,
abstract = {Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. },
author = {Field, David and Barrett, Spencer},
journal = {Molecular Ecology},
number = {15},
pages = {3640 -- 3643},
publisher = {Wiley-Blackwell},
title = {{Disassortative mating and the maintenance of sexual polymorphism in painted maple}},
doi = {10.1111/j.1365-294X.2012.05643.x},
volume = {21},
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},
}
@inproceedings{3134,
abstract = {It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. },
author = {Edelsbrunner, Herbert and Fasy, Brittany and Rote, Günter},
booktitle = {Proceedings of the twenty-eighth annual symposium on Computational geometry },
location = {Chapel Hill, NC, USA},
pages = {91 -- 100},
publisher = {ACM},
title = {{Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions}},
doi = {10.1145/2261250.2261265},
year = {2012},
}
@article{3242,
abstract = {Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”).},
author = {Konrad, Matthias and Vyleta, Meghan and Theis, Fabian and Stock, Miriam and Tragust, Simon and Klatt, Martina and Drescher, Verena and Marr, Carsten and Ugelvig, Line V and Cremer, Sylvia},
journal = {PLoS Biology},
number = {4},
publisher = {Public Library of Science},
title = {{Social transfer of pathogenic fungus promotes active immunisation in ant colonies}},
doi = {10.1371/journal.pbio.1001300},
volume = {10},
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{3160,
abstract = {There is a long-running controversy about how early cell fate decisions are made in the developing mammalian embryo. 1,2 In particular, it is controversial when the first events that can predict the establishment of the pluripotent and extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur. It has long been proposed that the position and polarity of cells at the 16- to 32-cell stage embryo influence their decision to either give rise to the pluripotent cell lineage that eventually contributes to the inner cell mass (ICM), comprising the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm (TE) surrounding the blastocoel. The positioning of cells in the embryo at this developmental stage could largely be the result of random events, making this a stochastic model of cell lineage allocation. Contrary to such a stochastic model, some studies have detected putative differences in the lineage potential of individual blastomeres before compaction, indicating that the first cell fate decisions may occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a key transcription factor (TF) controlling pre-implantation development in the mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications of such molecular heterogeneities in early development and offer potential avenues toward a mechanistic understanding of these observations, contributing to the resolution of the controversy of developmental cell lineage allocation.},
author = {Pantazis, Periklis and Bollenbach, Tobias},
journal = {Cell Cycle},
number = {11},
pages = {2055 -- 2058},
publisher = {Taylor and Francis},
title = {{Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo}},
doi = {10.4161/cc.20118},
volume = {11},
year = {2012},
}
@inproceedings{3280,
abstract = {The (decisional) learning with errors problem (LWE) asks to distinguish "noisy" inner products of a secret vector with random vectors from uniform. The learning parities with noise problem (LPN) is the special case where the elements of the vectors are bits. In recent years, the LWE and LPN problems have found many applications in cryptography. In this paper we introduce a (seemingly) much stronger adaptive assumption, called "subspace LWE" (SLWE), where the adversary can learn the inner product of the secret and random vectors after they were projected into an adaptively and adversarially chosen subspace. We prove that, surprisingly, the SLWE problem mapping into subspaces of dimension d is almost as hard as LWE using secrets of length d (the other direction is trivial.) This result immediately implies that several existing cryptosystems whose security is based on the hardness of the LWE/LPN problems are provably secure in a much stronger sense than anticipated. As an illustrative example we show that the standard way of using LPN for symmetric CPA secure encryption is even secure against a very powerful class of related key attacks. },
author = {Pietrzak, Krzysztof Z},
location = {Taormina, Sicily, Italy},
pages = {548 -- 563},
publisher = {Springer},
title = {{Subspace LWE}},
doi = {10.1007/978-3-642-28914-9_31},
volume = {7194},
year = {2012},
}
@article{3317,
abstract = {The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission.},
author = {Eggermann, Emmanuel and Bucurenciu, Iancu and Goswami, Sarit and Jonas, Peter M},
journal = {Nature Reviews Neuroscience},
number = {1},
pages = {7 -- 21},
publisher = {Nature Publishing Group},
title = {{Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses}},
doi = {10.1038/nrn3125},
volume = {13},
year = {2012},
}
@article{3247,
abstract = {The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species.},
author = {Vilaça, Sibelle and Fernandes Redondo, Rodrigo A and Lins, Lívia and Santos, Fabrício},
journal = {Conservation Genetics},
number = {1},
pages = {293 -- 298},
publisher = {Springer},
title = {{Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)}},
doi = {10.1007/s10592-011-0262-5},
volume = {13},
year = {2012},
}
@article{3331,
abstract = {Computing the topology of an algebraic plane curve C means computing a combinatorial graph that is isotopic to C and thus represents its topology in R2. We prove that, for a polynomial of degree n with integer coefficients bounded by 2ρ, the topology of the induced curve can be computed with bit operations ( indicates that we omit logarithmic factors). Our analysis improves the previous best known complexity bounds by a factor of n2. The improvement is based on new techniques to compute and refine isolating intervals for the real roots of polynomials, and on the consequent amortized analysis of the critical fibers of the algebraic curve.},
author = {Kerber, Michael and Sagraloff, Michael},
journal = { Journal of Symbolic Computation},
number = {3},
pages = {239 -- 258},
publisher = {Elsevier},
title = {{A worst case bound for topology computation of algebraic curves}},
doi = {10.1016/j.jsc.2011.11.001},
volume = {47},
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{3836,
abstract = {Hierarchical Timing Language (HTL) is a coordination language for distributed, hard real-time applications. HTL is a hierarchical extension of Giotto and, like its predecessor, based on the logical execution time (LET) paradigm of real-time programming. Giotto is compiled into code for a virtual machine, called the EmbeddedMachine (or E machine). If HTL is targeted to the E machine, then the hierarchicalprogram structure needs to be flattened; the flattening makes separatecompilation difficult, and may result in E machinecode of exponential size. In this paper, we propose a generalization of the E machine, which supports a hierarchicalprogram structure at runtime through real-time trigger mechanisms that are arranged in a tree. We present the generalized E machine, and a modular compiler for HTL that generates code of linear size. The compiler may generate code for any part of a given HTL program separately in any order.},
author = {Ghosal, Arkadeb and Iercan, Daniel and Kirsch, Christoph and Henzinger, Thomas A and Sangiovanni Vincentelli, Alberto},
journal = {Science of Computer Programming},
number = {2},
pages = {96 -- 112},
publisher = {Elsevier},
title = {{Separate compilation of hierarchical real-time programs into linear-bounded embedded machine code}},
doi = {10.1016/j.scico.2010.06.004},
volume = {77},
year = {2012},
}
@article{494,
abstract = {We solve the longstanding open problems of the blow-up involved in the translations, when possible, of a nondeterministic Büchi word automaton (NBW) to a nondeterministic co-Büchi word automaton (NCW) and to a deterministic co-Büchi word automaton (DCW). For the NBW to NCW translation, the currently known upper bound is 2o(nlog n) and the lower bound is 1.5n. We improve the upper bound to n2n and describe a matching lower bound of 2ω(n). For the NBW to DCW translation, the currently known upper bound is 2o(nlog n). We improve it to 2 o(n), which is asymptotically tight. Both of our upper-bound constructions are based on a simple subset construction, do not involve intermediate automata with richer acceptance conditions, and can be implemented symbolically. We continue and solve the open problems of translating nondeterministic Streett, Rabin, Muller, and parity word automata to NCW and to DCW. Going via an intermediate NBW is not optimal and we describe direct, simple, and asymptotically tight constructions, involving a 2o(n) blow-up. The constructions are variants of the subset construction, providing a unified approach for translating all common classes of automata to NCW and DCW. Beyond the theoretical importance of the results, we point to numerous applications of the new constructions. In particular, they imply a simple subset-construction based translation, when possible, of LTL to deterministic Büchi word automata.},
author = {Boker, Udi and Kupferman, Orna},
journal = {ACM Transactions on Computational Logic (TOCL)},
number = {4},
publisher = {ACM},
title = {{Translating to Co-Büchi made tight, unified, and useful}},
doi = {10.1145/2362355.2362357},
volume = {13},
year = {2012},
}
@inproceedings{2888,
abstract = {Formal verification aims to improve the quality of hardware and software by detecting errors before they do harm. At the basis of formal verification lies the logical notion of correctness, which purports to capture whether or not a circuit or program behaves as desired. We suggest that the boolean partition into correct and incorrect systems falls short of the practical need to assess the behavior of hardware and software in a more nuanced fashion against multiple criteria.},
author = {Henzinger, Thomas A},
booktitle = {Conference proceedings MODELS 2012},
location = {Innsbruck, Austria},
pages = {1 -- 2},
publisher = {Springer},
title = {{Quantitative reactive models}},
doi = {10.1007/978-3-642-33666-9_1},
volume = {7590},
year = {2012},
}
@inproceedings{2890,
abstract = {Systems are often specified using multiple requirements on their behavior. In practice, these requirements can be contradictory. The classical approach to specification, verification, and synthesis demands more detailed specifications that resolve any contradictions in the requirements. These detailed specifications are usually large, cumbersome, and hard to maintain or modify. In contrast, quantitative frameworks allow the formalization of the intuitive idea that what is desired is an implementation that comes "closest" to satisfying the mutually incompatible requirements, according to a measure of fit that can be defined by the requirements engineer. One flexible framework for quantifying how "well" an implementation satisfies a specification is offered by simulation distances that are parameterized by an error model. We introduce this framework, study its properties, and provide an algorithmic solution for the following quantitative synthesis question: given two (or more) behavioral requirements specified by possibly incompatible finite-state machines, and an error model, find the finite-state implementation that minimizes the maximal simulation distance to the given requirements. Furthermore, we generalize the framework to handle infinite alphabets (for example, realvalued domains). We also demonstrate how quantitative specifications based on simulation distances might lead to smaller and easier to modify specifications. Finally, we illustrate our approach using case studies on error correcting codes and scheduler synthesis.},
author = {Cerny, Pavol and Gopi, Sivakanth and Henzinger, Thomas A and Radhakrishna, Arjun and Totla, Nishant},
booktitle = {Proceedings of the tenth ACM international conference on Embedded software},
location = {Tampere, Finland},
pages = {53 -- 62},
publisher = {ACM},
title = {{Synthesis from incompatible specifications}},
doi = {10.1145/2380356.2380371},
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{3165,
abstract = {Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is Õ(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n·m) boundary by presenting a new technique that reduces the running time to O(n 2). This bound also leads to O(n 2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n 3)), and (3) in Markov decision processes (improving for m > n 4/3 an earlier bound of O(min(m 1.5, m·n 2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n 2), which is an improvement over earlier bounds for m > n 4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem.},
author = {Chatterjee, Krishnendu and Henzinger, Monika},
booktitle = {Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms},
location = {Kyoto, Japan},
pages = {1386 -- 1399},
publisher = {SIAM},
title = {{An O(n2) time algorithm for alternating Büchi games}},
doi = {10.1137/1.9781611973099.109},
year = {2012},
}
@article{3254,
abstract = {The theory of graph games with ω-regular winning conditions is the foundation for modeling and synthesizing reactive processes. In the case of stochastic reactive processes, the corresponding stochastic graph games have three players, two of them (System and Environment) behaving adversarially, and the third (Uncertainty) behaving probabilistically. We consider two problems for stochastic graph games: the qualitative problem asks for the set of states from which a player can win with probability 1 (almost-sure winning); and the quantitative problem asks for the maximal probability of winning (optimal winning) from each state. We consider ω-regular winning conditions formalized as Müller winning conditions. We present optimal memory bounds for pure (deterministic) almost-sure winning and optimal winning strategies in stochastic graph games with Müller winning conditions. We also study the complexity of stochastic Müller games and show that both the qualitative and quantitative analysis problems are PSPACE-complete. Our results are relevant in synthesis of stochastic reactive processes.},
author = {Chatterjee, Krishnendu},
journal = {Information and Computation},
pages = {29 -- 48},
publisher = {Elsevier},
title = {{The complexity of stochastic Müller games}},
doi = {10.1016/j.ic.2011.11.004},
volume = {211},
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},
}
@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},
}
@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},
journal = {Journal de Theorie des Nombres des Bordeaux},
number = {3},
pages = {729 -- 749},
publisher = {Universite de Bordeaux III},
title = {{Weak multipliers for generalized van der Corput sequences}},
doi = {10.5802/jtnb.819},
volume = {24},
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},
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},
}
@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{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},
}
@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{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{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},
}
@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{3166,
abstract = {There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)},
author = {Vladar, Harold},
journal = {Biology Direct},
publisher = {BioMed Central},
title = {{Amino acid fermentation at the origin of the genetic code}},
doi = {10.1186/1745-6150-7-6},
volume = {7},
year = {2012},
}
@article{3262,
abstract = {Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point.},
author = {Tkacik, Gasper and Walczak, Aleksandra and Bialek, William},
journal = { Physical Review E statistical nonlinear and soft matter physics },
number = {4},
publisher = {American Institute of Physics},
title = {{Optimizing information flow in small genetic networks. III. A self-interacting gene}},
doi = {10.1103/PhysRevE.85.041903},
volume = {85},
year = {2012},
}
@article{3274,
abstract = {A boundary element model of a tunnel running through horizontally layered soil with anisotropic material properties is presented. Since there is no analytical fundamental solution for wave propagation inside a layered orthotropic medium in 3D, the fundamental displacements and stresses have to be calculated numerically. In our model this is done in the Fourier domain with respect to space and time. The assumption of a straight tunnel with infinite extension in the x direction makes it possible to decouple the system for every wave number kx, leading to a 2.5D-problem, which is suited for parallel computation. The special form of the fundamental solution, resulting from our Fourier ansatz, and the fact, that the calculation of the boundary integral equation is performed in the Fourier domain, enhances the stability and efficiency of the numerical calculations.},
author = {Rieckh, Georg and Kreuzer, Wolfgang and Waubke, Holger and Balazs, Peter},
journal = { Engineering Analysis with Boundary Elements},
number = {6},
pages = {960 -- 967},
publisher = {Elsevier},
title = {{A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil}},
doi = {10.1016/j.enganabound.2011.12.014},
volume = {36},
year = {2012},
}
@inproceedings{3279,
abstract = {We show a hardness-preserving construction of a PRF from any length doubling PRG which improves upon known constructions whenever we can put a non-trivial upper bound q on the number of queries to the PRF. Our construction requires only O(logq) invocations to the underlying PRG with each query. In comparison, the number of invocations by the best previous hardness-preserving construction (GGM using Levin's trick) is logarithmic in the hardness of the PRG. For example, starting from an exponentially secure PRG {0,1} n → {0,1} 2n, we get a PRF which is exponentially secure if queried at most q = exp(√n)times and where each invocation of the PRF requires Θ(√n) queries to the underlying PRG. This is much less than the Θ(n) required by known constructions.
},
author = {Jain, Abhishek and Pietrzak, Krzysztof Z and Tentes, Aris},
location = {Taormina, Sicily, Italy},
pages = {369 -- 382},
publisher = {Springer},
title = {{Hardness preserving constructions of pseudorandom functions}},
doi = {10.1007/978-3-642-28914-9_21},
volume = {7194},
year = {2012},
}
@inproceedings{3281,
abstract = {We consider the problem of amplifying the "lossiness" of functions. We say that an oracle circuit C*: {0,1} m → {0,1}* amplifies relative lossiness from ℓ/n to L/m if for every function f:{0,1} n → {0,1} n it holds that 1 If f is injective then so is C f. 2 If f has image size of at most 2 n-ℓ, then C f has image size at most 2 m-L. The question is whether such C* exists for L/m ≫ ℓ/n. This problem arises naturally in the context of cryptographic "lossy functions," where the relative lossiness is the key parameter. We show that for every circuit C* that makes at most t queries to f, the relative lossiness of C f is at most L/m ≤ ℓ/n + O(log t)/n. In particular, no black-box method making a polynomial t = poly(n) number of queries can amplify relative lossiness by more than an O(logn)/n additive term. We show that this is tight by giving a simple construction (cascading with some randomization) that achieves such amplification.},
author = {Pietrzak, Krzysztof Z and Rosen, Alon and Segev, Gil},
location = {Taormina, Sicily, Italy},
pages = {458 -- 475},
publisher = {Springer},
title = {{Lossy functions do not amplify well}},
doi = {10.1007/978-3-642-28914-9_26},
volume = {7194},
year = {2012},
}
@inproceedings{3250,
abstract = {The Learning Parity with Noise (LPN) problem has recently found many applications in cryptography as the hardness assumption underlying the constructions of "provably secure" cryptographic schemes like encryption or authentication protocols. Being provably secure means that the scheme comes with a proof showing that the existence of an efficient adversary against the scheme implies that the underlying hardness assumption is wrong. LPN based schemes are appealing for theoretical and practical reasons. On the theoretical side, LPN based schemes offer a very strong security guarantee. The LPN problem is equivalent to the problem of decoding random linear codes, a problem that has been extensively studied in the last half century. The fastest known algorithms run in exponential time and unlike most number-theoretic problems used in cryptography, the LPN problem does not succumb to known quantum algorithms. On the practical side, LPN based schemes are often extremely simple and efficient in terms of code-size as well as time and space requirements. This makes them prime candidates for light-weight devices like RFID tags, which are too weak to implement standard cryptographic primitives like the AES block-cipher. This talk will be a gentle introduction to provable security using simple LPN based schemes as examples. Starting from pseudorandom generators and symmetric key encryption, over secret-key authentication protocols, and, if time admits, touching on recent constructions of public-key identification, commitments and zero-knowledge proofs.},
author = {Pietrzak, Krzysztof Z},
location = {Špindlerův Mlýn, Czech Republic},
pages = {99 -- 114},
publisher = {Springer},
title = {{Cryptography from learning parity with noise}},
doi = {10.1007/978-3-642-27660-6_9},
volume = {7147},
year = {2012},
}
@article{3248,
abstract = {We describe RTblob, a high speed vision system that detects objects in cluttered scenes based on their color and shape at a speed of over 800 frames/s. Because the system is available as open-source software and relies only on off-the-shelf PC hardware components, it can provide the basis for multiple application scenarios. As an illustrative example, we show how RTblob can be used in a robotic table tennis scenario to estimate ball trajectories through 3D space simultaneously from four cameras images at a speed of 200 Hz.},
author = {Lampert, Christoph and Peters, Jan},
journal = {Journal of Real-Time Image Processing},
number = {1},
pages = {31 -- 41},
publisher = {Springer},
title = {{Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components}},
doi = {10.1007/s11554-010-0168-3},
volume = {7},
year = {2012},
}
@article{3243,
author = {Danowski, Patrick},
journal = {Büchereiperspektiven},
pages = {11},
publisher = {Buchereiverband Österreichs},
title = {{Zwischen Technologie und Information}},
volume = {1/2012},
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{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},
}
@inproceedings{2942,
abstract = {Interface theories provide a formal framework for component-based development of software and hardware which supports the incremental design of systems and the independent implementability of components. These capabilities are ensured through mathematical properties of the parallel composition operator and the refinement relation for components. More recently, a conjunction operation was added to interface theories in order to provide support for handling multiple viewpoints, requirements engineering, and component reuse. Unfortunately, the conjunction operator does not allow independent implementability in general. In this paper, we study conditions that need to be imposed on interface models in order to enforce independent implementability with respect to conjunction. We focus on multiple viewpoint specifications and propose a new compatibility criterion between two interfaces, which we call orthogonality. We show that orthogonal interfaces can be refined separately, while preserving both orthogonality and composability with other interfaces. We illustrate the independent implementability of different viewpoints with a FIFO buffer example.},
author = {Henzinger, Thomas A and Nickovic, Dejan},
booktitle = { Conference proceedings Monterey Workshop 2012},
location = {Oxford, UK},
pages = {380 -- 395},
publisher = {Springer},
title = {{Independent implementability of viewpoints}},
doi = {10.1007/978-3-642-34059-8_20},
volume = {7539},
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{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{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{3255,
abstract = {In this paper we survey results of two-player games on graphs and Markov decision processes with parity, mean-payoff and energy objectives, and the combination of mean-payoff and energy objectives with parity objectives. These problems have applications in verification and synthesis of reactive systems in resource-constrained environments.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
location = {Lednice, Czech Republic},
pages = {37 -- 46},
publisher = {Springer},
title = {{Games and Markov decision processes with mean payoff parity and energy parity objectives}},
doi = {10.1007/978-3-642-25929-6_3},
volume = {7119},
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},
}
@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{3270,
abstract = {The persistence diagram of a filtered simplicial com- plex is usually computed by reducing the boundary matrix of the complex. We introduce a simple op- timization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new al- gorithm which yields to sub-cubic asymptotic bounds under certain assumptions.},
author = {Chen, Chao and Kerber, Michael},
location = {Morschach, Switzerland},
pages = {197 -- 200},
publisher = {TU Dortmund},
title = {{Persistent homology computation with a twist}},
year = {2011},
}
@phdthesis{3275,
abstract = {Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. },
author = {Schumann, Kathrin},
pages = {141},
publisher = {IST Austria},
title = {{The role of chemotactic gradients in dendritic cell migration}},
year = {2011},
}
@article{3287,
abstract = {Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion.},
author = {Ruprecht, Verena and Axmann, Markus and Wieser, Stefan and Schuetz, Gerhard},
journal = {Current Protein & Peptide Science},
number = {8},
pages = {714 -- 724},
publisher = {Bentham Science Publishers},
title = {{What can we learn from single molecule trajectories?}},
doi = {10.2174/138920311798841753},
volume = {12},
year = {2011},
}
@inproceedings{3299,
abstract = {We introduce propagation models, a formalism designed to support general and efficient data structures for the transient analysis of biochemical reaction networks. We give two use cases for propagation abstract data types: the uniformization method and numerical integration. We also sketch an implementation of a propagation abstract data type, which uses abstraction to approximate states.},
author = {Henzinger, Thomas A and Mateescu, Maria},
location = {Paris, France},
pages = {1 -- 3},
publisher = {Springer},
title = {{Propagation models for computing biochemical reaction networks}},
doi = {10.1145/2037509.2037510},
year = {2011},
}
@inproceedings{3302,
abstract = {Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We present a new job execution environment Flextic that exploits scal- able static scheduling techniques to provide the user with a flexible pricing model, such as a tradeoff between dif- ferent degrees of execution speed and execution price, and at the same time, reduce scheduling overhead for the cloud provider. We have evaluated a prototype of Flextic on Amazon EC2 and compared it against Hadoop. For various data parallel jobs from machine learning, im- age processing, and gene sequencing that we considered, Flextic has low scheduling overhead and reduces job du- ration by up to 15% compared to Hadoop, a dynamic cloud scheduler.},
author = {Henzinger, Thomas A and Singh, Anmol and Singh, Vasu and Wies, Thomas and Zufferey, Damien},
pages = {1 -- 6},
publisher = {USENIX},
title = {{Static scheduling in clouds}},
year = {2011},
}
@article{3352,
abstract = {Exploring the connection of biology with reactive systems to better understand living systems.},
author = {Fisher, Jasmin and Harel, David and Henzinger, Thomas A},
journal = {Communications of the ACM},
number = {10},
pages = {72 -- 82},
publisher = {ACM},
title = {{Biology as reactivity}},
doi = {10.1145/2001269.2001289},
volume = {54},
year = {2011},
}
@inproceedings{3319,
abstract = {We address the problem of metric learning for multi-view data, namely the construction of embedding projections from data in different representations into a shared feature space, such that the Euclidean distance in this space provides a meaningful within-view as well as between-view similarity. Our motivation stems from the problem of cross-media retrieval tasks, where the availability of a joint Euclidean distance function is a pre-requisite to allow fast, in particular hashing-based, nearest neighbor queries. We formulate an objective function that expresses the intuitive concept that matching samples are mapped closely together in the output space, whereas non-matching samples are pushed apart, no matter in which view they are available. The resulting optimization problem is not convex, but it can be decomposed explicitly into a convex and a concave part, thereby allowing efficient optimization using the convex-concave procedure. Experiments on an image retrieval task show that nearest-neighbor based cross-view retrieval is indeed possible, and the proposed technique improves the retrieval accuracy over baseline techniques.},
author = {Quadrianto, Novi and Lampert, Christoph},
location = {Bellevue, USA},
pages = {425 -- 432},
publisher = {Omnipress},
title = {{Learning multi-view neighborhood preserving projections}},
year = {2011},
}
@inproceedings{3326,
abstract = {Weighted automata map input words to numerical values. Ap- plications of weighted automata include formal verification of quantitative properties, as well as text, speech, and image processing. A weighted au- tomaton is defined with respect to a semiring. For the tropical semiring, the weight of a run is the sum of the weights of the transitions taken along the run, and the value of a word is the minimal weight of an accepting run on it. In the 90’s, Krob studied the decidability of problems on rational series defined with respect to the tropical semiring. Rational series are strongly related to weighted automata, and Krob’s results apply to them. In par- ticular, it follows from Krob’s results that the universality problem (that is, deciding whether the values of all words are below some threshold) is decidable for weighted automata defined with respect to the tropical semir- ing with domain ∪ {∞}, and that the equality problem is undecidable when the domain is ∪ {∞}. In this paper we continue the study of the borders of decidability in weighted automata, describe alternative and direct proofs of the above results, and tighten them further. Unlike the proofs of Krob, which are algebraic in their nature, our proofs stay in the terrain of state machines, and the reduction is from the halting problem of a two-counter machine. This enables us to significantly simplify Krob’s reasoning, make the un- decidability result accessible to the automata-theoretic community, and strengthen it to apply already to a very simple class of automata: all the states are accepting, there are no initial nor final weights, and all the weights on the transitions are from the set {−1, 0, 1}. The fact we work directly with the automata enables us to tighten also the decidability re- sults and to show that the universality problem for weighted automata defined with respect to the tropical semiring with domain ∪ {∞}, and in fact even with domain ≥0 ∪ {∞}, is PSPACE-complete. Our results thus draw a sharper picture about the decidability of decision problems for weighted automata, in both the front of containment vs. universality and the front of the ∪ {∞} vs. the ∪ {∞} domains.},
author = {Almagor, Shaull and Boker, Udi and Kupferman, Orna},
editor = {Bultan, Tevfik and Hsiung, Pao-Ann},
location = {Taipei, Taiwan},
pages = {482 -- 491},
publisher = {Springer},
title = {{What’s decidable about weighted automata }},
doi = {10.1007/978-3-642-24372-1_37},
volume = {6996},
year = {2011},
}
@inproceedings{3357,
abstract = {We consider two-player graph games whose objectives are request-response condition, i.e conjunctions of conditions of the form "if a state with property Rq is visited, then later a state with property Rp is visited". The winner of such games can be decided in EXPTIME and the problem is known to be NP-hard. In this paper, we close this gap by showing that this problem is, in fact, EXPTIME-complete. We show that the problem becomes PSPACE-complete if we only consider games played on DAGs, and NP-complete or PTIME-complete if there is only one player (depending on whether he wants to enforce or spoil the request-response condition). We also present near-optimal bounds on the memory needed to design winning strategies for each player, in each case.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Horn, Florian},
editor = {Dediu, Adrian-Horia and Inenaga, Shunsuke and Martín-Vide, Carlos},
location = {Tarragona, Spain},
pages = {227 -- 237},
publisher = {Springer},
title = {{The complexity of request-response games}},
doi = {10.1007/978-3-642-21254-3_17},
volume = {6638},
year = {2011},
}
@article{3383,
author = {Heisenberg, Carl-Philipp J},
journal = {FEBS Journal},
number = {S1},
pages = {24 -- 24},
publisher = {Wiley-Blackwell},
title = {{Invited Lectures ‐ Symposia Area}},
doi = {10.1111/j.1742-4658.2011.08136.x},
volume = {278},
year = {2011},
}
@article{3388,
abstract = {Background: Fragmentation of terrestrial ecosystems has had detrimental effects on metapopulations of habitat specialists. Maculinea butterflies have been particularly affected because of their specialized lifecycles, requiring both specific food-plants and host-ants. However, the interaction between dispersal, effective population size, and long-term genetic erosion of these endangered butterflies remains unknown. Using non-destructive sampling, we investigated the genetic diversity of the last extant population of M. arion in Denmark, which experienced critically low numbers in the 1980s. Results: Using nine microsatellite markers, we show that the population is genetically impoverished compared to nearby populations in Sweden, but less so than monitoring programs suggested. Ten additional short repeat microsatellites were used to reconstruct changes in genetic diversity and population structure over the last 77 years from museum specimens. We also tested amplification efficiency in such historical samples as a function of repeat length and sample age. Low population numbers in the 1980s did not affect genetic diversity, but considerable turnover of alleles has characterized this population throughout the time-span of our analysis. Conclusions: Our results suggest that M. arion is less sensitive to genetic erosion via population bottlenecks than previously thought, and that managing clusters of high quality habitat may be key for long-term conservation.},
author = {Ugelvig, Line V and Nielsen, Per and Boomsma, Jacobus and Nash, David},
journal = {BMC Evolutionary Biology},
number = {201},
publisher = {BioMed Central},
title = {{Reconstructing eight decades of genetic variation in an isolated Danish population of the large blue butterfly Maculinea arion}},
doi = {10.1186/1471-2148-11-201},
volume = {11},
year = {2011},
}
@article{3390,
abstract = {What determines the genetic contribution that an individual makes to future generations? With biparental reproduction, each individual leaves a 'pedigree' of descendants, determined by the biparental relationships in the population. The pedigree of an individual constrains the lines of descent of each of its genes. An individual's reproductive value is the expected number of copies of each of its genes that is passed on to distant generations conditional on its pedigree. For the simplest model of biparental reproduction analogous to the Wright-Fisher model, an individual's reproductive value is determined within ~10 generations, independent of population size. Partial selfing and subdivision do not greatly slow this convergence. Our central result is that the probability that a gene will survive is proportional to the reproductive value of the individual that carries it, and that conditional on survival, after a few tens of generations, the distribution of the number of surviving copies is the same for all individuals, whatever their reproductive value. These results can be generalized to the joint distribution of surviving blocks of ancestral genome. Selection on unlinked loci in the genetic background may greatly increase the variance in reproductive value, but the above results nevertheless still hold. The almost linear relationship between survival probability and reproductive value also holds for weakly favored alleles. Thus, the influence of the complex pedigree of descendants on an individual's genetic contribution to the population can be summarized through a single number: its reproductive value.},
author = {Barton, Nicholas H and Etheridge, Alison},
journal = {Genetics},
number = {4},
pages = {953 -- 973},
publisher = {Genetics Society of America},
title = {{The relation between reproductive value and genetic contribution}},
doi = {10.1534/genetics.111.127555},
volume = {188},
year = {2011},
}
@article{3395,
abstract = {Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life-history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life-history parameters when evaluating population connectivity levels from genetic data.},
author = {Palero, Ferran and Abello, Pere and Macpherson, Enrique and Beaumont, Mark and Pascual, Marta},
journal = {Biological Journal of the Linnean Society},
number = {2},
pages = {407 -- 418},
publisher = {Wiley-Blackwell},
title = {{Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster Palinurus elephas }},
doi = {10.1111/j.1095-8312.2011.01728.x},
volume = {104},
year = {2011},
}
@article{3376,
abstract = {Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations.},
author = {Bollenbach, Mark Tobias and Kishony, Roy},
journal = {Molecular Cell},
number = {4},
pages = {413 -- 425},
publisher = {Cell Press},
title = {{Resolution of gene regulatory conflicts caused by combinations of antibiotics}},
doi = {10.1016/j.molcel.2011.04.016},
volume = {42},
year = {2011},
}
@article{3369,
abstract = {Rab3 interacting molecules (RIMs) are highly enriched in the active zones of presynaptic terminals. It is generally thought that they operate as effectors of the small G protein Rab3. Three recent papers, by Han et al. (this issue of Neuron), Deng et al. (this issue of Neuron), and Kaeser et al. (a recent issue of Cell), shed new light on the functional role of RIM in presynaptic terminals. First, RIM tethers Ca2+ channels to active zones. Second, RIM contributes to priming of synaptic vesicles by interacting with another presynaptic protein, Munc13.},
author = {Pernia-Andrade, Alejandro and Jonas, Peter M},
journal = {Neuron},
number = {2},
pages = {185 -- 187},
publisher = {Elsevier},
title = {{The multiple faces of RIM}},
doi = {10.1016/j.neuron.2011.01.010},
volume = {69},
year = {2011},
}
@article{3371,
abstract = {The Minisymposium “Cell Migration and Motility” was attended by approximately 500 visitors and covered a broad range of questions in the field using diverse model systems. Topics comprised actin dynamics, cell polarity, force transduction, signal transduction, bar- rier transmigration, and chemotactic guidance.},
author = {Sixt, Michael K and Parent, Carole},
journal = {Molecular Biology and Evolution},
number = {6},
pages = {724},
publisher = {Oxford University Press},
title = {{Cells on the move in Philadelphia}},
doi = {10.1091/mbc.E10-12-0958},
volume = {22},
year = {2011},
}
@article{3965,
abstract = {The elevation function on a smoothly embedded 2-manifold in R-3 reflects the multiscale topography of cavities and protrusions as local maxima. The function has been useful in identifying coarse docking configurations for protein pairs. Transporting the concept from the smooth to the piecewise linear category, this paper describes an algorithm for finding all local maxima. While its worst-case running time is the same as of the algorithm used in prior work, its performance in practice is orders of magnitudes superior. We cast light on this improvement by relating the running time to the total absolute Gaussian curvature of the 2-manifold.},
author = {Wang, Bei and Edelsbrunner, Herbert and Morozov, Dmitriy},
journal = {Journal of Experimental Algorithmics},
number = {2.2},
pages = {1 -- 13},
publisher = {ACM},
title = {{Computing elevation maxima by searching the Gauss sphere}},
doi = {10.1145/1963190.1970375},
volume = {16},
year = {2011},
}
@article{3364,
abstract = {Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete-state continuous-time stochastic models (CTMC) can be used to describe such effects, but the calculation of the probabilities of certain events is computationally expensive. We present a comparison of two analysis approaches for CTMC. On one hand, we estimate the probabilities of interest using repeated Gillespie simulation and determine the statistical accuracy that we obtain. On the other hand, we apply a numerical reachability analysis that approximates the probability distributions of the system at several time instances. We use examples of cellular processes to demonstrate the superiority of the reachability analysis if accurate results are required.},
author = {Didier, Frédéric and Henzinger, Thomas A and Mateescu, Maria and Wolf, Verena},
journal = {Theoretical Computer Science},
number = {21},
pages = {2128 -- 2141},
publisher = {Elsevier},
title = {{Approximation of event probabilities in noisy cellular processes}},
doi = {10.1016/j.tcs.2010.10.022},
volume = {412},
year = {2011},
}
@article{491,
abstract = {In their search for antigens, lymphocytes continuously shuttle among blood vessels, lymph vessels, and lymphatic tissues. Chemokines mediate entry of lymphocytes into lymphatic tissues, and sphingosine 1-phosphate (S1P) promotes localization of lymphocytes to the vasculature. Both signals are sensed through G protein-coupled receptors (GPCRs). Most GPCRs undergo ligand-dependent homologous receptor desensitization, a process that decreases their signaling output after previous exposure to high ligand concentration. Such desensitization can explain why lymphocytes do not take an intermediate position between two signals but rather oscillate between them. The desensitization of S1P receptor 1 (S1PR1) is mediated by GPCR kinase 2 (GRK2). Deletion of GRK2 in lymphocytes compromises desensitization by high vascular S1P concentrations, thereby reducing responsiveness to the chemokine signal and trapping the cells in the vascular compartment. The desensitization kinetics of S1PR1 allows lymphocytes to dynamically shuttle between vasculature and lymphatic tissue, although the positional information in both compartments is static.},
author = {Eichner, Alexander and Sixt, Michael K},
journal = {Science Signaling},
number = {198},
publisher = {American Association for the Advancement of Science},
title = {{Setting the clock for recirculating lymphocytes}},
doi = {10.1126/scisignal.2002617},
volume = {4},
year = {2011},
}
@article{504,
abstract = {Populations living in a spatially and temporally changing environment can adapt to the changing optimum and/or migrate toward favorable habitats. Here we extend previous analyses with a static optimum to allow the environment to vary in time as well as in space. The model follows both population dynamics and the trait mean under stabilizing selection, and the outcomes can be understood by comparing the loads due to genetic variance, dispersal, and temporal change. With fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform along the environmental gradient and that responds to the moving optimum as expected for panmictic populations and when the spatial gradient is sufficiently steep, and (2) a population with limited range that adapts more slowly than the environmental optimum changes in both time and space; the population therefore becomes locally extinct and migrates toward suitable habitat. We also use a population‐genetic model with many loci to allow genetic variance to evolve, and we show that the only solution now has uniform adaptation.},
author = {Polechova, Jitka and Barton, Nicholas H and Marion, Glenn},
journal = {American Naturalist},
number = {4},
pages = {546 -- 547},
publisher = {University of Chicago Press},
title = {{Erratum: Species' range: Adaptation in space and time (American Naturalist 174 (E186 E204)) }},
doi = {10.1086/659642},
volume = {177},
year = {2011},
}
@unpublished{3338,
abstract = {We consider 2-player games played on a finite state space for an infinite number of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves inde- pendently and simultaneously; the current state and the two moves determine the successor state. We study concurrent games with ω-regular winning conditions specified as parity objectives. We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respec- tively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). We study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies. In terms of precision, strategies can be deterministic, uniform, finite-precision or infinite- precision; and in terms of memory, strategies can be memoryless, finite-memory or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as power- ful as infinite-precision finite-memory strategies. We show that the winning sets can be computed in O(n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. While this complexity is the same as for the simpler class of turn-based parity games, where in each state only one of the two players has a choice of moves, our algorithms, that are obtained by characterization of the winning sets as μ-calculus formulas, are considerably more involved than those for turn-based games.},
author = {Chatterjee, Krishnendu},
booktitle = {arXiv},
pages = {1 -- 51},
publisher = {ArXiv},
title = {{Bounded rationality in concurrent parity games}},
year = {2011},
}
@misc{5384,
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 for every ε > 0 there is a word that is accepted with probability at least 1 − ε. 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 words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions.},
author = {Chatterjee, Krishnendu and Tracol, Mathieu},
issn = {2664-1690},
pages = {30},
publisher = {IST Austria},
title = {{Decidable problems for probabilistic automata on infinite words}},
doi = {10.15479/AT:IST-2011-0004},
year = {2011},
}
@inproceedings{3345,
abstract = {We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
location = {Warsaw, Poland},
pages = {206 -- 218},
publisher = {Springer},
title = {{Energy and mean-payoff parity Markov Decision Processes}},
doi = {10.1007/978-3-642-22993-0_21},
volume = {6907},
year = {2011},
}
@article{3269,
abstract = {The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss-Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi-resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi-projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods.},
author = {Sheng, Yu and Cutler, Barbara and Chen, Chao and Nasman, Joshua},
journal = {Computer Graphics Forum},
number = {4},
pages = {1261 -- 1268},
publisher = {Wiley-Blackwell},
title = {{Perceptual global illumination cancellation in complex projection environments}},
doi = {10.1111/j.1467-8659.2011.01985.x},
volume = {30},
year = {2011},
}
@inbook{3271,
abstract = {In this paper we present an efficient framework for computation of persis- tent homology of cubical data in arbitrary dimensions. An existing algorithm using simplicial complexes is adapted to the setting of cubical complexes. The proposed approach enables efficient application of persistent homology in domains where the data is naturally given in a cubical form. By avoiding triangulation of the data, we significantly reduce the size of the complex. We also present a data-structure de- signed to compactly store and quickly manipulate cubical complexes. By means of numerical experiments, we show high speed and memory efficiency of our ap- proach. We compare our framework to other available implementations, showing its superiority. Finally, we report performance on selected 3D and 4D data-sets.},
author = {Wagner, Hubert and Chen, Chao and Vuçini, Erald},
booktitle = {Topological Methods in Data Analysis and Visualization II},
editor = {Peikert, Ronald and Hauser, Helwig and Carr, Hamish and Fuchs, Raphael},
pages = {91 -- 106},
publisher = {Springer},
title = {{Efficient computation of persistent homology for cubical data}},
doi = {10.1007/978-3-642-23175-9_7},
year = {2011},
}