@article{2931, abstract = {In this paper, we present a new approach for establishing correspondences between sparse image features related by an unknown nonrigid mapping and corrupted by clutter and occlusion, such as points extracted from images of different instances of the same object category. We formulate this matching task as an energy minimization problem by defining an elaborate objective function of the appearance and the spatial arrangement of the features. Optimization of this energy is an instance of graph matching, which is in general an NP-hard problem. We describe a novel graph matching optimization technique, which we refer to as dual decomposition (DD), and demonstrate on a variety of examples that this method outperforms existing graph matching algorithms. In the majority of our examples, DD is able to find the global minimum within a minute. The ability to globally optimize the objective allows us to accurately learn the parameters of our matching model from training examples. We show on several matching tasks that our learned model yields results superior to those of state-of-the-art methods. }, author = {Torresani, Lorenzo and Kolmogorov, Vladimir and Rother, Carsten}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {2}, pages = {259 -- 271}, publisher = {IEEE}, title = {{A dual decomposition approach to feature correspondence}}, doi = {10.1109/TPAMI.2012.105}, volume = {35}, year = {2012}, } @inproceedings{2937, abstract = {Developers building cryptography into security-sensitive applications face a daunting task. Not only must they understand the security guarantees delivered by the constructions they choose, they must also implement and combine them correctly and efficiently. Cryptographic compilers free developers from this task by turning high-level specifications of security goals into efficient implementations. Yet, trusting such tools is hard as they rely on complex mathematical machinery and claim security properties that are subtle and difficult to verify. In this paper we present ZKCrypt, an optimizing cryptographic compiler achieving an unprecedented level of assurance without sacrificing practicality for a comprehensive class of cryptographic protocols, known as Zero-Knowledge Proofs of Knowledge. The pipeline of ZKCrypt integrates purpose-built verified compilers and verifying compilers producing formal proofs in the CertiCrypt framework. By combining the guarantees delivered by each stage, ZKCrypt provides assurance that the output implementation securely realizes the abstract proof goal given as input. We report on the main characteristics of ZKCrypt, highlight new definitions and concepts at its foundations, and illustrate its applicability through a representative example of an anonymous credential system.}, author = {Almeida, José and Barbosa, Manuel and Bangerter, Endre and Barthe, Gilles and Krenn, Stephan and Béguelin, Santiago}, booktitle = {Proceedings of the 2012 ACM conference on Computer and communications security}, location = {Raleigh, NC, USA}, pages = {488 -- 500}, publisher = {ACM}, title = {{Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols}}, doi = {10.1145/2382196.2382249}, year = {2012}, } @article{2938, abstract = {Social insects have a very high potential to become invasive pest species. Here, we explore how their social lifestyle and their interaction with parasites may contribute to this invasive success. Similar to solitary species, parasite release followed by the evolution of increased competitive ability can promote establishment of introduced social insect hosts in their introduced range. Genetic bottlenecks during introduction of low numbers of founder individuals decrease the genetic diversity at three levels: the population, the colony and the individual, with the colony level being specific to social insects. Reduced genetic diversity can affect both the individual immune system and the collective colony-level disease defences (social immunity). Still, the dual immune system is likely to make social insects more robust to parasite attack. Changes in social structure from small, family-based, territorially aggressive societies in native populations towards huge networks of cooperating nests (unicoloniality) occur in some invasive social insects, for example, most invasive ants and some termites. Unicoloniality is likely to affect disease dynamics in multiple ways. The free exchange of individuals within the population leads to an increased genetic heterogeneity among individuals of a single nest, thereby decreasing disease transmission. However, the multitude of reproductively active queens per colony buffers the effect of individual diseased queens and their offspring, which may result in a higher level of vertical disease transmission in unicolonial societies. Lastly, unicoloniality provides a competitive advantage over native species, allowing them to quickly become the dominant species in the habitat, which in turn selects for parasite adaptation to this common host genotype and thus eventually a high parasite pressure. Overall, invasions by insect societies are characterized by general features applying to all introduced species, as well as idiosyncrasies that emerge from their social lifestyle. It is important to study these effects in concert to be able to develop efficient management and biocontrol strategies. © 2012 British Ecological Society.}, author = {Ugelvig, Line V and Cremer, Sylvia}, journal = {Functional Ecology}, number = {6}, pages = {1300 -- 1312}, publisher = {Wiley-Blackwell}, title = {{Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies}}, doi = {10.1111/1365-2435.12013}, volume = {26}, year = {2012}, } @article{2941, author = {Dolbilin, Nikolai and Edelsbrunner, Herbert and Musin, Oleg}, journal = {Russian Mathematical Surveys}, number = {4}, pages = {781 -- 783}, publisher = {IOP Publishing}, title = {{On the optimality of functionals over triangulations of Delaunay sets}}, doi = {10.1070/RM2012v067n04ABEH004807}, volume = {67}, year = {2012}, } @article{2943, abstract = {We examine whether the Escherichia coli chromosome is folded into a self-adherent nucleoprotein complex, or alternately is a confined but otherwise unconstrained self-avoiding polymer. We address this through in vivo visualization, using an inducible GFP fusion to the nucleoid-associated protein Fis to non-specifically decorate the entire chromosome. For a range of different growth conditions, the chromosome is a compact structure that does not fill the volume of the cell, and which moves from the new pole to the cell centre. During rapid growth, chromosome segregation occurs well before cell division, with daughter chromosomes coupled by a thin inter-daughter filament before complete segregation, whereas during slow growth chromosomes stay adjacent until cell division occurs. Image correlation analysis indicates that sub-nucleoid structure is stable on a 1min timescale, comparable to the timescale for redistribution time measured for GFP-Fis after photobleaching. Optical deconvolution and writhe calculation analysis indicate that the nucleoid has a large-scale coiled organization rather than being an amorphous mass. Our observations are consistent with the chromosome having a self-adherent filament organization.}, author = {Hadizadeh Yazdi, Nastaran and Guet, Calin C and Johnson, Reid and Marko, John}, journal = {Molecular Microbiology}, number = {6}, pages = {1318 -- 1333}, publisher = {Wiley-Blackwell}, title = {{Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions}}, doi = {10.1111/mmi.12071}, volume = {86}, year = {2012}, } @article{2945, abstract = {In search of foreign antigens, lymphocytes recirculate from the blood, through lymph nodes, into lymphatics and back to the blood. Dendritic cells also migrate to lymph nodes for optimal interaction with lymphocytes. This continuous trafficking of immune cells into and out of lymph nodes is essential for immune surveillance of foreign invaders. In this article, we review our current understanding of the functions of high endothelial venules (HEVs), stroma and lymphatics in the entry, positioning and exit of immune cells in lymph nodes during homeostasis, and we highlight the unexpected role of dendritic cells in the control of lymphocyte homing through HEVs.}, author = {Girard, Jean and Moussion, Christine and Förster, Reinhold}, journal = {Nature Reviews Immunology}, number = {11}, pages = {762 -- 773}, publisher = {Nature Publishing Group}, title = {{HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes}}, doi = {10.1038/nri3298}, volume = {12}, year = {2012}, } @article{2946, abstract = {MicroRNAs (miRNAs) are small noncoding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3′-untranslated region (3′-UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected.}, author = {Dueck, Anne and Ziegler, Christian and Eichner, Alexander and Berezikov, Eugène and Meister, Gunter}, journal = {Nucleic Acids Research}, number = {19}, pages = {9850 -- 9862}, publisher = {Oxford University Press}, title = {{MicroRNAs associated with the different human Argonaute proteins}}, doi = {10.1093/nar/gks705}, volume = {40}, year = {2012}, } @inproceedings{2947, abstract = {We introduce games with probabilistic uncertainty, a model for controller synthesis in which the controller observes the state through imprecise sensors that provide correct information about the current state with a fixed probability. That is, in each step, the sensors return an observed state, and given the observed state, there is a probability distribution (due to the estimation error) over the actual current state. The controller must base its decision on the observed state (rather than the actual current state, which it does not know). On the other hand, we assume that the environment can perfectly observe the current state. We show that controller synthesis for qualitative ω-regular objectives in our model can be reduced in polynomial time to standard partial-observation stochastic games, and vice-versa. As a consequence we establish the precise decidability frontier for the new class of games, and establish optimal complexity results for all the decidable problems.}, author = {Chatterjee, Krishnendu and Chmelik, Martin and Majumdar, Ritankar}, location = {Thiruvananthapuram, India}, pages = {385 -- 399}, publisher = {Springer}, title = {{Equivalence of games with probabilistic uncertainty and partial observation games}}, doi = {10.1007/978-3-642-33386-6_30}, volume = {7561}, year = {2012}, } @article{2949, author = {Dupret, David and Csicsvari, Jozsef L}, journal = {Nature Neuroscience}, number = {11}, pages = {1471 -- 1472}, publisher = {Nature Publishing Group}, title = {{The medial entorhinal cortex keeps Up}}, doi = {10.1038/nn.3245}, volume = {15}, year = {2012}, } @article{2951, abstract = {Differential cell adhesion and cortex tension are thought to drive cell sorting by controlling cell-cell contact formation. Here, we show that cell adhesion and cortex tension have different mechanical functions in controlling progenitor cell-cell contact formation and sorting during zebrafish gastrulation. Cortex tension controls cell-cell contact expansion by modulating interfacial tension at the contact. By contrast, adhesion has little direct function in contact expansion, but instead is needed to mechanically couple the cortices of adhering cells at their contacts, allowing cortex tension to control contact expansion. The coupling function of adhesion is mediated by E-cadherin and limited by the mechanical anchoring of E-cadherin to the cortex. Thus, cell adhesion provides the mechanical scaffold for cell cortex tension to drive cell sorting during gastrulation.}, author = {Maître, Jean-Léon and Berthoumieux, Hélène and Krens, Gabriel and Salbreux, Guillaume and Julicher, Frank and Paluch, Ewa and Heisenberg, Carl-Philipp J}, journal = {Science}, number = {6104}, pages = {253 -- 256}, publisher = {American Association for the Advancement of Science}, title = {{Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells}}, doi = {10.1126/science.1225399}, volume = {338}, year = {2012}, } @article{2952, abstract = {Body axis elongation represents a common and fundamental morphogenetic process in development. A key mechanism triggering body axis elongation without additional growth is convergent extension (CE), whereby a tissue undergoes simultaneous narrowing and extension. Both collective cell migration and cell intercalation are thought to drive CE and are used to different degrees in various species as they elongate their body axis. Here, we provide an overview of CE as a general strategy for body axis elongation and discuss conserved and divergent mechanisms underlying CE among different species.}, author = {Tada, Masazumi and Heisenberg, Carl-Philipp J}, journal = {Development}, number = {21}, pages = {3897 -- 3904}, publisher = {Company of Biologists}, title = {{Convergent extension Using collective cell migration and cell intercalation to shape embryos}}, doi = {10.1242/dev.073007}, volume = {139}, 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}, } @inproceedings{2956, abstract = {Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and parity objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two-player pushdown games. Finally we also show that all the problems have the same computational complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.}, author = {Chatterjee, Krishnendu and Velner, Yaron}, booktitle = {Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science}, location = {Dubrovnik, Croatia }, publisher = {IEEE}, title = {{Mean payoff pushdown games}}, doi = {10.1109/LICS.2012.30}, year = {2012}, } @inproceedings{2957, abstract = {We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether words are accepted with probability arbitrarily close to 1. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape (regular) words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions. For most decidable problems we show an optimal PSPACE-complete complexity bound.}, author = {Chatterjee, Krishnendu and Tracol, Mathieu}, booktitle = {Proceedings of the 2012 27th Annual ACM/IEEE Symposium on Logic in Computer Science}, location = {Dubrovnik, Croatia }, publisher = {IEEE}, title = {{Decidable problems for probabilistic automata on infinite words}}, doi = {10.1109/LICS.2012.29}, year = {2012}, } @article{2958, abstract = {The activity of hippocampal pyramidal cells reflects both the current position of the animal and information related to its current behavior. Here we investigated whether single hippocampal neurons can encode several independent features defining trials during a memory task. We also tested whether task-related information is represented by partial remapping of the place cell population or, instead, via firing rate modulation of spatially stable place cells. To address these two questions, the activity of hippocampal neurons was recorded in rats performing a conditional discrimination task on a modified T-maze in which the identity of a food reward guided behavior. When the rat was on the central arm of the maze, the firing rate of pyramidal cells changed depending on two independent factors: (1) the identity of the food reward given to the animal and (2) the previous location of the animal on the maze. Importantly, some pyramidal cells encoded information relative to both factors. This trial-type specific and retrospective coding did not interfere with the spatial representation of the maze: hippocampal cells had stable place fields and their theta-phase precession profiles were unaltered during the task, indicating that trial-related information was encoded via rate remapping. During error trials, encoding of both trial-related information and spatial location was impaired. Finally, we found that pyramidal cells also encode trial-related information via rate remapping during the continuous version of the rewarded alternation task without delays. These results suggest that hippocampal neurons can encode several task-related cognitive aspects via rate remapping.}, author = {Allen, Kevin and Rawlins, J Nick and Bannerman, David and Csicsvari, Jozsef L}, journal = {Journal of Neuroscience}, number = {42}, pages = {14752 -- 14766}, publisher = {Society for Neuroscience}, title = {{Hippocampal place cells can encode multiple trial-dependent features through rate remapping}}, doi = {10.1523/JNEUROSCI.6175-11.2012}, volume = {32}, year = {2012}, } @article{2959, abstract = {We study maximum likelihood estimation in Gaussian graphical models from a geometric point of view. An algebraic elimination criterion allows us to find exact lower bounds on the number of observations needed to ensure that the maximum likelihood estimator (MLE) exists with probability one. This is applied to bipartite graphs, grids and colored graphs. We also study the ML degree, and we present the first instance of a graph for which the MLE exists with probability one, even when the number of observations equals the treewidth.}, author = {Uhler, Caroline}, journal = {Annals of Statistics}, number = {1}, pages = {238 -- 261}, publisher = {Institute of Mathematical Statistics}, title = {{Geometry of maximum likelihood estimation in Gaussian graphical models}}, doi = {10.1214/11-AOS957}, volume = {40}, year = {2012}, } @article{2962, abstract = {The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates.}, author = {Aeschbacher, Simon and Beaumont, Mark and Futschik, Andreas}, journal = {Genetics}, number = {3}, pages = {1027 -- 1047}, publisher = {Genetics Society of America}, title = {{A novel approach for choosing summary statistics in approximate Bayesian computation}}, doi = {10.1534/genetics.112.143164}, volume = {192}, year = {2012}, } @article{2963, abstract = {Zebra finches are an ubiquitous model system for the study of vocal learning in animal communication. Their song has been well described, but its possible function(s) in social communication are only partly understood. The so-called ‘directed song’ is a high-intensity, high-performance song given during courtship in close proximity to the female, which is known to mediate mate choice and mating. However, this singing mode constitutes only a fraction of zebra finch males’ prolific song output. Potential communicative functions of their second, ‘undirected’ singing mode remain unresolved in the face of contradicting reports of both facilitating and inhibiting effects of social company on singing. We addressed this issue by experimentally manipulating social contexts in a within-subject design, comparing a solo versus male or female only company condition, each lasting for 24 hours. Males’ total song output was significantly higher when a conspecific was in audible and visible distance than when they were alone. Male and female company had an equally facilitating effect on song output. Our findings thus indicate that singing motivation is facilitated rather than inhibited by social company, suggesting that singing in zebra finches might function both in inter- and intrasexual communication. }, author = {Jesse, Fabienne and Riebel, Katharina}, journal = {Behavioural Processes}, number = {3}, pages = {262 -- 266}, publisher = {Elsevier}, title = {{Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata}}, doi = {10.1016/j.beproc.2012.09.006}, volume = {91}, 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}, issn = {2663-337X}, pages = {65}, publisher = {Institute of Science and Technology Austria}, title = {{Active properties of hippocampal CA3 pyramidal neuron dendrites}}, 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}, }