@inproceedings{3361, abstract = {In this paper, we investigate the computational complexity of quantitative information flow (QIF) problems. Information-theoretic quantitative relaxations of noninterference (based on Shannon entropy)have been introduced to enable more fine-grained reasoning about programs in situations where limited information flow is acceptable. The QIF bounding problem asks whether the information flow in a given program is bounded by a constant $d$. Our first result is that the QIF bounding problem is PSPACE-complete. The QIF memoryless synthesis problem asks whether it is possible to resolve nondeterministic choices in a given partial program in such a way that in the resulting deterministic program, the quantitative information flow is bounded by a given constant $d$. Our second result is that the QIF memoryless synthesis problem is also EXPTIME-complete. The QIF memoryless synthesis problem generalizes to QIF general synthesis problem which does not impose the memoryless requirement (that is, by allowing the synthesized program to have more variables then the original partial program). Our third result is that the QIF general synthesis problem is EXPTIME-hard.}, author = {Cerny, Pavol and Chatterjee, Krishnendu and Henzinger, Thomas A}, location = {Cernay-la-Ville, France}, pages = {205 -- 217}, publisher = {IEEE}, title = {{The complexity of quantitative information flow problems}}, doi = {10.1109/CSF.2011.21}, year = {2011}, } @inproceedings{3358, abstract = {The static scheduling problem often arises as a fundamental problem in real-time systems and grid computing. We consider the problem of statically scheduling a large job expressed as a task graph on a large number of computing nodes, such as a data center. This paper solves the large-scale static scheduling problem using abstraction refinement, a technique commonly used in formal verification to efficiently solve computationally hard problems. A scheduler based on abstraction refinement first attempts to solve the scheduling problem with abstract representations of the job and the computing resources. As abstract representations are generally small, the scheduling can be done reasonably fast. If the obtained schedule does not meet specified quality conditions (like data center utilization or schedule makespan) then the scheduler refines the job and data center abstractions and, again solves the scheduling problem. We develop different schedulers based on abstraction refinement. We implemented these schedulers and used them to schedule task graphs from various computing domains on simulated data centers with realistic topologies. We compared the speed of scheduling and the quality of the produced schedules with our abstraction refinement schedulers against a baseline scheduler that does not use any abstraction. We conclude that abstraction refinement techniques give a significant speed-up compared to traditional static scheduling heuristics, at a reasonable cost in the quality of the produced schedules. We further used our static schedulers in an actual system that we deployed on Amazon EC2 and compared it against the Hadoop dynamic scheduler for large MapReduce jobs. Our experiments indicate that there is great potential for static scheduling techniques.}, author = {Henzinger, Thomas A and Singh, Vasu and Wies, Thomas and Zufferey, Damien}, location = {Salzburg, Austria}, pages = {329 -- 342}, publisher = {ACM}, title = {{Scheduling large jobs by abstraction refinement}}, doi = {10.1145/1966445.1966476}, year = {2011}, } @inproceedings{3359, abstract = {Motivated by improvements in constraint-solving technology and by the increase of routinely available computational power, partial-program synthesis is emerging as an effective approach for increasing programmer productivity. The goal of the approach is to allow the programmer to specify a part of her intent imperatively (that is, give a partial program) and a part of her intent declaratively, by specifying which conditions need to be achieved or maintained. The task of the synthesizer is to construct a program that satisfies the specification. As an example, consider a partial program where threads access shared data without using any synchronization mechanism, and a declarative specification that excludes data races and deadlocks. The task of the synthesizer is then to place locks into the program code in order for the program to meet the specification. In this paper, we argue that quantitative objectives are needed in partial-program synthesis in order to produce higher-quality programs, while enabling simpler specifications. Returning to the example, the synthesizer could construct a naive solution that uses one global lock for shared data. This can be prevented either by constraining the solution space further (which is error-prone and partly defeats the point of synthesis), or by optimizing a quantitative objective that models performance. Other quantitative notions useful in synthesis include fault tolerance, robustness, resource (memory, power) consumption, and information flow.}, author = {Cerny, Pavol and Henzinger, Thomas A}, location = {Taipei; Taiwan}, pages = {149 -- 154}, publisher = {ACM}, title = {{From boolean to quantitative synthesis}}, doi = {10.1145/2038642.2038666}, 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{336, abstract = {The growth kinetics of colloidal Bi2S3 nanorods was investigated. After nucleation, the length distribution of the growing Bi 2S3 nanorods narrows with the reaction time until a bimodal length distribution appears. From this critical reaction time on, the smallest nanorods of the ensemble dissolve, feeding with monomer the growth of the largest ones. A comprehensive characterization of the size-distribution evolution of Bi2S3 nanorods is used here to illustrate the dependences of the anisotropic growth rates of cylindrical nanoparticles on the nanoparticle dimensions and the monomer concentration in solution. With this goal in mind, a diffusion-reaction model is presented to explain the origin of the experimentally obtained length distribution focusing mechanism. The model is able to reproduce the decrease of the growth rate in the nanorod axial direction with both its thickness and length. On the other hand, low lateral reaction rates prevent the nanorod thickness distribution to be focused. In both crystallographic growth directions, a concentration-dependent critical thickness exists, which discriminates between nanorods with positive growth rates and those dissolving in the reaction solution. }, author = {Ibáñez, Maria and Guardia, Pablo and Shavel, Alexey and Cadavid, Doris and Arbiol, Jordi and Morante, Joan and Cabot, Andreu}, journal = {Journal of Physical Chemistry C}, number = {16}, pages = {7947 -- 7955}, publisher = {American Chemical Society}, title = {{Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods}}, doi = {10.1021/jp2002904}, volume = {115}, year = {2011}, } @article{3379, abstract = {The process of gastrulation is highly conserved across vertebrates on both the genetic and morphological levels, despite great variety in embryonic shape and speed of development. This mechanism spatially separates the germ layers and establishes the organizational foundation for future development. Mesodermal identity is specified in a superficial layer of cells, the epiblast, where cells maintain an epithelioid morphology. These cells involute to join the deeper hypoblast layer where they adopt a migratory, mesenchymal morphology. Expression of a cascade of related transcription factors orchestrates the parallel genetic transition from primitive to mature mesoderm. Although the early and late stages of this process are increasingly well understood, the transition between them has remained largely mysterious. We present here the first high resolution in vivo observations of the blebby transitional morphology of involuting mesodermal cells in a vertebrate embryo. We further demonstrate that the zebrafish spadetail mutation creates a reversible block in the maturation program, stalling cells in the transition state. This mutation creates an ideal system for dissecting the specific properties of cells undergoing the morphological transition of maturing mesoderm, as we demonstrate with a direct measurement of cell–cell adhesion.}, author = {Row, Richard and Maître, Jean-Léon and Martin, Benjamin and Stockinger, Petra and Heisenberg, Carl-Philipp J and Kimelman, David}, journal = {Developmental Biology}, number = {1}, pages = {102 -- 110}, publisher = {Elsevier}, title = {{Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail}}, doi = {10.1016/j.ydbio.2011.03.025}, volume = {354}, 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{3380, abstract = {Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds.}, author = {Logeswaran, Sayanthan and Barton, Nicholas H}, journal = {Genetical Research}, number = {3}, pages = {221 -- 232}, publisher = {Cambridge University Press}, title = {{Mapping Mendelian traits in asexual progeny using changes in marker allele frequency}}, doi = {10.1017/S0016672311000115}, volume = {93}, year = {2011}, } @article{3377, abstract = {By definition, transverse intersections are stable under in- finitesimal perturbations. Using persistent homology, we ex- tend this notion to sizeable perturbations. Specifically, we assign to each homology class of the intersection its robust- ness, the magnitude of a perturbation necessary to kill it, and prove that robustness is stable. Among the applications of this result is a stable notion of robustness for fixed points of continuous mappings and a statement of stability for con- tours of smooth mappings.}, author = {Edelsbrunner, Herbert and Morozov, Dmitriy and Patel, Amit}, journal = {Foundations of Computational Mathematics}, number = {3}, pages = {345 -- 361}, publisher = {Springer}, title = {{Quantifying transversality by measuring the robustness of intersections}}, doi = {10.1007/s10208-011-9090-8}, volume = {11}, year = {2011}, } @article{3378, abstract = {The theory of intersection homology was developed to study the singularities of a topologically stratified space. This paper in- corporates this theory into the already developed framework of persistent homology. We demonstrate that persistent intersec- tion homology gives useful information about the relationship between an embedded stratified space and its singularities. We give, and prove the correctness of, an algorithm for the computa- tion of the persistent intersection homology groups of a filtered simplicial complex equipped with a stratification by subcom- plexes. We also derive, from Poincare ́ Duality, some structural results about persistent intersection homology.}, author = {Bendich, Paul and Harer, John}, journal = {Foundations of Computational Mathematics}, number = {3}, pages = {305 -- 336}, publisher = {Springer}, title = {{Persistent intersection homology}}, doi = {10.1007/s10208-010-9081-1}, volume = {11}, 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{3384, abstract = {Here we introduce a database of calibrated natural images publicly available through an easy-to-use web interface. Using a Nikon D70 digital SLR camera, we acquired about six-megapixel images of Okavango Delta of Botswana, a tropical savanna habitat similar to where the human eye is thought to have evolved. Some sequences of images were captured unsystematically while following a baboon troop, while others were designed to vary a single parameter such as aperture, object distance, time of day or position on the horizon. Images are available in the raw RGB format and in grayscale. Images are also available in units relevant to the physiology of human cone photoreceptors, where pixel values represent the expected number of photoisomerizations per second for cones sensitive to long (L), medium (M) and short (S) wavelengths. This database is distributed under a Creative Commons Attribution-Noncommercial Unported license to facilitate research in computer vision, psychophysics of perception, and visual neuroscience.}, author = {Tkacik, Gasper and Garrigan, Patrick and Ratliff, Charles and Milcinski, Grega and Klein, Jennifer and Seyfarth, Lucia and Sterling, Peter and Brainard, David and Balasubramanian, Vijay}, journal = {PLoS One}, number = {6}, publisher = {Public Library of Science}, title = {{Natural images from the birthplace of the human eye}}, doi = {10.1371/journal.pone.0020409}, volume = {6}, year = {2011}, } @article{3387, abstract = {Background: Supertree methods combine overlapping input trees into a larger supertree. Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny. Well known split-based supertree methods are matrix representation with parsimony and matrix representation with compatibility. Combining input trees on the same taxon set, as in the consensus setting, is a well-studied task and it is thus desirable to generalize consensus methods to supertree methods. Results: Here, three variants of majority-rule (MR) supertrees that generalize majority-rule consensus trees are investigated. I provide simple formulas for computing the respective score for bifurcating input- and supertrees. These score computations, together with a heuristic tree search minmizing the scores, were implemented in the python program PluMiST (Plus- and Minus SuperTrees) available from http://www.cibiv.at/software/ plumist. The different MR methods were tested by simulation and on real data sets. The search heuristic was successful in combining compatible input trees. When combining incompatible input trees, especially one variant, MR(-) supertrees, performed well. Conclusions: The presented framework allows for an efficient score computation of three majority-rule supertree variants and input trees. I combined the score computation with a heuristic search over the supertree space. The implementation was tested by simulation and on real data sets and showed promising results. Especially the MR(-) variant seems to be a reasonable score for supertree reconstruction. Generalizing these computations to multifurcating trees is an open problem, which may be tackled using this framework.}, author = {Kupczok, Anne}, journal = {BMC Evolutionary Biology}, number = {205}, publisher = {BioMed Central}, title = {{Split based computation of majority rule supertrees}}, doi = {10.1186/1471-2148-11-205}, volume = {11}, year = {2011}, } @article{3389, abstract = {Kernel canonical correlation analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying process that generates the data and can ignore high-variance noise directions. However, for data where acquisition in one or more modalities is expensive or otherwise limited, KCCA may suffer from small sample effects. We propose to use semi-supervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of KCCA on human fMRI data, with regression to single and multi-variate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of KCCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing.}, author = {Blaschko, Matthew and Shelton, Jacquelyn and Bartels, Andreas and Lampert, Christoph and Gretton, Arthur}, journal = {Pattern Recognition Letters}, number = {11}, pages = {1572 -- 1583}, publisher = {Elsevier}, title = {{Semi supervised kernel canonical correlation analysis with application to human fMRI}}, doi = {10.1016/j.patrec.2011.02.011}, volume = {32}, year = {2011}, } @article{3382, abstract = {Dynamic tactile sensing is a fundamental ability to recognize materials and objects. However, while humans are born with partially developed dynamic tactile sensing and quickly master this skill, today's robots remain in their infancy. The development of such a sense requires not only better sensors but the right algorithms to deal with these sensors' data as well. For example, when classifying a material based on touch, the data are noisy, high-dimensional, and contain irrelevant signals as well as essential ones. Few classification methods from machine learning can deal with such problems. In this paper, we propose an efficient approach to infer suitable lower dimensional representations of the tactile data. In order to classify materials based on only the sense of touch, these representations are autonomously discovered using visual information of the surfaces during training. However, accurately pairing vision and tactile samples in real-robot applications is a difficult problem. The proposed approach, therefore, works with weak pairings between the modalities. Experiments show that the resulting approach is very robust and yields significantly higher classification performance based on only dynamic tactile sensing.}, author = {Kroemer, Oliver and Lampert, Christoph and Peters, Jan}, journal = {IEEE Transactions on Robotics}, number = {3}, pages = {545 -- 557}, publisher = {IEEE}, title = {{Learning dynamic tactile sensing with robust vision based training}}, doi = {10.1109/TRO.2011.2121130}, volume = {27}, year = {2011}, } @article{3386, abstract = {Evolutionary theories of ageing predict that life span increases with decreasing extrinsic mortality, and life span variation among queens in ant species seems to corroborate this prediction: queens, which are the only reproductive in a colony, live much longer than queens in multi-queen colonies. The latter often inhabit ephemeral nest sites and accordingly are assumed to experience a higher mortality risk. Yet, all prior studies compared queens from different single- and multi-queen species. Here, we demonstrate an effect of queen number on longevity and fecundity within a single, socially plastic species, where queens experience the similar level of extrinsic mortality. Queens from single- and two-queen colonies had significantly longer lifespan and higher fecundity than queens living in associations of eight queens. As queens also differ neither in morphology nor the mode of colony foundation, our study shows that the social environment itself strongly affects ageing rate.}, author = {Schrempf, Alexandra and Cremer, Sylvia and Heinze, Jürgen}, journal = {Journal of Evolutionary Biology}, number = {7}, pages = {1455 -- 1461}, publisher = {Wiley-Blackwell}, title = {{Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies}}, doi = {10.1111/j.1420-9101.2011.02278.x}, volume = {24}, year = {2011}, } @article{3385, author = {Sixt, Michael K}, journal = {Immunology Letters}, number = {1}, pages = {32 -- 34}, publisher = {Elsevier}, title = {{Interstitial locomotion of leukocytes}}, doi = {10.1016/j.imlet.2011.02.013}, volume = {138}, 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{3399, abstract = {Context-dependent adjustment of mating tactics can drastically increase the mating success of behaviourally flexible animals. We used the ant Cardiocondyla obscurior as a model system to study adaptive adjustment of male mating tactics. This species shows a male diphenism of wingless fighter males and peaceful winged males. Whereas the wingless males stay and exclusively mate in the maternal colony, the mating behaviour of winged males is plastic. They copulate with female sexuals in their natal nests early in life but later disperse in search for sexuals outside. In this study, we observed the nest-leaving behaviour of winged males under different conditions and found that they adaptively adjust the timing of their dispersal to the availability of mating partners, as well as the presence, and even the type of competitors in their natal nests. In colonies with virgin female queens winged males stayed longest when they were the only male in the nest. They left earlier when mating partners were not available or when other males were present. In the presence of wingless, locally mating fighter males, winged males dispersed earlier than in the presence of docile, winged competitors. This suggests that C. obscurior males are capable of estimating their local breeding chances and adaptively adjust their dispersal behaviour in both an opportunistic and a risk-sensitive way, thus showing hitherto unknown behavioural plasticity in social insect males.}, author = {Cremer, Sylvia and Schrempf, Alexandra and Heinze, Jürgen}, journal = {PLoS One}, number = {3}, publisher = {Public Library of Science}, title = {{Competition and opportunity shape the reproductive tactics of males in the ant Cardiocondyla obscurior}}, doi = {10.1371/journal.pone.0017323}, volume = {6}, year = {2011}, } @article{3401, abstract = {The Bicoid morphogen gradient directs the patterning of cell fates along the anterior-posterior axis of the syncytial Drosophila embryo and serves as a paradigm of morphogen-mediated patterning. The simplest models of gradient formation rely on constant protein synthesis and diffusion from anteriorly localized source mRNA, coupled with uniform protein degradation. However, currently such models cannot account for all known gradient characteristics. Recent work has proposed that bicoid mRNA spatial distribution is sufficient to produce the observed protein gradient, minimizing the role of protein transport. Here, we adapt a novel method of fluorescent in situ hybridization to quantify the global spatio-temporal dynamics of bicoid mRNA particles. We determine that >90% of all bicoid mRNA is continuously present within the anterior 20% of the embryo. bicoid mRNA distribution along the body axis remains nearly unchanged despite dynamic mRNA translocation from the embryo core to the cortex. To evaluate the impact of mRNA distribution on protein gradient dynamics, we provide detailed quantitative measurements of nuclear Bicoid levels during the formation of the protein gradient. We find that gradient establishment begins 45 minutes after fertilization and that the gradient requires about 50 minutes to reach peak levels. In numerical simulations of gradient formation, we find that incorporating the actual bicoid mRNA distribution yields a closer prediction of the observed protein dynamics compared to modeling protein production from a point source at the anterior pole. We conclude that the spatial distribution of bicoid mRNA contributes to, but cannot account for, protein gradient formation, and therefore that protein movement, either active or passive, is required for gradient formation.}, author = {Little, Shawn and Tkacik, Gasper and Kneeland, Thomas and Wieschaus, Eric and Gregor, Thomas}, journal = {PLoS Biology}, number = {3}, publisher = {Public Library of Science}, title = {{The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized source}}, doi = {10.1371/journal.pbio.1000596}, volume = {9}, year = {2011}, } @inbook{3724, abstract = {Small photochromic molecules are widespread in nature and serve as switches for a plethora of light-controlled processes. In a typical photoreceptor, the different geometries and polarities of the photochrome isomers are tightly coupled to functionally relevant conformational changes in the proteins. The past decade has seen extensive efforts to mimic nature and create proteins controlled by synthetic photochromes in the laboratory. Here, we discuss the role of molecular modeling to gain a structural understanding of photochromes and to design light-controlled peptides and proteins. We address several fundamental questions: What are the molecular structures of photochromes, particularly for metastable isomers that cannot be addressed experimentally? How are the structures of bistable photoisomers coupled to the conformational states of peptides and proteins? Can we design light-controlled proteins rapidly and reliably? After an introduction to the principles of molecular modeling, we answer these questions by examining systems that range from the size of isolated photochromes, to that of peptides and large cell surface receptors, each from its unique computational perspective.}, author = {Harald Janovjak and Isacoff, Ehud Y}, booktitle = {Photosensitive Molecules for the Control of Biological Function}, pages = {233 -- 266}, publisher = {Springer}, title = {{Structure-based design of light-controlled proteins}}, doi = {10.1007/978-1-61779-031-7_13}, volume = {55}, year = {2011}, } @article{3770, abstract = {The pink dolphin (Inia geoffrensis) is widely distributed along the Amazon and Orinoco basins, covering an area of approximately 7 million km2. Previous morphological and genetic studies have proposed the existence of at least two evolutionary significant units: one distributed across the Orinoco and Amazon basins and another confined to the Bolivian Amazon. The presence of barriers in the riverine environment has been suggested to play a significant role in shaping present-day patterns of ecological and genetic structure for this species. In the present study, we examined the phylogeographic structure, lineage divergence time and historical demography using mitochondrial (mt)DNA sequences in different pink dolphin populations distributed in large and small spatial scales, including two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis revealed that the Brazilian haplotypes occupy an intermediate position compared to three previously studied geographic locations: the Colombian Amazon, the Colombian Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern of maternal isolation between two neighbouring populations from Brazil. Six mtDNA CR haplotypes were identified in Brazil with no sharing between the two populations, as well as specific cytochrome b (cyt b) haplotypes identified in each locality. In addition, we analyzed autosomal microsatellites to investigate male-mediated gene flow and demographic changes within the study area in Brazil. Data analysis of 14 microsatellite loci failed to detect significant population subdivision, suggesting that male-mediated gene flow may maintain homogeneity between these two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages through time, whereas a population decline was demonstrated in the Colombian Orinoco lineage. Moreover, BSP and Tajima's D and Fu's Fs tests revealed a recent population expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and continued throughout the Pleistocene.}, author = {Hollatz, Claudia and Vilaça, Sibelle and Fernandes Redondo, Rodrigo A and Marmontel, Míriam and Baker, Cyndi and Santos, Fabrício}, journal = {Biological Journal of the Linnean Society}, number = {4}, pages = {812 -- 827}, publisher = {Wiley}, title = {{The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)}}, doi = {10.1111/j.1095-8312.2011.01616.x}, volume = {102}, year = {2011}, } @article{3771, abstract = {The small-sized frugivorous bat Carollia perspicillata is an understory specialist and occurs in a wide range of lowland habitats, tending to be more common in tropical dry or moist forests of South and Central America. Its sister species, Carollia brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic study proposed a hypothesis of origin and subsequent diversification for C. perspicillata along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene sequences and a more extensive sampling to test hypotheses related to the origin and diversification of C. perspicillata plus C. brevicauda clade in South America. The results obtained indicate that there are two sympatric evolutionary lineages within each species. In C. perspicillata, one lineage is limited to the Southern Atlantic Forest, whereas the other is widely distributed. Coalescent analysis points to a simultaneous origin for C. perspicillata and C. brevicauda, although no place for the diversification of each species can be firmly suggested. The phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene refugia hypothesis as a likely vicariant phenomenon shaping the present distribution of its intraspecific lineages.}, author = {Pavan, Ana and Martins, Felipe and Santos, Fabrício and Ditchfield, Albert and Fernandes Redondo, Rodrigo A}, journal = {Biological Journal of the Linnean Society}, number = {3}, pages = {527 -- 539}, publisher = {Wiley-Blackwell}, title = {{Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.}}, doi = {10.1111/j.1095-8312.2010.01601.x}, volume = {102}, year = {2011}, } @article{3778, author = {Barton, Nicholas H}, journal = {Heredity}, number = {2}, pages = {205 -- 206}, publisher = {Nature Publishing Group}, title = {{Estimating linkage disequilibria}}, doi = {10.1038/hdy.2010.67}, volume = {106}, year = {2011}, } @inbook{3791, abstract = {During the development of multicellular organisms, cell fate specification is followed by the sorting of different cell types into distinct domains from where the different tissues and organs are formed. Cell sorting involves both the segregation of a mixed population of cells with different fates and properties into distinct domains, and the active maintenance of their segregated state. Because of its biological importance and apparent resemblance to fluid segregation in physics, cell sorting was extensively studied by both biologists and physicists over the last decades. Different theories were developed that try to explain cell sorting on the basis of the physical properties of the constituent cells. However, only recently the molecular and cellular mechanisms that control the physical properties driving cell sorting, have begun to be unraveled. In this review, we will provide an overview of different cell-sorting processes in development and discuss how these processes can be explained by the different sorting theories, and how these theories in turn can be connected to the molecular and cellular mechanisms driving these processes.}, author = {Krens, Gabriel and Heisenberg, Carl-Philipp J}, booktitle = {Forces and Tension in Development}, editor = {Labouesse, Michel}, pages = {189 -- 213}, publisher = {Elsevier}, title = {{Cell sorting in development}}, doi = {10.1016/B978-0-12-385065-2.00006-2}, volume = {95}, 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{469, abstract = {Spontaneous release of glutamate is important for maintaining synaptic strength and controlling spike timing in the brain. Mechanisms regulating spontaneous exocytosis remain poorly understood. Extracellular calcium concentration ([Ca2+]o) regulates Ca2+ entry through voltage-activated calcium channels (VACCs) and consequently is a pivotal determinant of action potential-evoked vesicle fusion. Extracellular Ca 2+ also enhances spontaneous release, but via unknown mechanisms. Here we report that external Ca2+ triggers spontaneous glutamate release more weakly than evoked release in mouse neocortical neurons. Blockade of VACCs has no effect on the spontaneous release rate or its dependence on [Ca2+]o. Intracellular [Ca2+] slowly increases in a minority of neurons following increases in [Ca2+]o. Furthermore, the enhancement of spontaneous release by extracellular calcium is insensitive to chelation of intracellular calcium by BAPTA. Activation of the calcium-sensing receptor (CaSR), a G-protein-coupled receptor present in nerve terminals, by several specific agonists increased spontaneous glutamate release. The frequency of spontaneous synaptic transmission was decreased in CaSR mutant neurons. The concentration-effect relationship for extracellular calcium regulation of spontaneous release was well described by a combination of CaSR-dependent and CaSR-independent mechanisms. Overall these results indicate that extracellular Ca2+ does not trigger spontaneous glutamate release by simply increasing calcium influx but stimulates CaSR and thereby promotes resting spontaneous glutamate release. }, author = {Vyleta, Nicholas and Smith, Stephen}, journal = {European Journal of Neuroscience}, number = {12}, pages = {4593 -- 4606}, publisher = {Wiley-Blackwell}, title = {{Spontaneous glutamate release is independent of calcium influx and tonically activated by the calcium-sensing receptor}}, doi = {10.1523/JNEUROSCI.6398-10.2011}, volume = {31}, year = {2011}, } @article{490, abstract = {BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals. }, author = {Schlögl, Alois and Vidaurre, Carmen and Sander, Tilmann}, journal = {Computational Intelligence and Neuroscience}, publisher = {Hindawi Publishing Corporation}, title = {{BioSig: The free and open source software library for biomedical signal processing}}, doi = {10.1155/2011/935364}, volume = {2011}, 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{518, abstract = {Cancer stem cells or cancer initiating cells are believed to contribute to cancer recurrence after therapy. MicroRNAs (miRNAs) are short RNA molecules with fundamental roles in gene regulation. The role of miRNAs in cancer stem cells is only poorly understood. Here, we report miRNA expression profiles of glioblastoma stem cell-containing CD133 + cell populations. We find that miR-9, miR-9 * (referred to as miR-9/9 *), miR-17 and miR-106b are highly abundant in CD133 + cells. Furthermore, inhibition of miR-9/9 * or miR-17 leads to reduced neurosphere formation and stimulates cell differentiation. Calmodulin-binding transcription activator 1 (CAMTA1) is a putative transcription factor, which induces the expression of the anti-proliferative cardiac hormone natriuretic peptide A (NPPA). We identify CAMTA1 as an miR-9/9 * and miR-17 target. CAMTA1 expression leads to reduced neurosphere formation and tumour growth in nude mice, suggesting that CAMTA1 can function as tumour suppressor. Consistently, CAMTA1 and NPPA expression correlate with patient survival. Our findings could provide a basis for novel strategies of glioblastoma therapy.}, author = {Schraivogel, Daniel and Weinmann, Lasse and Beier, Dagmar and Tabatabai, Ghazaleh and Eichner, Alexander and Zhu, Jia and Anton, Martina and Sixt, Michael K and Weller, Michael and Beier, Christoph and Meister, Gunter}, journal = {EMBO Journal}, number = {20}, pages = {4309 -- 4322}, publisher = {Wiley-Blackwell}, title = {{CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells}}, doi = {10.1038/emboj.2011.301}, volume = {30}, year = {2011}, } @article{531, abstract = {Software transactional memories (STM) are described in the literature with assumptions of sequentially consistent program execution and atomicity of high level operations like read, write, and abort. However, in a realistic setting, processors use relaxed memory models to optimize hardware performance. Moreover, the atomicity of operations depends on the underlying hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We describe RML, a simple language for expressing concurrent programs. We develop a semantics of RML parametrized by a relaxed memory model. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm restricted to two threads and two variables, and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the restricted STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order for two threads and two variables. Finally, we extend the verification results for DSTM and TL2 to an arbitrary number of threads and variables by manually proving that the structural properties of STMs are satisfied at the hardware level of atomicity under the considered relaxed memory models.}, author = {Guerraoui, Rachid and Henzinger, Thomas A and Singh, Vasu}, journal = {Formal Methods in System Design}, number = {3}, pages = {297 -- 331}, publisher = {Springer}, title = {{Verification of STM on relaxed memory models}}, doi = {10.1007/s10703-011-0131-3}, volume = {39}, year = {2011}, } @misc{5379, 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 ̃O(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 ̃O(n·m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2) 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 O(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m > n4/3 an earlier bound of O(min(m1.5, m·n2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n2), which is an improvement over earlier bounds for m > n4/3. 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 H}, issn = {2664-1690}, pages = {20}, publisher = {IST Austria}, title = {{An O(n2) time algorithm for alternating Büchi games}}, doi = {10.15479/AT:IST-2011-0009}, year = {2011}, } @misc{5381, abstract = {In two-player finite-state stochastic games of partial obser- vation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distri- bution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or pos- itively (i.e., with positive probability), no matter the strategy of the second player. We classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two- sided with (c) both players having partial observation. On the basis of randomization, (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. Our main results for pure strategies are as follows: (1) For one-sided games with player 2 perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strate- gies are not sufficient, and present an exponential upper bound on mem- ory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algo- rithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 perfect observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and posi- tive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence re- sult exhibit serious flaws in previous results in the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed.}, author = {Chatterjee, Krishnendu and Doyen, Laurent}, issn = {2664-1690}, pages = {43}, publisher = {IST Austria}, title = {{Partial-observation stochastic games: How to win when belief fails}}, doi = {10.15479/AT:IST-2011-0007}, year = {2011}, } @misc{5380, 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 independently 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, respectively. 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 powerful 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}, issn = {2664-1690}, pages = {53}, publisher = {IST Austria}, title = {{Bounded rationality in concurrent parity games}}, doi = {10.15479/AT:IST-2011-0008}, year = {2011}, } @misc{5382, abstract = {We consider two-player stochastic games played on a finite state space for an infinite num- ber of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with ω-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity games with respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition func- tion is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal).}, author = {Chatterjee, Krishnendu}, issn = {2664-1690}, pages = {18}, publisher = {IST Austria}, title = {{Robustness of structurally equivalent concurrent parity games}}, doi = {10.15479/AT:IST-2011-0006}, 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}, } @inproceedings{3356, abstract = {There is recently a significant effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions, aiming for a general and flexible framework for quantitative-oriented specifications. In the heart of quantitative objectives lies the accumulation of values along a computation. It is either the accumulated summation, as with the energy objectives, or the accumulated average, as with the mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point of time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire computation. We study the border of decidability for extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by prefix-accumulation assertions and extending LTL with path-accumulation assertions, result in temporal logics whose model-checking problem is decidable. The extended logics allow to significantly extend the currently known energy and mean-payoff objectives. Moreover, the prefix-accumulation assertions may be refined with "controlled-accumulation", allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that the fragment we point to is, in a sense, the maximal logic whose extension with prefix-accumulation assertions permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, and in particular CTL and LTL, makes the problem undecidable.}, author = {Boker, Udi and Chatterjee, Krishnendu and Henzinger, Thomas A and Kupferman, Orna}, location = {Toronto, Canada}, publisher = {IEEE}, title = {{Temporal specifications with accumulative values}}, doi = {10.1109/LICS.2011.33}, year = {2011}, } @misc{5385, abstract = {There is recently a significant effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions, aiming for a general and flexible framework for quantitative-oriented specifications. In the heart of quantitative objectives lies the accumulation of values along a computation. It is either the accumulated summation, as with the energy objectives, or the accumulated average, as with the mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point of time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire computation. We study the border of decidability for extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by prefix-accumulation assertions and extending LTL with path-accumulation assertions, result in temporal logics whose model-checking problem is decidable. The extended logics allow to significantly extend the currently known energy and mean-payoff objectives. Moreover, the prefix-accumulation assertions may be refined with “controlled-accumulation”, allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that the fragment we point to is, in a sense, the maximal logic whose extension with prefix-accumulation assertions permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, and in particular CTL and LTL, makes the problem undecidable.}, author = {Boker, Udi and Chatterjee, Krishnendu and Henzinger, Thomas A and Kupferman, Orna}, issn = {2664-1690}, pages = {14}, publisher = {IST Austria}, title = {{Temporal specifications with accumulative values}}, doi = {10.15479/AT:IST-2011-0003}, year = {2011}, } @misc{5386, abstract = {We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.}, author = {Chen, Chao and Freedman, Daniel and Lampert, Christoph}, issn = {2664-1690}, pages = {69}, publisher = {IST Austria}, title = {{Enforcing topological constraints in random field image segmentation}}, doi = {10.15479/AT:IST-2011-0002}, year = {2011}, } @misc{5383, abstract = {We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures.}, author = {Wies, Thomas and Muñiz, Marco and Kuncak, Viktor}, issn = {2664-1690}, pages = {25}, publisher = {IST Austria}, title = {{On an efficient decision procedure for imperative tree data structures}}, doi = {10.15479/AT:IST-2011-0005}, 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{3336, abstract = {We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.}, author = {Chen, Chao and Freedman, Daniel and Lampert, Christoph}, booktitle = {CVPR: Computer Vision and Pattern Recognition}, isbn = {978-1-4577-0394-2}, location = {Colorado Springs, CO, United States}, pages = {2089 -- 2096}, publisher = {IEEE}, title = {{Enforcing topological constraints in random field image segmentation}}, doi = {10.1109/CVPR.2011.5995503}, year = {2011}, } @inproceedings{3323, abstract = {We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures.}, author = {Wies, Thomas and Muñiz, Marco and Kuncak, Viktor}, location = {Wrocław, Poland}, pages = {476 -- 491}, publisher = {Springer}, title = {{An efficient decision procedure for imperative tree data structures}}, doi = {10.1007/978-3-642-22438-6_36}, volume = {6803}, year = {2011}, } @inproceedings{3366, abstract = {We present an algorithmic method for the quantitative, performance-aware synthesis of concurrent programs. The input consists of a nondeterministic partial program and of a parametric performance model. The nondeterminism allows the programmer to omit which (if any) synchronization construct is used at a particular program location. The performance model, specified as a weighted automaton, can capture system architectures by assigning different costs to actions such as locking, context switching, and memory and cache accesses. The quantitative synthesis problem is to automatically resolve the nondeterminism of the partial program so that both correctness is guaranteed and performance is optimal. As is standard for shared memory concurrency, correctness is formalized "specification free", in particular as race freedom or deadlock freedom. For worst-case (average-case) performance, we show that the problem can be reduced to 2-player graph games (with probabilistic transitions) with quantitative objectives. While we show, using game-theoretic methods, that the synthesis problem is Nexp-complete, we present an algorithmic method and an implementation that works efficiently for concurrent programs and performance models of practical interest. We have implemented a prototype tool and used it to synthesize finite-state concurrent programs that exhibit different programming patterns, for several performance models representing different architectures. }, author = {Cerny, Pavol and Chatterjee, Krishnendu and Henzinger, Thomas A and Radhakrishna, Arjun and Singh, Rohit}, editor = {Gopalakrishnan, Ganesh and Qadeer, Shaz}, location = {Snowbird, USA}, pages = {243 -- 259}, publisher = {Springer}, title = {{Quantitative synthesis for concurrent programs}}, doi = {10.1007/978-3-642-22110-1_20}, volume = {6806}, 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}, } @misc{5387, 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}, issn = {2664-1690}, pages = {20}, publisher = {IST Austria}, title = {{Energy and mean-payoff parity Markov decision processes}}, doi = {10.15479/AT:IST-2011-0001}, year = {2011}, } @article{580, author = {Onur Hosten}, journal = {Nature}, number = {7350}, pages = {170 -- 171}, publisher = {Nature Publishing Group}, title = {{Quantum physics: How to catch a wave}}, doi = {10.1038/474170a}, volume = {474}, year = {2011}, } @inproceedings{585, abstract = {We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements. }, author = {Schmid, David and Hazrat, Shiraz and Rangarajan, Radhika and Onur Hosten and Quint, Stephan and Kwiat, Paul G}, publisher = {OSA}, title = {{Methods towards achieving precise birefringent focusing}}, doi = {10.1364/CLEO_AT.2011.JThB130}, year = {2011}, } @article{586, abstract = {We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a high-finesse optical cavity. We observe robust continuous wave lasing in the atypical regime where single atoms can considerably affect the cavity field. Consequently, we discover unusual lasing threshold behavior in the system causing jumps in lasing power, and propose a model to explain the effect. We also measure the intermode laser linewidth, and observe values as low as 80Hz. The tunable gain properties of this laser suggest multiple directions for future research.}, author = {Vrijsen, Geert and Onur Hosten and Lee, Jongmin and Bernon, Simon and Kasevich, Mark A}, journal = {Physical Review Letters}, number = {6}, publisher = {American Physical Society}, title = {{Raman lasing with a cold atom gain medium in a high-finesse optical cavity}}, doi = {10.1103/PhysRevLett.107.063904}, volume = {107}, year = {2011}, } @article{597, abstract = {The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.}, author = {Bernecky, Carrie A and Grob, Patricia and Ebmeier, Christopher and Nogales, Eva and Taatjes, Dylan}, journal = {PLoS Biology}, number = {3}, publisher = {Public Library of Science}, title = {{Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly}}, doi = {10.1371/journal.pbio.1000603}, volume = {9}, year = {2011}, } @article{6140, abstract = {Genome sequence comparisons have highlighted many novel gene families that are conserved across animal phyla but whose biological function is unknown. Here, we functionally characterize a member of one such family, the macoilins. Macoilins are characterized by several highly conserved predicted transmembrane domains towards the N-terminus and by coiled-coil regions C-terminally. They are found throughout Eumetazoa but not in other organisms. Mutants for the single Caenorhabditis elegans macoilin, maco-1, exhibit a constellation of behavioral phenotypes, including defects in aggregation, O2 responses, and swimming. MACO-1 protein is expressed broadly and specifically in the nervous system and localizes to the rough endoplasmic reticulum; it is excluded from dendrites and axons. Apart from subtle synapse defects, nervous system development appears wild-type in maco-1 mutants. However, maco-1 animals are resistant to the cholinesterase inhibitor aldicarb and sensitive to levamisole, suggesting pre-synaptic defects. Using in vivo imaging, we show that macoilin is required to evoke Ca2+ transients, at least in some neurons: in maco-1 mutants the O2-sensing neuron PQR is unable to generate a Ca2+ response to a rise in O2. By genetically disrupting neurotransmission, we show that pre-synaptic input is not necessary for PQR to respond to O2, indicating that the response is mediated by cell-intrinsic sensory transduction and amplification. Disrupting the sodium leak channels NCA-1/NCA-2, or the N-,P/Q,R-type voltage-gated Ca2+ channels, also fails to disrupt Ca2+ responses in the PQR cell body to O2 stimuli. By contrast, mutations in egl-19, which encodes the only Caenorhabditis elegans L-type voltage-gated Ca2+ channel α1 subunit, recapitulate the Ca2+ response defect we see in maco-1 mutants, although we do not see defects in localization of EGL-19. Together, our data suggest that macoilin acts in the ER to regulate assembly or traffic of ion channels or ion channel regulators.}, author = {Arellano-Carbajal, Fausto and Briseño-Roa, Luis and Couto, Africa and Cheung, Benny H. H. and Labouesse, Michel and de Bono, Mario}, issn = {1553-7404}, journal = {PLoS Genetics}, number = {3}, publisher = {Public Library of Science}, title = {{Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability}}, doi = {10.1371/journal.pgen.1001341}, volume = {7}, year = {2011}, } @article{6137, abstract = {Variation in food quality and abundance requires animals to decide whether to stay on a poor food patch or leave in search of better food. An important question in behavioral ecology asks when is it optimal for an animal to leave a food patch it is depleting. Although optimal foraging is central to evolutionary success, the neural and molecular mechanisms underlying it are poorly understood. Here we investigate the neuronal basis for adaptive food-leaving behavior in response to resource depletion in Caenorhabditis elegans, and identify several of the signaling pathways involved. The ASE neurons, previously implicated in salt chemoattraction, promote food-leaving behavior via a cGMP pathway as food becomes limited. High ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX. Ectopic activation of these neurons using channelrhodopsin is sufficient to induce high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH neurons, and in the RMG interneuron to repress food-leaving. Finally, we show that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are necessary for adaptive food-leaving behavior. We suggest that animals integrate information about their nutritional state with ambient oxygen and gustatory stimuli to formulate optimal foraging strategies.}, author = {Milward, K. and Busch, K. E. and Murphy, R. J. and de Bono, Mario and Olofsson, B.}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {51}, pages = {20672--20677}, publisher = {National Academy of Sciences}, title = {{Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans}}, doi = {10.1073/pnas.1106134109}, volume = {108}, year = {2011}, } @article{6138, author = {Bretscher, Andrew Jonathan and Kodama-Namba, Eiji and Busch, Karl Emanuel and Murphy, Robin Joseph and Soltesz, Zoltan and Laurent, Patrick and de Bono, Mario}, issn = {0896-6273}, journal = {Neuron}, number = {6}, pages = {1099--1113}, publisher = {Elsevier BV}, title = {{Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior}}, doi = {10.1016/j.neuron.2011.02.023}, volume = {69}, year = {2011}, } @article{6298, abstract = {Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyalu-ronan (HA)-binding protein that plays important roles ininflammation and ovulation. TSG-6-mediated cross-linking ofHA has been proposed as a functional mechanism (e.g.for regu-lating leukocyte adhesion), but direct evidence for cross-linkingis lacking, and we know very little about its impact on HA ultra-structure. Here we used films of polymeric and oligomeric HAchains, end-grafted to a solid support, and a combination ofsurface-sensitive biophysical techniques to quantify the bindingof TSG-6 into HA films and to correlate binding to morpholog-ical changes. We find that full-length TSG-6 binds with pro-nounced positive cooperativity and demonstrate that it cancross-link HA at physiologically relevant concentrations. Ourdata indicate that cooperative binding of full-length TSG-6arises from HA-induced protein oligomerization and that theTSG-6 oligomers act as cross-linkers. In contrast, the HA-bind-ing domain of TSG-6 (the Link module) alone binds withoutpositive cooperativity and weaker than the full-length protein.Both the Link module and full-length TSG-6 condensed andrigidified HA films, and the degree of condensation scaled withthe affinity between the TSG-6 constructs and HA. We proposethat condensation is the result of protein-mediated HA cross-linking. Our findings firmly establish that TSG-6 is a potent HAcross-linking agent and might hence have important implica-tions for the mechanistic understanding of the biological func-tion of TSG-6 (e.g.in inflammation).}, author = {Baranova, Natalia and Nilebäck, Erik and Haller, F. Michael and Briggs, David C. and Svedhem, Sofia and Day, Anthony J. and Richter, Ralf P.}, issn = {0021-9258}, journal = {Journal of Biological Chemistry}, number = {29}, pages = {25675--25686}, publisher = {American Society for Biochemistry & Molecular Biology}, title = {{The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers}}, doi = {10.1074/jbc.m111.247395}, volume = {286}, year = {2011}, } @article{6496, abstract = {We report the switching behavior of the full bacterial flagellum system that includes the filament and the motor in wild-type Escherichia coli cells. In sorting the motor behavior by the clockwise bias, we find that the distributions of the clockwise (CW) and counterclockwise (CCW) intervals are either exponential or nonexponential with long tails. At low bias, CW intervals are exponentially distributed and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and CCW intervals are mainly exponentially distributed. A simple model suggests that these two distinct switching behaviors are governed by the presence of signaling noise within the chemotaxis network. Low noise yields exponentially distributed intervals, whereas large noise yields nonexponential behavior with long tails. These drastically different motor statistics may play a role in optimizing bacterial behavior for a wide range of environmental conditions.}, author = {Park, Heungwon and Oikonomou, Panos and Guet, Calin C and Cluzel, Philippe}, issn = {0006-3495}, journal = {Biophysical Journal}, number = {10}, pages = {2336--2340}, publisher = {Elsevier}, title = {{Noise underlies switching behavior of the bacterial flagellum}}, doi = {10.1016/j.bpj.2011.09.040}, volume = {101}, year = {2011}, } @article{6749, abstract = {This article refers to algorithms based on finite difference schemes for computing mean and affine curvature evolutions of digital images, introduced by Alvarez and Morel [L. Alvarez, J.M. Morel, “Formalization and computational aspects of image analysis”, Acta Numerica, pp. 159, 1994]. We discuss consistency, stability and convergence. Our analysis focuses on some possible choices of the parameters, choices that generate multiple variants in the implementations. Meaningful visual examples on how the algorithms actually work are provided.}, author = {Mondelli, Marco and Ciomaga, Adina}, issn = {2105-1232}, journal = {Image Processing On Line}, pages = {127--177}, publisher = {IPOL Image Processing On Line}, title = {{Finite difference schemes for MCM and AMSS}}, doi = {10.5201/ipol.2011.cm_fds}, volume = {1}, year = {2011}, } @inproceedings{6767, abstract = {In the present paper we give a thorough analysis of two finite difference schemes for the Mean Curvature Motion and its affine variant, the Affine Morphological Scale Space, schemes introduced in the Image Processing framework. This analysis brings in a series of parameters that allow us to compute an accurate discrete evolution of curvature motions. The choice of these parameters is based on intrinsic geometric properties of the evolution equations for linear, radial and elliptical functions. In the last part we present several examples, underlining the main advantages of the algorithms (the removal of pixelization effects and JPEG artifacts) as well as their major drawbacks (absence of contrast invariance and grid dependence). A detailed explanatory report, the ANSI C implementations and an on-line demo can be found at http://www.ipol.im/.}, author = {Mondelli, Marco and Ciomaga, Adina}, booktitle = {Proceedings of the International Student Conference on Pure and Applied Mathematics}, isbn = {978-973-703-602-5}, location = {Iasi, Romania}, pages = {137--156}, publisher = {Editura Universitãtii „Alexandru Ioan Cuza” Iasi}, title = {{On finite difference schemes for curvature motions}}, doi = {10.13140/2.1.1862.4646}, year = {2011}, } @article{7076, abstract = {Iron is a ubiquitous impurity in metamict (radiation-damaged and partially amorphized) materials such as titanite (CaSiTiO5). Using 57Fe Mössbauer spectroscopy we find that iron in metamict titanite is partitioned between amorphous and crystalline regions based on valence. Trivalent iron exists in the crystalline titanite matrix whereas divalent iron exists almost exclusively in radiation-amorphized regions. We find that the relative abundances of the oxidation states correlate with the volume fraction of amorphous and crystalline regions. Our data also show that oxidation of iron proceeds along with the recrystallization of the amorphized regions. Recrystallization is confirmed to occur over the range 700 °C < T < 925 °C, and no further structural changes are observed at higher temperatures. It is surprising that our Mössbauer measurements show divalent iron to be surrounded by titanite with a high degree of short-range structural order in the amorphized regions. This observation is fundamentally different from other metamict materials such as zircon (ZrSiO4), where amorphized regions show no short-range order.}, author = {Salje, E K H and Safarik, D J and Taylor, R D and Pasternak, M P and Modic, Kimberly A and Groat, L A and Lashley, J C}, issn = {0953-8984}, journal = {Journal of Physics: Condensed Matter}, number = {10}, publisher = {IOP Publishing}, title = {{Determination of iron sites and the amount of amorphization in radiation-damaged titanite (CaSiTiO5)}}, doi = {10.1088/0953-8984/23/10/105402}, volume = {23}, year = {2011}, } @article{7077, abstract = {Pb, Te, Ag and Se, when reacted in a 1:1:x:1 (x = 1.9, 2.0, 2.01) molar ratio, form a two phase composite which consists of a phase which crystallizes in the fcc cubic PbSe structure and a phase that crystallizes in the Ag2Te structure. In this article, we demonstrate that by varying the Ag concentration, we can manipulate which variant of the Ag2Te structure stabilizes at room temperature (monoclinic α-Ag2Te or cubic β-Ag1.9Te) and can consequently manipulate the electrical and thermal transport behavior of the composite and hence the thermoelectric performance. Additionally, we show that Cu-doping results in an overall improvement in thermoelectric performance. Our results suggest that formation of composites is a viable path for achieving a phonon-glass-electron-crystal (PGEC) alloy.}, author = {Capps, J. and Ma, B. and Drye, T. and Nucklos, C. and Lindsey, S. and Rhodes, D. and Zhang, Q. and Modic, Kimberly A and Cawthorne, S. and Drymiotis, F.}, issn = {0925-8388}, journal = {Journal of Alloys and Compounds}, number = {5}, pages = {1544--1549}, publisher = {Elsevier}, title = {{The effect of Ag concentration on the structural, electrical and thermal transport behavior of Pb:Te:Ag:Se mixtures and improvement of thermoelectric performance via Cu doping}}, doi = {10.1016/j.jallcom.2010.10.187}, volume = {509}, year = {2011}, } @article{7313, abstract = {Li-ion batteries have transformed portable electronics and will play a key role in the electrification of transport. However, the highest energy storage possible for Li-ion batteries is insufficient for the long-term needs of society, for example, extended-range electric vehicles. To go beyond the horizon of Li-ion batteries is a formidable challenge; there are few options. Here we consider two: Li–air (O2) and Li–S. The energy that can be stored in Li–air (based on aqueous or non-aqueous electrolytes) and Li–S cells is compared with Li-ion; the operation of the cells is discussed, as are the significant hurdles that will have to be overcome if such batteries are to succeed. Fundamental scientific advances in understanding the reactions occurring in the cells as well as new materials are key to overcoming these obstacles. The potential benefits of Li–air and Li–S justify the continued research effort that will be needed.}, author = {Bruce, Peter G. and Freunberger, Stefan Alexander and Hardwick, Laurence J. and Tarascon, Jean-Marie}, issn = {1476-1122}, journal = {Nature Materials}, number = {1}, pages = {19--29}, publisher = {Springer Nature}, title = {{Li–O2 and Li–S batteries with high energy storage}}, doi = {10.1038/nmat3191}, volume = {11}, year = {2011}, } @article{7314, abstract = {The electrolyte is one of the greatest challenges facing the development of the non‐aqueous Li–O2 battery. Although ether‐based electrolytes do from Li2O2 on the first discharge, it is shown by various techniques that they also decompose and that decomposition increases while Li2O2 decreases on cycling (see picture). Thus, these electrolytes are not suitable. }, author = {Freunberger, Stefan Alexander and Chen, Yuhui and Drewett, Nicholas E. and Hardwick, Laurence J. and Bardé, Fanny and Bruce, Peter G.}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, number = {37}, pages = {8609--8613}, publisher = {Wiley}, title = {{The Lithium-Oxygen battery with ether-based electrolytes}}, doi = {10.1002/anie.201102357}, volume = {50}, year = {2011}, } @article{7317, abstract = {Lithium-metal oxides with a high formal Li2O content, such as Li5FeO4 (5Li2O•Fe2O3) and a Li2MnO3•LiFeO2 composite ({Li2O•MnO2}•{Li2O•Fe2O3}) have been explored as electrocatalysts for primary and rechargeable Li-O2 cells. Activation occurs predominantly by Li2O removal, either electrochemically or chemically by acid-treatment. Superior electrochemical behavior is obtained if activation occurs by acid-treatment; Li2MnO3•LiFeO2 catalysts provide 2516 mAh/g (carbon) corresponding to 931 mAh/g (electrocatalyst + carbon) during the initial discharge. The reaction is reasonably reversible during the early cycles. The approach has implications for designing electrocatalysts that participate through electrochemical Li2O extraction/reformation reactions, offering exceptionally high capacities.}, author = {Trahey, L. and Johnson, C. S. and Vaughey, J. T. and Kang, S.-H. and Hardwick, L. J. and Freunberger, Stefan Alexander and Bruce, P. G. and Thackeray, M. M.}, issn = {1099-0062}, journal = {Electrochemical and Solid-State Letters}, number = {5}, publisher = {The Electrochemical Society}, title = {{Activated Lithium-Metal-Oxides as catalytic electrodes for Li–O2 cells}}, doi = {10.1149/1.3555366}, volume = {14}, year = {2011}, } @article{7316, abstract = {The nonaqueous rechargeable lithium–O2 battery containing an alkyl carbonate electrolyte discharges by formation of C3H6(OCO2Li)2, Li2CO3, HCO2Li, CH3CO2Li, CO2, and H2O at the cathode, due to electrolyte decomposition. Charging involves oxidation of C3H6(OCO2Li)2, Li2CO3, HCO2Li, CH3CO2Li accompanied by CO2 and H2O evolution. Mechanisms are proposed for the reactions on discharge and charge. The different pathways for discharge and charge are consistent with the widely observed voltage gap in Li–O2 cells. Oxidation of C3H6(OCO2Li)2 involves terminal carbonate groups leaving behind the OC3H6O moiety that reacts to form a thick gel on the Li anode. Li2CO3, HCO2Li, CH3CO2Li, and C3H6(OCO2Li)2 accumulate in the cathode on cycling correlating with capacity fading and cell failure. The latter is compounded by continuous consumption of the electrolyte on each discharge.}, author = {Freunberger, Stefan Alexander and Chen, Yuhui and Peng, Zhangquan and Griffin, John M. and Hardwick, Laurence J. and Bardé, Fanny and Novák, Petr and Bruce, Peter G.}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {20}, pages = {8040--8047}, publisher = {ACS}, title = {{Reactions in the rechargeable Lithium–O2 battery with alkyl carbonate electrolytes}}, doi = {10.1021/ja2021747}, volume = {133}, year = {2011}, } @article{7315, abstract = {Spectroscopic data (see picture) provide direct evidence that in non‐aqueous Li+ electrolyte, O2 is reduced to O2−, which then forms LiO2 on the electrode surface which disproportionates to Li2O2. On charging, Li2O2 decomposes directly, in a one‐step reaction to evolve O2 and does not pass through LiO2 as an intermediate. }, author = {Peng, Zhangquan and Freunberger, Stefan Alexander and Hardwick, Laurence J. and Chen, Yuhui and Giordani, Vincent and Bardé, Fanny and Novák, Petr and Graham, Duncan and Tarascon, Jean-Marie and Bruce, Peter G.}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, number = {28}, pages = {6351--6355}, publisher = {Wiley}, title = {{Oxygen reactions in a non-aqueous Li+ electrolyte}}, doi = {10.1002/anie.201100879}, volume = {50}, year = {2011}, } @inproceedings{757, abstract = {Synchronous distributed algorithms are easier to design and prove correct than algorithms that tolerate asynchrony. Yet, in the real world, networks experience asynchrony and other timing anomalies. In this paper, we address the question of how to efficiently transform an algorithm that relies on synchronization into an algorithm that tolerates asynchronous executions. We introduce a transformation technique from synchronous algorithms to indulgent algorithms [1], which induces only a constant overhead in terms of time complexity in well-behaved executions. Our technique is based on a new abstraction we call an asynchrony detector, which the participating processes implement collectively. The resulting transformation works for a large class of colorless tasks, including consensus and set agreement. Interestingly, we also show that our technique is relevant for colored tasks, by applying it to the renaming problem, to obtain the first indulgent renaming algorithm.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Travers, Corentin}, pages = {41 -- 52}, publisher = {Springer}, title = {{Generating fast indulgent algorithms}}, doi = {10.1007/978-3-642-17679-1_4}, volume = {6522 LNCS}, year = {2011}, } @inproceedings{759, abstract = {We study the complexity of renaming, a fundamental problem in distributed computing in which a set of processes need to pick distinct names from a given namespace. We prove an individual lower bound of Ω(k) process steps for deterministic renaming into any namespace of size sub-exponential in k, where k is the number of participants. This bound is tight: it draws an exponential separation between deterministic and randomized solutions, and implies new tight bounds for deterministic fetch-and-increment registers, queues and stacks. The proof of the bound is interesting in its own right, for it relies on the first reduction from renaming to another fundamental problem in distributed computing: mutual exclusion. We complement our individual bound with a global lower bound of Ω(k log (k/c)) on the total step complexity of renaming into a namespace of size ck, for any c ≥ 1. This applies to randomized algorithms against a strong adversary, and helps derive new global lower bounds for randomized approximate counter and fetch-and-increment implementations, all tight within logarithmic factors.}, author = {Alistarh, Dan-Adrian and Aspnes, James and Gilbert, Seth and Guerraoui, Rachid}, pages = {718 -- 727}, publisher = {IEEE}, title = {{The complexity of renaming}}, doi = {10.1109/FOCS.2011.66}, year = {2011}, } @inproceedings{761, abstract = {We give two new randomized algorithms for strong renaming, both of which work against an adaptive adversary in asynchronous shared memory. The first uses repeated sampling over a sequence of arrays of decreasing size to assign unique names to each of n processes with step complexity O(log3 n). The second transforms any sorting network into a strong adaptive renaming protocol, with an expected cost equal to the depth of the sorting network. Using an AKS sorting network, this gives a strong adaptive renaming algorithm with step complexity O(log k), where k is the contention in the current execution. We show this to be optimal based on a classic lower bound of Jayanti. We also show that any such strong renaming protocol can be used to build a monotone-consistent counter with logarithmic step complexity (at the cost of adding a max register) or a linearizable fetch-and-increment register (at the cost of increasing the step complexity by a logarithmic factor).}, author = {Alistarh, Dan-Adrian and Aspnes, James and Censor Hillel, Keren and Gilbert, Seth and Zadimoghaddam, Morteza}, pages = {239 -- 248}, publisher = {ACM}, title = {{Optimal-time adaptive strong renaming, with applications to counting}}, doi = {10.1145/1993806.1993850}, year = {2011}, } @inproceedings{760, abstract = {A randomized implementation is given of a test-and-set register with O(log log n) individual step complexity and O(n) total step complexity against an oblivious adversary. The implementation is linearizable and multi-shot, and shows an exponential complexity improvement over previous solutions designed to work against a strong adversary.}, author = {Alistarh, Dan-Adrian and Aspnes, James}, pages = {97 -- 109}, publisher = {Springer}, title = {{Sub-logarithmic test-and-set against a weak adversary}}, doi = {10.1007/978-3-642-24100-0_7}, volume = {6950 LNCS}, year = {2011}, } @article{7750, author = {Robinson, Matthew Richard}, issn = {1465-7279}, journal = {Behavioral Ecology}, number = {6}, pages = {1143--1144}, publisher = {Oxford University Press}, title = {{Understanding intrasexual competition and sexual selection requires an evolutionary ecology framework}}, doi = {10.1093/beheco/arr110}, volume = {22}, year = {2011}, } @article{8025, abstract = {Chandelier (axoaxonic) cells (ChCs) are a distinct group of GABAergic interneurons that innervate the axon initial segments of pyramidal cells. However, their circuit role and the function of their clearly defined anatomical specificity remain unclear. Recent work has demonstrated that chandelier cells can produce depolarizing GABAergic PSPs, occasionally driving postsynaptic targets to spike. On the other hand, other work suggests that ChCs are hyperpolarizing and may have an inhibitory role. These disparate functional effects may reflect heterogeneity among ChCs. Here, using brain slices from transgenic mouse strains, we first demonstrate that, across different neocortical areas and genetic backgrounds, upper Layer 2/3 ChCs belong to a single electrophysiologically and morphologically defined population, extensively sampling Layer 1 inputs with asymmetric dendrites. Consistent with being a single cell type, we find electrical coupling between ChCs. We then investigate the effect of chandelier cell activation on pyramidal neuron spiking in several conditions, ranging from the resting membrane potential to stimuli designed to approximate in vivo membrane potential dynamics. We find that under quiescent conditions, chandelier cells are capable of both promoting and inhibiting spike generation, depending on the postsynaptic membrane potential. However, during in vivo-like membrane potential fluctuations, the dominant postsynaptic effect was a strong inhibition. Thus, neocortical chandelier cells, even from within a homogeneous population, appear to play a dual role in the circuit, helping to activate quiescent pyramidal neurons, while at the same time inhibiting active ones.}, author = {Woodruff, A. R. and McGarry, L. M. and Vogels, Tim P and Inan, M. and Anderson, S. A. and Yuste, R.}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {49}, pages = {17872--17886}, publisher = {Society for Neuroscience}, title = {{State-dependent function of neocortical chandelier cells}}, doi = {10.1523/jneurosci.3894-11.2011}, volume = {31}, year = {2011}, } @article{8074, abstract = {Cortical neurons receive balanced excitatory and inhibitory synaptic currents. Such a balance could be established and maintained in an experience-dependent manner by synaptic plasticity at inhibitory synapses. We show that this mechanism provides an explanation for the sparse firing patterns observed in response to natural stimuli and fits well with a recently observed interaction of excitatory and inhibitory receptive field plasticity. The introduction of inhibitory plasticity in suitable recurrent networks provides a homeostatic mechanism that leads to asynchronous irregular network states. Further, it can accommodate synaptic memories with activity patterns that become indiscernible from the background state but can be reactivated by external stimuli. Our results suggest an essential role of inhibitory plasticity in the formation and maintenance of functional cortical circuitry.}, author = {Vogels, Tim P and Sprekeler, H. and Zenke, F. and Clopath, C. and Gerstner, W.}, issn = {0036-8075}, journal = {Science}, number = {6062}, pages = {1569--1573}, publisher = {American Association for the Advancement of Science}, title = {{Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks}}, doi = {10.1126/science.1211095}, volume = {334}, year = {2011}, } @article{8469, abstract = {The accurate experimental determination of dipolar-coupling constants for one-bond heteronuclear dipolar couplings in solids is a key for the quantification of the amplitudes of motional processes. Averaging of the dipolar coupling reports on motions on time scales up to the inverse of the coupling constant, in our case tens of microseconds. Combining dipolar-coupling derived order parameters that characterize the amplitudes of the motion with relaxation data leads to a more precise characterization of the dynamical parameters and helps to disentangle the amplitudes and the time scales of the motional processes, which impact relaxation rates in a highly correlated way. Here. we describe and characterize an improved experimental protocol – based on REDOR – to measure these couplings in perdeuterated proteins with a reduced sensitivity to experimental missettings. Because such effects are presently the dominant source of systematic errors in experimental dipolar-coupling measurements, these compensated experiments should help to significantly improve the precision of such data. A detailed comparison with other commonly used pulse sequences (T-MREV, phase-inverted CP,R18 5/2, and R18 7/1) is provided.}, author = {Schanda, Paul and Meier, Beat H. and Ernst, Matthias}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics}, number = {2}, pages = {246--259}, publisher = {Elsevier}, title = {{Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR}}, doi = {10.1016/j.jmr.2011.03.015}, volume = {210}, year = {2011}, } @article{8470, abstract = {Adding a new dimension: 4D or 3D proton‐detected spectra of perdeuterated protein samples with 1H labelled amides and methyl groups permit collecting unambiguous distance restraints with high sensitivity and determining protein structure by solid‐state NMR (see picture).}, author = {Huber, Matthias and Hiller, Sebastian and Schanda, Paul and Ernst, Matthias and Böckmann, Anja and Verel, René and Meier, Beat H.}, issn = {1439-4235}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {5}, pages = {915--918}, publisher = {Wiley}, title = {{A proton-detected 4D solid-state NMR experiment for protein structure determination}}, doi = {10.1002/cphc.201100062}, volume = {12}, year = {2011}, } @article{8464, abstract = {Nonsymmetric motion: Solid‐state NMR measurements of dipolar coupling tensors provide insight into protein dynamics. The hitherto ignored asymmetry of the dipolar coupling tensor contains valuable information about motional asymmetry, which was used in the first direct site‐resolved measurement of such tensors. Important motions such as rotamer jumps can now be directly detected in the solid state.}, author = {Schanda, Paul and Huber, Matthias and Boisbouvier, Jérôme and Meier, Beat H. and Ernst, Matthias}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, number = {46}, pages = {11005--11009}, publisher = {Wiley}, title = {{Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion}}, doi = {10.1002/anie.201103944}, volume = {50}, year = {2011}, } @article{8468, author = {Lalli, Daniela and Schanda, Paul and Chowdhury, Anup and Retel, Joren and Hiller, Matthias and Higman, Victoria A. and Handel, Lieselotte and Agarwal, Vipin and Reif, Bernd and van Rossum, Barth and Akbey, Ümit and Oschkinat, Hartmut}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, number = {4}, pages = {477--485}, publisher = {Springer Nature}, title = {{Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins}}, doi = {10.1007/s10858-011-9578-1}, volume = {51}, year = {2011}, } @article{890, abstract = {Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered.}, author = {Koblik, Evgeniy A and Red'Kin, Yaroslav A and Meer, Margarita S and Derelle, Romain and Golenkina, Sofia A and Fyodor Kondrashov and Arkhipov, Vladimir Y}, journal = {PLoS One}, number = {4}, publisher = {Public Library of Science}, title = {{Acrocephalus orinus: A case of Mistaken identity}}, doi = {10.1371/journal.pone.0017716}, volume = {6}, year = {2011}, } @article{90, abstract = {A popular method for generating micron-sized aerosols is to submerge ultrasonic (ω ∼ MHz) piezoelectric oscillators in a water bath. The submerged oscillator atomizes the fluid, creating droplets with radii proportional to the wavelength of the standing wave at the fluid surface. Classical theory for the Faraday instability predicts a parametric instability driving a capillary wave at the subharmonic (ω / 2) frequency. For many applications it is desirable to reduce the size of the droplets; however, using higher frequency oscillators becomes impractical beyond a few MHz. Observations are presented that demonstrate that smaller droplets may also be created by increasing the driving amplitude of the oscillator, and that this effect becomes more pronounced for large driving frequencies. It is shown that these observations are consistent with a transition from droplets associated with subharmonic (ω/2) capillary waves to harmonic (ω) capillary waves induced by larger driving frequencies and amplitudes, as predicted by a stability analysis of the capillary waves.}, author = {Higginbotham, Andrew P and Guillen, A and Jones, Nick and Donnelly, Tom and Bernoff, Andrew}, journal = {Journal of the Acoustical Society of America}, number = {5}, pages = {2694 -- 2699}, publisher = {Acoustical Society of America}, title = {{Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid}}, doi = {10.1121/1.3643816}, volume = {130}, year = {2011}, } @article{9144, abstract = {A cloud-resolving model is used to investigate the effect of warming on high percentiles of precipitation (precipitation extremes) in the idealized setting of radiative-convective equilibrium. While this idealized setting does not allow for several factors that influence precipitation in the tropics, it does allow for an evaluation of the response of precipitation extremes to warming in simulations with resolved rather than parameterized convection. The methodology developed should also be applicable to less idealized simulations. Modeled precipitation extremes are found to increase in magnitude in response to an increase in sea surface temperature. A dry static energy budget is used to relate the changes in precipitation extremes to changes in atmospheric temperature, vertical velocity, and precipitation efficiency. To first order, the changes in precipitation extremes are captured by changes in the mean temperature structure of the atmosphere. Changes in vertical velocities play a secondary role and tend to weaken the strength of precipitation extremes, despite an intensification of updraft velocities in the upper troposphere. The influence of changes in condensate transports on precipitation extremes is quantified in terms of a precipitation efficiency; it does not change greatly with warming. Tropical precipitation extremes have previously been found to increase at a greater fractional rate than the amount of atmospheric water vapor in observations of present-day variability and in some climate model simulations with parameterized convection. But the fractional increases in precipitation extremes in the cloud-resolving simulations are comparable in magnitude to those in surface water vapor concentrations (owing to a partial cancellation between dynamical and thermodynamical changes), and are substantially less than the fractional increases in column water vapor.}, author = {Muller, Caroline J and O’Gorman, Paul A. and Back, Larissa E.}, issn = {1520-0442}, journal = {Journal of Climate}, keywords = {Atmospheric Science}, number = {11}, pages = {2784--2800}, publisher = {American Meteorological Society}, title = {{Intensification of precipitation extremes with warming in a cloud-resolving model}}, doi = {10.1175/2011jcli3876.1}, volume = {24}, year = {2011}, } @article{9143, abstract = {Understanding and predicting the response of the hydrological cycle to climate change is a major challenge with important societal implications. Much progress has been made in understanding the response of global average precipitation by considering the energy balances of the atmosphere and the surface1,2,3,4,5,6. This energetic perspective reveals that changes in temperature, greenhouse gases, aerosols, solar forcing and cloud feedbacks can all affect the global average rate of precipitation5,7,8,9,10,11. Local precipitation changes have conventionally been analysed using the water vapour budget, but here we show that the energetic approach can be extended to local changes in precipitation by including changes in horizontal energy transport. In simulations of twenty-first century climate change, this energy transport accounts for much of the spatial variability in precipitation change. We show that changes in radiative and surface sensible heat fluxes are a guide to the local precipitation response over land and at large scales, but not at small scales over the ocean, where cloud and water vapour radiative feedbacks dampen the response. The energetic approach described here helps bridge the gap between our understanding of global and regional precipitation changes. It could be applied to better understand the response of regional precipitation to different radiative forcings, including geo-engineering schemes, as well as to understand the differences between the fast and slow responses of regional precipitation to such forcings.}, author = {Muller, Caroline J and O’Gorman, P. A.}, issn = {1758-678X}, journal = {Nature Climate Change}, number = {5}, pages = {266--271}, publisher = {Springer Nature}, title = {{An energetic perspective on the regional response of precipitation to climate change}}, doi = {10.1038/nclimate1169}, volume = {1}, year = {2011}, } @article{923, abstract = {The conserved role of Notch signaling in controlling intestinal cell fate specification and homeostasis has been extensively studied. Nevertheless, the precise identity of the cells in which Notch signaling is active and the role of different Notch receptor paralogues in the intestine remain ambiguous, due to the lack of reliable tools to investigate Notch expression and function in vivo. We generated a new series of transgenic mice that allowed us, by lineage analysis, to formally prove that Notch1 and Notch2 are specifically expressed in crypt stem cells. In addition, a novel Notch reporter mouse, Hes1-EmGFP SAT, demonstrated exclusive Notch activity in crypt stem cells and absorptive progenitors. This roster of knock-in and reporter mice represents a valuable resource to functionally explore the Notch pathway in vivo in virtually all tissues.}, author = {Fré, Silvia and Hannezo, Edouard B and Šale, Sanja and Huyghe, Mathilde and Lafkas, Daniel and Kissel, Holger and Louvi, Angeliki and Greve, Jeffrey and Louvard, Daniel and Artavanis Tsakonas, Spyros}, journal = {PLoS One}, number = {10}, publisher = {Public Library of Science}, title = {{Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice}}, doi = {10.1371/journal.pone.0025785}, volume = {6}, year = {2011}, } @article{9483, abstract = {Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development.}, author = {Hsieh, Tzung-Fu and Shin, Juhyun and Uzawa, Rie and Silva, Pedro and Cohen, Stephanie and Bauer, Matthew J. and Hashimoto, Meryl and Kirkbride, Ryan C. and Harada, John J. and Zilberman, Daniel and Fischer, Robert L.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {5}, pages = {1755--1762}, publisher = {National Academy of Sciences}, title = {{Regulation of imprinted gene expression in Arabidopsis endosperm}}, doi = {10.1073/pnas.1019273108}, volume = {108}, year = {2011}, } @article{967, abstract = {Motivated by recent experiments on the material Ba3NiSb 2O9, we consider a spin-one quantum antiferromagnet on a triangular lattice with the Heisenberg bilinear and biquadratic exchange interactions and a single-ion anisotropy. Using a fermionic "triplon" representation for spins, we study the phase diagram within mean-field theory. In addition to a fully gapped spin-liquid ground state, we find a state where one gapless triplon mode with a Fermi surface coexists with d+id topological pairing of the other triplons. Despite the existence of a Fermi surface, this ground state has fully gapped bulk spin excitations. Such a state has linear in-temperature specific heat and constant in-plane spin susceptibility, with an unusually high Wilson ratio.}, author = {Maksym Serbyn and Senthil, Todadri S and Lee, Patrick}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {18}, publisher = {American Physical Society}, title = {{Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice}}, doi = {10.1103/PhysRevB.84.180403}, volume = {84}, year = {2011}, } @article{969, abstract = {We investigate the isotope effect on the London penetration depth of a superconductor which measures n S/m*, the ratio of superfluid density to effective mass. We use a simplified model of electrons weakly coupled to a single phonon frequency ω E, but assume that the energy gap Δ does not have any isotope effect. Nevertheless, we find an isotope effect for n S/m* which is significant if Δ is sufficiently large that it becomes comparable to ω E, a regime of interest to high-T c cuprate superconductors and possibly other families of unconventional superconductors with relatively high T c. Our model is too simple to describe the cuprates and it gives the wrong sign of the isotope effect when compared with experiment, but it is a proof of principle that the isotope effect exists for n S/m* in materials where the pairing gap and T c are not of phonon origin and have no isotope effect.}, author = {Maksym Serbyn and Lee, Patrick}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {2}, publisher = {American Physical Society}, title = {{Isotope effect on the superfluid density in conventional and high-temperature superconductors}}, doi = {10.1103/PhysRevB.83.024506}, volume = {83}, year = {2011}, } @article{8471, abstract = {Despite the importance of protein fibrils in the context of conformational diseases, information on their structure is still sparse. Hydrogen/deuterium exchange measurements of backbone amide protons allow the identification hydrogen-bonding patterns and reveal pertinent information on the amyloid β-sheet architecture. However, they provide only little information on the identity of residues exposed to solvent or buried inside the fibril core. NMR spectroscopy is a potent method for identifying solvent-accessible residues in proteins via observation of polarization transfer between chemically exchanging side-chain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning greatly attenuates unwanted spin diffusion and allows identification of polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218–289) prion fibrils under different conditions (including physiological pH, where protofibrils assemble together into thicker fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded by water, thus excluding the existence of extended dry interfibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into the detailed structural features of amyloid fibrils in general.}, author = {Van Melckebeke, Hélène and Schanda, Paul and Gath, Julia and Wasmer, Christian and Verel, René and Lange, Adam and Meier, Beat H. and Böckmann, Anja}, issn = {0022-2836}, journal = {Journal of Molecular Biology}, number = {3}, pages = {765--772}, publisher = {Elsevier}, title = {{Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR}}, doi = {10.1016/j.jmb.2010.11.004}, volume = {405}, year = {2011}, } @article{8505, abstract = {The classical principle of least action says that orbits of mechanical systems extremize action; an important subclass are those orbits that minimize action. In this paper we utilize this principle along with Aubry-Mather theory to construct (Birkhoff) regions of instability for a certain three-body problem, given by a Hamiltonian system of 2 degrees of freedom. We believe that these methods can be applied to construct instability regions for a variety of Hamiltonian systems with 2 degrees of freedom. The Hamiltonian model we consider describes dynamics of a Sun-Jupiter-comet system, and under some simplifying assumptions, we show the existence of instabilities for the orbit of the comet. In particular, we show that a comet which starts close to an orbit in the shape of an ellipse of eccentricity e=0.66 can increase in eccentricity up to e=0.96. In the sequels to this paper, we extend the result to beyond e=1 and show the existence of ejection orbits. Such orbits are initially well within the range of our solar system. This might give an indication of why most objects rotating around the Sun in our solar system have relatively low eccentricity.}, author = {Galante, Joseph and Kaloshin, Vadim}, issn = {0012-7094}, journal = {Duke Mathematical Journal}, keywords = {General Mathematics}, number = {2}, pages = {275--327}, publisher = {Duke University Press}, title = {{Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action}}, doi = {10.1215/00127094-1415878}, volume = {159}, year = {2011}, } @inbook{881, author = {Fyodor Kondrashov}, booktitle = {Evolution after Gene Duplication}, pages = {57 -- 76}, publisher = {Wiley-Blackwell}, title = {{Gene Dosage and Duplication}}, doi = {10.1002/9780470619902.ch4}, year = {2011}, } @article{919, abstract = {Collective cell migration in tissues occurs throughout embryonic development, during wound healing, and in cancerous tumor invasion, yet most detailed knowledge of cell migration comes from single-cell studies. As single cells migrate, the shape of the cell body fluctuates dramatically through cyclic processes of extension, adhesion, and retraction, accompanied by erratic changes in migration direction. Within confluent cell layers, such subcellular motions must be coupled between neighbors, yet the influence of these subcellular motions on collective migration is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously measuring collective migration and subcellular motions, covering a broad range of length scales, time scales, and cell densities. At large length scales and time scales collective migration slows as cell density rises, yet the fastest cells move in large, multicell groups whose scale grows with increasing cell density. This behavior has an intriguing analogy to dynamic heterogeneities found in particulate systems as they become more crowded and approach a glass transition. In addition we find a diminishing self-diffusivity of short-wavelength motions within the cell layer, and growing peaks in the vibrational density of states associated with cooperative cell-shape fluctuations. Both of these observations are also intriguingly reminiscent of a glass transition. Thus, these results provide a broad and suggestive analogy between cell motion within a confluent layer and the dynamics of supercooled colloidal and molecular fluids approaching a glass transition.}, author = {Angelini, Thomas and Hannezo, Edouard B and Trepatc, Xavier and Marquez, Manuel and Fredberg, Jeffrey and Weitz, David}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {12}, pages = {4714 -- 4719}, publisher = {PNAS}, title = {{Glass-like dynamics of collective cell migration}}, doi = {10.1073/pnas.1010059108}, volume = {108}, year = {2011}, } @article{918, abstract = {We study theoretically the shapes of a dividing epithelial monolayer of cells lying on top of an elastic stroma. The negative tension created by cell division provokes a buckling instability at a finite wave vector leading to the formation of periodic arrays of villi and crypts. The instability is similar to the buckling of a metallic plate under compression. We use the results to rationalize the various structures of the intestinal lining observed in vivo. Taking into account the coupling between cell division and local curvature, we obtain different patterns of villi and crypts, which could explain the different morphologies of the small intestine and the colon.}, author = {Hannezo, Edouard B and Prost, Jacques and Joanny, Jean}, journal = {Physical Review Letters}, number = {7}, publisher = {American Physical Society}, title = {{Instabilities of monolayered epithelia Shape and structure of villi and crypts}}, doi = {10.1103/PhysRevLett.107.078104}, volume = {107}, year = {2011}, } @misc{9522, abstract = {Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo.}, author = {Zilberman, Daniel}, booktitle = {Developmental Cell}, issn = {1878-1551}, number = {6}, pages = {735--736}, publisher = {Elsevier}, title = {{Balancing parental contributions in plant embryonic gene activation}}, doi = {10.1016/j.devcel.2011.05.018}, volume = {20}, year = {2011}, } @inproceedings{9648, abstract = {In this paper, we establish a correspondence between the incremental algorithm for computing AT-models [8,9] and the one for computing persistent homology [6,14,15]. We also present a decremental algorithm for computing AT-models that allows to extend the persistence computation to a wider setting. Finally, we show how to combine incremental and decremental techniques for persistent homology computation.}, author = {Gonzalez-Diaz, Rocio and Ion, Adrian and Jimenez, Maria Jose and Poyatos, Regina}, booktitle = {Computer Analysis of Images and Patterns}, isbn = {9783642236716}, issn = {16113349}, location = {Seville, Spain}, pages = {286--293}, publisher = {Springer Nature}, title = {{Incremental-decremental algorithm for computing AT-models and persistent homology}}, doi = {10.1007/978-3-642-23672-3_35}, volume = {6854}, year = {2011}, } @article{968, abstract = {A Reply to the Comment by Andrei Sergeev, M. Reizer, and V. Mitin.}, author = {Maksym Serbyn and Skvortsov, Mikhail A and Varlamov, Andrei A and Galitski, Victor M}, journal = {Physical Review Letters}, number = {13}, publisher = {American Physical Society}, title = {{Serbyn et al. Reply:}}, doi = {10.1103/PhysRevLett.106.139702}, volume = {106}, 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}, } @misc{9762, 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 to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 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 showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating 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}, publisher = {IST Austria}, title = {{Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)}}, doi = {10.5061/dryad.299h8}, year = {2011}, } @inproceedings{9943, abstract = {Segmentation is the process of partitioning digital images into meaningful regions. The analysis of biological high content images often requires segmentation as a first step. We propose ilastik as an easy-to-use tool which allows the user without expertise in image processing to perform segmentation and classification in a unified way. ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, ilastik infers a problem specific segmentation. A random forest classifier is used in the learning step, in which each pixel's neighborhood is characterized by a set of generic (nonlinear) features. ilastik supports up to three spatial plus one spectral dimension and makes use of all dimensions in the feature calculation. ilastik provides realtime feedback that enables the user to interactively refine the segmentation result and hence further fine-tune the classifier. An uncertainty measure guides the user to ambiguous regions in the images. Real time performance is achieved by multi-threading which fully exploits the capabilities of modern multi-core machines. Once a classifier has been trained on a set of representative images, it can be exported and used to automatically process a very large number of images (e.g. using the CellProfiler pipeline). ilastik is an open source project and released under the BSD license at www.ilastik.org.}, author = {Sommer, Christoph M and Straehle, Christoph and Köthe, Ullrich and Hamprecht, Fred A.}, booktitle = {2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro}, isbn = {978-1-4244-4127-3}, issn = {1945-8452}, keywords = {image segmentation, biomedical imaging, three dimensional displays, neurons, retina, observers, image color analysis}, location = {Chicago, Illinois, USA}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Ilastik: Interactive learning and segmentation toolkit}}, doi = {10.1109/isbi.2011.5872394}, year = {2011}, } @inproceedings{10907, abstract = {This paper presents a method to create a model of an articulated object using the planar motion in an initialization video. The model consists of rigid parts connected by points of articulation. The rigid parts are described by the positions of salient feature-points tracked throughout the video. Following a filtering step that identifies points that belong to different objects, rigid parts are found by a grouping process in a graph pyramid. Valid articulation points are selected by verifying multiple hypotheses for each pair of parts.}, author = {Artner, Nicole M. and Ion, Adrian and Kropatsch, Walter G.}, booktitle = {Graph-Based Representations in Pattern Recognition}, editor = {Jiang, Xiaoyi and Ferrer, Miquel and Torsello, Andrea}, isbn = {9783642208430}, issn = {1611-3349}, location = {Münster, Germany}, pages = {215--224}, publisher = {Springer}, title = {{Spatio-temporal extraction of articulated models in a graph pyramid}}, doi = {10.1007/978-3-642-20844-7_22}, volume = {6658}, 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}, issn = {2663-337X}, pages = {141}, publisher = {Institute of Science and Technology Austria}, title = {{The role of chemotactic gradients in dendritic cell migration}}, year = {2011}, } @phdthesis{3273, author = {Maître, Jean-Léon}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors}}, year = {2011}, } @inproceedings{3238, abstract = {We construct efficient authentication protocols and message-authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work - starting with the HB protocol of Hopper and Blum in 2001 - until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle (MIM) attacks. A MAC implies such a (two-round) protocol. © 2011 International Association for Cryptologic Research}, author = {Kiltz, Eike and Pietrzak, Krzysztof Z and Cash, David and Jain, Abhishek and Venturi, Daniele}, location = {Tallinn, Estonia}, pages = {7 -- 26}, publisher = {Springer}, title = {{Efficient authentication from hard learning problems}}, doi = {10.1007/978-3-642-20465-4_3}, volume = {6632}, year = {2011}, } @article{3392, abstract = {Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing edge, or uropod. Although in vitro experiments in cell lines or activated primary cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional surfaces and nuclear propulsion through narrow pores in three-dimensional matrices, less is known about the role of these two events during the recirculation of primary, nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin II, we report that inhibition of uropod contractility blocked integrin-independent mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling on chemokine-coated endothelial cells under shear was severely impaired by ROCK inhibition, whereas transendothelial migration was only reduced through endothelial cells with high, but not low, barrier properties. Using three-dimensional thick-tissue imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue, we demonstrated a significant role for uropod contractility in intraluminal crawling and transendothelial migration through lymph node, but not bone marrow, endothelial cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or integrin-independent interactions, reduced parenchymal motility of inhibitor-treated T cells within the dense lymphoid microenvironment, thus assigning context-dependent roles for uropod contraction during lymphocyte recirculation.}, author = {Soriano, Silvia and Hons, Miroslav and Schumann, Kathrin and Kumar, Varsha and Dennier, Timo and Lyck, Ruth and Sixt, Michael K and Stein, Jens}, issn = {1550-6606}, journal = {Journal of Immunology}, number = {5}, pages = {2356 -- 2364}, publisher = {American Association of Immunologists}, title = {{In vivo analysis of uropod function during physiological T cell trafficking}}, doi = {10.4049/jimmunol.1100935}, volume = {187}, year = {2011}, } @inproceedings{3163, abstract = {We study multi-label prediction for structured output sets, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multilabel classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label set, which is infeasible in case of structured outputs. Relying on techniques originally designed for single-label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds.}, author = {Lampert, Christoph}, location = {Granada, Spain}, publisher = {Neural Information Processing Systems}, title = {{Maximum margin multi-label structured prediction}}, year = {2011}, }