@article{8510, abstract = {In this paper, using the ideas of Bessi and Mather, we present a simple mechanical system exhibiting Arnold diffusion. This system of a particle in a small periodic potential can be also interpreted as ray propagation in a periodic optical medium with a near-constant index of refraction. Arnold diffusion in this context manifests itself as an arbitrary finite change of direction for nearly constant index of refraction.}, author = {Kaloshin, Vadim and Levi, Mark}, issn = {0273-0979}, journal = {Bulletin of the American Mathematical Society}, keywords = {Applied Mathematics, General Mathematics}, number = {3}, pages = {409--427}, publisher = {American Mathematical Society}, title = {{An example of Arnold diffusion for near-integrable Hamiltonians}}, doi = {10.1090/s0273-0979-08-01211-1}, volume = {45}, year = {2008}, } @article{895, abstract = {Background. The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex (CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior.}, author = {Donaldson, Zoe R and Fyodor Kondrashov and Putnam, Andrea S and Bai, Yaohui and Stoinski, Tara S and Hammock, Elizabeth A and Young, Larry}, journal = {BMC Evolutionary Biology}, number = {1}, publisher = {BioMed Central}, title = {{Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene}}, doi = {10.1186/1471-2148-8-180}, volume = {8}, year = {2008}, } @article{907, abstract = {The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process.}, author = {Assis, Raquel and Kondrashov, Alexey S and Koonin, Eugene V and Fyodor Kondrashov}, journal = {Trends in Genetics}, number = {10}, pages = {475 -- 478}, publisher = {Elsevier}, title = {{Nested genes and increasing organizational complexity of metazoan genomes}}, doi = {10.1016/j.tig.2008.08.003}, volume = {24}, year = {2008}, } @article{9457, abstract = {Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.}, author = {Zilberman, Daniel and Coleman-Derr, Devin and Ballinger, Tracy and Henikoff, Steven}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7218}, pages = {125--129}, publisher = {Springer Nature}, title = {{Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks}}, doi = {10.1038/nature07324}, volume = {456}, year = {2008}, } @article{9537, abstract = {DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more.}, author = {Zilberman, Daniel}, issn = {1369-5266}, journal = {Current Opinion in Plant Biology}, number = {5}, pages = {554--559}, publisher = {Elsevier }, title = {{The evolving functions of DNA methylation}}, doi = {10.1016/j.pbi.2008.07.004}, volume = {11}, year = {2008}, } @article{965, abstract = {We give many examples of applying Bogoliubov's forest formula to iterative solutions of various nonlinear equations. The same formula describes an extremely wide class of objects, from an ordinary quadratic equation to renormalization in quantum field theory.}, author = {Morozov, Alexei Y and Maksym Serbyn}, journal = {Theoretical and Mathematical Physics}, number = {2}, pages = {270 -- 293}, publisher = {Elsevier}, title = {{Nonlinear algebra and Bogoliubov's recursion}}, doi = {10.1007/s11232-008-0026-7}, volume = {154}, year = {2008}, } @article{581, abstract = {We have detected a spin-dependent displacement perpendicular to the refractive index gradient for photons passing through an air-glass interface. The effect is the photonic version of the spin Hall effect in electronic systems, indicating the universality of the effect for particles of different nature. Treating the effect as a weak measurement of the spin projection of the photons, we used a preselection and postselection technique on the spin state to enhance the original displacement by nearly four orders of magnitude, attaining sensitivity to displacements of ∼1 angstrom. The spin Hall effect can be used for manipulating photonic angular momentum states, and the measurement technique holds promise for precision metrology.}, author = {Onur Hosten and Kwiat, Paul}, journal = {Science}, number = {5864}, pages = {787 -- 790}, publisher = {American Association for the Advancement of Science}, title = {{Observation of the spin hall effect of light via weak measurements}}, doi = {10.1126/science.1152697}, volume = {319}, year = {2008}, } @inproceedings{584, abstract = {Using “quantum weak-measurements” as a coherent enhancement technique for small signals, we have measured the recently proposed “spin Hall effect” of light at an air-glass interface, and are working on the smoothly varying refractive-index case.}, author = {Hosten, Onur and Kwiat, Paul}, isbn = {978-155752859-9}, issn = {21622701}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Spin hall effect of light via weak measurements: Sharp and smooth index variations}}, year = {2008}, } @article{6146, abstract = {Homeostasis of internal carbon dioxide (CO2) and oxygen (O2) levels is fundamental to all animals. Here we examine the CO2 response of the nematode Caenorhabditis elegans. This species inhabits rotting material, which typically has a broad CO2 concentration range. We show that well fed C. elegans avoid CO2 levels above 0.5%. Animals can respond to both absolute CO2 concentrations and changes in CO2 levels within seconds. Responses to CO2 do not reflect avoidance of acid pH but appear to define a new sensory response. Sensation of CO2 is promoted by the cGMP-gated ion channel subunits TAX-2 and TAX-4, but other pathways are also important. Robust CO2 avoidance in well fed animals requires inhibition of the DAF-16 forkhead transcription factor by the insulin-like receptor DAF-2. Starvation, which activates DAF-16, strongly suppresses CO2 avoidance. Exposure to hypoxia (<1% O2) also suppresses CO2 avoidance via activation of the hypoxia-inducible transcription factor HIF-1. The npr-1 215V allele of the naturally polymorphic neuropeptide receptor npr-1, besides inhibiting avoidance of high ambient O2 in feeding C. elegans, also promotes avoidance of high CO2. C. elegans integrates competing O2 and CO2 sensory inputs so that one response dominates. Food and allelic variation at NPR-1 regulate which response prevails. Our results suggest that multiple sensory inputs are coordinated by C. elegans to generate different coherent foraging strategies.}, author = {Bretscher, A. J. and Busch, K. E. and de Bono, Mario}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {23}, pages = {8044--8049}, publisher = {Proceedings of the National Academy of Sciences}, title = {{A carbon dioxide avoidance behavior is integrated with responses to ambient oxygen and food in Caenorhabditis elegans}}, doi = {10.1073/pnas.0707607105}, volume = {105}, year = {2008}, } @article{6148, author = {Kammenga, Jan E. and Phillips, Patrick C. and de Bono, Mario and Doroszuk, Agnieszka}, issn = {0168-9525}, journal = {Trends in Genetics}, number = {4}, pages = {178--185}, publisher = {Elsevier}, title = {{Beyond induced mutants: using worms to study natural variation in genetic pathways}}, doi = {10.1016/j.tig.2008.01.001}, volume = {24}, year = {2008}, } @article{6149, author = {Olofsson, Birgitta and de Bono, Mario}, issn = {0960-9822}, journal = {Current Biology}, number = {5}, pages = {R204--R206}, publisher = {Elsevier}, title = {{Sleep: dozy worms and sleepy flies}}, doi = {10.1016/j.cub.2008.01.002}, volume = {18}, year = {2008}, } @article{7320, abstract = {A comparative, experimental diffusivity study of gas diffusion layer (GDL) materials for polymer electrolyte fuel cells (PEFC) is presented for the first time. The GDL plays an important role for electrochemical losses due to gas transport limitations at high current densities. Characterization and optimization of these layers is therefore essential to improve power density. A recently developed method which allows for fast diffusimetry is applied and data compared to the literature values. Measurements are made as a function of direction and compression and the effect of different binder structures and hydrophobic treatments on effective diffusivities are discussed. A better understanding of the results is gained by including novel GDL cross-section images and a meaningful unit cell model for the interpretation of the data. The diffusivity data is valuable for GDL manufacturers and future PEFC models. The study reveals that a binder–fiber ratio larger than 50% has a negative impact on the effective diffusion properties. The hydrophobic treatment which is necessary to improve the water management can impede diffusion and thus reduce the power density. Furthermore binder has an isotropic effect while compression pronounces the in-plane orientation of the fibers.}, author = {Flückiger, Reto and Freunberger, Stefan Alexander and Kramer, Denis and Wokaun, Alexander and Scherer, Günther G. and Büchi, Felix N.}, issn = {0013-4686}, journal = {Electrochimica Acta}, number = {2}, pages = {551--559}, publisher = {Elsevier}, title = {{Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC}}, doi = {10.1016/j.electacta.2008.07.034}, volume = {54}, year = {2008}, } @article{7321, abstract = {Cell interaction phenomena in polymer electrolyte fuel cell stacks that arise from imbalance between adjacent cells are investigated in detail experimentally and theoretically. A specialized two-cell stack with advanced localized diagnostics was developed and used to analyze the mechanism and effect of cell-to-cell coupling as a result of operationally relevant variations in reactant feed flow. Contributions to overall and local voltage changes with respect to uniformly operated cells are scrutinized. Unequal operation of the cells causes in-plane current in the bipolar plate to redistribute current and result in inhomogeneous polarization. Both increasing and decreasing polarization along the air-flow path reduces cell power as compared to isopotential operation. A two-dimensional model based on a commercial computational fluid dynamics code is used to back and extend the experimental results to more general cases. Furthermore, the experimental setup presented allowed for the first time to perform simultaneous localized electrochemical impedance spectroscopy beyond the single-cell level. The mechanism of mutual cell interaction on local and integral spectra is revealed. Results show that virtually identical operation of the cells is essential to obtain meaningful integral spectra.}, author = {Freunberger, Stefan Alexander and Schneider, Ingo A. and Sui, Pang-Chieh and Wokaun, Alexander and Djilali, Nedjib and Büchi, Felix N.}, issn = {0013-4651}, journal = {Journal of The Electrochemical Society}, number = {7}, publisher = {The Electrochemical Society}, title = {{Cell interaction phenomena in polymer electrolyte fuel cell stacks}}, doi = {10.1149/1.2913095}, volume = {155}, year = {2008}, } @article{7322, abstract = {The gas diffusion layers (GDLs) of a membrane electrode assembly (MEA) serve as link between flow field and porous electrode within a polymer electrolyte fuel cell. Beside ensuring sufficient electrical and thermal contact between the whole electrode area and the flow field, these typically 200–400 μm thick porous structures enable the access of educts to the electrode area which would be occluded by the flow field lands if the flow field is directly attached to the electrode. Hence, the characterisation of properties pertaining to mass transport of educts and products through these structures is indispensable whilst examining the contribution of the GDLs to the overall electrochemical characteristics of a MEA. A fast and cost effective method to measure the effective diffusivity of a GDL is presented. Electrochemical impedance spectroscopy is applied to measure the effective ionic conductivity of an electrolyte-soaked GDL. Taking advantage of the analogy between Ficks and Ohms law, this provides a measure for the effective diffusivity. The method is described in detail, including experimental as well as theoretical aspects, and selected results, highlighting the anisotropy and dependence on the degree of compression, are shown. Moreover, a two-dimensional model consisting of regularly spaced ellipses is developed to represent the porous structure of the GDL, and by using conformal maps, the agreement between this model and experiment with respect to the sensitivity of the effective diffusivity towards compression is shown.}, author = {Kramer, Denis and Freunberger, Stefan Alexander and Flückiger, Reto and Schneider, Ingo A. and Wokaun, Alexander and Büchi, Felix N. and Scherer, Günther G.}, issn = {1572-6657}, journal = {Journal of Electroanalytical Chemistry}, number = {1}, pages = {63--77}, publisher = {Elsevier}, title = {{Electrochemical diffusimetry of fuel cell gas diffusion layers}}, doi = {10.1016/j.jelechem.2007.09.014}, volume = {612}, year = {2008}, } @inproceedings{7425, abstract = {The propagation of single cell performance losses to adjacent cells in a polymer electrolyte fuel cell stack is studied by means of local current density measurements in a two cell stack. In this stack, the working conditions of adjacent cells can be controlled independently in order to deliberately change the performance of one cell (inducing cell) and study the coupling effects to the adjacent cell (response cell), while keeping the working conditions of the later one unchanged. The experiments have shown that changes in the current density distribution caused by lowering of the air stoichiometry in the inducing cell cause changes in the current density distribution of the response cell in the order of 60% of the change of the inducing cell, even when the air stoichiometry of the response cell is kept constant. The losses in cell voltage of the inducing cell cause losses in cell voltage of the response cell in a magnitude between 30 and 50%.}, author = {Santis, Marco and Freunberger, Stefan Alexander and Papra, Matthias and Büchi, Felix N.}, booktitle = {3rd International Conference on Fuel Cell Science, Engineering and Technology}, isbn = {0791837645}, location = {Ypsilanti, MI, United States}, pages = {763--765}, publisher = {ASMEDC}, title = {{Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks}}, doi = {10.1115/fuelcell2005-74116}, year = {2008}, } @inproceedings{753, abstract = {This paper addresses the following question: what is the minimum-sized synchronous window needed to solve consensus in an otherwise asynchronous system? In answer to this question, we present the first optimally-resilient algorithm ASAP that solves consensus as soon as possible in an eventually synchronous system, i.e., a system that from some time GST onwards, delivers messages in a timely fashion. ASAP guarantees that, in an execution with at most f failures, every process decides no later than round GST + f + 2, which is optimal.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Travers, Corentin}, pages = {32 -- 46}, publisher = {Springer}, title = {{How to solve consensus in the smallest window of synchrony}}, doi = {10.1007/978-3-540-87779-0_3}, volume = {5218 LNCS}, year = {2008}, } @article{3435, abstract = {We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ~0.43.}, author = {Jonathan Bollback and York, Thomas L and Nielsen, Rasmus}, journal = {Genetics}, number = {1}, pages = {497 -- 502}, publisher = {Genetics Society of America}, title = {{Estimation of 2Nes From Temporal Allele Frequency Data}}, doi = {10.1534/genetics.107.085019}, volume = {179}, year = {2008}, } @inproceedings{3501, abstract = {The Wikipedia is a collaborative encyclopedia: anyone can contribute to its articles simply by clicking on an "edit" button. The open nature of the Wikipedia has been key to its success, but has also created a challenge: how can readers develop an informed opinion on its reliability? We propose a system that computes quantitative values of trust for the text in Wikipedia articles; these trust values provide an indication of text reliability. The system uses as input the revision history of each article, as well as information about the reputation of the contributing authors, as provided by a reputation system. The trust of a word in an article is computed on the basis of the reputation of the original author of the word, as well as the reputation of all authors who edited text near the word. The algorithm computes word trust values that vary smoothly across the text; the trust values can be visualized using varying text-background colors. The algorithm ensures that all changes to an article's text are reflected in the trust values, preventing surreptitious content changes. We have implemented the proposed system, and we have used it to compute and display the trust of the text of thousands of articles of the English Wikipedia. To validate our trust-computation algorithms, we show that text labeled as low-trust has a significantly higher probability of being edited in the future than text labeled as high-trust.}, author = {Adler, B Thomas and Krishnendu Chatterjee and de Alfaro, Luca and Faella, Marco and Pye, Ian and Raman, Vishwanath}, publisher = {ACM}, title = {{Assigning trust to Wikipedia content}}, doi = {10.1145/1822258.1822293}, year = {2008}, } @inproceedings{3502, abstract = {In content-driven reputation systems for collaborative content, users gain or lose reputation according to how their contributions fare: authors of long-lived contributions gain reputation, while authors of reverted contributions lose reputation. Existing content-driven systems are prone to Sybil attacks, in which multiple identities, controlled by the same person, perform coordinated actions to increase their reputation. We show that content-driven reputation systems can be made resistant to such attacks by taking advantage of thefact that the reputation increments and decrements depend on content modifications, which are visible to all. We present an algorithm for content-driven reputation that prevents a set of identities from increasing their maximum reputation without doing any useful work. Here, work is considered useful if it causes content to evolve in a direction that is consistent with the actions of high-reputation users. We argue that the content modifications that require no effort, such as the insertion or deletion of arbitrary text, are invariably non-useful. We prove a truthfullness result for the resulting system, stating that users who wish to perform a contribution do not gain by employing complex contribution schemes, compared to simply performing the contribution at once. In particular, splitting the contribution in multiple portions, or employing the coordinated actions of multiple identities, do not yield additional reputation. Taken together, these results indicate that content-driven systems can be made robust with respect to Sybil attacks. Copyright 2008 ACM.}, author = {Krishnendu Chatterjee and de Alfaro, Luca and Pye, Ian}, pages = {33 -- 42}, publisher = {ACM}, title = {{Robust content-driven reputation}}, doi = {10.1145/1456377.1456387 }, year = {2008}, } @inproceedings{3504, abstract = {Simulation and bisimulation metrics for stochastic systems provide a quantitative gen- eralization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative μ-calculus and related probabilistic logics. We present algorithms for computing the metrics on Markov decision processes (MDPs), turn- based stochastic games, and concurrent games. For turn-based games and MDPs, we provide a polynomial-time algorithm based on linear programming for the computation of the one-step metric distance between states. The algorithm improves on the previously known exponential-time algo- rithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known bound for Markov chains. For the bisimulation kernel of the metric, which corresponds to probabilistic bisimulation, our algorithm works in time O(n4) for both turn-based games and MDPs; improving the previously best known O(n9 · log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance between states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be accomplished via a reduction to the theory of real closed fields, involving a formula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity, improving the previously known reduction with O(|G|O(|G|7)) time complexity. These algorithms can be iterated to approximate the metrics using binary search.}, author = {Chatterjee, Krishnendu and De Alfaro, Luca and Majumdar, Ritankar and Raman, Vishwanath}, pages = {107 -- 118}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Algorithms for game metrics}}, doi = {10.4230/LIPIcs.FSTTCS.2008.1745}, volume = {2}, year = {2008}, }