@article{2781, abstract = {We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs, that is, graphs on N vertices where every edge is chosen independently and with probability p = p(N). We rescale the matrix so that its bulk eigenvalues are of order one. We prove that, as long as pN→∞(with a speed at least logarithmic in N), the density of eigenvalues of the Erdős-Rényi ensemble is given by the Wigner semicircle law for spectral windows of length larger than N-1 (up to logarithmic corrections). As a consequence, all eigenvectors are proved to be completely delocalized in the sense that the ℓ∞-norms of the ℓ2-normalized eigenvectors are at most of order N-1/2 with a very high probability. The estimates in this paper will be used in the companion paper [Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues (2011) Preprint] to prove the universality of eigenvalue distributions both in the bulk and at the spectral edges under the further restriction that pN »N2/3.}, author = {László Erdös and Knowles, Antti and Yau, Horng-Tzer and Yin, Jun}, journal = {Annals of Probability}, number = {3 B}, pages = {2279 -- 2375}, publisher = {Institute of Mathematical Statistics}, title = {{Spectral statistics of Erdős-Rényi graphs I: Local semicircle law}}, doi = {10.1214/11-AOP734}, volume = {41}, year = {2013}, } @article{2782, abstract = {We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2}, where X and Y have independent entries with zero mean and variance one. These matrices are the natural generalization of the Gaussian case, which are known as MANOVA matrices and which have joint eigenvalue density given by the third classical ensemble, the Jacobi ensemble. We show that, away from the spectral edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble even on the shortest possible scales of order 1/n (up to log n factors). This result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur law for general MANOVA matrices.}, author = {Erdös, László and Farrell, Brendan}, journal = {Journal of Statistical Physics}, number = {6}, pages = {1003 -- 1032}, publisher = {Springer}, title = {{Local eigenvalue density for general MANOVA matrices}}, doi = {10.1007/s10955-013-0807-8}, volume = {152}, year = {2013}, } @inproceedings{2807, abstract = {We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov's result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \no holes up to dimension k-1" (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. }, author = {Čadek, Martin and Krcál, Marek and Matoušek, Jiří and Vokřínek, Lukáš and Wagner, Uli}, booktitle = {45th Annual ACM Symposium on theory of computing}, location = {Palo Alto, CA, United States}, pages = {595 -- 604}, publisher = {ACM}, title = {{Extending continuous maps: Polynomiality and undecidability}}, doi = {10.1145/2488608.2488683}, year = {2013}, } @article{2808, abstract = {In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.}, author = {Landberg, Katarina and Pederson, Eric and Viaene, Tom and Bozorg, Behruz and Friml, Jirí and Jönsson, Henrik and Thelander, Mattias and Sundberg, Eva}, journal = {Plant Physiology}, number = {3}, pages = {1406 -- 1419}, publisher = {American Society of Plant Biologists}, title = {{The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain}}, doi = {10.1104/pp.113.214023}, volume = {162}, year = {2013}, } @article{2810, abstract = {The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data.}, author = {De Vos, Marjon and Poelwijk, Frank and Battich, Nico and Ndika, Joseph and Tans, Sander}, journal = {PLoS Genetics}, number = {6}, publisher = {Public Library of Science}, title = {{Environmental dependence of genetic constraint}}, doi = {10.1371/journal.pgen.1003580}, volume = {9}, year = {2013}, } @article{2811, abstract = {In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.}, author = {Avila, Marc and Hof, Björn}, journal = {Physical Review E}, number = {6}, publisher = {American Institute of Physics}, title = {{Nature of laminar-turbulence intermittency in shear flows}}, doi = {10.1103/PhysRevE.87.063012}, volume = {87}, year = {2013}, } @inproceedings{2812, abstract = {We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.}, author = {Attali, Dominique and Bauer, Ulrich and Devillers, Olivier and Glisse, Marc and Lieutier, André}, booktitle = {Proceedings of the 29th annual symposium on Computational Geometry}, location = {Rio de Janeiro, Brazil}, pages = {117 -- 125}, publisher = {ACM}, title = {{Homological reconstruction and simplification in R3}}, doi = {10.1145/2462356.2462373}, year = {2013}, } @article{2813, abstract = {Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called "maximum drag reduction" asymptote, which is exhibited by a wide range of viscoelastic fluids.}, author = {Samanta, Devranjan and Dubief, Yves and Holzner, Markus and Schäfer, Christof and Morozov, Alexander and Wagner, Christian and Hof, Björn}, journal = {PNAS}, number = {26}, pages = {10557 -- 10562}, publisher = {National Academy of Sciences}, title = {{Elasto-inertial turbulence}}, doi = {10.1073/pnas.1219666110}, volume = {110}, year = {2013}, } @article{2814, abstract = {We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing "reset" action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. We also discuss the memory requirement for deterministic strategies and extensions of our results to other models, such as pushdown systems and timed systems.}, author = {Chatterjee, Krishnendu and Alfaro, Luca and Majumdar, Ritankar}, journal = {International Journal of Foundations of Computer Science}, number = {2}, pages = {165 -- 185}, publisher = {World Scientific Publishing}, title = {{The complexity of coverage}}, doi = {10.1142/S0129054113400066}, volume = {24}, year = {2013}, } @article{2815, abstract = {The fact that a sum of isotropic Gaussian kernels can have more modes than kernels is surprising. Extra (ghost) modes do not exist in ℝ1 and are generally not well studied in higher dimensions. We study a configuration of n+1 Gaussian kernels for which there are exactly n+2 modes. We show that all modes lie on a finite set of lines, which we call axes, and study the restriction of the Gaussian mixture to these axes in order to discover that there are an exponential number of critical points in this configuration. Although the existence of ghost modes remained unknown due to the difficulty of finding examples in ℝ2, we show that the resilience of ghost modes grows like the square root of the dimension. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes.}, author = {Edelsbrunner, Herbert and Fasy, Brittany Terese and Rote, Günter}, issn = {1432-0444}, journal = {Discrete & Computational Geometry}, number = {4}, pages = {797 -- 822}, publisher = {Springer}, title = {{Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions}}, doi = {10.1007/s00454-013-9517-x}, volume = {49}, year = {2013}, } @article{2816, abstract = {In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics.}, author = {Božić, Ivana and Reiter, Johannes and Allen, Benjamin and Antal, Tibor and Chatterjee, Krishnendu and Shah, Preya and Moon, Yo and Yaqubie, Amin and Kelly, Nicole and Le, Dung and Lipson, Evan and Chapman, Paul and Diaz, Luis and Vogelstein, Bert and Nowak, Martin}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Evolutionary dynamics of cancer in response to targeted combination therapy}}, doi = {10.7554/eLife.00747}, volume = {2}, year = {2013}, } @article{2817, abstract = {The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle.}, author = {Novak, Sebastian and Chatterjee, Krishnendu and Nowak, Martin}, journal = {Journal of Theoretical Biology}, pages = {26 -- 34}, publisher = {Elsevier}, title = {{Density games}}, doi = {10.1016/j.jtbi.2013.05.029}, volume = {334}, year = {2013}, } @article{2818, abstract = {Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus.}, author = {Rajan, Kanaka and Marre, Olivier and Tkacik, Gasper}, journal = {Neural Computation}, number = {7}, pages = {1661 -- 1692}, publisher = {MIT Press }, title = {{Learning quadratic receptive fields from neural responses to natural stimuli}}, doi = {10.1162/NECO_a_00463}, volume = {25}, year = {2013}, } @inproceedings{2819, abstract = {We introduce quantatitive timed refinement metrics and quantitative timed simulation functions, incorporating zenoness checks, for timed systems. These functions assign positive real numbers between zero and infinity which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximum timing mismatch that can arise, (2) the "steady-state" maximum timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation functions to within any desired degree of accuracy. In order to compute the values of the quantitative simulation functions, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives for player 1, and then use these algorithms to compute the values of the quantitative timed simulation functions. }, author = {Chatterjee, Krishnendu and Prabhu, Vinayak}, booktitle = {Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control}, location = {Philadelphia, PA USA}, pages = {273 -- 282}, publisher = {Springer}, title = {{Quantitative timed simulation functions and refinement metrics for real-time systems}}, doi = {10.1145/2461328.2461370}, volume = {1}, year = {2013}, } @article{2821, abstract = {Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells.}, author = {Remy, Estelle and Cabrito, Tânia and Baster, Pawel and Batista, Rita and Teixeira, Miguel and Friml, Jirí and Sá Correia, Isabel and Duque, Paula}, journal = {Plant Cell}, number = {3}, pages = {901 -- 926}, publisher = {American Society of Plant Biologists}, title = {{A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis}}, doi = {10.1105/tpc.113.110353}, volume = {25}, year = {2013}, } @article{2822, abstract = {Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.}, author = {Topp, Christopher and Iyer Pascuzzi, Anjali and Anderson, Jill and Lee, Cheng and Zurek, Paul and Symonova, Olga and Zheng, Ying and Bucksch, Alexander and Mileyko, Yuriy and Galkovskyi, Taras and Moore, Brad and Harer, John and Edelsbrunner, Herbert and Mitchell Olds, Thomas and Weitz, Joshua and Benfey, Philip}, journal = {PNAS}, number = {18}, pages = {E1695 -- E1704}, publisher = {National Academy of Sciences}, title = {{3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture}}, doi = {10.1073/pnas.1304354110}, volume = {110}, year = {2013}, } @article{2826, abstract = {Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent analyses identified three additional mutations in three highly myopic unrelated individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential gene expression in a developmental mouse model, we induced myopia by applying a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for a copper homeostasis protein influential in mitochondrial cytochrome c oxidase activity. Copper deficiencies have been linked with photoreceptor loss and myopia with increased scleral wall elasticity. Retinal thinning has been reported with an SC02 variant. Human mutation identification with support from an induced myopic animal provides biological insights of myopic development.}, author = {Tran Viet, Khanh and Powell, Caldwell and Barathi, Veluchamy and Klemm, Thomas and Maurer Stroh, Sebastian and Limviphuvadh, Vachiranee and Soler, Vincent and Ho, Candice and Yanovitch, Tammy and Schneider, Georg and Li, Yi and Nading, Erica and Metlapally, Ravikanth and Saw, Seang and Goh, Liang and Rozen, Steve and Young, Terri}, journal = {American Journal of Human Genetics}, number = {5}, pages = {820 -- 826}, publisher = {Cell Press}, title = {{Mutations in SCO2 are associated with autosomal-dominant high-grade myopia}}, doi = {10.1016/j.ajhg.2013.04.005}, volume = {92}, year = {2013}, } @article{2827, abstract = {Removal of cargos from the cell surface via endocytosis is an efficient mechanism to regulate activities of plasma membrane (PM)-resident proteins, such as receptors or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally associated with pathogen defense. Here, we describe an unanticipated effect of SA on subcellular endocytic cycling of proteins. Both exogenous treatments and endogenously enhanced SA levels repressed endocytosis of different PM proteins. The SA effect on endocytosis did not involve transcription or known components of the SA signaling pathway for transcriptional regulation. SA likely targets an endocytic mechanism that involves the coat protein clathrin, because SA interfered with the clathrin incidence at the PM and clathrin-deficient mutants were less sensitive to the impact of SA on the auxin distribution and root bending during the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data suggest that the established SA impact on transcription in plant immunity and the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent mechanisms by which SA regulates distinct aspects of plant physiology.}, author = {Du, Yunlong and Tejos, Ricardo and Beck, Martina and Himschoot, Ellie and Li, Hongjiang and Robatzek, Silke and Vanneste, Steffen and Friml, Jirí}, journal = {PNAS}, number = {19}, pages = {7946 -- 7951}, publisher = {National Academy of Sciences}, title = {{Salicylic acid interferes with clathrin-mediated endocytic protein trafficking}}, doi = {10.1073/pnas.1220205110}, volume = {110}, year = {2013}, } @article{2828, abstract = {We study the complexity of valued constraint satisfaction problems (VCSPs) parametrized by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimize the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well understood, see Raghavendra [2008]. However, there is no characterization of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimization perspective. We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e., relations), such languages have been called conservative and studied by Bulatov [2003, 2011] and recently by Barto [2011]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [2006] for languages over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a Max-CSP), and by Takhanov [2010a] for {0, ∞}-valued languages containing all finite-valued unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimor-phisms), then any instance can be solved in polynomial time (via a new algorithm developed in this article), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains are significantly harder than the Boolean cases. The polynomial-time algorithm we present for the tractable cases is a generalization of the submodular minimization problem and a result of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a] and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [2008], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.}, author = {Kolmogorov, Vladimir and Živný, Stanislav}, journal = {Journal of the ACM}, number = {2}, publisher = {ACM}, title = {{The complexity of conservative valued CSPs}}, doi = {10.1145/2450142.2450146}, volume = {60}, year = {2013}, } @article{2829, abstract = {Laminar-turbulent intermittency is intrinsic to the transitional regime of a wide range of fluid flows including pipe, channel, boundary layer, and Couette flow. In the latter turbulent spots can grow and form continuous stripes, yet in the stripe-normal direction they remain interspersed by laminar fluid. We carry out direct numerical simulations in a long narrow domain and observe that individual turbulent stripes are transient. In agreement with recent observations in pipe flow, we find that turbulence becomes sustained at a distinct critical point once the spatial proliferation outweighs the inherent decaying process. By resolving the asymptotic size distributions close to criticality we can for the first time demonstrate scale invariance at the onset of turbulence.}, author = {Shi, Liang and Avila, Marc and Hof, Björn}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{Scale invariance at the onset of turbulence in couette flow}}, doi = {10.1103/PhysRevLett.110.204502}, volume = {110}, year = {2013}, }