@article{1173, abstract = {We introduce the Voronoi functional of a triangulation of a finite set of points in the Euclidean plane and prove that among all geometric triangulations of the point set, the Delaunay triangulation maximizes the functional. This result neither extends to topological triangulations in the plane nor to geometric triangulations in three and higher dimensions.}, author = {Edelsbrunner, Herbert and Glazyrin, Alexey and Musin, Oleg and Nikitenko, Anton}, issn = {02099683}, journal = {Combinatorica}, number = {5}, pages = {887 -- 910}, publisher = {Springer}, title = {{The Voronoi functional is maximized by the Delaunay triangulation in the plane}}, doi = {10.1007/s00493-016-3308-y}, volume = {37}, year = {2017}, } @inproceedings{1174, abstract = {Security of cryptographic applications is typically defined by security games. The adversary, within certain resources, cannot win with probability much better than 0 (for unpredictability applications, like one-way functions) or much better than 1/2 (indistinguishability applications for instance encryption schemes). In so called squared-friendly applications the winning probability of the adversary, for different values of the application secret randomness, is not only close to 0 or 1/2 on average, but also concentrated in the sense that its second central moment is small. The class of squared-friendly applications, which contains all unpredictability applications and many indistinguishability applications, is particularly important for key derivation. Barak et al. observed that for square-friendly applications one can beat the "RT-bound", extracting secure keys with significantly smaller entropy loss. In turn Dodis and Yu showed that in squared-friendly applications one can directly use a "weak" key, which has only high entropy, as a secure key. In this paper we give sharp lower bounds on square security assuming security for "weak" keys. We show that any application which is either (a) secure with weak keys or (b) allows for entropy savings for keys derived by universal hashing, must be square-friendly. Quantitatively, our lower bounds match the positive results of Dodis and Yu and Barak et al. (TCC\'13, CRYPTO\'11) Hence, they can be understood as a general characterization of squared-friendly applications. While the positive results on squared-friendly applications where derived by one clever application of the Cauchy-Schwarz Inequality, for tight lower bounds we need more machinery. In our approach we use convex optimization techniques and some theory of circular matrices.}, author = {Skórski, Maciej}, issn = {18688969}, location = {Hannover, Germany}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Lower bounds on key derivation for square-friendly applications}}, doi = {10.4230/LIPIcs.STACS.2017.57}, volume = {66}, year = {2017}, } @inproceedings{1175, abstract = {We study space complexity and time-space trade-offs with a focus not on peak memory usage but on overall memory consumption throughout the computation. Such a cumulative space measure was introduced for the computational model of parallel black pebbling by [Alwen and Serbinenko ’15] as a tool for obtaining results in cryptography. We consider instead the non- deterministic black-white pebble game and prove optimal cumulative space lower bounds and trade-offs, where in order to minimize pebbling time the space has to remain large during a significant fraction of the pebbling. We also initiate the study of cumulative space in proof complexity, an area where other space complexity measures have been extensively studied during the last 10–15 years. Using and extending the connection between proof complexity and pebble games in [Ben-Sasson and Nordström ’08, ’11] we obtain several strong cumulative space results for (even parallel versions of) the resolution proof system, and outline some possible future directions of study of this, in our opinion, natural and interesting space measure.}, author = {Alwen, Joel F and De Rezende, Susanna and Nordstrom, Jakob and Vinyals, Marc}, editor = {Papadimitriou, Christos}, issn = {18688969}, location = {Berkeley, CA, United States}, pages = {38:1--38--21}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Cumulative space in black-white pebbling and resolution}}, doi = {10.4230/LIPIcs.ITCS.2017.38}, volume = {67}, year = {2017}, } @inproceedings{1176, abstract = {The algorithm Argon2i-B of Biryukov, Dinu and Khovratovich is currently being considered by the IRTF (Internet Research Task Force) as a new de-facto standard for password hashing. An older version (Argon2i-A) of the same algorithm was chosen as the winner of the recent Password Hashing Competition. An important competitor to Argon2i-B is the recently introduced Balloon Hashing (BH) algorithm of Corrigan-Gibs, Boneh and Schechter. A key security desiderata for any such algorithm is that evaluating it (even using a custom device) requires a large amount of memory amortized across multiple instances. Alwen and Blocki (CRYPTO 2016) introduced a class of theoretical attacks against Argon2i-A and BH. While these attacks yield large asymptotic reductions in the amount of memory, it was not, a priori, clear if (1) they can be extended to the newer Argon2i-B, (2) the attacks are effective on any algorithm for practical parameter ranges (e.g., 1GB of memory) and (3) if they can be effectively instantiated against any algorithm under realistic hardware constrains. In this work we answer all three of these questions in the affirmative for all three algorithms. This is also the first work to analyze the security of Argon2i-B. In more detail, we extend the theoretical attacks of Alwen and Blocki (CRYPTO 2016) to the recent Argon2i-B proposal demonstrating severe asymptotic deficiencies in its security. Next we introduce several novel heuristics for improving the attack's concrete memory efficiency even when on-chip memory bandwidth is bounded. We then simulate our attacks on randomly sampled Argon2i-A, Argon2i-B and BH instances and measure the resulting memory consumption for various practical parameter ranges and for a variety of upperbounds on the amount of parallelism available to the attacker. Finally we describe, implement, and test a new heuristic for applying the Alwen-Blocki attack to functions employing a technique developed by Corrigan-Gibs et al. for improving concrete security of memory-hard functions. We analyze the collected data and show the effects various parameters have on the memory consumption of the attack. In particular, we can draw several interesting conclusions about the level of security provided by these functions. · For the Alwen-Blocki attack to fail against practical memory parameters, Argon2i-B must be instantiated with more than 10 passes on memory - beyond the "paranoid" parameter setting in the current IRTF proposal. · The technique of Corrigan-Gibs for improving security can also be overcome by the Alwen-Blocki attack under realistic hardware constraints. · On a positive note, both the asymptotic and concrete security of Argon2i-B seem to improve on that of Argon2i-A.}, author = {Alwen, Joel F and Blocki, Jeremiah}, isbn = {978-150905761-0}, location = {Paris, France}, publisher = {IEEE}, title = {{Towards practical attacks on Argon2i and balloon hashing}}, doi = {10.1109/EuroSP.2017.47}, year = {2017}, } @inproceedings{1178, abstract = {For any pair (X, Z) of correlated random variables we can think of Z as a randomized function of X. If the domain of Z is small, one can make this function computationally efficient by allowing it to be only approximately correct. In folklore this problem is known as simulating auxiliary inputs. This idea of simulating auxiliary information turns out to be a very usefull tool, finding applications in complexity theory, cryptography, pseudorandomness and zero-knowledge. In this paper we revisit this problem, achieving the following results: (a) We present a novel boosting algorithm for constructing the simulator. This boosting proof is of independent interest, as it shows how to handle “negative mass” issues when constructing probability measures by shifting distinguishers in descent algorithms. Our technique essentially fixes the flaw in the TCC’14 paper “How to Fake Auxiliary Inputs”. (b) The complexity of our simulator is better than in previous works, including results derived from the uniform min-max theorem due to Vadhan and Zheng. To achieve (s,ϵ) -indistinguishability we need the complexity O(s⋅25ℓϵ−2) in time/circuit size, which improve previous bounds by a factor of ϵ−2. In particular, with we get meaningful provable security for the EUROCRYPT’09 leakage-resilient stream cipher instantiated with a standard 256-bit block cipher, like }, author = {Skórski, Maciej}, pages = {159 -- 179}, publisher = {Springer}, title = {{Simulating auxiliary inputs, revisited}}, doi = {10.1007/978-3-662-53641-4_7}, volume = {9985}, year = {2017}, } @article{1180, abstract = {In this article we define an algebraic vertex of a generalized polyhedron and show that the set of algebraic vertices is the smallest set of points needed to define the polyhedron. We prove that the indicator function of a generalized polytope P is a linear combination of indicator functions of simplices whose vertices are algebraic vertices of P. We also show that the indicator function of any generalized polyhedron is a linear combination, with integer coefficients, of indicator functions of cones with apices at algebraic vertices and line-cones. The concept of an algebraic vertex is closely related to the Fourier–Laplace transform. We show that a point v is an algebraic vertex of a generalized polyhedron P if and only if the tangent cone of P, at v, has non-zero Fourier–Laplace transform.}, author = {Akopyan, Arseniy and Bárány, Imre and Robins, Sinai}, issn = {00018708}, journal = {Advances in Mathematics}, pages = {627 -- 644}, publisher = {Academic Press}, title = {{Algebraic vertices of non-convex polyhedra}}, doi = {10.1016/j.aim.2016.12.026}, volume = {308}, year = {2017}, } @article{1187, 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 (Formula presented.) 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 attacks. A MAC implies such a (two-round) protocol.}, author = {Kiltz, Eike and Pietrzak, Krzysztof Z and Venturi, Daniele and Cash, David and Jain, Abhishek}, journal = {Journal of Cryptology}, number = {4}, pages = {1238 -- 1275}, publisher = {Springer}, title = {{Efficient authentication from hard learning problems}}, doi = {10.1007/s00145-016-9247-3}, volume = {30}, year = {2017}, } @article{1191, abstract = {Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed.}, author = {Kollár, Richard and Novak, Sebastian}, journal = {Bulletin of Mathematical Biology}, number = {3}, pages = {525--559}, publisher = {Springer}, title = {{Existence of traveling waves for the generalized F–KPP equation}}, doi = {10.1007/s11538-016-0244-3}, volume = {79}, year = {2017}, } @inproceedings{1192, abstract = {The main result of this paper is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even Δ-matroid constraints allows us to extend the tractability result to a larger class of Δ-matroids that includes many classes that were known to be tractable before, namely co-independent, compact, local and binary.}, author = {Kazda, Alexandr and Kolmogorov, Vladimir and Rolinek, Michal}, isbn = {978-161197478-2}, location = {Barcelona, Spain}, pages = {307 -- 326}, publisher = {SIAM}, title = {{Even delta-matroids and the complexity of planar Boolean CSPs}}, doi = {10.1137/1.9781611974782.20}, year = {2017}, } @inproceedings{1194, abstract = {Termination is one of the basic liveness properties, and we study the termination problem for probabilistic programs with real-valued variables. Previous works focused on the qualitative problem that asks whether an input program terminates with probability~1 (almost-sure termination). A powerful approach for this qualitative problem is the notion of ranking supermartingales with respect to a given set of invariants. The quantitative problem (probabilistic termination) asks for bounds on the termination probability. A fundamental and conceptual drawback of the existing approaches to address probabilistic termination is that even though the supermartingales consider the probabilistic behavior of the programs, the invariants are obtained completely ignoring the probabilistic aspect. In this work we address the probabilistic termination problem for linear-arithmetic probabilistic programs with nondeterminism. We define the notion of {\em stochastic invariants}, which are constraints along with a probability bound that the constraints hold. We introduce a concept of {\em repulsing supermartingales}. First, we show that repulsing supermartingales can be used to obtain bounds on the probability of the stochastic invariants. Second, we show the effectiveness of repulsing supermartingales in the following three ways: (1)~With a combination of ranking and repulsing supermartingales we can compute lower bounds on the probability of termination; (2)~repulsing supermartingales provide witnesses for refutation of almost-sure termination; and (3)~with a combination of ranking and repulsing supermartingales we can establish persistence properties of probabilistic programs. We also present results on related computational problems and an experimental evaluation of our approach on academic examples. }, author = {Chatterjee, Krishnendu and Novotny, Petr and Zikelic, Djordje}, issn = {07308566}, location = {Paris, France}, number = {1}, pages = {145 -- 160}, publisher = {ACM}, title = {{Stochastic invariants for probabilistic termination}}, doi = {10.1145/3009837.3009873}, volume = {52}, year = {2017}, } @article{1198, abstract = {We consider a model of fermions interacting via point interactions, defined via a certain weighted Dirichlet form. While for two particles the interaction corresponds to infinite scattering length, the presence of further particles effectively decreases the interaction strength. We show that the model becomes trivial in the thermodynamic limit, in the sense that the free energy density at any given particle density and temperature agrees with the corresponding expression for non-interacting particles.}, author = {Moser, Thomas and Seiringer, Robert}, issn = {03779017}, journal = {Letters in Mathematical Physics}, number = {3}, pages = { 533 -- 552}, publisher = {Springer}, title = {{Triviality of a model of particles with point interactions in the thermodynamic limit}}, doi = {10.1007/s11005-016-0915-x}, volume = {107}, year = {2017}, } @article{1199, abstract = {Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.}, author = {Barton, Nicholas H}, journal = {Heredity}, pages = {96 -- 109}, publisher = {Nature Publishing Group}, title = {{How does epistasis influence the response to selection?}}, doi = {10.1038/hdy.2016.109}, volume = {118}, year = {2017}, } @article{1207, abstract = {The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix.}, author = {Bao, Zhigang and Erdös, László and Schnelli, Kevin}, issn = {00103616}, journal = {Communications in Mathematical Physics}, number = {3}, pages = {947 -- 990}, publisher = {Springer}, title = {{Local law of addition of random matrices on optimal scale}}, doi = {10.1007/s00220-016-2805-6}, volume = {349}, year = {2017}, } @article{1208, abstract = {We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd.}, author = {Zwiernik, Piotr and Uhler, Caroline and Richards, Donald}, issn = {13697412}, journal = {Journal of the Royal Statistical Society. Series B: Statistical Methodology}, number = {4}, pages = {1269 -- 1292}, publisher = {Wiley-Blackwell}, title = {{Maximum likelihood estimation for linear Gaussian covariance models}}, doi = {10.1111/rssb.12217}, volume = {79}, year = {2017}, } @article{1211, abstract = {Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.}, author = {Budanur, Nazmi B and Cvitanović, Predrag}, journal = {Journal of Statistical Physics}, number = {3-4}, pages = {636--655}, publisher = {Springer}, title = {{Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system}}, doi = {10.1007/s10955-016-1672-z}, volume = {167}, year = {2017}, } @article{1228, abstract = {Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.}, author = {Sauerzopf, Ulrich and Sacco, Roberto and Novarino, Gaia and Niello, Marco and Weidenauer, Ana and Praschak Rieder, Nicole and Sitte, Harald and Willeit, Matthaeus}, journal = {European Journal of Neuroscience}, number = {1}, pages = {45 -- 57}, publisher = {Wiley-Blackwell}, title = {{Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence}}, doi = {10.1111/ejn.13418}, volume = {45}, year = {2017}, } @article{123, abstract = {The Leidenfrost effect occurs when an object near a hot surface vaporizes rapidly enough to lift itself up and hover. Although well understood for liquids and stiff sublimable solids, nothing is known about the effect with materials whose stiffness lies between these extremes. Here we introduce a new phenomenon that occurs with vaporizable soft solids - the elastic Leidenfrost effect. By dropping hydrogel spheres onto hot surfaces we find that, rather than hovering, they energetically bounce several times their diameter for minutes at a time. With high-speed video during a single impact, we uncover high-frequency microscopic gap dynamics at the sphere/substrate interface. We show how these otherwise-hidden agitations constitute work cycles that harvest mechanical energy from the vapour and sustain the bouncing. Our findings suggest a new strategy for injecting mechanical energy into a widely used class of soft materials, with potential relevance to fields such as active matter, soft robotics and microfluidics.}, author = {Waitukaitis, Scott R and Zuiderwijk, Antal and Souslov, Anton and Coulais, Corentin and Van Hecke, Martin}, journal = {Nature Physics}, number = {11}, pages = {1095 -- 1099}, publisher = {Nature Publishing Group}, title = {{Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing}}, doi = {10.1038/nphys4194}, volume = {13}, year = {2017}, } @article{909, abstract = {We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor &#xbd; cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape.}, author = {Akopyan, Arseniy and Vysotsky, Vladislav}, issn = {00029890}, journal = {The American Mathematical Monthly}, number = {7}, pages = {588 -- 596}, publisher = {Mathematical Association of America}, title = {{On the lengths of curves passing through boundary points of a planar convex shape}}, doi = {10.4169/amer.math.monthly.124.7.588}, volume = {124}, year = {2017}, } @article{910, abstract = {Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear. }, author = {Novak, Sebastian and Barton, Nicholas H}, journal = {Genetics}, number = {2}, pages = {653 -- 668}, publisher = {Genetics Society of America}, title = {{When does frequency-independent selection maintain genetic variation?}}, doi = {10.1534/genetics.117.300129}, volume = {207}, year = {2017}, } @inproceedings{911, abstract = {We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset.}, author = {Royer, Amélie and Kolesnikov, Alexander and Lampert, Christoph}, location = {London, United Kingdom}, pages = {85.1--85.12}, publisher = {BMVA Press}, title = {{Probabilistic image colorization}}, doi = {10.5244/c.31.85}, year = {2017}, } @article{912, abstract = {We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals. }, author = {Deuchert, Andreas}, issn = {00222488}, journal = { Journal of Mathematical Physics}, number = {8}, publisher = {AIP}, title = {{A lower bound for the BCS functional with boundary conditions at infinity}}, doi = {10.1063/1.4996580}, volume = {58}, year = {2017}, } @article{9137, abstract = {Pools of air cooled by partial rain evaporation span up to several hundreds of kilometers in nature and typically last less than 1 day, ultimately losing their identity to the large-scale flow. These fundamentally differ in character from the radiatively-driven dry pools defining convective aggregation. Advancement in remote sensing and in computer capabilities has promoted exploration of how precipitation-induced cold pool processes modify the convective spectrum and life cycle. This contribution surveys current understanding of such cold pools over the tropical and subtropical oceans. In shallow convection with low rain rates, the cold pools moisten, preserving the near-surface equivalent potential temperature or increasing it if the surface moisture fluxes cannot ventilate beyond the new surface layer; both conditions indicate downdraft origin air from within the boundary layer. When rain rates exceed ∼ 2 mm h−1, convective-scale downdrafts can bring down drier air of lower equivalent potential temperature from above the boundary layer. The resulting density currents facilitate the lifting of locally thermodynamically favorable air and can impose an arc-shaped mesoscale cloud organization. This organization allows clouds capable of reaching 4–5 km within otherwise dry environments. These are more commonly observed in the northern hemisphere trade wind regime, where the flow to the intertropical convergence zone is unimpeded by the equator. Their near-surface air properties share much with those shown from cold pools sampled in the equatorial Indian Ocean. Cold pools are most effective at influencing the mesoscale organization when the atmosphere is moist in the lower free troposphere and dry above, suggesting an optimal range of water vapor paths. Outstanding questions on the relationship between cold pools, their accompanying moisture distribution and cloud cover are detailed further. Near-surface water vapor rings are documented in one model inside but near the cold pool edge; these are not consistent with observations, but do improve with smaller horizontal grid spacings.}, author = {Zuidema, Paquita and Torri, Giuseppe and MULLER, Caroline J and Chandra, Arunchandra}, issn = {0169-3298}, journal = {Surveys in Geophysics}, keywords = {Geochemistry and Petrology, Geophysics}, number = {6}, pages = {1283--1305}, publisher = {Springer Nature}, title = {{A survey of precipitation-induced atmospheric cold pools over oceans and their interactions with the larger-scale environment}}, doi = {10.1007/s10712-017-9447-x}, volume = {38}, year = {2017}, } @article{9138, abstract = {Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network.}, author = {Holloway, Christopher E. and Wing, Allison A. and Bony, Sandrine and MULLER, Caroline J and Masunaga, Hirohiko and L’Ecuyer, Tristan S. and Turner, David D. and Zuidema, Paquita}, issn = {0169-3298}, journal = {Surveys in Geophysics}, keywords = {Geochemistry and Petrology, Geophysics}, number = {6}, pages = {1199--1236}, publisher = {Springer Nature}, title = {{Observing convective aggregation}}, doi = {10.1007/s10712-017-9419-1}, volume = {38}, year = {2017}, } @article{914, abstract = {Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect.}, author = {Giehr, Julia and Grasse, Anna V and Cremer, Sylvia and Heinze, Jürgen and Schrempf, Alexandra}, issn = {20545703}, journal = {Royal Society Open Science}, number = {7}, publisher = {Royal Society, The}, title = {{Ant queens increase their reproductive efforts after pathogen infection}}, doi = {10.1098/rsos.170547}, volume = {4}, year = {2017}, } @inproceedings{915, abstract = {We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.}, author = {Swoboda, Paul and Andres, Bjoern}, isbn = {978-153860457-1}, location = {Honolulu, HA, United States}, pages = {4990--4999}, publisher = {IEEE}, title = {{A message passing algorithm for the minimum cost multicut problem}}, doi = {10.1109/CVPR.2017.530}, volume = {2017}, year = {2017}, } @article{9152, abstract = {Previous numerical studies of the dissipation of internal tides in idealized settings suggest the existence of a critical latitude (~29°) where dissipation is enhanced. But observations only indicate a modest enhancement at this latitude. To resolve this difference between observational and numerical results, the authors study the latitudinal dependence of internal tides’ dissipation in more realistic conditions. In particular, the ocean is not a quiescent medium; the presence of large-scale currents or mesoscale eddies can impact the propagation and dissipation of internal tides. This paper investigates the impact of a weak background mean current in numerical simulations. The authors focus on the local dissipation of high spatial mode internal waves near their generation site. The vertical profile of dissipation and its variation with latitude without the mean current are consistent with earlier studies. But adding a weak mean current has a major impact on the latitudinal distribution of dissipation. The peak at the critical latitude disappears, and the dissipation is closer to a constant, albeit with two weak peaks at ~25° and ~35° latitude. This disappearance results from the Doppler shift of the internal tides’ frequency, which hinders the nonlinear transfer of energy to small-scale secondary waves via the parametric subharmonic instability (PSI). The new two weak peaks correspond to the Doppler-shifted critical latitudes of the left- and right-propagating waves. The results are confirmed in simulations with simple sinusoidal topography. Thus, although nonlinear transfers via PSI are efficient at dissipating internal tides, the exact location of the dissipation is sensitive to large-scale oceanic conditions.}, author = {Richet, O. and MULLER, Caroline J and Chomaz, J.-M.}, issn = {0022-3670}, journal = {Journal of Physical Oceanography}, keywords = {Oceanography}, number = {6}, pages = {1457--1472}, publisher = {American Meteorological Society}, title = {{Impact of a mean current on the internal tide energy dissipation at the critical latitude}}, doi = {10.1175/jpo-d-16-0197.1}, volume = {47}, year = {2017}, } @inproceedings{916, abstract = {We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each.}, author = {Swoboda, Paul and Rother, Carsten and Abu Alhaija, Carsten and Kainmueller, Dagmar and Savchynskyy, Bogdan}, isbn = {978-153860457-1}, location = {Honolulu, HA, United States}, pages = {7062--7071}, publisher = {IEEE}, title = {{A study of lagrangean decompositions and dual ascent solvers for graph matching}}, doi = {10.1109/CVPR.2017.747}, volume = {2017}, year = {2017}, } @inproceedings{917, abstract = {We propose a general dual ascent framework for Lagrangean decomposition of combinatorial problems. Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers.}, author = {Swoboda, Paul and Kuske, Jan and Savchynskyy, Bogdan}, isbn = {978-153860457-1}, location = {Honolulu, HA, United States}, pages = {4950--4960}, publisher = {IEEE}, title = {{A dual ascent framework for Lagrangean decomposition of combinatorial problems}}, doi = {10.1109/CVPR.2017.526}, volume = {2017}, year = {2017}, } @article{93, abstract = {An electro-optomechanical device capable of microwave-to-optics conversion has recently been demonstrated, with the vision of enabling optical networks of superconducting qubits. Here we present an improved converter design that uses a three-dimensional microwave cavity for coupling between the microwave transmission line and an integrated LC resonator on the converter chip. The new design simplifies the optical assembly and decouples it from the microwave part of the setup. Experimental demonstrations show that the modular device assembly allows us to flexibly tune the microwave coupling to the converter chip while maintaining small loss. We also find that electromechanical experiments are not impacted by the additional microwave cavity. Our design is compatible with a high-finesse optical cavity and will improve optical performance.}, author = {Menke, Tim and Burns, Peter and Higginbotham, Andrew P and Kampel, N S and Peterson, Robert and Cicak, Katarina and Simmonds, Raymond and Regal, Cindy and Lehnert, Konrad}, journal = {Review of Scientific Instruments}, number = {9}, publisher = {American Institute of Physics}, title = {{Reconfigurable re-entrant cavity for wireless coupling to an electro-optomechanical device}}, doi = {10.1063/1.5000973}, volume = {88}, year = {2017}, } @phdthesis{938, abstract = {The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin.}, author = {Adamowski, Maciek}, pages = {117}, publisher = {IST Austria}, title = {{Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana }}, doi = {10.15479/AT:ISTA:th_842}, year = {2017}, } @article{939, abstract = {We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding.}, author = {Midya, Bikashkali and Konotop, Vladimir}, issn = {00319007}, journal = {Physical Review Letters}, number = {3}, publisher = {American Physical Society}, title = {{Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons}}, doi = {10.1103/PhysRevLett.119.033905}, volume = {119}, year = {2017}, } @article{94, abstract = {We introduce a method for breaking Lorentz reciprocity based upon the noncommutation of frequency conversion and delay. The method requires no magnetic materials or resonant physics, allowing for the design of scalable and broadband nonreciprocal circuits. With this approach, two types of gyrators - universal building blocks for linear, nonreciprocal circuits - are constructed. Using one of these gyrators, we create a circulator with >15 dB of isolation across the 5-9 GHz band. Our designs may be readily extended to any platform with suitable frequency conversion elements, including semiconducting devices for telecommunication or an on-chip superconducting implementation for quantum information processing.}, author = {Rosenthal, Eric and Chapman, Benjamin and Higginbotham, Andrew P and Kerckhoff, Joseph and Lehnert, Konrad}, journal = {APS Physics, Physical Review Letters}, number = {14}, publisher = {American Physical Society}, title = {{Breaking Lorentz reciprocity with frequency conversion and delay}}, doi = {10.1103/PhysRevLett.119.147703}, volume = {119}, year = {2017}, } @article{943, abstract = {Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation.}, author = {Zagórski, Marcin P and Tabata, Yoji and Brandenberg, Nathalie and Lutolf, Matthias and Tkacik, Gasper and Bollenbach, Tobias and Briscoe, James and Kicheva, Anna}, issn = {00368075}, journal = {Science}, number = {6345}, pages = {1379 -- 1383}, publisher = {American Association for the Advancement of Science}, title = {{Decoding of position in the developing neural tube from antiparallel morphogen gradients}}, doi = {10.1126/science.aam5887}, volume = {356}, year = {2017}, } @article{945, abstract = {While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.}, author = {Huylmans, Ann K and Macon, Ariana and Vicoso, Beatriz}, issn = {07374038}, journal = {Molecular Biology and Evolution}, number = {10}, pages = {2637 -- 2649}, publisher = {Oxford University Press}, title = {{Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome}}, doi = {10.1093/molbev/msx190}, volume = {34}, year = {2017}, } @article{946, abstract = {Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.}, author = {Von Wangenheim, Daniel and Hauschild, Robert and Fendrych, Matyas and Barone, Vanessa and Benková, Eva and Friml, Jirí}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Live tracking of moving samples in confocal microscopy for vertically grown roots}}, doi = {10.7554/eLife.26792}, volume = {6}, year = {2017}, } @article{947, abstract = {Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.}, author = {De Martino, Daniele and Capuani, Fabrizio and De Martino, Andrea}, issn = {24700045}, journal = { Physical Review E Statistical Nonlinear and Soft Matter Physics }, number = {1}, publisher = {American Institute of Physics}, title = {{Quantifying the entropic cost of cellular growth control}}, doi = {10.1103/PhysRevE.96.010401}, volume = {96}, year = {2017}, } @inproceedings{950, abstract = {Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\in [0,1] such that if\PO's budget exceeds $t$, he can win the game, and if\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. }, author = {Avni, Guy and Henzinger, Thomas A and Chonev, Ventsislav K}, issn = {1868-8969}, location = {Berlin, Germany}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Infinite-duration bidding games}}, doi = {10.4230/LIPIcs.CONCUR.2017.21}, volume = {85}, year = {2017}, } @article{951, abstract = {Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo}, author = {Schmidt, Tom and Barton, Nicholas H and Rasic, Gordana and Turley, Andrew and Montgomery, Brian and Iturbe Ormaetxe, Inaki and Cook, Peter and Ryan, Peter and Ritchie, Scott and Hoffmann, Ary and O’Neill, Scott and Turelli, Michael}, issn = {15449173}, journal = {PLoS Biology}, number = {5}, publisher = {Public Library of Science}, title = {{Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti}}, doi = {10.1371/journal.pbio.2001894}, volume = {15}, year = {2017}, } @article{952, abstract = {A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area.}, author = {Turelli, Michael and Barton, Nicholas H}, issn = {00405809}, journal = {Theoretical Population Biology}, pages = {45 -- 60}, publisher = {Elsevier}, title = {{Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti}}, doi = {10.1016/j.tpb.2017.03.003}, volume = {115}, year = {2017}, } @article{953, abstract = {The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.}, author = {Charlesworth, Deborah and Barton, Nicholas H and Charlesworth, Brian}, journal = {Proceedings of the Royal Society of London Series B Biological Sciences}, number = {1855}, publisher = {Royal Society, The}, title = {{The sources of adaptive evolution}}, doi = {10.1098/rspb.2016.2864}, volume = {284}, year = {2017}, } @article{954, abstract = {Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for.}, author = {Lagator, Mato and Paixao, Tiago and Barton, Nicholas H and Bollback, Jonathan P and Guet, Calin C}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{On the mechanistic nature of epistasis in a canonical cis-regulatory element}}, doi = {10.7554/eLife.25192}, volume = {6}, year = {2017}, } @article{955, abstract = {Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.}, author = {Friedlander, Tamar and Prizak, Roshan and Barton, Nicholas H and Tkacik, Gasper}, issn = {20411723}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{Evolution of new regulatory functions on biophysically realistic fitness landscapes}}, doi = {10.1038/s41467-017-00238-8}, volume = {8}, year = {2017}, } @article{956, abstract = {We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance.}, author = {Carlen, Eric and Maas, Jan}, issn = {00221236}, journal = {Journal of Functional Analysis}, number = {5}, pages = {1810 -- 1869}, publisher = {Academic Press}, title = {{Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance}}, doi = {10.1016/j.jfa.2017.05.003}, volume = {273}, year = {2017}, } @article{959, abstract = {In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions.}, author = {De Martino, Daniele}, issn = {24700045}, journal = { Physical Review E Statistical Nonlinear and Soft Matter Physics }, number = {6}, pages = {062419}, publisher = {American Institute of Physics}, title = {{Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics}}, doi = {10.1103/PhysRevE.95.062419}, volume = {95}, year = {2017}, } @article{960, abstract = {The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.}, author = {Hansen, Andi H and Düllberg, Christian F and Mieck, Christine and Loose, Martin and Hippenmeyer, Simon}, issn = {16625102}, journal = {Frontiers in Cellular Neuroscience}, publisher = {Frontiers Research Foundation}, title = {{Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks}}, doi = {10.3389/fncel.2017.00176}, volume = {11}, year = {2017}, } @phdthesis{961, abstract = {Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation.}, author = {Barone, Vanessa}, pages = {109}, publisher = {IST Austria}, title = {{Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation}}, doi = {10.15479/AT:ISTA:th_825}, year = {2017}, } @inproceedings{963, abstract = {Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. }, author = {Avni, Guy and Guha, Shibashis and Kupferman, Orna}, issn = {18688969}, location = {Aalborg, Denmark}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Timed network games with clocks}}, doi = {10.4230/LIPIcs.MFCS.2017.37}, volume = {83}, year = {2017}, } @article{988, abstract = {The current-phase relation (CPR) of a Josephson junction (JJ) determines how the supercurrent evolves with the superconducting phase difference across the junction. Knowledge of the CPR is essential in order to understand the response of a JJ to various external parameters. Despite the rising interest in ultraclean encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we use a fully gate-tunable graphene superconducting quantum intereference device (SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently controlling the critical current of the JJs, we can operate the SQUID either in a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found to be skewed, deviating significantly from a sinusoidal form. The skewness can be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance oscillations of the ballistic graphene cavity. We compare our experiments with tight-binding calculations that include realistic graphene-superconductor interfaces and find a good qualitative agreement.}, author = {Nanda, Gaurav and Aguilera Servin, Juan L and Rakyta, Péter and Kormányos, Andor and Kleiner, Reinhold and Koelle, Dieter and Watanabe, Kazuo and Taniguchi, Takashi and Vandersypen, Lieven and Goswami, Srijit}, issn = {15306984}, journal = {Nano Letters}, number = {6}, pages = {3396 -- 3401}, publisher = {American Chemical Society}, title = {{Current-phase relation of ballistic graphene Josephson junctions}}, doi = {10.1021/acs.nanolett.7b00097}, volume = {17}, year = {2017}, } @article{990, abstract = {Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.}, author = {Sachdeva, Himani and Barton, Nicholas H}, issn = {00143820}, journal = {Evolution; International Journal of Organic Evolution}, number = {6}, pages = {1478 -- 1493 }, publisher = {Wiley-Blackwell}, title = {{Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow}}, doi = {10.1111/evo.13252}, volume = {71}, year = {2017}, } @phdthesis{992, abstract = {An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of variables, a finite domain of labels, and a set of constraints, each constraint acting on a subset of the variables. The goal is to find an assignment of labels to its variables that satisfies all constraints (or decide whether one exists). If we allow more general “soft” constraints, which come with (possibly infinite) costs of particular assignments, we obtain instances from a richer class called Valued Constraint Satisfaction Problem (VCSP). There the goal is to find an assignment with minimum total cost. In this thesis, we focus (assuming that P 6 = NP) on classifying computational com- plexity of CSPs and VCSPs under certain restricting conditions. Two results are the core content of the work. In one of them, we consider VCSPs parametrized by a constraint language, that is the set of “soft” constraints allowed to form the instances, and finish the complexity classification modulo (missing pieces of) complexity classification for analogously parametrized CSP. The other result is a generalization of Edmonds’ perfect matching algorithm. This generalization contributes to complexity classfications in two ways. First, it gives a new (largest known) polynomial-time solvable class of Boolean CSPs in which every variable may appear in at most two constraints and second, it settles full classification of Boolean CSPs with planar drawing (again parametrized by a constraint language).}, author = {Rolinek, Michal}, pages = {97}, publisher = {IST Austria}, title = {{Complexity of constraint satisfaction}}, doi = {10.15479/AT:ISTA:th_815}, year = {2017}, } @article{993, abstract = {In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development.}, author = {Levina (Martius), Anna and Priesemann, Viola}, issn = {20411723}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Subsampling scaling}}, doi = {10.1038/ncomms15140}, volume = {8}, year = {2017}, } @article{994, abstract = {The formation of vortices is usually considered to be the main mechanism of angular momentum disposal in superfluids. Recently, it was predicted that a superfluid can acquire angular momentum via an alternative, microscopic route -- namely, through interaction with rotating impurities, forming so-called `angulon quasiparticles' [Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to transfer of a small number of angular momentum quanta from the impurity to the superfluid, as opposed to vortex instabilities, where angular momentum is quantized in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules) represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically 3D as well, as opposed to a merely planar rotation which is inherent to vortices. Herein we show that the angulon theory can explain the anomalous broadening of the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities in experiment.}, author = {Cherepanov, Igor and Lemeshko, Mikhail}, journal = {Physical Review Materials}, number = {3}, publisher = {American Physical Society}, title = {{Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules}}, doi = {10.1103/PhysRevMaterials.1.035602}, volume = {1}, year = {2017}, } @article{995, abstract = {Recently it was shown that an impurity exchanging orbital angular momentum with a surrounding bath can be described in terms of the angulon quasiparticle [Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor dressed by a many-particle field of boson excitations, and can be formed out of, for example, a molecule or a nonspherical atom in superfluid helium, or out of an electron coupled to lattice phonons or a Bose condensate. Here we develop an approach to the angulon based on the path-integral formalism, which sets the ground for a systematic, perturbative treatment of the angulon problem. The resulting perturbation series can be interpreted in terms of Feynman diagrams, from which, in turn, one can derive a set of diagrammatic rules. These rules extend the machinery of the graphical theory of angular momentum - well known from theoretical atomic spectroscopy - to the case where an environment with an infinite number of degrees of freedom is present. In particular, we show that each diagram can be interpreted as a 'skeleton', which enforces angular momentum conservation, dressed by an additional many-body contribution. This connection between the angulon theory and the graphical theory of angular momentum is particularly important as it allows to systematically and substantially simplify the analytical representation of each diagram. In order to exemplify the technique, we calculate the 1- and 2-loop contributions to the angulon self-energy, the spectral function, and the quasiparticle weight. The diagrammatic theory we develop paves the way to investigate next-to-leading order quantities in a more compact way compared to the variational approaches.}, author = {Bighin, Giacomo and Lemeshko, Mikhail}, issn = {24699950}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {8}, publisher = {American Physical Society}, title = {{Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment}}, doi = {10.1103/PhysRevB.96.085410}, volume = {96}, year = {2017}, } @article{996, abstract = {Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160 ps long laser pulse. The highest degree of alignment, occurring at the peak of the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas of isolated molecules each with an effective rotational constant of 0.6 times the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using the angulon quasiparticle to describe rotating molecules in superfluid helium rationalizes why the alignment mechanism is similar to that of isolated molecules with an effective rotational constant. A major advantage of molecules in He droplets is that their 0.4 K temperature leads to stronger alignment than what can generally be achieved for gas phase molecules -- here demonstrated by a direct comparison of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated molecules. This point is further illustrated for more complex system by measurements on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. }, author = {Shepperson, Benjamin and Chatterley, Adam and Søndergaard, Anders and Christiansen, Lars and Lemeshko, Mikhail and Stapelfeldt, Henrik}, issn = {00219606}, journal = {The Journal of Chemical Physics}, number = {1}, publisher = {AIP}, title = {{Strongly aligned molecules inside helium droplets in the near-adiabatic regime}}, doi = {10.1063/1.4983703}, volume = {147}, year = {2017}, } @article{997, abstract = {Recently it was shown that molecules rotating in superfluid helium can be described in terms of the angulon quasiparticles (Phys. Rev. Lett. 118, 095301 (2017)). Here we demonstrate that in the experimentally realized regime the angulon can be seen as a point charge on a 2-sphere interacting with a gauge field of a non-abelian magnetic monopole. Unlike in several other settings, the gauge fields of the angulon problem emerge in the real coordinate space, as opposed to the momentum space or some effective parameter space. Furthermore, we find a topological transition associated with making the monopole abelian, which takes place in the vicinity of the previously reported angulon instabilities. These results pave the way for studying topological phenomena in experiments on molecules trapped in superfluid helium nanodroplets, as well as on other realizations of orbital impurity problems.}, author = {Yakaboylu, Enderalp and Deuchert, Andreas and Lemeshko, Mikhail}, issn = {00319007}, journal = {APS Physics, Physical Review Letters}, number = {23}, publisher = {American Physiological Society}, title = {{Emergence of non-abelian magnetic monopoles in a quantum impurity problem}}, doi = {10.1103/PhysRevLett.119.235301}, volume = {119}, year = {2017}, } @inproceedings{998, abstract = {A major open problem on the road to artificial intelligence is the development of incrementally learning systems that learn about more and more concepts over time from a stream of data. In this work, we introduce a new training strategy, iCaRL, that allows learning in such a class-incremental way: only the training data for a small number of classes has to be present at the same time and new classes can be added progressively. iCaRL learns strong classifiers and a data representation simultaneously. This distinguishes it from earlier works that were fundamentally limited to fixed data representations and therefore incompatible with deep learning architectures. We show by experiments on CIFAR-100 and ImageNet ILSVRC 2012 data that iCaRL can learn many classes incrementally over a long period of time where other strategies quickly fail. }, author = {Rebuffi, Sylvestre Alvise and Kolesnikov, Alexander and Sperl, Georg and Lampert, Christoph}, isbn = {978-153860457-1}, location = {Honolulu, HA, United States}, pages = {5533 -- 5542}, publisher = {IEEE}, title = {{iCaRL: Incremental classifier and representation learning}}, doi = {10.1109/CVPR.2017.587}, volume = {2017}, year = {2017}, } @inproceedings{999, abstract = {In multi-task learning, a learner is given a collection of prediction tasks and needs to solve all of them. In contrast to previous work, which required that annotated training data must be available for all tasks, we consider a new setting, in which for some tasks, potentially most of them, only unlabeled training data is provided. Consequently, to solve all tasks, information must be transferred between tasks with labels and tasks without labels. Focusing on an instance-based transfer method we analyze two variants of this setting: when the set of labeled tasks is fixed, and when it can be actively selected by the learner. We state and prove a generalization bound that covers both scenarios and derive from it an algorithm for making the choice of labeled tasks (in the active case) and for transferring information between the tasks in a principled way. We also illustrate the effectiveness of the algorithm on synthetic and real data. }, author = {Pentina, Anastasia and Lampert, Christoph}, issn = {978-151085514-4}, location = {Sydney, Australia}, pages = {2807 -- 2816}, publisher = {Omnipress}, title = {{Multi-task learning with labeled and unlabeled tasks}}, volume = {70}, year = {2017}, } @article{392, abstract = {We used femtosecond optical pump-probe spectroscopy to study the photoinduced change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4 (LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above Tc, we observe fluence-dependent relaxation rates that begin at a temperature similar to the one where transport measurements first show signatures of antiferromagnetic correlations. Upon suppressing superconductivity with a magnetic field, it is found that the fluence and temperature dependence of relaxation rates are consistent with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating from antiferromagnetic correlations which comprise the pseudogap in electron-doped cuprates. This can be used to learn about coupling between electrons and high-energy (ω>2ΔAF) excitations in these compounds and set limits on the time scales on which antiferromagnetic correlations are static.}, author = {Vishik, Inna and Mahmood, Fahad and Alpichshev, Zhanybek and Gedik, Nuh and Higgins, Joshu and Greene, Richard}, journal = {Physical Review B}, number = {11}, publisher = {American Physical Society}, title = {{Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ}}, doi = {10.1103/PhysRevB.95.115125}, volume = {95}, year = {2017}, } @article{393, abstract = {We use a three-pulse ultrafast optical spectroscopy to study the relaxation processes in a frustrated Mott insulator Na2IrO3. By being able to independently produce the out-of-equilibrium bound states (excitons) of doublons and holons with the first pulse and suppress the underlying antiferromagnetic order with the second one, we were able to elucidate the relaxation mechanism of quasiparticles in this system. By observing the difference in the exciton dynamics in the magnetically ordered and disordered phases we found that the mass of this quasiparticle is mostly determined by its interaction with the surrounding spins. }, author = {Alpichshev, Zhanybek and Sie, Edbert and Mahmood, Fahad and Cao, Gang and Gedik, Nuh}, journal = {Physical Review B}, number = {23}, publisher = {American Physical Society}, title = {{Origin of the exciton mass in the frustrated Mott insulator Na2IrO3}}, doi = {10.1103/PhysRevB.96.235141}, volume = {96}, year = {2017}, } @inbook{424, abstract = {We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b, d) such that the following holds. If F is a finite family of subsets of Rd such that βi(∩G)≤b for any G⊊F and every 0 ≤ i ≤ [d/2]-1 then F has Helly number at most h(b, d). Here βi denotes the reduced Z2-Betti numbers (with singular homology). These topological conditions are sharp: not controlling any of these [d/2] first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map C*(K)→C*(Rd).}, author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, booktitle = {A Journey through Discrete Mathematics: A Tribute to Jiri Matousek}, editor = {Loebl, Martin and Nešetřil, Jaroslav and Thomas, Robin}, isbn = {978-331944479-6}, pages = {407 -- 447}, publisher = {Springer}, title = {{Bounding helly numbers via betti numbers}}, doi = {10.1007/978-3-319-44479-6_17}, year = {2017}, } @inproceedings{431, abstract = {Parallel implementations of stochastic gradient descent (SGD) have received significant research attention, thanks to its excellent scalability properties. A fundamental barrier when parallelizing SGD is the high bandwidth cost of communicating gradient updates between nodes; consequently, several lossy compresion heuristics have been proposed, by which nodes only communicate quantized gradients. Although effective in practice, these heuristics do not always converge. In this paper, we propose Quantized SGD (QSGD), a family of compression schemes with convergence guarantees and good practical performance. QSGD allows the user to smoothly trade off communication bandwidth and convergence time: nodes can adjust the number of bits sent per iteration, at the cost of possibly higher variance. We show that this trade-off is inherent, in the sense that improving it past some threshold would violate information-theoretic lower bounds. QSGD guarantees convergence for convex and non-convex objectives, under asynchrony, and can be extended to stochastic variance-reduced techniques. When applied to training deep neural networks for image classification and automated speech recognition, QSGD leads to significant reductions in end-to-end training time. For instance, on 16GPUs, we can train the ResNet-152 network to full accuracy on ImageNet 1.8 × faster than the full-precision variant. }, author = {Alistarh, Dan-Adrian and Grubic, Demjan and Li, Jerry and Tomioka, Ryota and Vojnović, Milan}, issn = {10495258}, location = {Long Beach, CA, United States}, pages = {1710--1721}, publisher = {Neural Information Processing Systems Foundation, Inc.}, title = {{QSGD: Communication-efficient SGD via gradient quantization and encoding}}, volume = {2017}, year = {2017}, } @inproceedings{432, abstract = {Recently there has been significant interest in training machine-learning models at low precision: by reducing precision, one can reduce computation and communication by one order of magnitude. We examine training at reduced precision, both from a theoretical and practical perspective, and ask: is it possible to train models at end-to-end low precision with provable guarantees? Can this lead to consistent order-of-magnitude speedups? We mainly focus on linear models, and the answer is yes for linear models. We develop a simple framework called ZipML based on one simple but novel strategy called double sampling. Our ZipML framework is able to execute training at low precision with no bias, guaranteeing convergence, whereas naive quanti- zation would introduce significant bias. We val- idate our framework across a range of applica- tions, and show that it enables an FPGA proto- type that is up to 6.5 × faster than an implemen- tation using full 32-bit precision. We further de- velop a variance-optimal stochastic quantization strategy and show that it can make a significant difference in a variety of settings. When applied to linear models together with double sampling, we save up to another 1.7 × in data movement compared with uniform quantization. When training deep networks with quantized models, we achieve higher accuracy than the state-of-the- art XNOR-Net. }, author = {Zhang, Hantian and Li, Jerry and Kara, Kaan and Alistarh, Dan-Adrian and Liu, Ji and Zhang, Ce}, booktitle = {Proceedings of Machine Learning Research}, isbn = {978-151085514-4}, location = {Sydney, Australia}, pages = {4035 -- 4043}, publisher = { PMLR}, title = {{ZipML: Training linear models with end-to-end low precision, and a little bit of deep learning}}, volume = { 70}, year = {2017}, } @article{443, abstract = {Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited.}, author = {Hardie, Rae and Van Dam, Ellen and Cowley, Mark and Han, Ting and Balaban, Seher and Pajic, Marina and Pinese, Mark and Iconomou, Mary and Shearer, Robert and Mckenna, Jessie and Miller, David and Waddell, Nicola and Pearson, John and Grimmond, Sean and Sazanov, Leonid A and Biankin, Andrew and Villas Boas, Silas and Hoy, Andrew and Turner, Nigel and Saunders, Darren}, journal = {Cancer & Metabolism}, number = {2}, publisher = {BioMed Central}, title = {{Mitochondrial mutations and metabolic adaptation in pancreatic cancer}}, doi = {10.1186/s40170-017-0164-1}, volume = {5}, year = {2017}, } @article{445, abstract = {The Loschmidt echo, defined as the overlap between quantum wave function evolved with different Hamiltonians, quantifies the sensitivity of quantum dynamics to perturbations and is often used as a probe of quantum chaos. In this work we consider the behavior of the Loschmidt echo in the many-body localized phase, which is characterized by emergent local integrals of motion and provides a generic example of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt echo decay as a power law in time in the many-body localized phase, in contrast to the exponential decay in few-body ergodic systems. We consider the spin-echo generalization of the Loschmidt echo and argue that the corresponding correlation function saturates to a finite value in localized systems. Slow, power-law decay of fluctuations of such spin-echo-type overlap is related to the operator spreading and is present only in the many-body localized phase, but not in a noninteracting Anderson insulator. While most of the previously considered probes of dephasing dynamics could be understood by approximating physical spin operators with local integrals of motion, the Loschmidt echo and its generalizations crucially depend on the full expansion of the physical operators via local integrals of motion operators, as well as operators which flip local integrals of motion. Hence these probes allow one to get insights into the relation between physical operators and local integrals of motion and access the operator spreading in the many-body localized phase.}, author = {Maksym Serbyn and Abanin, Dimitry A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {1}, publisher = {American Physical Society}, title = {{Loschmidt echo in many body localized phases}}, doi = {10.1103/PhysRevB.96.014202}, volume = {96}, year = {2017}, } @article{447, abstract = {We consider last passage percolation (LPP) models with exponentially distributed random variables, which are linked to the totally asymmetric simple exclusion process (TASEP). The competition interface for LPP was introduced and studied in Ferrari and Pimentel (2005a) for cases where the corresponding exclusion process had a rarefaction fan. Here we consider situations with a shock and determine the law of the fluctuations of the competition interface around its deter- ministic law of large number position. We also study the multipoint distribution of the LPP around the shock, extending our one-point result of Ferrari and Nejjar (2015).}, author = {Ferrari, Patrik and Nejjar, Peter}, journal = {Revista Latino-Americana de Probabilidade e Estatística}, pages = {299 -- 325}, publisher = {ALEA Network}, title = {{Fluctuations of the competition interface in presence of shocks}}, volume = {9}, year = {2017}, } @article{453, abstract = {Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.}, author = {Fallesen, Todd and Roostalu, Johanna and Düllberg, Christian F and Pruessner, Gunnar and Surrey, Thomas}, journal = {Biophysical Journal}, number = {9}, pages = {2055 -- 2067}, publisher = {Biophysical Society}, title = {{Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement}}, doi = {10.1016/j.bpj.2017.09.006}, volume = {113}, year = {2017}, } @article{459, abstract = {The social insects bees, wasps, ants, and termites are species-rich, occur in many habitats, and often constitute a large part of the biomass. Many are also invasive, including species of termites, the red imported fire ant, and the Argentine ant. While invasive social insects have been a problem in Southern Europe for some time, Central Europa was free of invasive ant species until recently because most ants are adapted to warmer climates. Only in the 1990s, did Lasius neglectus, a close relative of the common black garden ant, arrive in Germany. First described in 1990 based on individuals collected in Budapest, the species has since been detected for example in France, Germany, Spain, England, and Kyrgyzstan. The species is spread with soil during construction work or plantings, and L. neglectus therefore is often found in parks and botanical gardens. Another invasive ant now spreading in southern Germany is Formica fuscocinerea, which occurs along rivers, including in the sandy floodplains of the river Isar. As is typical of pioneer species, F. fuscocinerea quickly becomes extremely abundant and therefore causes problems for example on playgrounds in Munich. All invasive ant species are characterized by cooperation across nests, leading to strongly interconnected, very large super-colonies. The resulting dominance results in the extinction of native ant species as well as other arthropod species and thus in the reduction of biodiversity.}, author = {Cremer, Sylvia}, journal = {Rundgespräche Forum Ökologie}, pages = {105 -- 116}, publisher = {Pfeil}, title = {{Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern}}, volume = {46}, year = {2017}, } @inproceedings{313, abstract = {Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron.}, author = {Camus, Nicolas and Yakaboylu, Enderalp and Fechner, Lutz and Klaiber, Michael and Laux, Martin and Mi, Yonghao and Hatsagortsyan, Karen and Pfeifer, Thomas and Keitel, Cristoph and Moshammer, Robert}, issn = {17426588}, location = {Kazan, Russian Federation}, number = {1}, publisher = {American Physical Society}, title = {{Experimental evidence for Wigner's tunneling time}}, doi = {10.1088/1742-6596/999/1/012004}, volume = {999}, year = {2017}, } @phdthesis{6291, abstract = {Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population.}, author = {Payne, Pavel}, pages = {83}, publisher = {IST Austria}, title = {{Bacterial herd and social immunity to phages}}, year = {2017}, } @phdthesis{1127, abstract = {Plant hormone auxin and its transport between cells belong to the most important mechanisms controlling plant development. Auxin itself could change localization of PINs and thereby control direction of its own flow. We performed an expression profiling experiment in Arabidopsis roots to identify potential regulators of PIN polarity which are transcriptionally regulated by auxin signalling. We identified several novel regulators and performed a detailed characterization of the transcription factor WRKY23 (At2g47260) and its role in auxin feedback on PIN polarity. Gain-of-function and dominant-negative mutants revealed that WRKY23 plays a crucial role in mediating the auxin effect on PIN polarity. In concordance, typical polar auxin transport processes such as gravitropism and leaf vascular pattern formation were disturbed by interfering with WRKY23 function. In order to identify direct targets of WRKY23, we performed consequential expression profiling experiments using a WRKY23 inducible gain-of-function line and dominant-negative WRKY23 line that is defunct in PIN re-arrangement. Among several genes mostly related to the groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE TRANSPORTER 1 (LHT1; At5g40780), a small amino acid permease gene from the amino acid/auxin permease family (AAAP), we present its detailed characterisation in auxin feedback on PIN repolarization, identified its transcriptional regulation, we propose a potential mechanism of its action. Moreover, we identified also a member of receptor-like protein kinase LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1; LRRK1; At1g05700), which also affects auxin-dependent PIN re-arrangement. We described its transcriptional behaviour, subcellular localization. Based on global expression data, we tried to identify ligand responsible for mechanism of signalling and suggest signalling partner and interactors. Additionally, we described role of novel phytohormone group, strigolactone, in auxin-dependent PIN re-arrangement, that could be a fundament for future studies in this field. Our results provide first insights into an auxin transcriptional network targeting PIN localization and thus regulating plant development. We highlighted WRKY23 transcriptional network and characterised its mediatory role in plant development. We identified direct effectors of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement and PIN-dependent auxin transport processes.}, author = {Prat, Tomas}, pages = {131}, publisher = {IST Austria}, title = {{Identification of novel regulators of PIN polarity and development of novel auxin sensor}}, year = {2017}, } @article{9190, abstract = {Plant meristems carry pools of continuously active stem cells, whose activity is controlled by developmental and environmental signals. After stem cell division, daughter cells that exit the stem cell domain acquire transit amplifying cell identity before they are incorporated into organs and differentiate. In this study, we used an integrated approach to elucidate the role of HECATE (HEC) genes in regulating developmental trajectories of shoot stem cells in Arabidopsis thaliana. Our work reveals that HEC function stabilizes cell fate in distinct zones of the shoot meristem thereby controlling the spatio-temporal dynamics of stem cell differentiation. Importantly, this activity is concomitant with the local modulation of cellular responses to cytokinin and auxin, two key phytohormones regulating cell behaviour. Mechanistically, we show that HEC factors transcriptionally control and physically interact with MONOPTEROS (MP), a key regulator of auxin signalling, and modulate the autocatalytic stabilization of auxin signalling output.}, author = {Gaillochet, Christophe and Stiehl, Thomas and Wenzl, Christian and Ripoll, Juan-José and Bailey-Steinitz, Lindsay J and Li, Lanxin and Pfeiffer, Anne and Miotk, Andrej and Hakenjos, Jana P and Forner, Joachim and Yanofsky, Martin F and Marciniak-Czochra, Anna and Lohmann, Jan U}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Control of plant cell fate transitions by transcriptional and hormonal signals}}, doi = {10.7554/elife.30135}, volume = {6}, year = {2017}, } @article{1029, abstract = {RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.}, author = {Lukacisin, Martin and Landon, Matthieu and Jajoo, Rishi}, issn = {19326203}, journal = {PLoS One}, number = {3}, publisher = {Public Library of Science}, title = {{Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast}}, doi = {10.1371/journal.pone.0174066}, volume = {12}, year = {2017}, } @article{696, abstract = {Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.}, author = {Lukacisinova, Marta and Novak, Sebastian and Paixao, Tiago}, issn = {1553734X}, journal = {PLoS Computational Biology}, number = {7}, publisher = {Public Library of Science}, title = {{Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes}}, doi = {10.1371/journal.pcbi.1005609}, volume = {13}, year = {2017}, } @article{1027, abstract = {The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance.}, author = {Lukacisinova, Marta and Bollenbach, Mark Tobias}, journal = {Current Opinion in Biotechnology}, pages = {90 -- 97}, publisher = {Elsevier}, title = {{Toward a quantitative understanding of antibiotic resistance evolution}}, doi = {10.1016/j.copbio.2017.02.013}, volume = {46}, year = {2017}, } @article{682, abstract = {Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry.}, author = {Ukai, Hikari and Kawahara, Aiko and Hirayama, Keiko and Case, Matthew J and Aino, Shotaro and Miyabe, Masahiro and Wakita, Ken and Oogi, Ryohei and Kasayuki, Michiyo and Kawashima, Shihomi and Sugimoto, Shunichi and Chikamatsu, Kanako and Nitta, Noritaka and Koga, Tsuneyuki and Shigemoto, Ryuichi and Takai, Toshiyuki and Ito, Isao}, issn = {19326203}, journal = {PLoS One}, number = {6}, publisher = {Public Library of Science}, title = {{PirB regulates asymmetries in hippocampal circuitry}}, doi = {10.1371/journal.pone.0179377}, volume = {12}, year = {2017}, } @article{1024, abstract = {The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.}, author = {Hurny, Andrej and Benková, Eva}, issn = {10643745}, journal = {Auxins and Cytokinins in Plant Biology}, pages = {1 -- 29}, publisher = {Springer}, title = {{Methodological advances in auxin and cytokinin biology}}, doi = {10.1007/978-1-4939-6831-2_1}, volume = {1569}, year = {2017}, } @inproceedings{949, abstract = {The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs.}, author = {Chatterjee, Krishnendu and Goharshady, Amir and Pavlogiannis, Andreas}, editor = {D'Souza, Deepak}, issn = {03029743}, location = {Pune, India}, pages = {59 -- 66}, publisher = {Springer}, title = {{JTDec: A tool for tree decompositions in soot}}, doi = {10.1007/978-3-319-68167-2_4}, volume = {10482}, year = {2017}, } @inproceedings{639, abstract = {We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.}, author = {Chatterjee, Krishnendu and Fu, Hongfei and Goharshady, Amir}, editor = {Majumdar, Rupak and Kunčak, Viktor}, isbn = {978-331963389-3}, location = {Heidelberg, Germany}, pages = {41 -- 63}, publisher = {Springer}, title = {{Non-polynomial worst case analysis of recursive programs}}, doi = {10.1007/978-3-319-63390-9_3}, volume = {10427}, year = {2017}, } @article{704, abstract = {How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.}, author = {Steinrück, Magdalena and Guet, Calin C}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection}}, doi = {10.7554/eLife.25100}, volume = {6}, year = {2017}, } @article{661, abstract = {During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo.}, author = {Smutny, Michael and Ákos, Zsuzsa and Grigolon, Silvia and Shamipour, Shayan and Ruprecht, Verena and Capek, Daniel and Behrndt, Martin and Papusheva, Ekaterina and Tada, Masazumi and Hof, Björn and Vicsek, Tamás and Salbreux, Guillaume and Heisenberg, Carl-Philipp J}, issn = {14657392}, journal = {Nature Cell Biology}, pages = {306 -- 317}, publisher = {Nature Publishing Group}, title = {{Friction forces position the neural anlage}}, doi = {10.1038/ncb3492}, volume = {19}, year = {2017}, } @article{676, abstract = {The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.}, author = {Krens, Gabriel and Veldhuis, Jim and Barone, Vanessa and Capek, Daniel and Maître, Jean-Léon and Brodland, Wayne and Heisenberg, Carl-Philipp J}, issn = {09501991}, journal = {Development}, number = {10}, pages = {1798 -- 1806}, publisher = {Company of Biologists}, title = {{Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation}}, doi = {10.1242/dev.144964}, volume = {144}, year = {2017}, } @article{262, abstract = {For any number field we calculate the exact proportion of rational numbers which are everywhere locally a norm but not globally a norm from the number field.}, author = {Timothy Browning and Newton, Rachel}, journal = {Mathematika}, number = {2}, pages = {337 -- 347}, publisher = {Cambridge University Press}, title = {{The proportion of failures of the Hasse norm principle}}, doi = {10.1112/S0025579315000261}, volume = {62}, year = {2016}, } @article{263, abstract = {We count rational points of bounded height on the Cayley ruled cubic surface and interpret the result in the context of general conjectures due to Batyrev and Tschinkel.}, author = {de la Bretèche, Régis and Timothy Browning and Salberger, Per}, journal = {European Journal of Mathematics}, number = {1}, pages = {55 -- 72}, publisher = {Springer Nature}, title = {{Counting rational points on the Cayley ruled cubic}}, doi = {10.1007/s40879-015-0049-1}, volume = {2}, year = {2016}, } @article{264, abstract = {Given a family of varieties over a number field, we determine conditions under which there is a Brauer-Manin obstruction to weak approximation for 100% of the fibres which are everywhere locally soluble.}, author = {Bright, Maritn J and Timothy Browning and Loughran, Daniel}, journal = {Compositio Mathematica}, number = {7}, pages = {1435 -- 1475}, publisher = {Cambridge University Press}, title = {{Failures of weak approximation in families}}, doi = {10.1112/S0010437X16007405}, volume = {152}, year = {2016}, } @article{8020, abstract = {Balance of cortical excitation and inhibition (EI) is thought to be disrupted in several neuropsychiatric conditions, yet it is not clear how it is maintained in the healthy human brain. When EI balance is disturbed during learning and memory in animal models, it can be restabilized via formation of inhibitory replicas of newly formed excitatory connections. Here we assess evidence for such selective inhibitory rebalancing in humans. Using fMRI repetition suppression we measure newly formed cortical associations in the human brain. We show that expression of these associations reduces over time despite persistence in behavior, consistent with inhibitory rebalancing. To test this, we modulated excitation/inhibition balance with transcranial direct current stimulation (tDCS). Using ultra-high-field (7T) MRI and spectroscopy, we show that reducing GABA allows cortical associations to be re-expressed. This suggests that in humans associative memories are stored in balanced excitatory-inhibitory ensembles that lie dormant unless latent inhibitory connections are unmasked.}, author = {Barron, H.C. and Vogels, Tim P and Emir, U.E. and Makin, T.R. and O’Shea, J. and Clare, S. and Jbabdi, S. and Dolan, R.J. and Behrens, T.E.J.}, issn = {0896-6273}, journal = {Neuron}, number = {1}, pages = {191--203}, publisher = {Elsevier}, title = {{Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories}}, doi = {10.1016/j.neuron.2016.02.031}, volume = {90}, year = {2016}, } @inproceedings{8094, abstract = {With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.}, author = {Martius, Georg S and Hostettler, Rafael and Knoll, Alois and Der, Ralf}, booktitle = {Proceedings of the Artificial Life Conference 2016}, isbn = {9780262339360}, location = {Cancun, Mexico}, pages = {142--143}, publisher = {MIT Press}, title = {{Self-organized control of an tendon driven arm by differential extrinsic plasticity}}, doi = {10.7551/978-0-262-33936-0-ch029}, volume = {28}, year = {2016}, } @unpublished{8128, abstract = {The stimulus selectivity of synaptic currents in cortical neurons often shows a co-tuning of excitation and inhibition, but the mechanisms that underlie the emergence and plasticity of this co-tuning are not fully understood. Using a computational model, we show that an interaction of excitatory and inhibitory synaptic plasticity reproduces both the developmental and – when combined with a disinhibitory gate – the adult plasticity of excitatory and inhibitory receptive fields in auditory cortex. The co-tuning arises from inhibitory plasticity that balances excitation and inhibition, while excitatory stimulus selectivity can result from two different mechanisms. Inhibitory inputs with a broad stimulus tuning introduce a sliding threshold as in Bienenstock-Cooper-Munro rules, introducing an excitatory stimulus selectivity at the cost of a broader inhibitory receptive field. Alternatively, input asymmetries can be amplified by synaptic competition. The latter leaves any receptive field plasticity transient, a prediction we verify in recordings in auditory cortex.}, author = {Clopath, Claudia and Vogels, Tim P and Froemke, Robert C. and Sprekeler, Henning}, booktitle = {bioRxiv}, pages = {43}, publisher = {Cold Spring Harbor Laboratory}, title = {{Receptive field formation by interacting excitatory and inhibitory synaptic plasticity}}, year = {2016}, } @article{8241, abstract = {Background: Anticancer vaccines could represent a valuable complementary strategy to established therapies, especially in settings of early stage and minimal residual disease. HER-2 is an important target for immunotherapy and addressed by the monoclonal antibody trastuzumab. We have previously generated HER-2 mimotope peptides from phage display libraries. The synthesized peptides were coupled to carriers and applied for epitope-specific induction of trastuzumab-like IgG. For simplification and to avoid methodological limitations of synthesis and coupling chemistry, we herewith present a novel and optimized approach by using adeno-associated viruses (AAV) as effective and high-density mimotope-display system, which can be directly used for vaccination. Methods: An AAV capsid display library was constructed by genetically incorporating random peptides in a plasmid encoding the wild-type AAV2 capsid protein. AAV clones, expressing peptides specifically reactive to trastuzumab, were employed to immunize BALB/c mice. Antibody titers against human HER-2 were determined, and the isotype composition and functional properties of these were tested. Finally, prophylactically immunized mice were challenged with human HER-2 transfected mouse D2F2/E2 cells. Results: HER-2 mimotope AAV-vaccines induced antibodies specific to human HER-2. Two clones were selected for immunization of mice, which were subsequently grafted D2F2/E2 cells. Both mimotope AAV clones delayed the growth of tumors significantly, as compared to controls. Conclusion: In this study, a novel mimotope AAV-based platform was created allowing the isolation of mimotopes, which can be directly used as anticancer vaccines. The example of trastuzumab AAV-mimotopes demonstrates that this vaccine strategy could help to establish active immunotherapy for breast-cancer patients.}, author = {Singer, Josef and Manzano-Szalai, Krisztina and Fazekas, Judit and Thell, Kathrin and Bentley-Lukschal, Anna and Stremnitzer, Caroline and Roth-Walter, Franziska and Weghofer, Margit and Ritter, Mirko and Pino Tossi, Kerstin and Hörer, Markus and Michaelis, Uwe and Jensen-Jarolim, Erika}, issn = {2162-402X}, journal = {OncoImmunology}, number = {7}, publisher = {Taylor & Francis}, title = {{Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform}}, doi = {10.1080/2162402x.2016.1171446}, volume = {5}, year = {2016}, } @inproceedings{8302, abstract = {While showing great promise, Bitcoin requires users to wait tens of minutes for transactions to commit, and even then, offering only probabilistic guarantees. This paper introduces ByzCoin, a novel Byzantine consensus protocol that leverages scalable collective signing to commit Bitcoin transactions irreversibly within seconds. ByzCoin achieves Byzantine consensus while preserving Bitcoin’s open membership by dynamically forming hash power-proportionate consensus groups that represent recently-successful block miners. ByzCoin employs communication trees to optimize transaction commitment and verification under normal operation while guaranteeing safety and liveness under Byzantine faults, up to a near-optimal tolerance of f faulty group members among 3f + 2 total. ByzCoin mitigates double spending and selfish mining attacks by producing collectively signed transaction blocks within one minute of transaction submission. Tree-structured communication further reduces this latency to less than 30 seconds. Due to these optimizations, ByzCoin achieves a throughput higher than Paypal currently handles, with a confirmation latency of 15-20 seconds.}, author = {Kokoris Kogias, Eleftherios and Jovanovic, Philipp and Gailly, Nicolas and Khoffi, Ismail and Gasser, Linus and Ford, Bryan}, booktitle = {Proceedings of the 25th USENIX Conference on Security Symposium}, isbn = {9781931971324}, location = {Austin, TX, United States}, pages = {279–296}, publisher = {USENIX Association}, title = {{Enhancing bitcoin security and performance with strong consistency via collective signing}}, year = {2016}, } @article{1705, abstract = {Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential.}, author = {Bogomolov, Sergiy and Donzé, Alexandre and Frehse, Goran and Grosu, Radu and Johnson, Taylor and Ladan, Hamed and Podelski, Andreas and Wehrle, Martin}, journal = {International Journal on Software Tools for Technology Transfer}, number = {4}, pages = {449 -- 467}, publisher = {Springer}, title = {{Guided search for hybrid systems based on coarse-grained space abstractions}}, doi = {10.1007/s10009-015-0393-y}, volume = {18}, year = {2016}, } @article{173, abstract = {We calculate admissible values of r such that a square-free polynomial with integer coefficients, no fixed prime divisor and irreducible factors of degree at most 3 takes infinitely many values that are a product of at most r distinct primes.}, author = {Browning, Timothy D and Booker, Andrew}, journal = {Discrete Analysis}, pages = {1 -- 18}, title = {{Square-free values of reducible polynomials}}, doi = {10.19086/da.732}, volume = {8}, year = {2016}, } @article{1794, abstract = {We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights.}, author = {Kolmogorov, Vladimir and Takhanov, Rustem}, journal = {Algorithmica}, number = {1}, pages = {17 -- 46}, publisher = {Springer}, title = {{Inference algorithms for pattern-based CRFs on sequence data}}, doi = {10.1007/s00453-015-0017-7}, volume = {76}, year = {2016}, } @article{1833, abstract = {Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in the table, and not necessarily containing the overall effect, that is, a common parameter in every cell. Similarly to log-linear models, relational models can be extended to non-negative distributions, but the extension requires more complex methods. An extended relational model is defined as an algebraic variety, and it turns out to be the closure of the original model with respect to the Bregman divergence. In the extended relational model, the MLE of the cell parameters always exists and is unique, but some of its properties may be different from those of the MLE under log-linear models. The MLE can be computed using a generalized iterative scaling procedure based on Bregman projections. }, author = {Klimova, Anna and Rudas, Tamás}, journal = {Journal of Multivariate Analysis}, pages = {440 -- 452}, publisher = {Elsevier}, title = {{On the closure of relational models}}, doi = {10.1016/j.jmva.2015.10.005}, volume = {143}, year = {2016}, } @article{1881, abstract = {We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal random matrix of size N with i.i.d.\ entries that are independent of W. We assume subexponential decay for the matrix entries of W and we choose λ∼1, so that the eigenvalues of W and λV are typically of the same order. Further, we assume that the density of the entries of V is supported on a single interval and is convex near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such that the largest eigenvalues of H are in the limit of large N determined by the order statistics of V for λ>λ+. In particular, the largest eigenvalue of H has a Weibull distribution in the limit N→∞ if λ>λ+. Moreover, for N sufficiently large, we show that the eigenvectors associated to the largest eigenvalues are partially localized for λ>λ+, while they are completely delocalized for λ<λ+. Similar results hold for the lowest eigenvalues. }, author = {Lee, Jioon and Schnelli, Kevin}, journal = {Probability Theory and Related Fields}, number = {1-2}, pages = {165 -- 241}, publisher = {Springer}, title = {{Extremal eigenvalues and eigenvectors of deformed Wigner matrices}}, doi = {10.1007/s00440-014-0610-8}, volume = {164}, year = {2016}, } @article{7279, abstract = {Kinetics of electrochemical reactions are several orders of magnitude slower in solids than in liquids as a result of the much lower ion diffusivity. Yet, the solid state maximizes the density of redox species, which is at least two orders of magnitude lower in liquids because of solubility limitations. With regard to electrochemical energy storage devices, this leads to high-energy batteries with limited power and high-power supercapacitors with a well-known energy deficiency. For such devices the ideal system should endow the liquid state with a density of redox species close to the solid state. Here we report an approach based on biredox ionic liquids to achieve bulk-like redox density at liquid-like fast kinetics. The cation and anion of these biredox ionic liquids bear moieties that undergo very fast reversible redox reactions. As a first demonstration of their potential for high-capacity/high-rate charge storage, we used them in redox supercapacitors. These ionic liquids are able to decouple charge storage from an ion-accessible electrode surface, by storing significant charge in the pores of the electrodes, to minimize self-discharge and leakage current as a result of retaining the redox species in the pores, and to raise working voltage due to their wide electrochemical window.}, author = {Mourad, Eléonore and Coustan, Laura and Lannelongue, Pierre and Zigah, Dodzi and Mehdi, Ahmad and Vioux, André and Freunberger, Stefan Alexander and Favier, Frédéric and Fontaine, Olivier}, issn = {1476-1122}, journal = {Nature Materials}, number = {4}, pages = {446--453}, publisher = {Springer Nature}, title = {{Biredox ionic liquids with solid-like redox density in the liquid state for high-energy supercapacitors}}, doi = {10.1038/nmat4808}, volume = {16}, year = {2016}, } @article{7297, abstract = {Redox mediators facilitate the oxidation of the highly insulating discharge product in metal–oxygen batteries during recharge and offer opportunities to achieve high reversible capacities. Now a design principle for selecting redox mediators that can recharge the batteries more efficiently is suggested.}, author = {Freunberger, Stefan Alexander}, issn = {2058-7546}, journal = {Nature Energy}, number = {6}, publisher = {Springer Nature}, title = {{Batteries: Charging ahead rationally}}, doi = {10.1038/nenergy.2016.74}, volume = {1}, year = {2016}, } @article{7599, abstract = {Normal leaf margin development is important for leaf morphogenesis and contributes to diverse leaf shapes in higher plants. We here show the crucial roles of an atypical type II phosphatidylinositol 4-kinase, PI4Kγ5, in Arabidopsis leaf margin development. PI4Kγ5 presents a dynamics expression pattern along with leaf development and a T-DNA mutant lacking PI4Kγ5, pi4kγ5–1, presents serrated leaves, which is resulted from the accelerated cell division and increased auxin concentration at serration tips. Studies revealed that PI4Kγ5 interacts with and phosphorylates a membrane-bound NAC transcription factor, ANAC078. Previous studies demonstrated that membrane-bound transcription factors regulate gene transcription by undergoing proteolytic process to translocate into nucleus, and ANAC078 undergoes proteolysis by cleaving off the transmembrane region and carboxyl terminal. Western blot analysis indeed showed that ANAC078 deleting of carboxyl terminal is significantly reduced in pi4kγ5–1, indicating that PI4Kγ5 is important for the cleavage of ANAC078. This is consistent with the subcellular localization observation showing that fluorescence by GFP-ANAC078 is detected at plasma membrane but not nucleus in pi4kγ5–1 mutant and that expression of ANAC078 deleting of carboxyl terminal, driven by PI4Kγ5 promoter, could rescue the leaf serration defects of pi4kγ5–1. Further analysis showed that ANAC078 suppresses the auxin synthesis by directly binding and regulating the expression of auxin synthesis-related genes. These results indicate that PI4Kγ5 interacts with ANAC078 to negatively regulate auxin synthesis and hence influences cell proliferation and leaf development, providing informative clues for the regulation of in situ auxin synthesis and cell division, as well as the cleavage and functional mechanism of membrane-bound transcription factors.}, author = {Tang, Yong and Zhao, Chun-Yan and Tan, Shutang and Xue, Hong-Wei}, issn = {1553-7404}, journal = {PLOS Genetics}, number = {8}, publisher = {Public Library of Science}, title = {{Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078}}, doi = {10.1371/journal.pgen.1006252}, volume = {12}, year = {2016}, } @article{7737, abstract = {Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human complex traits. However, the genes or functional DNA elements through which these variants exert their effects on the traits are often unknown. We propose a method (called SMR) that integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. We apply the method to five human complex traits using GWAS data on up to 339,224 individuals and eQTL data on 5,311 individuals, and we prioritize 126 genes (for example, TRAF1 and ANKRD55 for rheumatoid arthritis and SNX19 and NMRAL1 for schizophrenia), of which 25 genes are new candidates; 77 genes are not the nearest annotated gene to the top associated GWAS SNP. These genes provide important leads to design future functional studies to understand the mechanism whereby DNA variation leads to complex trait variation.}, author = {Zhu, Zhihong and Zhang, Futao and Hu, Han and Bakshi, Andrew and Robinson, Matthew Richard and Powell, Joseph E and Montgomery, Grant W and Goddard, Michael E and Wray, Naomi R and Visscher, Peter M and Yang, Jian}, issn = {1061-4036}, journal = {Nature Genetics}, number = {5}, pages = {481--487}, publisher = {Springer Nature}, title = {{Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets}}, doi = {10.1038/ng.3538}, volume = {48}, year = {2016}, } @article{786, abstract = {Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. Although obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most nonblocking commercial code is only lock-free. This article suggests a simple solution to this problem.We show that for a large class of lock-free algorithms, under scheduling conditions that approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can continue to design simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes to the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1 but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst-case adversary, in a stochastic model capturing their expected asymptotic behavior.}, author = {Alistarh, Dan-Adrian and Censor Hillel, Keren and Shavit, Nir}, journal = {Journal of the ACM}, number = {4}, publisher = {ACM}, title = {{Are lock free concurrent algorithms practically wait free }}, doi = {10.1145/2903136}, volume = {63}, year = {2016}, } @article{460, abstract = {NF-κB signaling is a central pathway of immunity and integrates signal transduction upon a wide array of inflammatory stimuli. Noncanonical NF-κB signaling is activated by a small subset of TNF family receptors and characterized by NF-κB2/p52 transcriptional activity. The medical relevance of this pathway has recently re-emerged from the discovery of primary immunodeficiency patients that have loss-of-function mutations in the MAP3K14 gene encoding NIK. Nevertheless, knowledge of protein interactions that regulate noncanonical NF-κB signaling is sparse. Here we report a detailed state-of-the-art mass spectrometry-based protein–protein interaction network including the noncanonical NF-κB signaling nodes TRAF2, TRAF3, IKKα, NIK, and NF-κB2/p100. The value of the data set was confirmed by the identification of interactions already known to regulate this pathway. In addition, a remarkable number of novel interactors were identified. We provide validation of the novel NIK and IKKα interactor FKBP8, which may regulate processes downstream of noncanonical NF-κB signaling. To understand perturbed noncanonical NF-κB signaling in the context of misregulated NIK in disease, we also provide a differential interactome of NIK mutants that cause immunodeficiency. Altogether, this data set not only provides critical insight into how protein–protein interactions can regulate immune signaling but also offers a novel resource on noncanonical NF-κB signaling.}, author = {Willmann, Katharina L and Roberto Sacco and Martins, Rui and Garncarz, Wojciech and Krolo, Ana and Knapp, Sylvia and Bennett, Keiryn L and Boztug, Kaan}, journal = {Journal of Proteome Research}, number = {9}, pages = {2900 -- 2909}, publisher = {American Chemical Society}, title = {{Expanding the interactome of the noncanonical NF-κB signaling pathway}}, doi = {10.1021/acs.jproteome.5b01004}, volume = {15}, year = {2016}, }