@article{1674,
abstract = {We consider N × N random matrices of the form H = W + V where W is a real symmetric Wigner matrix and V a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W and we choose V so that the eigenvalues of W and V are typically of the same order. For a large class of diagonal matrices V, we show that the rescaled distribution of the extremal eigenvalues is given by the Tracy-Widom distribution F1 in the limit of large N. Our proofs also apply to the complex Hermitian setting, i.e. when W is a complex Hermitian Wigner matrix.},
author = {Lee, Jioon and Schnelli, Kevin},
journal = {Reviews in Mathematical Physics},
number = {8},
publisher = {World Scientific Publishing},
title = {{Edge universality for deformed Wigner matrices}},
doi = {10.1142/S0129055X1550018X},
volume = {27},
year = {2015},
}
@inproceedings{1675,
abstract = {Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble).},
author = {Dziembowski, Stefan and Faust, Sebastian and Kolmogorov, Vladimir and Pietrzak, Krzysztof Z},
location = {Santa Barbara, CA, United States},
pages = {585 -- 605},
publisher = {Springer},
title = {{Proofs of space}},
doi = {10.1007/978-3-662-48000-7_29},
volume = {9216},
year = {2015},
}
@article{1676,
author = {Sixt, Michael K and Raz, Erez},
journal = {Current Opinion in Cell Biology},
number = {10},
pages = {4 -- 6},
publisher = {Elsevier},
title = {{Editorial overview: Cell adhesion and migration}},
doi = {10.1016/j.ceb.2015.09.004},
volume = {36},
year = {2015},
}
@article{1677,
abstract = {We consider real symmetric and complex Hermitian random matrices with the additional symmetry hxy = hN-y,N-x. The matrix elements are independent (up to the fourfold symmetry) and not necessarily identically distributed. This ensemble naturally arises as the Fourier transform of a Gaussian orthogonal ensemble. Italso occurs as the flip matrix model - an approximation of the two-dimensional Anderson model at small disorder. We show that the density of states converges to the Wigner semicircle law despite the new symmetry type. We also prove the local version of the semicircle law on the optimal scale.},
author = {Alt, Johannes},
journal = {Journal of Mathematical Physics},
number = {10},
publisher = {American Institute of Physics},
title = {{The local semicircle law for random matrices with a fourfold symmetry}},
doi = {10.1063/1.4932606},
volume = {56},
year = {2015},
}
@article{1678,
abstract = {High-throughput live-cell screens are intricate elements of systems biology studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted method that avoids the need for chemical activators and reporters, reduces the number of operational steps and increases information content in a cell-based small-molecule screen against human protein kinases, including an orphan receptor tyrosine kinase. This blueprint for all-optical screening can be adapted to many drug targets and cellular processes.},
author = {Inglés Prieto, Álvaro and Gschaider-Reichhart, Eva and Muellner, Markus and Nowak, Matthias and Nijman, Sebastian and Grusch, Michael and Janovjak, Harald L},
journal = {Nature Chemical Biology},
number = {12},
pages = {952 -- 954},
publisher = {Nature Publishing Group},
title = {{Light-assisted small-molecule screening against protein kinases}},
doi = {10.1038/nchembio.1933},
volume = {11},
year = {2015},
}
@article{1679,
author = {Lemoult, Grégoire M and Maier, Philipp and Hof, Björn},
journal = {Physics of Fluids},
number = {9},
publisher = {American Institute of Physics},
title = {{Taylor's Forest}},
doi = {10.1063/1.4930850},
volume = {27},
year = {2015},
}
@article{1680,
abstract = {We consider the satisfiability problem for modal logic over first-order definable classes of frames.We confirm the conjecture from Hemaspaandra and Schnoor [2008] that modal logic is decidable over classes definable by universal Horn formulae. We provide a full classification of Horn formulae with respect to the complexity of the corresponding satisfiability problem. It turns out, that except for the trivial case of inconsistent formulae, local satisfiability is eitherNP-complete or PSPACE-complete, and global satisfiability is NP-complete, PSPACE-complete, or ExpTime-complete. We also show that the finite satisfiability problem for modal logic over Horn definable classes of frames is decidable. On the negative side, we show undecidability of two related problems. First, we exhibit a simple universal three-variable formula defining the class of frames over which modal logic is undecidable. Second, we consider the satisfiability problem of bimodal logic over Horn definable classes of frames, and also present a formula leading to undecidability.},
author = {Michaliszyn, Jakub and Otop, Jan and Kieroňski, Emanuel},
journal = {ACM Transactions on Computational Logic},
number = {1},
publisher = {ACM},
title = {{On the decidability of elementary modal logics}},
doi = {10.1145/2817825},
volume = {17},
year = {2015},
}
@article{1681,
abstract = {In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game.},
author = {Priklopil, Tadeas and Chatterjee, Krishnendu},
journal = {Games},
number = {4},
pages = {413 -- 437},
publisher = {Multidisciplinary Digital Publishing Institute},
title = {{Evolution of decisions in population games with sequentially searching individuals}},
doi = {10.3390/g6040413},
volume = {6},
year = {2015},
}
@article{1682,
abstract = {We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f:K→ ℝn on a finite simplicial complex K and α > 0, it holds that each function g: K → ℝn such that ||g - f || ∞ < α, has a root in K. Via a reduction to the extension problem of maps into a sphere, we particularly show that this problem is decidable in polynomial time for every fixed n, assuming dimK ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction, we prove that the problem is undecidable when dim K > 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is simplexwise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings.},
author = {Franek, Peter and Krcál, Marek},
journal = {Journal of the ACM},
number = {4},
publisher = {ACM},
title = {{Robust satisfiability of systems of equations}},
doi = {10.1145/2751524},
volume = {62},
year = {2015},
}
@article{1683,
abstract = {The 1 MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5 Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8 Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated.},
author = {Letts, Jame A and Sazanov, Leonid A},
journal = {Current Opinion in Structural Biology},
number = {8},
pages = {135 -- 145},
publisher = {Elsevier},
title = {{Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions}},
doi = {10.1016/j.sbi.2015.08.008},
volume = {33},
year = {2015},
}
@article{1684,
abstract = {Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.},
author = {Vicoso, Beatriz and Bachtrog, Doris},
journal = {PLoS Biology},
number = {4},
publisher = {Public Library of Science},
title = {{Numerous transitions of sex chromosomes in Diptera}},
doi = {10.1371/journal.pbio.1002078},
volume = {13},
year = {2015},
}
@inproceedings{1685,
abstract = {Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3.
Our techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest.},
author = {Cohen Addad, Vincent and De Mesmay, Arnaud N},
location = {Patras, Greece},
pages = {386 -- 398},
publisher = {Springer},
title = {{A fixed parameter tractable approximation scheme for the optimal cut graph of a surface}},
doi = {10.1007/978-3-662-48350-3_33},
volume = {9294},
year = {2015},
}
@article{1686,
author = {Kiermaier, Eva and Sixt, Michael K},
journal = {Science},
number = {6252},
pages = {1055 -- 1056},
publisher = {American Association for the Advancement of Science},
title = {{Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection}},
doi = {10.1126/science.aad0867},
volume = {349},
year = {2015},
}
@article{1687,
abstract = {Guided cell movement is essential for development and integrity of animals and crucially involved in cellular immune responses. Leukocytes are professional migratory cells that can navigate through most types of tissues and sense a wide range of directional cues. The responses of these cells to attractants have been mainly explored in tissue culture settings. How leukocytes make directional decisions in situ, within the challenging environment of a tissue maze, is less understood. Here we review recent advances in how leukocytes sense chemical cues in complex tissue settings and make links with paradigms of directed migration in development and Dictyostelium discoideum amoebae.},
author = {Sarris, Milka and Sixt, Michael K},
journal = {Current Opinion in Cell Biology},
number = {10},
pages = {93 -- 102},
publisher = {Elsevier},
title = {{Navigating in tissue mazes: Chemoattractant interpretation in complex environments}},
doi = {10.1016/j.ceb.2015.08.001},
volume = {36},
year = {2015},
}
@article{1688,
abstract = {We estimate the selection constant in the following geometric selection theorem by Pach: For every positive integer d, there is a constant (Formula presented.) such that whenever (Formula presented.) are n-element subsets of (Formula presented.), we can find a point (Formula presented.) and subsets (Formula presented.) for every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices determined by (Formula presented.) simplices with one vertex in each Yi. We show a super-exponentially decreasing upper bound (Formula presented.). The ideas used in the proof of the upper bound also help us to prove Pach’s theorem with (Formula presented.), which is a lower bound doubly exponentially decreasing in d (up to some polynomial in the exponent). For comparison, Pach’s original approach yields a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem with (Formula presented.). In our construction for the upper bound, we use the fact that the minimum solid angle of every d-simplex is super-exponentially small. This fact was previously unknown and might be of independent interest. For the lower bound, we improve the ‘separation’ part of the argument by showing that in one of the key steps only d+1 separations are necessary, compared to 2d separations in the original proof. We also provide a measure version of Pach’s theorem.},
author = {Karasev, Roman and Kynčl, Jan and Paták, Pavel and Patakova, Zuzana and Tancer, Martin},
journal = {Discrete & Computational Geometry},
number = {3},
pages = {610 -- 636},
publisher = {Springer},
title = {{Bounds for Pach's selection theorem and for the minimum solid angle in a simplex}},
doi = {10.1007/s00454-015-9720-z},
volume = {54},
year = {2015},
}
@inproceedings{1689,
abstract = {We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. We demonstrate our approach on an illustrative case study.},
author = {Svoreňová, Mária and Kretinsky, Jan and Chmelik, Martin and Chatterjee, Krishnendu and Cěrná, Ivana and Belta, Cǎlin},
booktitle = {Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control},
location = {Seattle, WA, United States},
pages = {259 -- 268},
publisher = {ACM},
title = {{Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games}},
doi = {10.1145/2728606.2728608},
year = {2015},
}
@inproceedings{1690,
abstract = {A number of powerful and scalable hybrid systems model checkers have recently emerged. Although all of them honor roughly the same hybrid systems semantics, they have drastically different model description languages. This situation (a) makes it difficult to quickly evaluate a specific hybrid automaton model using the different tools, (b) obstructs comparisons of reachability approaches, and (c) impedes the widespread application of research results that perform model modification and could benefit many of the tools. In this paper, we present Hyst, a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently taking input in the SpaceEx model format, and translating to the formats of HyCreate, Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation passes that serve to both ease the translation and potentially improve reachability results for the supported tools. Although these model transformation passes could be implemented within each tool, the Hyst approach provides a single place for model modification, generating modified input sources for the unmodified target tools. Our evaluation demonstrates Hyst is capable of automatically translating benchmarks in several classes (including affine and nonlinear hybrid automata) to the input formats of several tools. Additionally, we illustrate a general model transformation pass based on pseudo-invariants implemented in Hyst that illustrates the reachability improvement.},
author = {Bak, Stanley and Bogomolov, Sergiy and Johnson, Taylor},
location = {Seattle, WA, United States},
pages = {128 -- 133},
publisher = {Springer},
title = {{HYST: A source transformation and translation tool for hybrid automaton models}},
doi = {10.1145/2728606.2728630},
year = {2015},
}
@inproceedings{1691,
abstract = {We consider a case study of the problem of deploying an autonomous air vehicle in a partially observable, dynamic, indoor environment from a specification given as a linear temporal logic (LTL) formula over regions of interest. We model the motion and sensing capabilities of the vehicle as a partially observable Markov decision process (POMDP). We adapt recent results for solving POMDPs with parity objectives to generate a control policy. We also extend the existing framework with a policy minimization technique to obtain a better implementable policy, while preserving its correctness. The proposed techniques are illustrated in an experimental setup involving an autonomous quadrotor performing surveillance in a dynamic environment.},
author = {Svoreňová, Mária and Chmelik, Martin and Leahy, Kevin and Eniser, Hasan and Chatterjee, Krishnendu and Cěrná, Ivana and Belta, Cǎlin},
booktitle = {Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control},
location = {Seattle, WA, United States},
pages = {233 -- 238},
publisher = {ACM},
title = {{Temporal logic motion planning using POMDPs with parity objectives: Case study paper}},
doi = {10.1145/2728606.2728617},
year = {2015},
}
@inproceedings{1692,
abstract = {Computing an approximation of the reachable states of a hybrid system is a challenge, mainly because overapproximating the solutions of ODEs with a finite number of sets does not scale well. Using template polyhedra can greatly reduce the computational complexity, since it replaces complex operations on sets with a small number of optimization problems. However, the use of templates may make the over-approximation too conservative. Spurious transitions, which are falsely considered reachable, are particularly detrimental to performance and accuracy, and may exacerbate the state explosion problem. In this paper, we examine how spurious transitions can be avoided with minimal computational effort. To this end, detecting spurious transitions is reduced to the well-known problem of showing that two convex sets are disjoint by finding a hyperplane that separates them. We generalize this to owpipes by considering hyperplanes that evolve with time in correspondence to the dynamics of the system. The approach is implemented in the model checker SpaceEx and demonstrated on examples.},
author = {Frehse, Goran and Bogomolov, Sergiy and Greitschus, Marius and Strump, Thomas and Podelski, Andreas},
booktitle = {Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control},
isbn = {978-1-4503-3433-4},
location = {Seattle, WA, United States},
pages = {149 -- 158},
publisher = {ACM},
title = {{Eliminating spurious transitions in reachability with support functions}},
doi = {10.1145/2728606.2728622},
year = {2015},
}
@article{1693,
abstract = {Quantum interference between energetically close states is theoretically investigated, with the state structure being observed via laser spectroscopy. In this work, we focus on hyperfine states of selected hydrogenic muonic isotopes, and on how quantum interference affects the measured Lamb shift. The process of photon excitation and subsequent photon decay is implemented within the framework of nonrelativistic second-order perturbation theory. Due to its experimental interest, calculations are performed for muonic hydrogen, deuterium, and helium-3. We restrict our analysis to the case of photon scattering by incident linear polarized photons and the polarization of the scattered photons not being observed. We conclude that while quantum interference effects can be safely neglected in muonic hydrogen and helium-3, in the case of muonic deuterium there are resonances with close proximity, where quantum interference effects can induce shifts up to a few percent of the linewidth, assuming a pointlike detector. However, by taking into account the geometry of the setup used by the CREMA collaboration, this effect is reduced to less than 0.2% of the linewidth in all possible cases, which makes it irrelevant at the present level of accuracy. © 2015 American Physical Society.},
author = {Amaro, Pedro and Franke, Beatrice and Krauth, Julian and Diepold, Marc and Fratini, Filippo and Safari, Laleh and Machado, Jorge and Antognini, Aldo and Kottmann, Franz and Indelicato, Paul and Pohl, Randolf and Santos, José},
journal = {Physical Review A},
number = {2},
publisher = {American Physical Society},
title = {{Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3}},
doi = {10.1103/PhysRevA.92.022514},
volume = {92},
year = {2015},
}
@article{1694,
abstract = {
We introduce quantitative timed refinement and timed simulation (directed) metrics, incorporating zenoness checks, for timed systems. These metrics assign positive real numbers which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximal timing mismatch that can arise, (2) the “steady-state” maximal timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation distances to within any desired degree of accuracy. In order to compute the values of the quantitative simulation distances, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite-state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives in graph games, and then use these algorithms to compute the values of the timed simulation distances over timed automata.
},
author = {Chatterjee, Krishnendu and Prabhu, Vinayak},
journal = {IEEE Transactions on Automatic Control},
number = {9},
pages = {2291 -- 2306},
publisher = {IEEE},
title = {{Quantitative temporal simulation and refinement distances for timed systems}},
doi = {10.1109/TAC.2015.2404612},
volume = {60},
year = {2015},
}
@article{1695,
abstract = {We give a comprehensive introduction into a diagrammatic method that allows for the evaluation of Gutzwiller wave functions in finite spatial dimensions. We discuss in detail some numerical schemes that turned out to be useful in the real-space evaluation of the diagrams. The method is applied to the problem of d-wave superconductivity in a two-dimensional single-band Hubbard model. Here, we discuss in particular the role of long-range contributions in our diagrammatic expansion. We further reconsider our previous analysis on the kinetic energy gain in the superconducting state.},
author = {Kaczmarczyk, Jan and Schickling, Tobias and Bünemann, Jörg},
journal = {Physica Status Solidi (B): Basic Solid State Physics},
number = {9},
pages = {2059 -- 2071},
publisher = {Wiley},
title = {{Evaluation techniques for Gutzwiller wave functions in finite dimensions}},
doi = {10.1002/pssb.201552082},
volume = {252},
year = {2015},
}
@article{1696,
abstract = {The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller wave function (GWF) is applied to the Anderson lattice model. This approach allows for a systematic evaluation of the expectation values with full Gutzwiller wave function in finite-dimensional systems. It introduces results extending in an essential manner those obtained by means of the standard Gutzwiller approximation (GA), which is variationally exact only in infinite dimensions. Within the DE-GWF approach we discuss the principal paramagnetic properties and their relevance to heavy-fermion systems. We demonstrate the formation of an effective, narrow f band originating from atomic f-electron states and subsequently interpret this behavior as a direct itineracy of f electrons; it represents a combined effect of both the hybridization and the correlations induced by the Coulomb repulsive interaction. Such a feature is absent on the level of GA, which is equivalent to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent narrow f band rationalizes the common assumption of such dispersion of f levels in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it is shown that the emerging f-electron direct itineracy leads in a natural manner to three physically distinct regimes within a single model that are frequently discussed for 4f- or 5f-electron compounds as separate model situations. We identify these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging correlated quantum liquid state are stressed.},
author = {Wysokiński, Marcin and Kaczmarczyk, Jan and Spałek, Jozef},
journal = {Physical Review B},
number = {12},
publisher = {American Physical Society},
title = {{Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states}},
doi = {10.1103/PhysRevB.92.125135},
volume = {92},
year = {2015},
}
@article{1697,
abstract = {Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits.},
author = {Marre, Olivier and Botella Soler, Vicente and Simmons, Kristina and Mora, Thierry and Tkacik, Gasper and Berry, Michael},
journal = {PLoS Computational Biology},
number = {7},
publisher = {Public Library of Science},
title = {{High accuracy decoding of dynamical motion from a large retinal population}},
doi = {10.1371/journal.pcbi.1004304},
volume = {11},
year = {2015},
}
@article{1698,
abstract = {In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Multi-mean-payoff and multi-energy games replace individual weights by tuples, and the limit average (resp., running sum) of each coordinate must be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy games and show inter-reducibility of multi-mean-payoff and multi-energy games for finite-memory strategies. We improve the computational complexity for solving both classes with finite-memory strategies: we prove coNP-completeness improving the previous known EXPSPACE bound. For memoryless strategies, we show that deciding the existence of a winning strategy for the protagonist is NP-complete. We present the first solution of multi-mean-payoff games with infinite-memory strategies: we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf objectives are coNP-complete.},
author = {Velner, Yaron and Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A and Rabinovich, Alexander and Raskin, Jean},
journal = {Information and Computation},
number = {4},
pages = {177 -- 196},
publisher = {Elsevier},
title = {{The complexity of multi-mean-payoff and multi-energy games}},
doi = {10.1016/j.ic.2015.03.001},
volume = {241},
year = {2015},
}
@article{1699,
abstract = {By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.},
author = {Uecker, Hildegard and Setter, Derek and Hermisson, Joachim},
journal = {Journal of Mathematical Biology},
number = {7},
pages = {1523 -- 1580},
publisher = {Springer},
title = {{Adaptive gene introgression after secondary contact}},
doi = {10.1007/s00285-014-0802-y},
volume = {70},
year = {2015},
}
@article{1700,
abstract = {We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms.},
author = {Van Loon, Erik and Katsnelson, Mikhail and Lemeshko, Mikhail},
journal = {Physical Review B},
number = {8},
publisher = {American Physical Society},
title = {{Ultralong-range order in the Fermi-Hubbard model with long-range interactions}},
doi = {10.1103/PhysRevB.92.081106},
volume = {92},
year = {2015},
}
@article{1701,
abstract = {The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance. },
author = {Tkacik, Gasper and Mora, Thierry and Marre, Olivier and Amodei, Dario and Palmer, Stephanie and Berry Ii, Michael and Bialek, William},
journal = {PNAS},
number = {37},
pages = {11508 -- 11513},
publisher = {National Academy of Sciences},
title = {{Thermodynamics and signatures of criticality in a network of neurons}},
doi = {10.1073/pnas.1514188112},
volume = {112},
year = {2015},
}
@article{1703,
abstract = {Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.},
author = {Broadhurst, Linda and Fifield, Graham and Vanzella, Bindi and Pickup, Melinda},
journal = {Australian Journal of Botany},
number = {5},
pages = {455 -- 466},
publisher = {CSIRO},
title = {{An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas}},
doi = {10.1071/BT15023},
volume = {63},
year = {2015},
}
@article{1704,
abstract = {Given a convex function (Formula presented.) and two hermitian matrices A and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative entropy defined by (Formula presented.). Among other things, they prove that the so-defined quantity is monotone if and only if (Formula presented.) is operator monotone. The monotonicity is then used to properly define (Formula presented.) for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional projections (Formula presented.) with (Formula presented.) strongly, the limit (Formula presented.) is shown to exist and to be independent of the sequence of projections (Formula presented.). The question whether this sequence converges to its "obvious" limit, namely (Formula presented.), has been left open. We answer this question in principle affirmatively and show that (Formula presented.). If the operators A and B are regular enough, that is (A − B), (Formula presented.) and (Formula presented.) are trace-class, the identity (Formula presented.) holds.},
author = {Deuchert, Andreas and Hainzl, Christian and Seiringer, Robert},
journal = {Letters in Mathematical Physics},
number = {10},
pages = {1449 -- 1466},
publisher = {Springer},
title = {{Note on a family of monotone quantum relative entropies}},
doi = {10.1007/s11005-015-0787-5},
volume = {105},
year = {2015},
}
@inproceedings{1706,
abstract = {We consider a problem of learning kernels for use in SVM classification in the multi-task and lifelong scenarios and provide generalization bounds on the error of a large margin classifier. Our results show that, under mild conditions on the family of kernels used for learning, solving several related tasks simultaneously is beneficial over single task learning. In particular, as the number of observed tasks grows, assuming that in the considered family of kernels there exists one that yields low approximation error on all tasks, the overhead associated with learning such a kernel vanishes and the complexity converges to that of learning when this good kernel is given to the learner.},
author = {Pentina, Anastasia and Ben David, Shai},
location = {Banff, AB, Canada},
pages = {194 -- 208},
publisher = {Springer},
title = {{Multi-task and lifelong learning of kernels}},
doi = {10.1007/978-3-319-24486-0_13},
volume = {9355},
year = {2015},
}
@article{1709,
abstract = {The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards.},
author = {Reiter, Johannes and Kanodia, Ayush and Gupta, Raghav and Nowak, Martin and Chatterjee, Krishnendu},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1812},
publisher = {Royal Society},
title = {{Biological auctions with multiple rewards}},
doi = {10.1098/rspb.2015.1041},
volume = {282},
year = {2015},
}
@article{1710,
abstract = {We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞.},
author = {Akopyan, Arseniy and Plakhov, Alexander},
journal = {Society for Industrial and Applied Mathematics},
number = {4},
pages = {2754 -- 2769},
publisher = {SIAM},
title = {{Minimal resistance of curves under the single impact assumption}},
doi = {10.1137/140993843},
volume = {47},
year = {2015},
}
@article{1712,
abstract = {The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses.},
author = {Ratheesh, Aparna and Belyaeva, Vera and Siekhaus, Daria E},
journal = {Current Opinion in Cell Biology},
number = {10},
pages = {71 -- 79},
publisher = {Elsevier},
title = {{Drosophila immune cell migration and adhesion during embryonic development and larval immune responses}},
doi = {10.1016/j.ceb.2015.07.003},
volume = {36},
year = {2015},
}
@inproceedings{1714,
abstract = {We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application.},
author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Kößler, Alexander and Schmid, Ulrich},
booktitle = {Real-Time Systems Symposium},
location = {Rome, Italy},
number = {January},
pages = {118 -- 127},
publisher = {IEEE},
title = {{A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks}},
doi = {10.1109/RTSS.2014.9},
volume = {2015},
year = {2015},
}
@article{1728,
abstract = {In the vertebrate neural tube, the morphogen Sonic Hedgehog (Shh) establishes a characteristic pattern of gene expression. Here we quantify the Shh gradient in the developing mouse neural tube and show that while the amplitude of the gradient increases over time, the activity of the pathway transcriptional effectors, Gli proteins, initially increases but later decreases. Computational analysis of the pathway suggests three mechanisms that could contribute to this adaptation: transcriptional upregulation of the inhibitory receptor Ptch1, transcriptional downregulation of Gli and the differential stability of active and inactive Gli isoforms. Consistent with this, Gli2 protein expression is downregulated during neural tube patterning and adaptation continues when the pathway is stimulated downstream of Ptch1. Moreover, the Shh-induced upregulation of Gli2 transcription prevents Gli activity levels from adapting in a different cell type, NIH3T3 fibroblasts, despite the upregulation of Ptch1. Multiple mechanisms therefore contribute to the intracellular dynamics of Shh signalling, resulting in different signalling dynamics in different cell types.},
author = {Cohen, Michael H and Anna Kicheva and Ribeiro, Ana C and Blassberg, Robert A and Page, Karen M and Barnes, Chris P and Briscoe, James},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms}},
doi = {10.1038/ncomms7709},
volume = {6},
year = {2015},
}
@inproceedings{1729,
abstract = {We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions.},
author = {Cerny, Pavol and Clarke, Edmund and Henzinger, Thomas A and Radhakrishna, Arjun and Ryzhyk, Leonid and Samanta, Roopsha and Tarrach, Thorsten},
location = {San Francisco, CA, United States},
pages = {180 -- 197},
publisher = {Springer},
title = {{From non-preemptive to preemptive scheduling using synchronization synthesis}},
doi = {10.1007/978-3-319-21668-3_11},
volume = {9207},
year = {2015},
}
@article{1730,
abstract = {How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations.},
author = {Colin De Verdière, Éric and Hubard, Alfredo and De Mesmay, Arnaud N},
journal = {Discrete & Computational Geometry},
number = {3},
pages = {587 -- 620},
publisher = {Springer},
title = {{Discrete systolic inequalities and decompositions of triangulated surfaces}},
doi = {10.1007/s00454-015-9679-9},
volume = {53},
year = {2015},
}
@article{1731,
abstract = {We consider two-player zero-sum games on graphs. These games can be classified on the basis of the information of the players and on the mode of interaction between them. On the basis of information the classification is as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided complete-observation (one player has complete observation); and (c) complete-observation (both players have complete view of the game). On the basis of mode of interaction we have the following classification: (a) concurrent (both players interact simultaneously); and (b) turn-based (both players interact in turn). The two sources of randomness in these games are randomness in transition function and randomness in strategies. In general, randomized strategies are more powerful than deterministic strategies, and randomness in transitions gives more general classes of games. In this work we present a complete characterization for the classes of games where randomness is not helpful in: (a) the transition function probabilistic transition can be simulated by deterministic transition); and (b) strategies (pure strategies are as powerful as randomized strategies). As consequence of our characterization we obtain new undecidability results for these games. },
author = {Chatterjee, Krishnendu and Doyen, Laurent and Gimbert, Hugo and Henzinger, Thomas A},
journal = {Information and Computation},
number = {12},
pages = {3 -- 16},
publisher = {Elsevier},
title = {{Randomness for free}},
doi = {10.1016/j.ic.2015.06.003},
volume = {245},
year = {2015},
}
@inproceedings{1732,
abstract = {We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty.},
author = {Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Raghav and Kanodia, Ayush},
location = {Seattle, WA, United States},
pages = {325 -- 330},
publisher = {IEEE},
title = {{Qualitative analysis of POMDPs with temporal logic specifications for robotics applications}},
doi = {10.1109/ICRA.2015.7139019},
year = {2015},
}
@article{1734,
abstract = {Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. "Image-based methods" try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. "Parametric methods" instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture.},
author = {Klehm, Oliver and Rousselle, Fabrice and Papas, Marios and Bradley, Derek and Hery, Christophe and Bickel, Bernd and Jarosz, Wojciech and Beeler, Thabo},
journal = {Computer Graphics Forum},
number = {2},
pages = {709 -- 733},
publisher = {Wiley-Blackwell},
title = {{Recent advances in facial appearance capture}},
doi = {10.1111/cgf.12594},
volume = {34},
year = {2015},
}
@article{1735,
abstract = {This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations.},
author = {Ando, Ryoichi and Thürey, Nils and Wojtan, Christopher J},
journal = {Computer Graphics Forum},
number = {2},
pages = {473 -- 480},
publisher = {Wiley},
title = {{A dimension-reduced pressure solver for liquid simulations}},
doi = {10.1111/cgf.12576},
volume = {34},
year = {2015},
}
@article{1788,
abstract = {We fabricate and characterize a microscale silicon opto-electromechanical system whose mechanical motion is coupled capacitively to an electrical circuit and optically via radiation pressure to a photonic crystal cavity. To achieve large electromechanical interaction strength, we implement an inverse shadow mask fabrication scheme which obtains capacitor gaps as small as 30 nm while maintaining a silicon surface quality necessary for minimizing optical loss. Using the sensitive optical read-out of the photonic crystal cavity, we characterize the linear and nonlinear capacitive coupling to the fundamental ωm=2π = 63 MHz in-plane flexural motion of the structure, showing that the large electromechanical coupling in such devices may be suitable for realizing efficient microwave-to-optical signal conversion.},
author = {Pitanti, Alessandro and Johannes Fink and Safavi-Naeini, Amir H and Hill, Jeff T and Lei, Chan U and Tredicucci, Alessandro and Painter, Oskar J},
journal = {Optics Express},
number = {3},
pages = {3196 -- 3208},
publisher = {Optical Society of America},
title = {{Strong opto-electro-mechanical coupling in a silicon photonic crystal cavity}},
doi = {10.1364/OE.23.003196},
volume = {23},
year = {2015},
}
@article{1789,
abstract = {Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID.},
author = {Kuechler, Alma and Zink, Alexander and Wieland, Thomas and Lüdecke, Hermann and Cremer, Kirsten and Salviati, Leonardo and Magini, Pamela and Najafi, Kimia and Zweier, Christiane and Czeschik, Johanna and Aretz, Stefan and Endele, Sabine and Tamburrino, Federica and Pinato, Claudia and Clementi, Maurizio and Gundlach, Jasmin and Maylahn, Carina and Mazzanti, Laura and Wohlleber, Eva and Schwarzmayr, Thomas and Kariminejad, Roxana and Schlessinger, Avner and Wieczorek, Dagmar and Strom, Tim and Novarino, Gaia and Engels, Hartmut},
journal = {European Journal of Human Genetics},
number = {6},
pages = {753 -- 760},
publisher = {Nature Publishing Group},
title = {{Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome}},
doi = {10.1038/ejhg.2014.165},
volume = {23},
year = {2015},
}
@article{1792,
abstract = {Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology.},
author = {Pausinger, Florian and Svane, Anne},
journal = {Journal of Complexity},
number = {6},
pages = {773 -- 797},
publisher = {Academic Press},
title = {{A Koksma-Hlawka inequality for general discrepancy systems}},
doi = {10.1016/j.jco.2015.06.002},
volume = {31},
year = {2015},
}
@article{1793,
abstract = {We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.},
author = {Symonova, Olga and Topp, Christopher and Edelsbrunner, Herbert},
journal = {PLoS One},
number = {6},
publisher = {Public Library of Science},
title = {{DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots}},
doi = {10.1371/journal.pone.0127657},
volume = {10},
year = {2015},
}
@article{1802,
abstract = {Noncoding variants in the human MIR137 gene locus increase schizophrenia risk with genome-wide significance. However, the functional consequence of these risk alleles is unknown. Here we examined induced human neurons harboring the minor alleles of four disease-associated single nucleotide polymorphisms in MIR137. We observed increased MIR137 levels compared to those in major allele–carrying cells. microRNA-137 gain of function caused downregulation of the presynaptic target genes complexin-1 (Cplx1), Nsf and synaptotagmin-1 (Syt1), leading to impaired vesicle release. In vivo, miR-137 gain of function resulted in changes in synaptic vesicle pool distribution, impaired induction of mossy fiber long-term potentiation and deficits in hippocampus-dependent learning and memory. By sequestering endogenous miR-137, we were able to ameliorate the synaptic phenotypes. Moreover, reinstatement of Syt1 expression partially restored synaptic plasticity, demonstrating the importance of Syt1 as a miR-137 target. Our data provide new insight into the mechanism by which miR-137 dysregulation can impair synaptic plasticity in the hippocampus.},
author = {Sandra Siegert and Seo, Jinsoo and Kwon, Ester J and Rudenko, Andrii and Cho, Sukhee and Wang, Wenyuan and Flood, Zachary C and Martorell, Anthony J and Ericsson, Maria and Mungenast, Alison E and Tsai, Lihuei},
journal = {Nature Neuroscience},
pages = {1008 -- 1016},
publisher = {Nature Publishing Group},
title = {{The schizophrenia risk gene product miR-137 alters presynaptic plasticity}},
doi = {10.1038/nn.4023},
volume = {18},
year = {2015},
}
@article{1803,
abstract = {Repeated stress has been suggested to underlie learning and memory deficits via the basolateral amygdala (BLA) and the hippocampus; however, the functional contribution of BLA inputs to the hippocampus and their molecular repercussions are not well understood. Here we show that repeated stress is accompanied by generation of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation of glucocorticoid receptors, increased HDAC2 expression, and reduced expression of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic approaches shows that BLA activation is both necessary and sufficient for stress-associated molecular changes and memory impairments. Furthermore, we show that this effect relies on direct glutamatergic projections from the BLA to the dorsal hippocampus. Finally, we show that p25 generation is necessary for the stress-induced memory dysfunction. Taken together, our data provide a neural circuit model for stress-induced hippocampal memory deficits through BLA activity-dependent p25 generation.},
author = {Rei, Damien and Mason, Xenos and Seo, Jinsoo and Gräff, Johannes and Rudenko, Andrii and Wang, Jùn and Rueda, Richard and Sandra Siegert and Cho, Sukhee and Canter, Rebecca G and Mungenast, Alison E and Deisseroth, Karl A and Tsai, Lihuei},
journal = {PNAS},
number = {23},
pages = {7291 -- 7296},
publisher = {National Academy of Sciences},
title = {{Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway}},
doi = {10.1073/pnas.1415845112},
volume = {112},
year = {2015},
}
@article{1804,
abstract = {It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control.},
author = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Transition to turbulence in Taylor-Couette ferrofluidic flow}},
doi = {10.1038/srep10781},
volume = {5},
year = {2015},
}
@article{1805,
abstract = {We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.},
author = {Attali, Dominique and Bauer, Ulrich and Devillers, Olivier and Glisse, Marc and Lieutier, André},
journal = {Computational Geometry: Theory and Applications},
number = {8},
pages = {606 -- 621},
publisher = {Elsevier},
title = {{Homological reconstruction and simplification in R3}},
doi = {10.1016/j.comgeo.2014.08.010},
volume = {48},
year = {2015},
}