@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},
}
@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{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},
}
@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{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{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},
}
@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{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{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{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{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{1807,
abstract = {We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.},
author = {Goldman, Michael and Royo-Letelier, Jimena},
journal = {ESAIM - Control, Optimisation and Calculus of Variations},
number = {3},
pages = {603 -- 624},
publisher = {EDP Sciences},
title = {{Sharp interface limit for two components Bose-Einstein condensates}},
doi = {10.1051/cocv/2014040},
volume = {21},
year = {2015},
}
@article{1809,
abstract = {Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.},
author = {Trubenova, Barbora and Novak, Sebastian and Hager, Reinmar},
journal = {PLoS One},
number = {5},
publisher = {Public Library of Science},
title = {{Indirect genetic effects and the dynamics of social interactions}},
doi = {10.1371/journal.pone.0126907},
volume = {10},
year = {2015},
}
@article{1810,
abstract = {Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.},
author = {Bollenbach, Mark Tobias},
journal = {Current Opinion in Microbiology},
pages = {1 -- 9},
publisher = {Elsevier},
title = {{Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution}},
doi = {10.1016/j.mib.2015.05.008},
volume = {27},
year = {2015},
}
@article{1811,
abstract = {Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.},
author = {Safari, Laleh and Santos, José and Amaro, Pedro and Jänkälä, Kari and Fratini, Filippo},
journal = {Journal of Mathematical Physics},
number = {5},
publisher = {American Institute of Physics},
title = {{Analytical evaluation of atomic form factors: Application to Rayleigh scattering}},
doi = {10.1063/1.4921227},
volume = {56},
year = {2015},
}
@article{1812,
abstract = {We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.
},
author = {Lahrz, Martin and Lemeshko, Mikhail and Mathey, Ludwig},
journal = {New Journal of Physics},
number = {4},
publisher = {IOP Publishing Ltd.},
title = {{Exotic roton excitations in quadrupolar Bose–Einstein condensates }},
doi = {10.1088/1367-2630/17/4/045005},
volume = {17},
year = {2015},
}
@article{1813,
abstract = {We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.},
author = {Schmidt, Richard and Lemeshko, Mikhail},
journal = {Physical Review Letters},
number = {20},
publisher = {American Physical Society},
title = {{Rotation of quantum impurities in the presence of a many-body environment}},
doi = {10.1103/PhysRevLett.114.203001},
volume = {114},
year = {2015},
}
@article{1814,
abstract = {We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.},
author = {Jeschke, Stefan and Wojtan, Christopher J},
journal = {ACM Transactions on Graphics},
number = {3},
publisher = {ACM},
title = {{Water wave animation via wavefront parameter interpolation}},
doi = {10.1145/2714572},
volume = {34},
year = {2015},
}
@article{1817,
abstract = {Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. },
author = {Porazinski, Sean and Wang, Huijia and Asaoka, Yoichi and Behrndt, Martin and Miyamoto, Tatsuo and Morita, Hitoshi and Hata, Shoji and Sasaki, Takashi and Krens, Gabriel and Osada, Yumi and Asaka, Satoshi and Momoi, Akihiro and Linton, Sarah and Miesfeld, Joel and Link, Brian and Senga, Takeshi and Castillo Morales, Atahualpa and Urrutia, Araxi and Shimizu, Nobuyoshi and Nagase, Hideaki and Matsuura, Shinya and Bagby, Stefan and Kondoh, Hisato and Nishina, Hiroshi and Heisenberg, Carl-Philipp J and Furutani Seiki, Makoto},
journal = {Nature},
number = {7551},
pages = {217 -- 221},
publisher = {Nature Publishing Group},
title = {{YAP is essential for tissue tension to ensure vertebrate 3D body shape}},
doi = {10.1038/nature14215},
volume = {521},
year = {2015},
}
@article{1818,
abstract = {Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.},
author = {Polechova, Jitka and Barton, Nicholas H},
journal = {PNAS},
number = {20},
pages = {6401 -- 6406},
publisher = {National Academy of Sciences},
title = {{Limits to adaptation along environmental gradients}},
doi = {10.1073/pnas.1421515112},
volume = {112},
year = {2015},
}
@inproceedings{1820,
abstract = {We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.},
author = {Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Raghav and Kanodia, Ayush},
booktitle = {Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence },
location = {Austin, TX, USA},
pages = {3496--3502},
publisher = {AAAI Press},
title = {{Optimal cost almost-sure reachability in POMDPs}},
volume = {5},
year = {2015},
}
@article{1823,
abstract = {Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways.},
author = {Chevereau, Guillaume and Bollenbach, Mark Tobias},
journal = {Molecular Systems Biology},
number = {4},
publisher = {Nature Publishing Group},
title = {{Systematic discovery of drug interaction mechanisms}},
doi = {10.15252/msb.20156098},
volume = {11},
year = {2015},
}
@article{1824,
abstract = {Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates.},
author = {Knebel, Johannes and Weber, Markus and Krüger, Torben H and Frey, Erwin},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Evolutionary games of condensates in coupled birth-death processes}},
doi = {10.1038/ncomms7977},
volume = {6},
year = {2015},
}
@article{1827,
abstract = {Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.},
author = {Friedlander, Tamar and Mayo, Avraham and Tlusty, Tsvi and Alon, Uri},
journal = {PLoS Computational Biology},
number = {3},
publisher = {Public Library of Science},
title = {{Evolution of bow-tie architectures in biology}},
doi = {10.1371/journal.pcbi.1004055},
volume = {11},
year = {2015},
}
@article{1828,
abstract = {We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory.},
author = {Akopyan, Arseniy and Pirogov, Sergey and Rybko, Aleksandr},
journal = {Journal of Statistical Physics},
number = {1},
pages = {163 -- 167},
publisher = {Springer},
title = {{Invariant measures of genetic recombination process}},
doi = {10.1007/s10955-015-1238-5},
volume = {160},
year = {2015},
}
@article{1830,
abstract = {To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.},
author = {Theis, Fabian and Ugelvig, Line V and Marr, Carsten and Cremer, Sylvia},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1669},
publisher = {Royal Society, The},
title = {{Opposing effects of allogrooming on disease transmission in ant societies}},
doi = {10.1098/rstb.2014.0108},
volume = {370},
year = {2015},
}
@article{1831,
abstract = {This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research.},
author = {Kappeler, Peter and Cremer, Sylvia and Nunn, Charles},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1669},
publisher = {Royal Society},
title = {{Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies}},
doi = {10.1098/rstb.2014.0116},
volume = {370},
year = {2015},
}
@article{1832,
abstract = {Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on the identification of the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates. In response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof. },
author = {Chakraborty, Soham and Henzinger, Thomas A and Sezgin, Ali and Vafeiadis, Viktor},
journal = {Logical Methods in Computer Science},
number = {1},
publisher = {International Federation of Computational Logic},
title = {{Aspect-oriented linearizability proofs}},
doi = {10.2168/LMCS-11(1:20)2015},
volume = {11},
year = {2015},
}
@article{1834,
abstract = {Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks.},
author = {Chen, Chong and Wang, Chao and Zhao, Xuan and Zhou, Tao and Xu, Dao and Wang, Zhi and Wang, Ying},
journal = {ASN Neuro},
number = {2},
publisher = {SAGE},
title = {{Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats}},
doi = {10.1177/1759091415575845},
volume = {7},
year = {2015},
}
@inproceedings{1835,
abstract = {The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.},
author = {Giacobbe, Mirco and Guet, Calin C and Gupta, Ashutosh and Henzinger, Thomas A and Paixao, Tiago and Petrov, Tatjana},
location = {London, United Kingdom},
pages = {469 -- 483},
publisher = {Springer},
title = {{Model checking gene regulatory networks}},
doi = {10.1007/978-3-662-46681-0_47},
volume = {9035},
year = {2015},
}
@article{1837,
abstract = {Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.},
author = {Kühnen, Jakob and Braunshier, P and Schwegel, M and Kuhlmann, Hendrik and Hof, Björn},
journal = {Journal of Fluid Mechanics},
number = {5},
publisher = {Cambridge University Press},
title = {{Subcritical versus supercritical transition to turbulence in curved pipes}},
doi = {10.1017/jfm.2015.184},
volume = {770},
year = {2015},
}
@inproceedings{1838,
abstract = {Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples.},
author = {Bloem, Roderick and Chatterjee, Krishnendu and Jacobs, Swen and Könighofer, Robert},
location = {London, United Kingdom},
pages = {517 -- 532},
publisher = {Springer},
title = {{Assume-guarantee synthesis for concurrent reactive programs with partial information}},
doi = {10.1007/978-3-662-46681-0_50},
volume = {9035},
year = {2015},
}
@inproceedings{1839,
abstract = {We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies.},
author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín},
location = {London, United Kingdom},
pages = {181 -- 187},
publisher = {Springer},
title = {{Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives}},
doi = {10.1007/978-3-662-46681-0_12},
volume = {9035},
year = {2015},
}
@article{1840,
abstract = {In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.},
author = {Geiger, Bernhard and Petrov, Tatjana and Kubin, Gernot and Koeppl, Heinz},
issn = {0018-9286},
journal = {IEEE Transactions on Automatic Control},
number = {4},
pages = {1010 -- 1022},
publisher = {IEEE},
title = {{Optimal Kullback-Leibler aggregation via information bottleneck}},
doi = {10.1109/TAC.2014.2364971},
volume = {60},
year = {2015},
}
@article{1841,
abstract = {We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results.},
author = {Kolmogorov, Vladimir},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
number = {5},
pages = {919 -- 930},
publisher = {IEEE},
title = {{A new look at reweighted message passing}},
doi = {10.1109/TPAMI.2014.2363465},
volume = {37},
year = {2015},
}
@article{1845,
abstract = {Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression.},
author = {Vandael, David H and Espinoza Martinez, Claudia M and Jonas, Peter M},
journal = {Neuron},
number = {6},
pages = {1149 -- 1151},
publisher = {Elsevier},
title = {{Excitement about inhibitory presynaptic terminals}},
doi = {10.1016/j.neuron.2015.03.006},
volume = {85},
year = {2015},
}
@article{1846,
abstract = {Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS.},
author = {Beneš, Nikola and Kretinsky, Jan and Larsen, Kim and Möller, Mikael and Sickert, Salomon and Srba, Jiří},
journal = {Acta Informatica},
number = {2-3},
pages = {269 -- 297},
publisher = {Springer},
title = {{Refinement checking on parametric modal transition systems}},
doi = {10.1007/s00236-015-0215-4},
volume = {52},
year = {2015},
}
@article{1848,
abstract = {The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis.},
author = {Schwamb, Bettina and Pick, Robert and Fernández, Sara and Völp, Kirsten and Heering, Jan and Dötsch, Volker and Bösser, Susanne and Jung, Jennifer and Beinoravičiute Kellner, Rasa and Wesely, Josephine and Zörnig, Inka and Hammerschmidt, Matthias and Nowak, Matthias and Penzel, Roland and Zatloukal, Kurt and Joos, Stefan and Rieker, Ralf and Agaimy, Abbas and Söder, Stephan and Reid Lombardo, Kmarie and Kendrick, Michael and Bardsley, Michael and Hayashi, Yujiro and Asuzu, David and Syed, Sabriya and Ördög, Tamás and Zörnig, Martin},
journal = {International Journal of Cancer},
number = {6},
pages = {1318 -- 1329},
publisher = {Wiley},
title = {{FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors}},
doi = {10.1002/ijc.29498},
volume = {137},
year = {2015},
}
@article{1850,
abstract = {Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.},
author = {Novak, Sebastian and Cremer, Sylvia},
journal = {Journal of Theoretical Biology},
number = {5},
pages = {54 -- 64},
publisher = {Elsevier},
title = {{Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates}},
doi = {10.1016/j.jtbi.2015.02.018},
volume = {372},
year = {2015},
}
@article{1851,
abstract = {We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them.},
author = {Priklopil, Tadeas and Kisdi, Eva and Gyllenberg, Mats},
journal = {Evolution},
number = {4},
pages = {1015 -- 1026},
publisher = {Wiley-Blackwell},
title = {{Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating}},
doi = {10.1111/evo.12618},
volume = {69},
year = {2015},
}
@article{1855,
abstract = {Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.},
author = {Mcmahon, Dino and Fürst, Matthias and Caspar, Jesicca and Theodorou, Panagiotis and Brown, Mark and Paxton, Robert},
journal = {Journal of Animal Ecology},
number = {3},
pages = {615 -- 624},
publisher = {Wiley},
title = {{A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees}},
doi = {10.1111/1365-2656.12345},
volume = {84},
year = {2015},
}
@article{1856,
abstract = {The traditional synthesis question given a specification asks for the automatic construction of a system that satisfies the specification, whereas often there exists a preference order among the different systems that satisfy the given specification. Under a probabilistic assumption about the possible inputs, such a preference order is naturally expressed by a weighted automaton, which assigns to each word a value, such that a system is preferred if it generates a higher expected value. We solve the following optimal synthesis problem: given an omega-regular specification, a Markov chain that describes the distribution of inputs, and a weighted automaton that measures how well a system satisfies the given specification under the input assumption, synthesize a system that optimizes the measured value. For safety specifications and quantitative measures that are defined by mean-payoff automata, the optimal synthesis problem reduces to finding a strategy in a Markov decision process (MDP) that is optimal for a long-run average reward objective, which can be achieved in polynomial time. For general omega-regular specifications along with mean-payoff automata, the solution rests on a new, polynomial-time algorithm for computing optimal strategies in MDPs with mean-payoff parity objectives. Our algorithm constructs optimal strategies that consist of two memoryless strategies and a counter. The counter is in general not bounded. To obtain a finite-state system, we show how to construct an ε-optimal strategy with a bounded counter, for all ε > 0. Furthermore, we show how to decide in polynomial time if it is possible to construct an optimal finite-state system (i.e., a system without a counter) for a given specification. We have implemented our approach and the underlying algorithms in a tool that takes qualitative and quantitative specifications and automatically constructs a system that satisfies the qualitative specification and optimizes the quantitative specification, if such a system exists. We present some experimental results showing optimal systems that were automatically generated in this way.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara and Singh, Rohit},
journal = {Journal of the ACM},
number = {1},
publisher = {ACM},
title = {{Measuring and synthesizing systems in probabilistic environments}},
doi = {10.1145/2699430},
volume = {62},
year = {2015},
}
@inproceedings{1857,
abstract = {Sharing information between multiple tasks enables algorithms to achieve good generalization performance even from small amounts of training data. However, in a realistic scenario of multi-task learning not all tasks are equally related to each other, hence it could be advantageous to transfer information only between the most related tasks. In this work we propose an approach that processes multiple tasks in a sequence with sharing between subsequent tasks instead of solving all tasks jointly. Subsequently, we address the question of curriculum learning of tasks, i.e. finding the best order of tasks to be learned. Our approach is based on a generalization bound criterion for choosing the task order that optimizes the average expected classification performance over all tasks. Our experimental results show that learning multiple related tasks sequentially can be more effective than learning them jointly, the order in which tasks are being solved affects the overall performance, and that our model is able to automatically discover the favourable order of tasks. },
author = {Pentina, Anastasia and Sharmanska, Viktoriia and Lampert, Christoph},
location = {Boston, MA, United States},
pages = {5492 -- 5500},
publisher = {IEEE},
title = {{Curriculum learning of multiple tasks}},
doi = {10.1109/CVPR.2015.7299188},
year = {2015},
}
@inproceedings{1858,
abstract = {We study the problem of predicting the future, though only in the probabilistic sense of estimating a future state of a time-varying probability distribution. This is not only an interesting academic problem, but solving this extrapolation problem also has many practical application, e.g. for training classifiers that have to operate under time-varying conditions. Our main contribution is a method for predicting the next step of the time-varying distribution from a given sequence of sample sets from earlier time steps. For this we rely on two recent machine learning techniques: embedding probability distributions into a reproducing kernel Hilbert space, and learning operators by vector-valued regression. We illustrate the working principles and the practical usefulness of our method by experiments on synthetic and real data. We also highlight an exemplary application: training a classifier in a domain adaptation setting without having access to examples from the test time distribution at training time.},
author = {Lampert, Christoph},
location = {Boston, MA, United States},
pages = {942 -- 950},
publisher = {IEEE},
title = {{Predicting the future behavior of a time-varying probability distribution}},
doi = {10.1109/CVPR.2015.7298696},
year = {2015},
}
@inproceedings{1859,
abstract = {Structural support vector machines (SSVMs) are amongst the best performing models for structured computer vision tasks, such as semantic image segmentation or human pose estimation. Training SSVMs, however, is computationally costly, because it requires repeated calls to a structured prediction subroutine (called \emph{max-oracle}), which has to solve an optimization problem itself, e.g. a graph cut.
In this work, we introduce a new algorithm for SSVM training that is more efficient than earlier techniques when the max-oracle is computationally expensive, as it is frequently the case in computer vision tasks. The main idea is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm with efficient hyperplane caching, and (ii) use an automatic selection rule for deciding whether to call the exact max-oracle or to rely on an approximate one based on the cached hyperplanes.
We show experimentally that this strategy leads to faster convergence to the optimum with respect to the number of requires oracle calls, and that this translates into faster convergence with respect to the total runtime when the max-oracle is slow compared to the other steps of the algorithm. },
author = {Shah, Neel and Kolmogorov, Vladimir and Lampert, Christoph},
location = {Boston, MA, USA},
pages = {2737 -- 2745},
publisher = {IEEE},
title = {{A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle}},
doi = {10.1109/CVPR.2015.7298890},
year = {2015},
}
@inproceedings{1860,
abstract = {Classifiers for object categorization are usually evaluated by their accuracy on a set of i.i.d. test examples. This provides us with an estimate of the expected error when applying the classifiers to a single new image. In real application, however, classifiers are rarely only used for a single image and then discarded. Instead, they are applied sequentially to many images, and these are typically not i.i.d. samples from a fixed data distribution, but they carry dependencies and their class distribution varies over time. In this work, we argue that the phenomenon of correlated data at prediction time is not a nuisance, but a blessing in disguise. We describe a probabilistic method for adapting classifiers at prediction time without having to retrain them. We also introduce a framework for creating realistically distributed image sequences, which offers a way to benchmark classifier adaptation methods, such as the one we propose. Experiments on the ILSVRC2010 and ILSVRC2012 datasets show that adapting object classification systems at prediction time can significantly reduce their error rate, even with no additional human feedback.},
author = {Royer, Amélie and Lampert, Christoph},
location = {Boston, MA, United States},
pages = {1401 -- 1409},
publisher = {IEEE},
title = {{Classifier adaptation at prediction time}},
doi = {10.1109/CVPR.2015.7298746},
year = {2015},
}
@article{1864,
abstract = {The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive regime, a universal power law behaviour for the correlation functions of the mesoscopic eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013), we prove these formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013) we introduced a diagrammatic approach and presented robust estimates on general diagrams under certain simplifying assumptions. In this paper, we remove these assumptions by giving a general estimate of the subleading diagrams. We also give a precise analysis of the leading diagrams which give rise to the Altschuler–Shklovskii power laws. Moreover, we introduce a family of general random band matrices which interpolates between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track the transition for the mesoscopic density–density correlation. Finally, we address the higher-order correlation functions by proving that they behave asymptotically according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii formulas.
},
author = {Erdös, László and Knowles, Antti},
journal = {Annales Henri Poincare},
number = {3},
pages = {709 -- 799},
publisher = {Springer},
title = {{The Altshuler–Shklovskii formulas for random band matrices II: The general case}},
doi = {10.1007/s00023-014-0333-5},
volume = {16},
year = {2015},
}
@article{1871,
abstract = {The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.},
author = {Grones, Peter and Friml, Jirí},
journal = {Journal of Cell Science},
number = {1},
pages = {1 -- 7},
publisher = {Company of Biologists},
title = {{Auxin transporters and binding proteins at a glance}},
doi = {10.1242/jcs.159418},
volume = {128},
year = {2015},
}
@article{1873,
abstract = {We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with every transition, and the payoff of an infinite path is the long-run average of the rewards. We consider two types of path constraints: (i) a quantitative constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples.},
author = {Chatterjee, Krishnendu and Chmelik, Martin},
journal = {Artificial Intelligence},
pages = {46 -- 72},
publisher = {Elsevier},
title = {{POMDPs under probabilistic semantics}},
doi = {10.1016/j.artint.2014.12.009},
volume = {221},
year = {2015},
}
@article{1879,
abstract = {When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.},
author = {Kremer, A and Lippens, Stefaan and Bartunkova, Sonia and Asselbergh, Bob and Blanpain, Cendric and Fendrych, Matyas and Goossens, A and Holt, Matthew and Janssens, Sophie and Krols, Michiel and Larsimont, Jean and Mc Guire, Conor and Nowack, Moritz and Saelens, Xavier and Schertel, Andreas and Schepens, B and Slezak, M and Timmerman, Vincent and Theunis, Clara and Van Brempt, Ronald and Visser, Y and Guérin, Christophe},
journal = {Journal of Microscopy},
number = {2},
pages = {80 -- 96},
publisher = {Wiley-Blackwell},
title = {{Developing 3D SEM in a broad biological context}},
doi = {10.1111/jmi.12211},
volume = {259},
year = {2015},
}
@article{1880,
abstract = {We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder},
author = {Könenberg, Martin and Moser, Thomas and Seiringer, Robert and Yngvason, Jakob},
journal = {New Journal of Physics},
publisher = {IOP Publishing Ltd.},
title = {{Superfluid behavior of a Bose-Einstein condensate in a random potential}},
doi = {10.1088/1367-2630/17/1/013022},
volume = {17},
year = {2015},
}
@inproceedings{1882,
abstract = {We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations.},
author = {Fahrenberg, Uli and Kretinsky, Jan and Legay, Axel and Traonouez, Louis},
location = {Bertinoro, Italy},
pages = {306 -- 324},
publisher = {Springer},
title = {{Compositionality for quantitative specifications}},
doi = {10.1007/978-3-319-15317-9_19},
volume = {8997},
year = {2015},
}
@article{1883,
abstract = {We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.
},
author = {Keller-Schmidt, Stephanie and Tugrul, Murat and Eguíluz, Víctor and Hernandez Garcia, Emilio and Klemm, Konstantin},
journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
number = {2},
publisher = {American Institute of Physics},
title = {{Anomalous scaling in an age-dependent branching model}},
doi = {10.1103/PhysRevE.91.022803},
volume = {91},
year = {2015},
}
@article{1885,
abstract = {The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. },
author = {Tkacik, Gasper and Dubuis, Julien and Petkova, Mariela and Gregor, Thomas},
journal = {Genetics},
number = {1},
pages = {39 -- 59},
publisher = {Genetics Society of America},
title = {{Positional information, positional error, and readout precision in morphogenesis: A mathematical framework}},
doi = {10.1534/genetics.114.171850},
volume = {199},
year = {2015},
}
@article{1940,
abstract = {We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.},
author = {Sokolowski, Thomas R and Tkacik, Gasper},
journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
number = {6},
publisher = {American Institute of Physics},
title = {{Optimizing information flow in small genetic networks. IV. Spatial coupling}},
doi = {10.1103/PhysRevE.91.062710},
volume = {91},
year = {2015},
}
@unpublished{8183,
abstract = {We study conditions under which a finite simplicial complex $K$ can be mapped to $\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\to \mathbb R^d$ such that the images of any $r$
pairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of
the $(d+1)(r-1)$-simplex in $\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\geq 3r$) based on a series of papers by M. \"Ozaydin, M. Gromov, P. Blagojevi\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\to \mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\to \mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \sqcup S^3\sqcup S^3\to \mathbb R^5$ up to ornament
concordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.},
author = {Avvakumov, Sergey and Mabillard, Isaac and Skopenkov, A. and Wagner, Uli},
pages = {24},
publisher = {arXiv},
title = {{Eliminating higher-multiplicity intersections, III. Codimension 2}},
year = {2015},
}
@article{1383,
abstract = {In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants.},
author = {Yu, Luo and Scholl, Stefan and Doering, Anett and Yi, Zhang and Irani, Niloufer and Di Rubbo, Simone and Neumetzler, Lutz and Krishnamoorthy, Praveen and Van Houtte, Isabelle and Mylle, Evelien and Bischoff, Volker and Vernhettes, Samantha and Winne, Johan and Friml, Jirí and Stierhof, York and Schumacher, Karin and Persson, Staffan and Russinova, Eugenia},
journal = {Nature Plants},
number = {7},
publisher = {Nature Publishing Group},
title = {{V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis}},
doi = {10.1038/nplants.2015.94},
volume = {1},
year = {2015},
}
@inproceedings{1424,
abstract = {We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data.},
author = {Kwitt, Roland and Huber, Stefan and Niethammer, Marc and Lin, Weili and Bauer, Ulrich},
location = {Montreal, Canada},
pages = {3070 -- 3078},
publisher = {Neural Information Processing Systems},
title = {{Statistical topological data analysis-A kernel perspective}},
volume = {28},
year = {2015},
}
@inproceedings{1425,
abstract = {In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm.},
author = {Pentina, Anastasia and Lampert, Christoph},
location = {Montreal, Canada},
pages = {1540 -- 1548},
publisher = {Neural Information Processing Systems},
title = {{Lifelong learning with non-i.i.d. tasks}},
volume = {2015},
year = {2015},
}
@inproceedings{1430,
abstract = {Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.},
author = {Paixao, Tiago and Sudholt, Dirk and Heredia, Jorge and Trubenova, Barbora},
booktitle = {Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation},
location = {Madrid, Spain},
pages = {1455 -- 1462},
publisher = {ACM},
title = {{First steps towards a runtime comparison of natural and artificial evolution}},
doi = {10.1145/2739480.2754758},
year = {2015},
}
@inproceedings{1474,
abstract = {Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data.},
author = {Ferrara, Anna and Fuchsbauer, Georg and Liu, Bin and Warinschi, Bogdan},
location = {Verona, Italy},
pages = {46--60},
publisher = {IEEE},
title = {{Policy privacy in cryptographic access control}},
doi = {10.1109/CSF.2015.11},
year = {2015},
}
@inproceedings{1481,
abstract = {Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in the development of mathematical and logical skills, but also in the emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. We present an approach that generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. The presence of such states for standard game variants like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played as the default start state is heavily biased. },
author = {Ahmed, Umair and Chatterjee, Krishnendu and Gulwani, Sumit},
booktitle = {Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence},
location = {Austin, TX, USA},
pages = {745 -- 752},
publisher = {AAAI Press},
title = {{Automatic generation of alternative starting positions for simple traditional board games}},
volume = {2},
year = {2015},
}
@inproceedings{1483,
abstract = {Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes.},
author = {Reininghaus, Jan and Huber, Stefan and Bauer, Ulrich and Kwitt, Roland},
location = {Boston, MA, USA},
pages = {4741 -- 4748},
publisher = {IEEE},
title = {{A stable multi-scale kernel for topological machine learning}},
doi = {10.1109/CVPR.2015.7299106},
year = {2015},
}
@inproceedings{1495,
abstract = {Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. },
author = {Edelsbrunner, Herbert and Iglesias Ham, Mabel and Kurlin, Vitaliy},
booktitle = {Proceedings of the 27th Canadian Conference on Computational Geometry},
location = {Ontario, Canada},
pages = {128--135},
publisher = {Queen's University},
title = {{Relaxed disk packing}},
volume = {2015-August},
year = {2015},
}
@article{1497,
abstract = {Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.},
author = {Andergassen, Daniel and Dotter, Christoph and Kulinski, Tomasz and Guenzl, Philipp and Bammer, Philipp and Barlow, Denise and Pauler, Florian and Hudson, Quanah},
journal = {Nucleic Acids Research},
number = {21},
publisher = {Oxford University Press},
title = {{Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data}},
doi = {10.1093/nar/gkv727},
volume = {43},
year = {2015},
}
@inproceedings{1498,
abstract = {Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea.},
author = {Dragoi, Cezara and Henzinger, Thomas A and Zufferey, Damien},
isbn = {978-3-939897-80-4 },
location = {Asilomar, CA, United States},
pages = {90 -- 102},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{The need for language support for fault-tolerant distributed systems}},
doi = {10.4230/LIPIcs.SNAPL.2015.90},
volume = {32},
year = {2015},
}
@inproceedings{1499,
abstract = {We consider weighted automata with both positive and negative integer weights on edges and
study the problem of synchronization using adaptive strategies that may only observe whether
the current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata.},
author = {Kretinsky, Jan and Larsen, Kim and Laursen, Simon and Srba, Jiří},
location = {Madrid, Spain},
pages = {142 -- 154},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Polynomial time decidability of weighted synchronization under partial observability}},
doi = {10.4230/LIPIcs.CONCUR.2015.142},
volume = {42},
year = {2015},
}
@article{1501,
abstract = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
author = {Chatterjee, Krishnendu and Chmelik, Martin and Daca, Przemyslaw},
journal = {Formal Methods in System Design},
number = {2},
pages = {230 -- 264},
publisher = {Springer},
title = {{CEGAR for compositional analysis of qualitative properties in Markov decision processes}},
doi = {10.1007/s10703-015-0235-2},
volume = {47},
year = {2015},
}
@inproceedings{1502,
abstract = {We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system.},
author = {Beneš, Nikola and Daca, Przemyslaw and Henzinger, Thomas A and Kretinsky, Jan and Nickovic, Dejan},
isbn = {978-1-4503-3471-6},
location = {Montreal, QC, Canada},
pages = {101 -- 110},
publisher = {ACM},
title = {{Complete composition operators for IOCO-testing theory}},
doi = {10.1145/2737166.2737175},
year = {2015},
}
@article{1505,
abstract = {This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed.},
author = {Bao, Zhigang and Pan, Guangming and Zhou, Wang},
journal = {Annals of Statistics},
number = {1},
pages = {382 -- 421},
publisher = {Institute of Mathematical Statistics},
title = {{Universality for the largest eigenvalue of sample covariance matrices with general population}},
doi = {10.1214/14-AOS1281},
volume = {43},
year = {2015},
}
@article{1506,
abstract = {Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).},
author = {Bao, Zhigang and Pan, Guangming and Zhou, Wang},
journal = {Bernoulli},
number = {3},
pages = {1600 -- 1628},
publisher = {Bernoulli Society for Mathematical Statistics and Probability},
title = {{The logarithmic law of random determinant}},
doi = {10.3150/14-BEJ615},
volume = {21},
year = {2015},
}
@article{1508,
abstract = {We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential.},
author = {Erdös, László and Yau, Horng},
journal = {Journal of the European Mathematical Society},
number = {8},
pages = {1927 -- 2036},
publisher = {European Mathematical Society},
title = {{Gap universality of generalized Wigner and β ensembles}},
doi = {10.4171/JEMS/548},
volume = {17},
year = {2015},
}
@article{1509,
abstract = {The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.},
author = {Michalko, Jaroslav and Dravecka, Marta and Bollenbach, Tobias and Friml, Jirí},
journal = {F1000 Research },
publisher = {F1000 Research Ltd. },
title = {{Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene}},
doi = {10.12688/f1000research.7143.1},
volume = {4},
year = {2015},
}
@inproceedings{1510,
abstract = {The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. },
author = {Franek, Peter and Krcál, Marek},
location = {Eindhoven, Netherlands},
pages = {842 -- 856},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{On computability and triviality of well groups}},
doi = {10.4230/LIPIcs.SOCG.2015.842},
volume = {34},
year = {2015},
}
@inproceedings{1511,
abstract = {The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel's conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.},
author = {Goaoc, Xavier and Mabillard, Isaac and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
location = {Eindhoven, Netherlands},
pages = {476 -- 490},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result}},
doi = {10.4230/LIPIcs.SOCG.2015.476},
volume = {34 },
year = {2015},
}
@inproceedings{1512,
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 R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these 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 from C_*(K) to C_*(R^d). Both techniques are of independent interest.},
author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
location = {Eindhoven, Netherlands},
pages = {507 -- 521},
publisher = {ACM},
title = {{Bounding Helly numbers via Betti numbers}},
doi = {10.4230/LIPIcs.SOCG.2015.507},
volume = {34},
year = {2015},
}
@article{1513,
abstract = {Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.
In this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. },
author = {Pal, Arka and Vicoso, Beatriz},
journal = {Genome Biology and Evolution},
number = {12},
pages = {3259 -- 3268},
publisher = {Oxford University Press},
title = {{The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression}},
doi = {10.1093/gbe/evv215},
volume = {7},
year = {2015},
}
@article{1517,
abstract = {We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.
},
author = {Erbar, Matthias and Maas, Jan and Renger, Michiel},
journal = {Electronic Communications in Probability},
publisher = {Institute of Mathematical Statistics},
title = {{From large deviations to Wasserstein gradient flows in multiple dimensions}},
doi = {10.1214/ECP.v20-4315},
volume = {20},
year = {2015},
}
@article{1519,
abstract = {Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so.},
author = {Barton, Nicholas H and Servedio, Maria},
journal = {Evolution},
number = {5},
pages = {1101 -- 1112},
publisher = {Wiley},
title = {{The interpretation of selection coefficients}},
doi = {10.1111/evo.12641},
volume = {69},
year = {2015},
}
@article{1525,
abstract = {Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.},
author = {Bauer, Bruno and Blechl, Guido and Bock, Christoph and Danowski, Patrick and Ferus, Andreas and Graschopf, Anton and König, Thomas and Mayer, Katja and Reckling, Falk and Rieck, Katharina and Seitz, Peter and Stöger, Herwig and Welzig, Elvira},
journal = {VÖB Mitteilungen},
number = {3},
pages = {580 -- 607},
publisher = {Verein Österreichischer Bibliothekare},
title = {{Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA}},
doi = {10.5281/zenodo.33178},
volume = {68},
year = {2015},
}
@article{1534,
abstract = {PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.},
author = {Wang, Hongzhe and Yang, Kezhen and Zou, Junjie and Zhu, Lingling and Xie, Zidian and Morita, Miyoterao and Tasaka, Masao and Friml, Jirí and Grotewold, Erich and Beeckman, Tom and Vanneste, Steffen and Sack, Fred and Le, Jie},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism}},
doi = {10.1038/ncomms9822},
volume = {6},
year = {2015},
}
@article{1535,
abstract = {Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress.},
author = {Vandael, David H and Marcantoni, Andrea and Carbone, Emilio},
journal = {Current Molecular Pharmacology},
number = {2},
pages = {149 -- 161},
publisher = {Bentham Science Publishers},
title = {{Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells}},
doi = {10.2174/1874467208666150507105443},
volume = {8},
year = {2015},
}
@article{1537,
abstract = {3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype.},
author = {Ruprecht, Verena and Wieser, Stefan and Callan Jones, Andrew and Smutny, Michael and Morita, Hitoshi and Sako, Keisuke and Barone, Vanessa and Ritsch Marte, Monika and Sixt, Michael K and Voituriez, Raphaël and Heisenberg, Carl-Philipp J},
journal = {Cell},
number = {4},
pages = {673 -- 685},
publisher = {Cell Press},
title = {{Cortical contractility triggers a stochastic switch to fast amoeboid cell motility}},
doi = {10.1016/j.cell.2015.01.008},
volume = {160},
year = {2015},
}
@article{1538,
abstract = {Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.},
author = {Ruess, Jakob and Parise, Francesca and Milias Argeitis, Andreas and Khammash, Mustafa and Lygeros, John},
journal = {PNAS},
number = {26},
pages = {8148 -- 8153},
publisher = {National Academy of Sciences},
title = {{Iterative experiment design guides the characterization of a light-inducible gene expression circuit}},
doi = {10.1073/pnas.1423947112},
volume = {112},
year = {2015},
}
@article{1539,
abstract = {Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. },
author = {Ruess, Jakob},
journal = {Journal of Chemical Physics},
number = {24},
publisher = {American Institute of Physics},
title = {{Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space}},
doi = {10.1063/1.4937937},
volume = {143},
year = {2015},
}
@article{1995,
abstract = {Optical transport represents a natural route towards fast communications, and it is currently used in large scale data transfer. The progressive miniaturization of devices for information processing calls for the microscopic tailoring of light transport and confinement at length scales appropriate for upcoming technologies. With this goal in mind, we present a theoretical analysis of a one-dimensional Fabry-Perot interferometer built with two highly saturable nonlinear mirrors: a pair of two-level systems. Our approach captures nonlinear and nonreciprocal effects of light transport that were not reported previously. Remarkably, we show that such an elementary device can operate as a microscopic integrated optical rectifier.},
author = {Fratini, Filippo and Mascarenhas, Eduardo and Safari, Laleh and Poizat, Jean and Valente, Daniel and Auffèves, Alexia and Gerace, Dario and Santos, Marcelo},
journal = {Physical Review Letters},
number = {24},
publisher = {American Physical Society},
title = {{Fabry-Perot interferometer with quantum mirrors: Nonlinear light transport and rectification}},
doi = {10.1103/PhysRevLett.113.243601},
volume = {113},
year = {2014},
}