@inproceedings{2293,
abstract = {Many computer vision problems have an asymmetric distribution of information between training and test time. In this work, we study the case where we are given additional information about the training data, which however will not be available at test time. This situation is called learning using privileged information (LUPI). We introduce two maximum-margin techniques that are able to make use of this additional source of information, and we show that the framework is applicable to several scenarios that have been studied in computer vision before. Experiments with attributes, bounding boxes, image tags and rationales as additional information in object classification show promising results.},
author = {Sharmanska, Viktoriia and Quadrianto, Novi and Lampert, Christoph},
location = {Sydney, Australia},
pages = {825 -- 832},
publisher = {IEEE},
title = {{Learning to rank using privileged information}},
doi = {10.1109/ICCV.2013.107},
year = {2013},
}
@inproceedings{2294,
abstract = {In this work we propose a system for automatic classification of Drosophila embryos into developmental stages.
While the system is designed to solve an actual problem in biological research, we believe that the principle underly-
ing it is interesting not only for biologists, but also for researchers in computer vision. The main idea is to combine two orthogonal sources of information: one is a classifier trained on strongly invariant features, which makes it applicable to images of very different conditions, but also leads to rather noisy predictions. The other is a label propagation step based on a more powerful similarity measure that however is only consistent within specific subsets of the data at a time.
In our biological setup, the information sources are the shape and the staining patterns of embryo images. We show
experimentally that while neither of the methods can be used by itself to achieve satisfactory results, their combina-
tion achieves prediction quality comparable to human performance.},
author = {Kazmar, Tomas and Kvon, Evgeny and Stark, Alexander and Lampert, Christoph},
location = {Sydney, Australia},
publisher = {IEEE},
title = {{Drosophila Embryo Stage Annotation using Label Propagation}},
doi = {10.1109/ICCV.2013.139},
year = {2013},
}
@inproceedings{2295,
abstract = {We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal EXPTIME-complete complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite-memory strategies. We also establish asymptotically optimal (exponential) memory bounds.},
author = {Chatterjee, Krishnendu and Chmelik, Martin and Tracol, Mathieu},
location = {Torino, Italy},
pages = {165 -- 180},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{What is decidable about partially observable Markov decision processes with omega-regular objectives}},
doi = {10.4230/LIPIcs.CSL.2013.165},
volume = {23},
year = {2013},
}
@article{2297,
abstract = {We present an overview of mathematical results on the low temperature properties of dilute quantum gases, which have been obtained in the past few years. The presentation includes a discussion of Bose-Einstein condensation, the excitation spectrum for trapped gases and its relation to superfluidity, as well as the appearance of quantized vortices in rotating systems. All these properties are intensely being studied in current experiments on cold atomic gases. We will give a description of the mathematics involved in understanding these phenomena, starting from the underlying many-body Schrödinger equation.},
author = {Seiringer, Robert},
journal = {Japanese Journal of Mathematics},
number = {2},
pages = {185 -- 232},
publisher = {Springer},
title = {{Hot topics in cold gases: A mathematical physics perspective}},
doi = {10.1007/s11537-013-1264-5},
volume = {8},
year = {2013},
}
@inproceedings{2298,
abstract = {We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. We have implemented this analysis in a prototype tool and applied it on several interesting case studies that manipulate overlaid and nested linked lists.
},
author = {Dragoi, Cezara and Enea, Constantin and Sighireanu, Mihaela},
location = {Seattle, WA, United States},
pages = {150 -- 171},
publisher = {Springer},
title = {{Local shape analysis for overlaid data structures}},
doi = {10.1007/978-3-642-38856-9_10},
volume = {7935},
year = {2013},
}
@article{2299,
abstract = {The standard hardware design flow involves: (a) design of an integrated circuit using a hardware description language, (b) extensive functional and formal verification, and (c) logical synthesis. However, the above-mentioned processes consume significant effort and time. An alternative approach is to use a formal specification language as a high-level hardware description language and synthesize hardware from formal specifications. Our work is a case study of the synthesis of the widely and industrially used AMBA AHB protocol from formal specifications. Bloem et al. presented the first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter circuit. However, in the first formal specification some important assumptions were missing. Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. Thus with systematic description we are able to automatically and completely synthesize an important and widely used industrial protocol.},
author = {Godhal, Yashdeep and Chatterjee, Krishnendu and Henzinger, Thomas A},
journal = {International Journal on Software Tools for Technology Transfer},
number = {5-6},
pages = {585 -- 601},
publisher = {Springer},
title = {{Synthesis of AMBA AHB from formal specification: A case study}},
doi = {10.1007/s10009-011-0207-9},
volume = {15},
year = {2013},
}
@article{2300,
abstract = {We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability.},
author = {Giuliani, Alessandro and Lieb, Élliott and Seiringer, Robert},
journal = {Physical Review B},
number = {6},
publisher = {American Physical Society},
title = {{Realization of stripes and slabs in two and three dimensions}},
doi = {10.1103/PhysRevB.88.064401},
volume = {88},
year = {2013},
}
@inproceedings{2305,
abstract = {We study the complexity of central controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize both the expected mean-payoff performance of the system and its stability. e argue that the basic theoretical notion of expressing the stability in terms of the variance of the mean-payoff (called global variance in our paper) is not always sufficient, since it ignores possible instabilities on respective runs. For this reason we propose alernative definitions of stability, which we call local and hybrid variance, and which express how rewards on each run deviate from the run's own mean-payoff and from the expected mean-payoff, respectively. We show that a strategy ensuring both the expected mean-payoff and the variance below given bounds requires randomization and memory, under all the above semantics of variance. We then look at the problem of determining whether there is a such a strategy. For the global variance, we show that the problem is in PSPACE, and that the answer can be approximated in pseudo-polynomial time. For the hybrid variance, the analogous decision problem is in NP, and a polynomial-time approximating algorithm also exists. For local variance, we show that the decision problem is in NP. Since the overall performance can be traded for stability (and vice versa), we also present algorithms for approximating the associated Pareto curve in all the three cases. Finally, we study a special case of the decision problems, where we require a given expected mean-payoff together with zero variance. Here we show that the problems can be all solved in polynomial time.},
author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín},
booktitle = {28th Annual ACM/IEEE Symposium},
location = {New Orleans, LA, United States},
pages = {331 -- 340},
publisher = {IEEE},
title = {{Trading performance for stability in Markov decision processes}},
doi = {10.1109/LICS.2013.39},
year = {2013},
}
@book{2306,
abstract = {Das Buch ist sowohl eine Einführung in die Themen Linked Data, Open Data und Open Linked Data als es auch den konkreten Bezug auf Bibliotheken behandelt. Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut sind.},
author = {Danowski, Patrick and Pohl, Adrian},
publisher = {De Gruyter},
title = {{(Open) Linked Data in Bibliotheken}},
doi = {10.1515/9783110278736},
volume = {50},
year = {2013},
}
@inproceedings{2315,
abstract = { We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the interval. },
author = {Seiringer, Robert and Yngvason, Jakob and Zagrebnov, Valentin},
pages = {610--619},
publisher = {World Scientific Publishing},
title = {{Disordered Bose-Einstein condensates with interaction}},
doi = {10.1142/9789814449243_0063},
year = {2013},
}
@inproceedings{2319,
abstract = {In a recent paper [7] we give the first rigorous derivation of the celebrated Ginzburg-Landau (GL)theory, starting from the microscopic Bardeen- Cooper-Schrieffer (BCS)model. Here we present our results in the simplified case of a one-dimensional system of particles interacting via a δ-potential.},
author = {Frank, Rupert L and Hainzl, Christian and Robert Seiringer and Solovej, Jan P},
pages = {57 -- 88},
publisher = {Springer},
title = {{ Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction}},
doi = {10.1007/978-3-0348-0531-5_3},
year = {2013},
}
@inproceedings{2327,
abstract = {We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M′ within distance ρ from M satisfy (or violate) φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.},
author = {Henzinger, Thomas A and Otop, Jan},
location = {Buenos Aires, Argentina},
pages = {273 -- 287},
publisher = {Springer},
title = {{From model checking to model measuring}},
doi = {10.1007/978-3-642-40184-8_20},
volume = {8052},
year = {2013},
}
@inproceedings{2328,
abstract = {Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying 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 = {Henzinger, Thomas A and Sezgin, Ali and Vafeiadis, Viktor},
location = {Buenos Aires, Argentina},
pages = {242 -- 256},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Aspect-oriented linearizability proofs}},
doi = {10.1007/978-3-642-40184-8_18},
volume = {8052},
year = {2013},
}
@inproceedings{2329,
abstract = {Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games.},
author = {Chatterjee, Krishnendu and Velner, Yaron},
location = {Buenos Aires, Argentinia},
pages = {500 -- 515},
publisher = {Springer},
title = {{Hyperplane separation technique for multidimensional mean-payoff games}},
doi = {10.1007/978-3-642-40184-8_35},
volume = {8052},
year = {2013},
}
@article{2404,
abstract = {The Lieb-Thirring inequalities give a bound on the negative eigenvalues of a Schrödinger operator in terms of an Lp-norm of the potential. These are dual to bounds on the H1-norms of a system of orthonormal functions. Here we extend these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting particles (i.e., for perturbations of the continuous spectrum of the Laplacian by local potentials).},
author = {Frank, Rupert L and Lewin, Mathieu and Lieb, Élliott H and Robert Seiringer},
journal = {Duke Mathematical Journal},
number = {3},
pages = {435 -- 495},
publisher = {Duke University Press},
title = {{A positive density analogue of the Lieb-Thirring inequality}},
doi = {10.1215/00127094-2019477},
volume = {162},
year = {2013},
}
@article{2405,
abstract = {We consider the bipolaron in the Pekar-Tomasevich approximation and address the question whether the ground state is spherically symmetric or not. Numerical analysis has, so far, not completely settled the question. Our contribution is to prove rigorously that the ground state remains spherical for small values of the electron-electron Coulomb repulsion.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {557 -- 573},
publisher = {Springer},
title = {{Symmetry of bipolaron bound states for small Coulomb repulsion}},
doi = {10.1007/s00220-012-1604-y},
volume = {319},
year = {2013},
}
@article{2408,
abstract = {We investigate the low-energy excitation spectrum of a Bose gas confined in a trap, with weak long-range repulsive interactions. In particular, we prove that the spectrum can be described in terms of the eigenvalues of an effective one-particle operator, as predicted by the Bogoliubov approximation.},
author = {Grech, Philip and Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {559 -- 591},
publisher = {Springer},
title = {{The excitation spectrum for weakly interacting Bosons in a trap}},
doi = {10.1007/s00220-013-1736-8},
volume = {322},
year = {2013},
}
@article{2410,
abstract = {Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. },
author = {Fernandes Redondo, Rodrigo A and Kupczok, Anne and Stift, Gertraud and Bollback, Jonathan P},
journal = {Genome Announcements},
number = {3},
publisher = {American Society for Microbiology},
title = {{Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis}},
doi = {10.1128/genomeA.00216-13},
volume = {1},
year = {2013},
}
@article{2412,
abstract = {Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.},
author = {Kupczok, Anne and Bollback, Jonathan P},
journal = {BMC Evolutionary Biology},
number = {1},
pages = {54 -- 54},
publisher = {BioMed Central},
title = {{Probabilistic models for CRISPR spacer content evolution }},
doi = {10.1186/1471-2148-13-54},
volume = {13},
year = {2013},
}
@inproceedings{2444,
abstract = {We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.},
author = {Chatterjee, Krishnendu and Ła̧Cki, Jakub},
location = {St. Petersburg, Russia},
pages = {543 -- 558},
publisher = {Springer},
title = {{Faster algorithms for Markov decision processes with low treewidth}},
doi = {10.1007/978-3-642-39799-8_36},
volume = {8044},
year = {2013},
}
@inproceedings{2445,
abstract = {We develop program synthesis techniques that can help programmers fix concurrency-related bugs. We make two new contributions to synthesis for concurrency, the first improving the efficiency of the synthesized code, and the second improving the efficiency of the synthesis procedure itself. The first contribution is to have the synthesis procedure explore a variety of (sequential) semantics-preserving program transformations. Classically, only one such transformation has been considered, namely, the insertion of synchronization primitives (such as locks). Based on common manual bug-fixing techniques used by Linux device-driver developers, we explore additional, more efficient transformations, such as the reordering of independent instructions. The second contribution is to speed up the counterexample-guided removal of concurrency bugs within the synthesis procedure by considering partial-order traces (instead of linear traces) as counterexamples. A partial-order error trace represents a set of linear (interleaved) traces of a concurrent program all of which lead to the same error. By eliminating a partial-order error trace, we eliminate in a single iteration of the synthesis procedure all linearizations of the partial-order trace. We evaluated our techniques on several simplified examples of real concurrency bugs that occurred in Linux device drivers.},
author = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun and Ryzhyk, Leonid and Tarrach, Thorsten},
location = {St. Petersburg, Russia},
pages = {951 -- 967},
publisher = {Springer},
title = {{Efficient synthesis for concurrency by semantics-preserving transformations}},
doi = {10.1007/978-3-642-39799-8_68},
volume = {8044},
year = {2013},
}
@inproceedings{2446,
abstract = {The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements.},
author = {Chatterjee, Krishnendu and Gaiser, Andreas and Kretinsky, Jan},
location = {St. Petersburg, Russia},
pages = {559 -- 575},
publisher = {Springer},
title = {{Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis}},
doi = {10.1007/978-3-642-39799-8_37},
volume = {8044},
year = {2013},
}
@inproceedings{2447,
abstract = {Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.
},
author = {Piskac, Ruzica and Wies, Thomas and Zufferey, Damien},
location = {St. Petersburg, Russia},
pages = {773 -- 789},
publisher = {Springer},
title = {{Automating separation logic using SMT}},
doi = {10.1007/978-3-642-39799-8_54},
volume = {8044},
year = {2013},
}
@article{2448,
abstract = {Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots.},
author = {Remy, Estelle and Baster, Pawel and Friml, Jirí and Duque, Paula},
journal = {Plant Signaling & Behavior},
number = {10},
publisher = {Landes Bioscience},
title = {{ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip}},
doi = {10.4161/psb.25688},
volume = {8},
year = {2013},
}
@article{245,
abstract = {For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ.},
author = {Baier, Stephan and Timothy Browning},
journal = {Journal fur die Reine und Angewandte Mathematik},
number = {680},
pages = {69 -- 151},
publisher = {Walter de Gruyter},
title = {{Inhomogeneous cubic congruences and rational points on del Pezzo surfaces}},
doi = {10.1515/crelle.2012.039},
year = {2013},
}
@article{2466,
abstract = {We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation.},
author = {Ando, Ryoichi and Thuerey, Nils and Wojtan, Christopher J},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Highly adaptive liquid simulations on tetrahedral meshes}},
doi = {10.1145/2461912.2461982},
volume = {32},
year = {2013},
}
@article{2467,
abstract = {This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors.},
author = {Bernstein, Gilbert and Wojtan, Christopher J},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Putting holes in holey geometry: Topology change for arbitrary surfaces}},
doi = {10.1145/2461912.2462027},
volume = {32},
year = {2013},
}
@article{2468,
abstract = {Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers.},
author = {Bojsen-Hansen, Morten and Wojtan, Christopher J},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Liquid surface tracking with error compensation}},
doi = {10.1145/2461912.2461991},
volume = {32},
year = {2013},
}
@article{2469,
abstract = {Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact.},
author = {Maître, Jean-Léon and Heisenberg, Carl-Philipp J},
journal = {Current Biology},
number = {14},
pages = {R626 -- R633},
publisher = {Cell Press},
title = {{Three functions of cadherins in cell adhesion}},
doi = {10.1016/j.cub.2013.06.019},
volume = {23},
year = {2013},
}
@article{2470,
abstract = {Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients.},
author = {Čovanová, Milada and Sauer, Michael and Rychtář, Jan and Friml, Jirí and Petrášek, Jan and Zažímalová, Eva},
journal = {PLoS One},
number = {7},
publisher = {Public Library of Science},
title = {{Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells}},
doi = {10.1371/journal.pone.0070050},
volume = {8},
year = {2013},
}
@article{2471,
abstract = {The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation.},
author = {Sanchez Romero, Inmaculada and Ariza, Antonio and Wilson, Keith and Skjøt, Michael and Vind, Jesper and De Maria, Leonardo and Skov, Lars and Sánchez Ruiz, Jose},
journal = {PLoS One},
number = {7},
publisher = {Public Library of Science},
title = {{Mechanism of protein kinetic stabilization by engineered disulfide crosslinks}},
doi = {10.1371/journal.pone.0070013},
volume = {8},
year = {2013},
}
@article{2472,
abstract = {Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.},
author = {Cazzonelli, Christopher and Vanstraelen, Marleen and Simon, Sibu and Yin, Kuide and Carron Arthur, Ashley and Nisar, Nazia and Tarle, Gauri and Cuttriss, Abby and Searle, Iain and Benková, Eva and Mathesius, Ulrike and Masle, Josette and Friml, Jirí and Pogson, Barry},
journal = {PLoS One},
number = {7},
publisher = {Public Library of Science},
title = {{Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development}},
doi = {10.1371/journal.pone.0070069},
volume = {8},
year = {2013},
}
@article{2473,
abstract = {When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift, . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis.},
author = {Barton, Nicholas H and Etheridge, Alison and Kelleher, Jerome and Véber, Amandine},
journal = {Theoretical Population Biology},
number = {8},
pages = {75 -- 89},
publisher = {Elsevier},
title = {{Genetic hitch-hiking in spatially extended populations}},
doi = {10.1016/j.tpb.2012.12.001},
volume = {87},
year = {2013},
}
@article{250,
abstract = {Châtelet surfaces provide a rich source of geometrically rational surfaces that do not always satisfy the Hasse principle. Restricting attention to a special class of Châtelet surfaces, we investigate the frequency that such counter-examples arise over the rational numbers.},
author = {de la Bretèche, Régis and Timothy Browning},
journal = {Proceedings of the London Mathematical Society},
number = {4},
pages = {1030 -- 1078},
publisher = {Oxford University Press},
title = {{Density of Châtelet surfaces failing the Hasse principle}},
doi = {10.1112/plms/pdt060},
volume = {108},
year = {2013},
}
@inproceedings{2517,
abstract = {Traditional formal methods are based on a Boolean satisfaction notion: a reactive system satisfies, or not, a given specification. We generalize formal methods to also address the quality of systems. As an adequate specification formalism we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F] formula is a number between 0 and 1, describing the quality of the satisfaction. The logic generalizes traditional LTL by augmenting it with a (parameterized) set F of arbitrary functions over the interval [0,1]. For example, F may contain the maximum or minimum between the satisfaction values of subformulas, their product, and their average. The classical decision problems in formal methods, such as satisfiability, model checking, and synthesis, are generalized to search and optimization problems in the quantitative setting. For example, model checking asks for the quality in which a specification is satisfied, and synthesis returns a system satisfying the specification with the highest quality. Reasoning about quality gives rise to other natural questions, like the distance between specifications. We formalize these basic questions and study them for LTL[F]. By extending the automata-theoretic approach for LTL to a setting that takes quality into an account, we are able to solve the above problems and show that reasoning about LTL[F] has roughly the same complexity as reasoning about traditional LTL.},
author = {Almagor, Shaull and Boker, Udi and Kupferman, Orna},
location = {Riga, Latvia},
number = {Part 2},
pages = {15 -- 27},
publisher = {Springer},
title = {{Formalizing and reasoning about quality}},
doi = {10.1007/978-3-642-39212-2_3},
volume = {7966},
year = {2013},
}
@inproceedings{2518,
abstract = {A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. An instance of the problem is specified by a sum of cost functions from the language with the goal to minimise the sum. We study which classes of finite-valued languages can be solved exactly by the basic linear programming relaxation (BLP). Thapper and Živný showed [20] that if BLP solves the language then the language admits a binary commutative fractional polymorphism. We prove that the converse is also true. This leads to a necessary and a sufficient condition which can be checked in polynomial time for a given language. In contrast, the previous necessary and sufficient condition due to [20] involved infinitely many inequalities. More recently, Thapper and Živný [21] showed (using, in particular, a technique introduced in this paper) that core languages that do not satisfy our condition are NP-hard. Taken together, these results imply that a finite-valued language can either be solved using Linear Programming or is NP-hard.},
author = {Kolmogorov, Vladimir},
location = {Riga, Latvia},
number = {1},
pages = {625 -- 636},
publisher = {Springer},
title = {{The power of linear programming for finite-valued CSPs: A constructive characterization}},
doi = {10.1007/978-3-642-39206-1_53},
volume = {7965},
year = {2013},
}
@inproceedings{2520,
abstract = {We propose a probabilistic model to infer supervised latent variables in
the Hamming space from observed data. Our model allows simultaneous
inference of the number of binary latent variables, and their values. The
latent variables preserve neighbourhood structure of the data in a sense
that objects in the same semantic concept have similar latent values, and
objects in different concepts have dissimilar latent values. We formulate
the supervised infinite latent variable problem based on an intuitive
principle of pulling objects together if they are of the same type, and
pushing them apart if they are not. We then combine this principle with a
flexible Indian Buffet Process prior on the latent variables. We show that
the inferred supervised latent variables can be directly used to perform a
nearest neighbour search for the purpose of retrieval. We introduce a new
application of dynamically extending hash codes, and show how to
effectively couple the structure of the hash codes with continuously
growing structure of the neighbourhood preserving infinite latent feature
space.},
author = {Quadrianto, Novi and Sharmanska, Viktoriia and Knowles, David and Ghahramani, Zoubin},
booktitle = {Proceedings of the 29th conference uncertainty in Artificial Intelligence},
isbn = {9780974903996},
location = {Bellevue, WA, United States},
pages = {527 -- 536},
publisher = {AUAI Press},
title = {{The supervised IBP: Neighbourhood preserving infinite latent feature models}},
year = {2013},
}
@article{450,
abstract = {Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.},
author = {Pickup, Melinda and Field, David and Rowell, David and Young, Andrew},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1750},
publisher = {Royal Society, The},
title = {{Source population characteristics affect heterosis following genetic rescue of fragmented plant populations}},
doi = {10.1098/rspb.2012.2058},
volume = {280},
year = {2013},
}
@article{476,
abstract = {Maternal exposure to infection occurring mid-gestation produces a three-fold increase in the risk of schizophrenia in the offspring. The critical initiating factor appears to be the maternal immune activation (MIA) that follows infection. This process can be induced in rodents by exposure of pregnant dams to the viral mimic Poly I:C, which triggers an immune response that results in structural, functional, behavioral, and electrophysiological phenotypes in the adult offspring that model those seen in schizophrenia. We used this model to explore the role of synchronization in brain neural networks, a process thought to be dysfunctional in schizophrenia and previously associated with positive, negative, and cognitive symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced an impairment in long-range neural synchrony in adult offspring between two regions implicated in schizophrenia pathology; the hippocampus and the medial prefrontal cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the antipsychotic clozapine. MIA animals have previously been shown to have impaired pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits in animal models. Our data showed that deficits in synchrony were positively correlated with the impairments in PPI. Subsequent analysis of LFP activity during the PPI response also showed that reduced coupling between the mPFC and the hippocampus following processing of the pre-pulse was associated with reduced PPI. The ability of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology provides a useful platform from which to investigate the ontogeny of aberrant synchronous processes. Further, the way in which the model expresses translatable deficits such as aberrant synchrony and reduced PPI will allow researchers to explore novel intervention strategies targeted to these changes. },
author = {Dickerson, Desiree and Bilkey, David},
journal = {Frontiers in Behavioral Neuroscience},
number = {DEC},
publisher = {Frontiers Research Foundation},
title = {{Aberrant neural synchrony in the maternal immune activation model: Using translatable measures to explore targeted interventions}},
doi = {10.3389/fnbeh.2013.00217},
volume = {7},
year = {2013},
}
@article{500,
abstract = {Background: Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded the emergence of pandemic strains. It has been suggested that productive viral infection requires a balance in the level of functional activity of HA and NA, arising from their closely interacting roles in the viral life cycle, and that this functional balance could be mediated by genetic changes in the HA and NA. Here, we investigate how the selective pressure varies for H7 avian influenza HA on different NA subtype backgrounds. Results: By extending Bayesian stochastic mutational mapping methods to calculate the ratio of the rate of non-synonymous change to the rate of synonymous change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1 region to be significantly greater on an N2 NA subtype background than on an N1, N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different NA subtype backgrounds could not be attributed to underlying differences between avian host species or virus pathogenicity. Examination of d N/d S values for each subtype on a site-by-site basis indicated that the elevated d N/d S on the N2 NA background was a result of increased selection, rather than a relaxation of selective constraint. Conclusions: Our results are consistent with the hypothesis that reassortment exposes influenza HA to significant changes in selective pressure through genetic interactions with NA. Such epistatic effects might be explicitly accounted for in future models of influenza evolution.},
author = {Ward, Melissa and Lycett, Samantha and Avila, Dorita and Bollback, Jonathan P and Leigh Brown, Andrew},
journal = {BMC Evolutionary Biology},
number = {1},
publisher = {BioMed Central},
title = {{Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza}},
doi = {10.1186/1471-2148-13-222},
volume = {13},
year = {2013},
}
@article{501,
abstract = {All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.},
author = {Cozzuol, Mario and Clozato, Camila and Holanda, Elizete and Rodrigues, Flávio and Nienow, Samuel and De Thoisy, Benoit and Fernandes Redondo, Rodrigo A and Santos, Fabrício},
journal = {Journal of Mammalogy},
number = {6},
pages = {1331 -- 1345},
publisher = {Oxford University Press},
title = {{A new species of tapir from the Amazon}},
doi = {10.1644/12-MAMM-A-169.1},
volume = {94},
year = {2013},
}
@article{507,
abstract = {Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs.},
author = {Kim, Soo and Xu, Zheng and Song, Kyungyoung and Kim, Dae and Kang, Hyangju and Reichardt, Ilka and Sohn, Eun and Friml, Jirí and Juergens, Gerd and Hwang, Inhwan},
journal = {Plant Cell},
number = {8},
pages = {2970 -- 2985},
publisher = {American Society of Plant Biologists},
title = {{Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis}},
doi = {10.1105/tpc.113.114264},
volume = {25},
year = {2013},
}
@article{508,
abstract = {The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.},
author = {Tarazona Santos, Eduardo and Machado, Moara and Magalhães, Wagner and Chen, Renee and Lyon, Fernanda and Burdett, Laurie and Crenshaw, Andrew and Fabbri, Cristina and Pereira, Latife and Pinto, Laelia and Fernandes Redondo, Rodrigo A and Sestanovich, Ben and Yeager, Meredith and Chanock, Stephen},
journal = {Molecular Biology and Evolution},
number = {9},
pages = {2157 -- 2167},
publisher = {Oxford University Press},
title = {{Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications}},
doi = {10.1093/molbev/mst119},
volume = {30},
year = {2013},
}
@article{509,
abstract = {Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. },
author = {Di Rubbo, Simone and Irani, Niloufer and Kim, Soo and Xu, Zheng and Gadeyne, Astrid and Dejonghe, Wim and Vanhoutte, Isabelle and Persiau, Geert and Eeckhout, Dominique and Simon, Sibu and Song, Kyungyoung and Kleine Vehn, Jürgen and Friml, Jirí and De Jaeger, Geert and Van Damme, Daniël and Hwang, Inhwan and Russinova, Eugenia},
journal = {Plant Cell},
number = {8},
pages = {2986 -- 2997},
publisher = {American Society of Plant Biologists},
title = {{The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis}},
doi = {10.1105/tpc.113.114058},
volume = {25},
year = {2013},
}
@article{511,
abstract = {The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.},
author = {Pěnčík, Aleš and Simonovik, Biljana and Petersson, Sara and Henyková, Eva and Simon, Sibu and Greenham, Kathleen and Zhang, Yi and Kowalczyk, Mariusz and Estelle, Mark and Zažímalová, Eva and Novák, Ondřej and Sandberg, Göran and Ljung, Karin},
journal = {Plant Cell},
number = {10},
pages = {3858 -- 3870},
publisher = {American Society of Plant Biologists},
title = {{Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid}},
doi = {10.1105/tpc.113.114421},
volume = {25},
year = {2013},
}
@article{516,
abstract = {In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.},
author = {Bargmann, Bastiaan and Vanneste, Steffen and Krouk, Gabriel and Nawy, Tal and Efroni, Idan and Shani, Eilon and Choe, Goh and Friml, Jirí and Bergmann, Dominique and Estelle, Mark and Birnbaum, Kenneth},
journal = {Molecular Systems Biology},
number = {1},
publisher = {Nature Publishing Group},
title = {{A map of cell type‐specific auxin responses}},
doi = {10.1038/msb.2013.40},
volume = {9},
year = {2013},
}
@misc{5399,
abstract = {In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.},
author = {Reiter, Johannes and Bozic, Ivana and Chatterjee, Krishnendu and Nowak, Martin},
issn = {2664-1690},
pages = {17},
publisher = {IST Austria},
title = {{TTP: Tool for Tumor Progression}},
doi = {10.15479/AT:IST-2013-104-v1-1},
year = {2013},
}
@misc{5400,
abstract = {We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages extends regular languages to infinite strings and provides a robust specification language to express all properties used in verification, and parity objectives are canonical forms to express ω-regular conditions. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satis- fied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite- memory strategies. We establish asymptotically optimal (exponential) memory bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives.},
author = {Chatterjee, Krishnendu and Chmelik, Martin and Tracol, Mathieu},
issn = {2664-1690},
pages = {41},
publisher = {IST Austria},
title = {{What is decidable about partially observable Markov decision processes with ω-regular objectives}},
doi = {10.15479/AT:IST-2013-109-v1-1},
year = {2013},
}
@techreport{5401,
abstract = {This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the actual initiatives, projects and standards related to the project. It supports the preparation of standards and specifications for the project, which should be considered and followed to ensure interoperability and visibility of the uploaded data.},
author = {Porsche, Jana},
publisher = {IST Austria},
title = {{Initiatives and projects related to RD}},
year = {2013},
}
@misc{5402,
abstract = {Linearizability requires that the outcome of calls by competing threads to a concurrent data structure is the same as some sequential execution where each thread has exclusive access to the data structure. In an ordered data structure, such as a queue or a stack, linearizability is ensured by requiring threads commit in the order dictated by the sequential semantics of the data structure; e.g., in a concurrent queue implementation a dequeue can only remove the oldest element.
In this paper, we investigate the impact of this strict ordering, by comparing what linearizability allows to what existing implementations do. We first give an operational definition for linearizability which allows us to build the most general linearizable implementation as a transition system for any given sequential specification. We then use this operational definition to categorize linearizable implementations based on whether they are bound or free. In a bound implementation, whenever all threads observe the same logical state, the updates to the logical state and the temporal order of commits coincide. All existing queue implementations we know of are bound. We then proceed to present, to the best of our knowledge, the first ever free queue implementation. Our experiments show that free implementations have the potential for better performance by suffering less from contention.},
author = {Henzinger, Thomas A and Sezgin, Ali},
issn = {2664-1690},
pages = {16},
publisher = {IST Austria},
title = {{How free is your linearizable concurrent data structure?}},
doi = {10.15479/AT:IST-2013-123-v1-1},
year = {2013},
}
@misc{5403,
abstract = {We consider concurrent games played by two-players on a finite state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to every transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of mean-payoff games) that is not known to be in polynomial time.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus},
issn = {2664-1690},
pages = {33},
publisher = {IST Austria},
title = {{Qualitative analysis of concurrent mean-payoff games}},
doi = {10.15479/AT:IST-2013-126-v1-1},
year = {2013},
}
@misc{5404,
abstract = {We study finite-state two-player (zero-sum) concurrent mean-payoff games played on a graph. We focus on the important sub-class of ergodic games where all states are visited infinitely often with probability 1. The algorithmic study of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic complexity questions have remained unresolved. Our main results for ergodic games are as follows: We establish (1) an optimal exponential bound on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy); (2) the approximation problem lie in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP and coNP is the long-standing best known bound). We show that the exact value can be expressed in the existential theory of the reals, and also establish square-root sum hardness for a related class of games.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus},
issn = {2664-1690},
pages = {29},
publisher = {IST Austria},
title = {{The complexity of ergodic games}},
doi = {10.15479/AT:IST-2013-127-v1-1},
year = {2013},
}
@misc{5405,
abstract = {The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2-1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2-1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic) with only parity objectives, or with only mean-payoff objectives. We present an algorithm running
in time O(d · n^{2d}·MeanGame) to compute the set of almost-sure winning states from which the objective
can be ensured with probability 1, where n is the number of states of the game, d the number of priorities
of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states
in 2-1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems
with both functional requirement (given as a qualitative objective) and performance requirement (given
as a quantitative objective).},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Gimbert, Hugo and Oualhadj, Youssouf},
issn = {2664-1690},
pages = {22},
publisher = {IST Austria},
title = {{Perfect-information stochastic mean-payoff parity games}},
doi = {10.15479/AT:IST-2013-128-v1-1},
year = {2013},
}
@misc{5406,
abstract = {We consider the distributed synthesis problem fortemporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTLand our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3)Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan and Pavlogiannis, Andreas},
issn = {2664-1690},
pages = {11},
publisher = {IST Austria},
title = {{Distributed synthesis for LTL Fragments}},
doi = {10.15479/AT:IST-2013-130-v1-1},
year = {2013},
}
@techreport{5407,
abstract = {This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the mandatory features, which need to be fulfilled to provide an institutional repository as a platform and also a service to the scientists at the institute. It also includes optional features, which would be of strong benefit for the scientists and would increase the usage of the repository, and hence the visibility of research at IST Austria.},
author = {Porsche, Jana},
publisher = {IST Austria},
title = {{Technical requirements and features}},
year = {2013},
}
@misc{5408,
abstract = {We consider two-player partial-observation stochastic games where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are omega-regular conditions specified as parity objectives. The qualitative analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, they were shown to be decidable in 2EXPTIME under finite-memory strategies. We improve the complexity and show that the qualitative analysis problems for partial-observation stochastic parity games under finite-memory strategies are
EXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis. },
author = {Chatterjee, Krishnendu and Doyen, Laurent and Nain, Sumit and Vardi, Moshe},
issn = {2664-1690},
pages = {17},
publisher = {IST Austria},
title = {{The complexity of partial-observation stochastic parity games with finite-memory strategies}},
doi = {10.15479/AT:IST-2013-141-v1-1},
year = {2013},
}
@misc{5409,
abstract = {The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition.
In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in timestamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than delta away from the parameter, for delta>0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and we show analogous decidability results for rectangular automata.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Majumdar, Rupak},
issn = {2664-1690},
pages = {12},
publisher = {IST Austria},
title = {{Edit distance for timed automata}},
doi = {10.15479/AT:IST-2013-144-v1-1},
year = {2013},
}
@misc{5410,
abstract = {Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in development of mathematical and logical skills, but also in 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.
Our approach 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. Also, the presence of such states for standard game variants like Tic-Tac-Toe on board size 4x4 opens up new games to be played that have not been played for ages since the default start state is heavily biased. },
author = {Ahmed, Umair and Chatterjee, Krishnendu and Gulwani, Sumit},
issn = {2664-1690},
pages = {13},
publisher = {IST Austria},
title = {{Automatic generation of alternative starting positions for traditional board games}},
doi = {10.15479/AT:IST-2013-146-v1-1},
year = {2013},
}
@inbook{5747,
author = {Dragoi, Cezara and Gupta, Ashutosh and Henzinger, Thomas A},
booktitle = {Computer Aided Verification},
isbn = {9783642397981},
issn = {0302-9743},
location = {Saint Petersburg, Russia},
pages = {174--190},
publisher = {Springer Berlin Heidelberg},
title = {{Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates}},
doi = {10.1007/978-3-642-39799-8_11},
volume = {8044},
year = {2013},
}
@article{595,
author = {Bernecky, Carrie A and Cramer, Patrick},
journal = {EMBO Journal},
number = {6},
pages = {771 -- 772},
publisher = {Wiley-Blackwell},
title = {{Struggling to let go: A non-coding RNA directs its own extension and destruction}},
doi = {10.1038/emboj.2013.36},
volume = {32},
year = {2013},
}
@article{6128,
abstract = {Different interoceptive systems must be integrated to ensure that multiple homeostatic insults evoke appropriate behavioral and physiological responses. Little is known about how this is achieved. Using C. elegans, we dissect cross-modulation between systems that monitor temperature, O2 and CO2. CO2 is less aversive to animals acclimated to 15°C than those grown at 22°C. This difference requires the AFD neurons, which respond to both temperature and CO2 changes. CO2 evokes distinct AFD Ca2+ responses in animals acclimated at 15°C or 22°C. Mutants defective in synaptic transmission can reprogram AFD CO2 responses according to temperature experience, suggesting reprogramming occurs cell autonomously. AFD is exquisitely sensitive to CO2. Surprisingly, gradients of 0.01% CO2/second evoke very different Ca2+ responses from gradients of 0.04% CO2/second. Ambient O2 provides further contextual modulation of CO2 avoidance. At 21% O2 tonic signalling from the O2-sensing neuron URX inhibits CO2 avoidance. This inhibition can be graded according to O2 levels. In a natural wild isolate, a switch from 21% to 19% O2 is sufficient to convert CO2 from a neutral to an aversive cue. This sharp tuning is conferred partly by the neuroglobin GLB-5. The modulatory effects of O2 on CO2 avoidance involve the RIA interneurons, which are post-synaptic to URX and exhibit CO2-evoked Ca2+ responses. Ambient O2 and acclimation temperature act combinatorially to modulate CO2 responsiveness. Our work highlights the integrated architecture of homeostatic responses in C. elegans.},
author = {Kodama-Namba, Eiji and Fenk, Lorenz A. and Bretscher, Andrew J. and Gross, Einav and Busch, K. Emanuel and de Bono, Mario},
issn = {1553-7404},
journal = {PLoS Genetics},
number = {12},
publisher = {Public Library of Science (PLoS)},
title = {{Cross-modulation of homeostatic responses to temperature, oxygen and carbon dioxide in C. elegans}},
doi = {10.1371/journal.pgen.1004011},
volume = {9},
year = {2013},
}
@article{6130,
abstract = {Cas9 is an RNA-guided double-stranded DNA nuclease that participates in clustered regularly interspaced short palindromic repeats (CRISPR)-mediated adaptive immunity in prokaryotes. CRISPR–Cas9 has recently been used to generate insertion and deletion mutations in Caenorhabditis elegans, but not to create tailored changes (knock-ins). We show that the CRISPR–CRISPR-associated (Cas) system can be adapted for efficient and precise editing of the C. elegans genome. The targeted double-strand breaks generated by CRISPR are substrates for transgene-instructed gene conversion. This allows customized changes in the C. elegans genome by homologous recombination: sequences contained in the repair template (the transgene) are copied by gene conversion into the genome. The possibility to edit the C. elegans genome at selected locations will facilitate the systematic study of gene function in this widely used model organism.},
author = {Chen, Changchun and Fenk, Lorenz A. and de Bono, Mario},
issn = {1362-4962},
journal = {Nucleic Acids Research},
number = {20},
publisher = {Oxford University Press},
title = {{Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination}},
doi = {10.1093/nar/gkt805},
volume = {41},
year = {2013},
}
@article{6133,
abstract = {cGMP signaling is widespread in the nervous system. However, it has proved difficult to visualize and genetically probe endogenously evoked cGMP dynamics in neurons in vivo. Here, we combine cGMP and Ca2+ biosensors to image and dissect a cGMP signaling network in a Caenorhabditis elegans oxygen-sensing neuron. We show that a rise in O2 can evoke a tonic increase in cGMP that requires an atypical O2-binding soluble guanylate cyclase and that is sustained until oxygen levels fall. Increased cGMP leads to a sustained Ca2+ response in the neuron that depends on cGMP-gated ion channels. Elevated levels of cGMP and Ca2+ stimulate competing negative feedback loops that shape cGMP dynamics. Ca2+-dependent negative feedback loops, including activation of phosphodiesterase-1 (PDE-1), dampen the rise of cGMP. A different negative feedback loop, mediated by phosphodiesterase-2 (PDE-2) and stimulated by cGMP-dependent kinase (PKG), unexpectedly promotes cGMP accumulation following a rise in O2, apparently by keeping in check gating of cGMP channels and limiting activation of Ca2+-dependent negative feedback loops. Simultaneous imaging of Ca2+ and cGMP suggests that cGMP levels can rise close to cGMP channels while falling elsewhere. O2-evoked cGMP and Ca2+ responses are highly reproducible when the same neuron in an individual animal is stimulated repeatedly, suggesting that cGMP transduction has high intrinsic reliability. However, responses vary substantially across individuals, despite animals being genetically identical and similarly reared. This variability may reflect stochastic differences in expression of cGMP signaling components. Our work provides in vivo insights into the architecture of neuronal cGMP signaling.},
author = {Couto, A. and Oda, S. and Nikolaev, V. O. and Soltesz, Z. and de Bono, Mario},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {35},
pages = {E3301--E3310},
publisher = {Proceedings of the National Academy of Sciences},
title = {{In vivo genetic dissection of O2-evoked cGMP dynamics in a Caenorhabditis elegans gas sensor}},
doi = {10.1073/pnas.1217428110},
volume = {110},
year = {2013},
}
@article{2697,
abstract = {We consider Hermitian and symmetric random band matrices H = (h xy ) in d⩾1 d ⩾ 1 dimensions. The matrix entries h xy , indexed by x,y∈(Z/LZ)d x , y ∈ ( Z / L Z ) d , are independent, centred random variables with variances sxy=E|hxy|2 s x y = E | h x y | 2 . We assume that s xy is negligible if |x − y| exceeds the band width W. In one dimension we prove that the eigenvectors of H are delocalized if W≫L4/5 W ≫ L 4 / 5 . We also show that the magnitude of the matrix entries |Gxy|2 | G x y | 2 of the resolvent G=G(z)=(H−z)−1 G = G ( z ) = ( H - z ) - 1 is self-averaging and we compute E|Gxy|2 E | G x y | 2 . We show that, as L→∞ L → ∞ and W≫L4/5 W ≫ L 4 / 5 , the behaviour of E|Gxy|2 E | G x y | 2 is governed by a diffusion operator whose diffusion constant we compute. Similar results are obtained in higher dimensions.},
author = {László Erdös and Knowles, Antti and Yau, Horng-Tzer and Yin, Jun},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {367 -- 416},
publisher = {Springer},
title = {{Delocalization and diffusion profile for random band matrices}},
doi = {10.1007/s00220-013-1773-3},
volume = {323},
year = {2013},
}
@article{2698,
abstract = {We consider non-interacting particles subject to a fixed external potential V and a self-generated magnetic field B. The total energy includes the field energy β∫B2 and we minimize over all particle states and magnetic fields. In the case of spin-1/2 particles this minimization leads to the coupled Maxwell-Pauli system. The parameter β tunes the coupling strength between the field and the particles and it effectively determines the strength of the field. We investigate the stability and the semiclassical asymptotics, h→0, of the total ground state energy E(β,h,V). The relevant parameter measuring the field strength in the semiclassical limit is κ=βh. We are not able to give the exact leading order semiclassical asymptotics uniformly in κ or even for fixed κ. We do however give upper and lower bounds on E with almost matching dependence on κ. In the simultaneous limit h→0 and κ→∞ we show that the standard non-magnetic Weyl asymptotics holds. The same result also holds for the spinless case, i.e. where the Pauli operator is replaced by the Schrödinger operator.},
author = {Erdös, László and Fournais, Søren and Solovej, Jan},
journal = {Journal of the European Mathematical Society},
number = {6},
pages = {2093 -- 2113},
publisher = {European Mathematical Society},
title = {{Stability and semiclassics in self-generated fields}},
doi = {10.4171/JEMS/416},
volume = {15},
year = {2013},
}
@inproceedings{2718,
abstract = {Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C.},
author = {Barton, Nicholas H and Paixao, Tiago},
booktitle = {Proceedings of the 15th annual conference on Genetic and evolutionary computation},
location = {Amsterdam, Netherlands},
pages = {1573 -- 1580},
publisher = {ACM},
title = {{Can quantitative and population genetics help us understand evolutionary computation?}},
doi = {10.1145/2463372.2463568},
year = {2013},
}
@article{2720,
abstract = {Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.},
author = {Long, Hongan and Paixao, Tiago and Azevedo, Ricardo and Zufall, Rebecca},
journal = {Genetics},
number = {2},
pages = {527--540},
publisher = {Genetics Society of America},
title = {{Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila}},
doi = {10.1534/genetics.113.153536},
volume = {195},
year = {2013},
}
@article{2780,
abstract = {We consider a general class of random matrices whose entries are centred random variables, independent up to a symmetry constraint. We establish precise high-probability bounds on the averages of arbitrary monomials in the resolvent matrix entries. Our results generalize the previous results of Erdős et al. (Ann Probab, arXiv:1103.1919, 2013; Commun Math Phys, arXiv:1103.3869, 2013; J Combin 1(2):15-85, 2011) which constituted a key step in the proof of the local semicircle law with optimal error bound in mean-field random matrix models. Our bounds apply to random band matrices and improve previous estimates from order 2 to order 4 in the cases relevant to applications. In particular, they lead to a proof of the diffusion approximation for the magnitude of the resolvent of random band matrices. This, in turn, implies new delocalization bounds on the eigenvectors. The applications are presented in a separate paper (Erdős et al., arXiv:1205.5669, 2013).},
author = {László Erdös and Knowles, Antti and Yau, Horng-Tzer},
journal = {Annales Henri Poincare},
number = {8},
pages = {1837 -- 1926},
publisher = {Birkhäuser},
title = {{Averaging fluctuations in resolvents of random band matrices}},
doi = {10.1007/s00023-013-0235-y},
volume = {14},
year = {2013},
}
@article{2781,
abstract = {We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs, that is, graphs on N vertices where every edge is chosen independently and with probability p = p(N). We rescale the matrix so that its bulk eigenvalues are of order one. We prove that, as long as pN→∞(with a speed at least logarithmic in N), the density of eigenvalues of the Erdős-Rényi ensemble is given by the Wigner semicircle law for spectral windows of length larger than N-1 (up to logarithmic corrections). As a consequence, all eigenvectors are proved to be completely delocalized in the sense that the ℓ∞-norms of the ℓ2-normalized eigenvectors are at most of order N-1/2 with a very high probability. The estimates in this paper will be used in the companion paper [Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues (2011) Preprint] to prove the universality of eigenvalue distributions both in the bulk and at the spectral edges under the further restriction that pN »N2/3.},
author = {László Erdös and Knowles, Antti and Yau, Horng-Tzer and Yin, Jun},
journal = {Annals of Probability},
number = {3 B},
pages = {2279 -- 2375},
publisher = {Institute of Mathematical Statistics},
title = {{Spectral statistics of Erdős-Rényi graphs I: Local semicircle law}},
doi = {10.1214/11-AOP734},
volume = {41},
year = {2013},
}
@article{2782,
abstract = {We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2}, where X and Y have independent entries with zero mean and variance one. These matrices are the natural generalization of the Gaussian case, which are known as MANOVA matrices and which have joint eigenvalue density given by the third classical ensemble, the Jacobi ensemble. We show that, away from the spectral edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble even on the shortest possible scales of order 1/n (up to log n factors). This result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur law for general MANOVA matrices.},
author = {Erdös, László and Farrell, Brendan},
journal = {Journal of Statistical Physics},
number = {6},
pages = {1003 -- 1032},
publisher = {Springer},
title = {{Local eigenvalue density for general MANOVA matrices}},
doi = {10.1007/s10955-013-0807-8},
volume = {152},
year = {2013},
}
@inproceedings{2807,
abstract = {We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov's result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \no holes up to dimension k-1" (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. },
author = {Čadek, Martin and Krcál, Marek and Matoušek, Jiří and Vokřínek, Lukáš and Wagner, Uli},
booktitle = {45th Annual ACM Symposium on theory of computing},
location = {Palo Alto, CA, United States},
pages = {595 -- 604},
publisher = {ACM},
title = {{Extending continuous maps: Polynomiality and undecidability}},
doi = {10.1145/2488608.2488683},
year = {2013},
}
@article{2808,
abstract = {In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.},
author = {Landberg, Katarina and Pederson, Eric and Viaene, Tom and Bozorg, Behruz and Friml, Jirí and Jönsson, Henrik and Thelander, Mattias and Sundberg, Eva},
journal = {Plant Physiology},
number = {3},
pages = {1406 -- 1419},
publisher = {American Society of Plant Biologists},
title = {{The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain}},
doi = {10.1104/pp.113.214023},
volume = {162},
year = {2013},
}
@article{2810,
abstract = {The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data.},
author = {De Vos, Marjon and Poelwijk, Frank and Battich, Nico and Ndika, Joseph and Tans, Sander},
journal = {PLoS Genetics},
number = {6},
publisher = {Public Library of Science},
title = {{Environmental dependence of genetic constraint}},
doi = {10.1371/journal.pgen.1003580},
volume = {9},
year = {2013},
}
@article{2811,
abstract = {In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.},
author = {Avila, Marc and Hof, Björn},
journal = {Physical Review E},
number = {6},
publisher = {American Institute of Physics},
title = {{Nature of laminar-turbulence intermittency in shear flows}},
doi = {10.1103/PhysRevE.87.063012},
volume = {87},
year = {2013},
}
@inproceedings{2812,
abstract = {We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.},
author = {Attali, Dominique and Bauer, Ulrich and Devillers, Olivier and Glisse, Marc and Lieutier, André},
booktitle = {Proceedings of the 29th annual symposium on Computational Geometry},
location = {Rio de Janeiro, Brazil},
pages = {117 -- 125},
publisher = {ACM},
title = {{Homological reconstruction and simplification in R3}},
doi = {10.1145/2462356.2462373},
year = {2013},
}
@article{2813,
abstract = {Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called "maximum drag reduction" asymptote, which is exhibited by a wide range of viscoelastic fluids.},
author = {Samanta, Devranjan and Dubief, Yves and Holzner, Markus and Schäfer, Christof and Morozov, Alexander and Wagner, Christian and Hof, Björn},
journal = {PNAS},
number = {26},
pages = {10557 -- 10562},
publisher = {National Academy of Sciences},
title = {{Elasto-inertial turbulence}},
doi = {10.1073/pnas.1219666110},
volume = {110},
year = {2013},
}
@article{2814,
abstract = {We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing "reset" action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. We also discuss the memory requirement for deterministic strategies and extensions of our results to other models, such as pushdown systems and timed systems.},
author = {Chatterjee, Krishnendu and Alfaro, Luca and Majumdar, Ritankar},
journal = {International Journal of Foundations of Computer Science},
number = {2},
pages = {165 -- 185},
publisher = {World Scientific Publishing},
title = {{The complexity of coverage}},
doi = {10.1142/S0129054113400066},
volume = {24},
year = {2013},
}
@article{2816,
abstract = {In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics.},
author = {Božić, Ivana and Reiter, Johannes and Allen, Benjamin and Antal, Tibor and Chatterjee, Krishnendu and Shah, Preya and Moon, Yo and Yaqubie, Amin and Kelly, Nicole and Le, Dung and Lipson, Evan and Chapman, Paul and Diaz, Luis and Vogelstein, Bert and Nowak, Martin},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Evolutionary dynamics of cancer in response to targeted combination therapy}},
doi = {10.7554/eLife.00747},
volume = {2},
year = {2013},
}
@article{2817,
abstract = {The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle.},
author = {Novak, Sebastian and Chatterjee, Krishnendu and Nowak, Martin},
journal = {Journal of Theoretical Biology},
pages = {26 -- 34},
publisher = {Elsevier},
title = {{Density games}},
doi = {10.1016/j.jtbi.2013.05.029},
volume = {334},
year = {2013},
}
@article{2818,
abstract = {Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus.},
author = {Rajan, Kanaka and Marre, Olivier and Tkacik, Gasper},
journal = {Neural Computation},
number = {7},
pages = {1661 -- 1692},
publisher = {MIT Press },
title = {{Learning quadratic receptive fields from neural responses to natural stimuli}},
doi = {10.1162/NECO_a_00463},
volume = {25},
year = {2013},
}
@inproceedings{2819,
abstract = {We introduce quantatitive timed refinement metrics and quantitative timed simulation functions, incorporating zenoness checks, for timed systems. These functions assign positive real numbers between zero and infinity which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximum timing mismatch that can arise, (2) the "steady-state" maximum timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation functions to within any desired degree of accuracy. In order to compute the values of the quantitative simulation functions, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives for player 1, and then use these algorithms to compute the values of the quantitative timed simulation functions. },
author = {Chatterjee, Krishnendu and Prabhu, Vinayak},
booktitle = {Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control},
location = {Philadelphia, PA USA},
pages = {273 -- 282},
publisher = {Springer},
title = {{Quantitative timed simulation functions and refinement metrics for real-time systems}},
doi = {10.1145/2461328.2461370},
volume = {1},
year = {2013},
}
@article{2821,
abstract = {Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells.},
author = {Remy, Estelle and Cabrito, Tânia and Baster, Pawel and Batista, Rita and Teixeira, Miguel and Friml, Jirí and Sá Correia, Isabel and Duque, Paula},
journal = {Plant Cell},
number = {3},
pages = {901 -- 926},
publisher = {American Society of Plant Biologists},
title = {{A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis}},
doi = {10.1105/tpc.113.110353},
volume = {25},
year = {2013},
}
@article{2822,
abstract = {Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.},
author = {Topp, Christopher and Iyer Pascuzzi, Anjali and Anderson, Jill and Lee, Cheng and Zurek, Paul and Symonova, Olga and Zheng, Ying and Bucksch, Alexander and Mileyko, Yuriy and Galkovskyi, Taras and Moore, Brad and Harer, John and Edelsbrunner, Herbert and Mitchell Olds, Thomas and Weitz, Joshua and Benfey, Philip},
journal = {PNAS},
number = {18},
pages = {E1695 -- E1704},
publisher = {National Academy of Sciences},
title = {{3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture}},
doi = {10.1073/pnas.1304354110},
volume = {110},
year = {2013},
}
@article{2826,
abstract = {Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent analyses identified three additional mutations in three highly myopic unrelated individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential gene expression in a developmental mouse model, we induced myopia by applying a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for a copper homeostasis protein influential in mitochondrial cytochrome c oxidase activity. Copper deficiencies have been linked with photoreceptor loss and myopia with increased scleral wall elasticity. Retinal thinning has been reported with an SC02 variant. Human mutation identification with support from an induced myopic animal provides biological insights of myopic development.},
author = {Tran Viet, Khanh and Powell, Caldwell and Barathi, Veluchamy and Klemm, Thomas and Maurer Stroh, Sebastian and Limviphuvadh, Vachiranee and Soler, Vincent and Ho, Candice and Yanovitch, Tammy and Schneider, Georg and Li, Yi and Nading, Erica and Metlapally, Ravikanth and Saw, Seang and Goh, Liang and Rozen, Steve and Young, Terri},
journal = {American Journal of Human Genetics},
number = {5},
pages = {820 -- 826},
publisher = {Cell Press},
title = {{Mutations in SCO2 are associated with autosomal-dominant high-grade myopia}},
doi = {10.1016/j.ajhg.2013.04.005},
volume = {92},
year = {2013},
}
@article{2827,
abstract = {Removal of cargos from the cell surface via endocytosis is an efficient mechanism to regulate activities of plasma membrane (PM)-resident proteins, such as receptors or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally associated with pathogen defense. Here, we describe an unanticipated effect of SA on subcellular endocytic cycling of proteins. Both exogenous treatments and endogenously enhanced SA levels repressed endocytosis of different PM proteins. The SA effect on endocytosis did not involve transcription or known components of the SA signaling pathway for transcriptional regulation. SA likely targets an endocytic mechanism that involves the coat protein clathrin, because SA interfered with the clathrin incidence at the PM and clathrin-deficient mutants were less sensitive to the impact of SA on the auxin distribution and root bending during the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data suggest that the established SA impact on transcription in plant immunity and the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent mechanisms by which SA regulates distinct aspects of plant physiology.},
author = {Du, Yunlong and Tejos, Ricardo and Beck, Martina and Himschoot, Ellie and Li, Hongjiang and Robatzek, Silke and Vanneste, Steffen and Friml, Jirí},
journal = {PNAS},
number = {19},
pages = {7946 -- 7951},
publisher = {National Academy of Sciences},
title = {{Salicylic acid interferes with clathrin-mediated endocytic protein trafficking}},
doi = {10.1073/pnas.1220205110},
volume = {110},
year = {2013},
}
@article{2828,
abstract = {We study the complexity of valued constraint satisfaction problems (VCSPs) parametrized by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimize the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well understood, see Raghavendra [2008]. However, there is no characterization of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimization perspective. We consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e., relations), such languages have been called conservative and studied by Bulatov [2003, 2011] and recently by Barto [2011]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [2006] for languages over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a Max-CSP), and by Takhanov [2010a] for {0, ∞}-valued languages containing all finite-valued unary cost functions (a.k.a. Min-Cost-Hom). We prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimor-phisms), then any instance can be solved in polynomial time (via a new algorithm developed in this article), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains are significantly harder than the Boolean cases. The polynomial-time algorithm we present for the tractable cases is a generalization of the submodular minimization problem and a result of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a] and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [2008], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.},
author = {Kolmogorov, Vladimir and Živný, Stanislav},
journal = {Journal of the ACM},
number = {2},
publisher = {ACM},
title = {{The complexity of conservative valued CSPs}},
doi = {10.1145/2450142.2450146},
volume = {60},
year = {2013},
}
@article{2829,
abstract = {Laminar-turbulent intermittency is intrinsic to the transitional regime of a wide range of fluid flows including pipe, channel, boundary layer, and Couette flow. In the latter turbulent spots can grow and form continuous stripes, yet in the stripe-normal direction they remain interspersed by laminar fluid. We carry out direct numerical simulations in a long narrow domain and observe that individual turbulent stripes are transient. In agreement with recent observations in pipe flow, we find that turbulence becomes sustained at a distinct critical point once the spatial proliferation outweighs the inherent decaying process. By resolving the asymptotic size distributions close to criticality we can for the first time demonstrate scale invariance at the onset of turbulence.},
author = {Shi, Liang and Avila, Marc and Hof, Björn},
journal = {Physical Review Letters},
number = {20},
publisher = {American Physical Society},
title = {{Scale invariance at the onset of turbulence in couette flow}},
doi = {10.1103/PhysRevLett.110.204502},
volume = {110},
year = {2013},
}
@article{2831,
abstract = {We consider Markov decision processes (MDPs) with Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning states from where the objective can be ensured with probability 1. Our contributions are as follows: First, we present the first subquadratic symbolic algorithm to compute the almost-sure winning set for MDPs with Büchi objectives; our algorithm takes O(n · √ m) symbolic steps as compared to the previous known algorithm that takes O(n 2) symbolic steps, where n is the number of states and m is the number of edges of the MDP. In practice MDPs have constant out-degree, and then our symbolic algorithm takes O(n · √ n) symbolic steps, as compared to the previous known O(n 2) symbolic steps algorithm. Second, we present a new algorithm, namely win-lose algorithm, with the following two properties: (a) the algorithm iteratively computes subsets of the almost-sure winning set and its complement, as compared to all previous algorithms that discover the almost-sure winning set upon termination; and (b) requires O(n · √ K) symbolic steps, where K is the maximal number of edges of strongly connected components (scc's) of the MDP. The win-lose algorithm requires symbolic computation of scc's. Third, we improve the algorithm for symbolic scc computation; the previous known algorithm takes linear symbolic steps, and our new algorithm improves the constants associated with the linear number of steps. In the worst case the previous known algorithm takes 5×n symbolic steps, whereas our new algorithm takes 4×n symbolic steps.},
author = {Chatterjee, Krishnendu and Henzinger, Monika and Joglekar, Manas and Shah, Nisarg},
journal = {Formal Methods in System Design},
number = {3},
pages = {301 -- 327},
publisher = {Springer},
title = {{Symbolic algorithms for qualitative analysis of Markov decision processes with Büchi objectives}},
doi = {10.1007/s10703-012-0180-2},
volume = {42},
year = {2013},
}
@article{2832,
abstract = {PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants. PIN localization is under extensive control by environmental or developmental cues, but mechanisms regulating PIN localization are not fully understood. Here we show that early endosomal components ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively required for polar PIN localization, for their dynamic repolarization, and consequently for auxin activity gradient formation and auxin-related developmental processes including embryonic patterning, organogenesis, and vasculature venation patterning. These results show that early endosomal trafficking is crucial for cell polarity and auxin-dependent regulation of plant architecture.},
author = {Tanaka, Hirokazu and Kitakura, Saeko and Rakusová, Hana and Uemura, Tomohiro and Feraru, Mugurel and De Rycke, Riet and Robert, Stéphanie and Kakimoto, Tatsuo and Friml, Jirí},
journal = {PLoS Genetics},
number = {5},
publisher = {Public Library of Science},
title = {{Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana}},
doi = {10.1371/journal.pgen.1003540},
volume = {9},
year = {2013},
}
@article{2834,
abstract = {Although the equations governing fluid flow are well known, there are no analytical expressions that describe the complexity of turbulent motion. A recent proposition is that in analogy to low dimensional chaotic systems, turbulence is organized around unstable solutions of the governing equations which provide the building blocks of the disordered dynamics. We report the discovery of periodic solutions which just like intermittent turbulence are spatially localized and show that turbulent transients arise from one such solution branch.},
author = {Avila, Marc and Mellibovsky, Fernando and Roland, Nicolas and Hof, Björn},
journal = {Physical Review Letters},
number = {22},
publisher = {American Physical Society},
title = {{Streamwise-localized solutions at the onset of turbulence in pipe flow}},
doi = {10.1103/PhysRevLett.110.224502},
volume = {110},
year = {2013},
}
@article{2835,
abstract = {The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The levels of the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1 (RUS1), a member of the conserved Domain of Unknown Function647 protein family found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane.},
author = {Yu, Hong and Karampelias, Michael and Robert, Stéphanie and Peer, Wendy and Swarup, Ranjan and Ye, Songqing and Ge, Lei and Cohen, Jerry and Murphy, Angus and Friml, Jirí and Estelle, Mark},
journal = {Plant Physiology},
number = {2},
pages = {965 -- 976},
publisher = {American Society of Plant Biologists},
title = {{Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis}},
doi = {10.1104/pp.113.217018},
volume = {162},
year = {2013},
}
@article{2836,
abstract = {We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents and the trusted third party as path formulas in linear temporal logic and prove that the satisfaction of these objectives imply fairness; a property required of fair exchange protocols. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of AGS as follows: (a) any solution of AGS is attack-free; no subset of participants can violate the objectives of the other participants; (b) the Asokan-Shoup-Waidner certified mail protocol that has known vulnerabilities is not a solution of AGS; (c) the Kremer-Markowitch non-repudiation protocol is a solution of AGS; and (d) AGS presents a new and symmetric fair non-repudiation protocol that is attack-free. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can both automatically discover vulnerabilities in protocols and generate correct protocols. The solution to AGS can be computed efficiently as the secure equilibrium solution of three-player graph games. },
author = {Chatterjee, Krishnendu and Raman, Vishwanath},
journal = {Formal Aspects of Computing},
number = {4},
pages = {825 -- 859},
publisher = {Springer},
title = {{Assume-guarantee synthesis for digital contract signing}},
doi = {10.1007/s00165-013-0283-6},
volume = {26},
year = {2013},
}
@article{2837,
abstract = {We consider a general class of N × N random matrices whose entries hij are independent up to a symmetry constraint, but not necessarily identically distributed. Our main result is a local semicircle law which improves previous results [17] both in the bulk and at the edge. The error bounds are given in terms of the basic small parameter of the model, maxi,j E|hij|2. As a consequence, we prove the universality of the local n-point correlation functions in the bulk spectrum for a class of matrices whose entries do not have comparable variances, including random band matrices with band width W ≫N1-εn with some εn > 0 and with a negligible mean-field component. In addition, we provide a coherent and pedagogical proof of the local semicircle law, streamlining and strengthening previous arguments from [17, 19, 6].},
author = {Erdös, László and Knowles, Antti and Yau, Horng and Yin, Jun},
journal = {Electronic Journal of Probability},
number = {59},
pages = {1--58},
publisher = {Institute of Mathematical Statistics},
title = {{The local semicircle law for a general class of random matrices}},
doi = {10.1214/EJP.v18-2473},
volume = {18},
year = {2013},
}
@article{2838,
abstract = {Individuals with Down syndrome (DS) present important motor deficits that derive from altered motor development of infants and young children. DYRK1A, a candidate gene for DS abnormalities has been implicated in motor function due to its expression in motor nuclei in the adult brain, and its overexpression in DS mouse models leads to hyperactivity and altered motor learning. However, its precise role in the adult motor system, or its possible involvement in postnatal locomotor development has not yet been clarified. During the postnatal period we observed time-specific expression of Dyrk1A in discrete subsets of brainstem nuclei and spinal cord motor neurons. Interestingly, we describe for the first time the presence of Dyrk1A in the presynaptic terminal of the neuromuscular junctions and its axonal transport from the facial nucleus, suggesting a function for Dyrk1A in these structures. Relevant to DS, Dyrk1A overexpression in transgenic mice (TgDyrk1A) produces motor developmental alterations possibly contributing to DS motor phenotypes and modifies the numbers of motor cholinergic neurons, suggesting that the kinase may have a role in the development of the brainstem and spinal cord motor system.},
author = {Arquè Fuste, Gloria and Casanovas, Anna and Dierssen, Mara},
journal = {PLoS One},
number = {1},
publisher = {Public Library of Science},
title = {{Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome}},
doi = {10.1371/journal.pone.0054285},
volume = {8},
year = {2013},
}
@article{2839,
abstract = {Directional guidance of cells via gradients of chemokines is considered crucial for embryonic development, cancer dissemination, and immune responses. Nevertheless, the concept still lacks direct experimental confirmation in vivo. Here, we identify endogenous gradients of the chemokine CCL21 within mouse skin and show that they guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots of CCL21 within lymphatic endothelial cells and steeply decaying gradients within the perilymphatic interstitium. These gradients match the migratory patterns of the dendritic cells, which directionally approach vessels from a distance of up to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and its experimental delocalization or swamping the endogenous gradients abolishes directed migration. These findings functionally establish the concept of haptotaxis, directed migration along immobilized gradients, in tissues.},
author = {Weber, Michele and Hauschild, Robert and Schwarz, Jan and Moussion, Christine and De Vries, Ingrid and Legler, Daniel and Luther, Sanjiv and Bollenbach, Mark Tobias and Sixt, Michael K},
journal = {Science},
number = {6117},
pages = {328 -- 332},
publisher = {American Association for the Advancement of Science},
title = {{Interstitial dendritic cell guidance by haptotactic chemokine gradients}},
doi = {10.1126/science.1228456},
volume = {339},
year = {2013},
}
@article{2842,
abstract = {We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a 'local scale', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2.},
author = {Barton, Nicholas H and Etheridge, Alison and Kelleher, Jerome and Véber, Amandine},
journal = {Theoretical Population Biology},
number = {1},
pages = {105 -- 119},
publisher = {Elsevier},
title = {{Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks}},
doi = {10.1016/j.tpb.2013.03.001},
volume = {87},
year = {2013},
}
@article{2846,
abstract = {The Red Queen hypothesis proposes that coevolving parasites select for outcrossing in the host. Outcrossing relies on males, which often show lower immune investment due to, for example, sexual selection. Here, we demonstrate that such sex differences in immunity interfere with parasite-mediated selection for outcrossing. Two independent coevolution experiments with Caenorhabditis elegans and its microparasite Bacillus thuringiensis produced decreased yet stable frequencies of outcrossing male hosts. A subsequent systematic analysis verified that male C. elegans suffered from a direct selective disadvantage under parasite pressure (i.e. lower resistance, decreased sexual activity, increased escape behaviour), which can reduce outcrossing and thus male frequencies. At the same time, males offered an indirect selective benefit, because male-mediated outcrossing increased offspring resistance, thus favouring male persistence in the evolving populations. As sex differences in immunity are widespread, such interference of opposing selective constraints is likely of central importance during host adaptation to a coevolving parasite.},
author = {El Masri, Leila and Schulte, Rebecca and Timmermeyer, Nadine and Thanisch, Stefanie and Crummenerl, Lena and Jansen, Gunther and Michiels, Nico and Schulenburg, Hinrich},
journal = {Ecology Letters},
number = {4},
pages = {461 -- 468},
publisher = {Wiley-Blackwell},
title = {{Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution}},
doi = {10.1111/ele.12068},
volume = {16},
year = {2013},
}
@inproceedings{2847,
abstract = {Depth-Bounded Systems form an expressive class of well-structured transition systems. They can model a wide range of concurrent infinite-state systems including those with dynamic thread creation, dynamically changing communication topology, and complex shared heap structures. We present the first method to automatically prove fair termination of depth-bounded systems. Our method uses a numerical abstraction of the system, which we obtain by systematically augmenting an over-approximation of the system’s reachable states with a finite set of counters. This numerical abstraction can be analyzed with existing termination provers. What makes our approach unique is the way in which it exploits the well-structuredness of the analyzed system. We have implemented our work in a prototype tool and used it to automatically prove liveness properties of complex concurrent systems, including nonblocking algorithms such as Treiber’s stack and several distributed processes. Many of these examples are beyond the scope of termination analyses that are based on traditional counter abstractions.},
author = {Bansal, Kshitij and Koskinen, Eric and Wies, Thomas and Zufferey, Damien},
editor = {Piterman, Nir and Smolka, Scott},
location = {Rome, Italy},
pages = {62 -- 77},
publisher = {Springer},
title = {{Structural Counter Abstraction}},
doi = {10.1007/978-3-642-36742-7_5},
volume = {7795},
year = {2013},
}
@article{2850,
abstract = {Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on capturing the measured correlations among pairs of neurons. Here we suggest an alternative, constructing models that are consistent with the distribution of global network activity, i.e. the probability that K out of N cells in the network generate action potentials in the same small time bin. The inverse problem that we need to solve in constructing the model is analytically tractable, and provides a natural 'thermodynamics' for the network in the limit of large N. We analyze the responses of neurons in a small patch of the retina to naturalistic stimuli, and find that the implied thermodynamics is very close to an unusual critical point, in which the entropy (in proper units) is exactly equal to the energy. © 2013 IOP Publishing Ltd and SISSA Medialab srl.
},
author = {Tkacik, Gasper and Marre, Olivier and Mora, Thierry and Amodei, Dario and Berry, Michael and Bialek, William},
journal = {Journal of Statistical Mechanics Theory and Experiment},
number = {3},
publisher = {IOP Publishing Ltd.},
title = {{The simplest maximum entropy model for collective behavior in a neural network}},
doi = {10.1088/1742-5468/2013/03/P03011},
volume = {2013},
year = {2013},
}
@article{2853,
abstract = {High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared with its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low, because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.},
author = {Refardt, Dominik and Bergmiller, Tobias and Kümmerli, Rolf},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1759},
publisher = {Royal Society, The},
title = {{Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection}},
doi = {10.1098/rspb.2012.3035},
volume = {280},
year = {2013},
}