@article{2107, abstract = {We present a method for fabrication-oriented design of actuated deformable characters that allows a user to automatically create physical replicas of digitally designed characters using rapid manufacturing technologies. Given a deformable character and a set of target poses as input, our method computes a small set of actuators along with their locations on the surface and optimizes the internal material distribution such that the resulting character exhibits the desired deformation behavior. We approach this problem with a dedicated algorithm that combines finite-element analysis, sparse regularization, and constrained optimization. We validate our pipeline on a set of two- and three-dimensional example characters and present results in simulation and physically-fabricated prototypes.}, author = {Skouras, Mélina and Thomaszewski, Bernhard and Coros, Stelian and Bernd Bickel and Groß, Markus S}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Computational design of actuated deformable characters}}, doi = {10.1145/2461912.2461979}, volume = {32}, year = {2013}, } @article{2112, abstract = {Force-deformation measurements of cloth exhibit significant hysteresis, and many researchers have identified internal friction as the source of this effect. However, it has not been incorporated into computer animation models of cloth. In this paper, we propose a model of internal friction based on an augmented reparameterization of Dahl's model, and we show that this model provides a good match to several important features of cloth hysteresis even with a minimal set of parameters. We also propose novel parameter estimation procedures that are based on simple and inexpensive setups and need only sparse data, as opposed to the complex hardware and dense data acquisition of previous methods. Finally, we provide an algorithm for the efficient simulation of internal friction, and we demonstrate it on simulation examples that show disparate behavior with and without internal friction.}, author = {Miguel, Eder and Tamstorf, Rasmus and Bradley, Derek J and Schvartzman, Sara C and Thomaszewski, Bernhard and Bernd Bickel and Matusik, Wojciech and Marschner, Steve and Otaduy, Miguel A}, journal = {ACM Transactions on Graphics}, number = {6}, publisher = {ACM}, title = {{Modeling and estimation of internal friction in cloth}}, doi = {10.1145/2508363.2508389 }, volume = {32}, year = {2013}, } @article{2117, abstract = {We prove new upper and lower bounds for Banach space-valued stochastic integrals with respect to a compensated Poisson random measure. Our estimates apply to Banach spaces with non-trivial martingale (co)type and extend various results in the literature. We also develop a Malliavin framework to interpret Poisson stochastic integrals as vector-valued Skorohod integrals, and prove a Clark-Ocone representation formula.}, author = {Dirksen, Sjoerd and Jan Maas and van Neerven, Jan M}, journal = {Electronic Journal of Probability}, publisher = {Institute of Mathematical Statistics}, title = {{Poisson stochastic integration in Banach spaces}}, doi = {10.1214/EJP.v18-2945 }, volume = {18}, year = {2013}, } @article{2113, abstract = {A new method fabricates custom surface reflectance and spatially varying bidirectional reflectance distribution functions (svBRDFs). Researchers optimize a microgeometry for a range of normal distribution functions and simulate the resulting surface's effective reflectance. Using the simulation's results, they reproduce an input svBRDF's appearance by distributing the microgeometry on the printed material's surface. This method lets people print svBRDFs on planar samples with current 3D printing technology, even with a limited set of printing materials. It extends naturally to printing svBRDFs on arbitrary shapes.}, author = {Rouiller, Olivier and Bernd Bickel and Kautz, Jan and Matusik, Wojciech and Alexa, Marc}, journal = {IEEE Computer Graphics and Applications}, number = {6}, pages = {48 -- 57}, publisher = {IEEE}, title = {{3D printing spatially varying BRDFs}}, doi = {10.1109/MCG.2013.82 }, volume = {33}, year = {2013}, } @article{2114, abstract = {3D printing is considered a disruptive technology with a potentially tremendous socioeconomic impact. The three articles in this special issue illustrate how novel computer graphics approaches are advancing such digital fabrication.}, author = {Bernd Bickel and Alexa, Marc}, journal = {IEEE Computer Graphics and Applications}, number = {6}, pages = {24 -- 25}, publisher = {IEEE}, title = {{Computational aspects of fabrication: Modeling, design and 3d printing}}, doi = {10.1109/MCG.2013.89}, volume = {33}, year = {2013}, } @article{2129, abstract = {This paper continues the investigation of `Wasserstein-like' transportation distances for probability measures on discrete sets. We prove that the discrete transportation metrics on the d-dimensional discrete torus with mesh size 1/N converge, when N→∞, to the standard 2-Wasserstein distance W_2 on the continuous torus in the sense of Gromov-Hausdorff. This is the first convergence result for the recently developed discrete transportation metrics. The result shows the compatibility between these metrics and the well-established 2-Wasserstein metric. }, author = {Gigli, Nicola and Jan Maas}, journal = {SIAM Journal on Mathematical Analysis}, number = {2}, pages = {879 -- 899}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Gromov-Hausdorff convergence of discrete transportation metrics}}, doi = {10.1137/120886315 }, volume = {45}, year = {2013}, } @article{2139, abstract = {Recently it has been shown that pairs of atoms can form metastable bonds due to non-conservative forces induced by dissipation [Lemeshko&Weimer, Nature Comm. 4, 2230 (2013)]. Here we study the dynamics of interaction-induced coherent population trapping - the process responsible for the formation of dissipatively bound molecules. We derive the effective dissipative potentials induced between ultracold atoms by laser light, and study the time evolution of the scattering states. We demonstrate that binding occurs on short timescales of ~10 microseconds, even if the initial kinetic energy of the atoms significantly exceeds the depth of the dissipative potential. Dissipatively-bound molecules with preordained bond lengths and vibrational wavefunctions can be created and detected in current experiments with ultracold atoms.}, author = {Mikhail Lemeshko}, journal = {Frontiers Physics}, number = {17}, publisher = {Frontiers Media}, title = {{Manipulating scattering of ultracold atoms with light-induced dissipation}}, doi = {10.3389/fphy.2013.00017}, volume = {1}, year = {2013}, } @inproceedings{2181, abstract = {There is a trade-off between performance and correctness in implementing concurrent data structures. Better performance may be achieved at the expense of relaxing correctness, by redefining the semantics of data structures. We address such a redefinition of data structure semantics and present a systematic and formal framework for obtaining new data structures by quantitatively relaxing existing ones. We view a data structure as a sequential specification S containing all "legal" sequences over an alphabet of method calls. Relaxing the data structure corresponds to defining a distance from any sequence over the alphabet to the sequential specification: the k-relaxed sequential specification contains all sequences over the alphabet within distance k from the original specification. In contrast to other existing work, our relaxations are semantic (distance in terms of data structure states). As an instantiation of our framework, we present two simple yet generic relaxation schemes, called out-of-order and stuttering relaxation, along with several ways of computing distances. We show that the out-of-order relaxation, when further instantiated to stacks, queues, and priority queues, amounts to tolerating bounded out-of-order behavior, which cannot be captured by a purely syntactic relaxation (distance in terms of sequence manipulation, e.g. edit distance). We give concurrent implementations of relaxed data structures and demonstrate that bounded relaxations provide the means for trading correctness for performance in a controlled way. The relaxations are monotonic which further highlights the trade-off: increasing k increases the number of permitted sequences, which as we demonstrate can lead to better performance. Finally, since a relaxed stack or queue also implements a pool, we actually have new concurrent pool implementations that outperform the state-of-the-art ones.}, author = {Henzinger, Thomas A and Kirsch, Christoph and Payer, Hannes and Sezgin, Ali and Sokolova, Ana}, booktitle = {Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language}, isbn = {978-1-4503-1832-7}, location = {Rome, Italy}, pages = {317 -- 328}, publisher = {ACM}, title = {{Quantitative relaxation of concurrent data structures}}, doi = {10.1145/2429069.2429109}, year = {2013}, } @inproceedings{2182, abstract = {We propose a general framework for abstraction with respect to quantitative properties, such as worst-case execution time, or power consumption. Our framework provides a systematic way for counter-example guided abstraction refinement for quantitative properties. The salient aspect of the framework is that it allows anytime verification, that is, verification algorithms that can be stopped at any time (for example, due to exhaustion of memory), and report approximations that improve monotonically when the algorithms are given more time. We instantiate the framework with a number of quantitative abstractions and refinement schemes, which differ in terms of how much quantitative information they keep from the original system. We introduce both state-based and trace-based quantitative abstractions, and we describe conditions that define classes of quantitative properties for which the abstractions provide over-approximations. We give algorithms for evaluating the quantitative properties on the abstract systems. We present algorithms for counter-example based refinements for quantitative properties for both state-based and segment-based abstractions. We perform a case study on worst-case execution time of executables to evaluate the anytime verification aspect and the quantitative abstractions we proposed.}, author = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun}, booktitle = {Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language}, location = {Rome, Italy}, pages = {115 -- 128}, publisher = {ACM}, title = {{Quantitative abstraction refinement}}, doi = {10.1145/2429069.2429085}, year = {2013}, } @inproceedings{2209, abstract = {A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon or planar straight-line graph. In this paper, we ask the reverse question: Given the straight skeleton (in form of a planar straight-line graph, with some rays to infinity), can we reconstruct a planar straight-line graph for which this was the straight skeleton? We show how to reduce this problem to the problem of finding a line that intersects a set of convex polygons. We can find these convex polygons and all such lines in $O(nlog n)$ time in the Real RAM computer model, where $n$ denotes the number of edges of the input graph. We also explain how our approach can be used for recognizing Voronoi diagrams of points, thereby completing a partial solution provided by Ash and Bolker in 1985. }, author = {Biedl, Therese and Held, Martin and Huber, Stefan}, location = {St. Petersburg, Russia}, pages = {37 -- 46}, publisher = {IEEE}, title = {{Recognizing straight skeletons and Voronoi diagrams and reconstructing their input}}, doi = {10.1109/ISVD.2013.11}, year = {2013}, } @article{2204, abstract = {We introduce a new platform for quantum simulation of many-body systems based on nonspherical atoms or molecules with zero dipole moments but possessing a significant value of electric quadrupole moments. We consider a quadrupolar Fermi gas trapped in a 2D square optical lattice, and show that the peculiar symmetry and broad tunability of the quadrupole-quadrupole interaction results in a rich phase diagram encompassing unconventional BCS and charge density wave phases, and opens up a perspective to create a topological superfluid. Quadrupolar species, such as metastable alkaline-earth atoms and homonuclear molecules, are stable against chemical reactions and collapse and are readily available in experiment at high densities.}, author = {Bhongale, Satyan and Mathey, Ludwig and Zhao, Erhai and Yelin, Susanne and Lemeshko, Mikhail}, journal = {Physical Review Letters}, number = {15}, publisher = {American Physical Society}, title = {{Quantum phases of quadrupolar fermi gases in optical lattices}}, doi = {10.1103/PhysRevLett.110.155301}, volume = {110}, year = {2013}, } @article{2206, abstract = {Magnetic impurities embedded in inert solids can exhibit long coherence times and interact with one another via their intrinsic anisotropic dipolar interaction. We argue that, as a consequence of these properties, disordered ensembles of magnetic impurities provide an effective platform for realizing a controllable, tunable version of the dipolar quantum spin glass seen in LiHoxY1-xF4. Specifically, we propose and analyze a system composed of dysprosium atoms embedded in solid helium. We describe the phase diagram of the system and discuss the realizability and detectability of the quantum spin glass and antiglass phases.}, author = {Mikhail Lemeshko and Yao, Norman Y and Gorshkov, Alexey V and Weimer, Hendrik and Bennett, Steven D and Momose, Takamasa and Gopalakrishnan, Sarang}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {1}, publisher = {American Physical Society}, title = {{Controllable quantum spin glasses with magnetic impurities embedded in quantum solids}}, doi = {10.1103/PhysRevB.88.014426}, volume = {88}, year = {2013}, } @misc{2205, abstract = {The goal of the present article is to review the major developments that have led to the current understanding of molecule-field interactions and experimental methods for manipulating molecules with electromagnetic fields. Molecule-field interactions are at the core of several, seemingly distinct areas of molecular physics. This is reflected in the organisation of this article, which includes sections on field control of molecular beams, external field traps for cold molecules, control of molecular orientation and molecular alignment, manipulation of molecules by non-conservative forces, ultracold molecules and ultracold chemistry, controlled many-body phenomena, entanglement of molecules and dipole arrays, and stability of molecular systems in high-frequency super-intense laser fields. The article contains 852 references.}, author = {Mikhail Lemeshko and Krems, Roman V and Doyle, John M and Kais, Sabre}, booktitle = {Molecular Physics}, number = {12-13}, pages = {1648 -- 1682}, publisher = {Taylor & Francis}, title = {{Manipulation of molecules with electromagnetic fields}}, doi = {10.1080/00268976.2013.813595}, volume = {111}, year = {2013}, } @article{2207, abstract = {The formation of molecules and supramolecular structures results from bonding by conservative forces acting among electrons and nuclei and giving rise to equilibrium configurations defined by minima of the interaction potential. Here we show that bonding can also occur by the non-conservative forces responsible for interaction-induced coherent population trapping. The bound state arises in a dissipative process and manifests itself as a stationary state at a preordained interatomic distance. Remarkably, such a dissipative bonding is present even when the interactions among the atoms are purely repulsive. The dissipative bound states can be created and studied spectroscopically in present-day experiments with ultracold atoms or molecules and can potentially serve for cooling strongly interacting quantum gases.}, author = {Mikhail Lemeshko and Weimer, Hendrik}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Dissipative binding of atoms by non-conservative forces}}, doi = {10.1038/ncomms3230}, volume = {4}, year = {2013}, } @inproceedings{2210, abstract = {A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon. In this paper, we ask the reverse question: Given the straight skeleton (in form of a tree with a drawing in the plane, but with the exact position of the leaves unspecified), can we reconstruct the polygon? We show that in most cases there exists at most one polygon; in the remaining case there is an infinite number of polygons determined by one angle that can range in an interval. We can find this (set of) polygon(s) in linear time in the Real RAM computer model.}, author = {Biedl, Therese and Held, Martin and Huber, Stefan}, booktitle = {29th European Workshop on Computational Geometry}, location = {Braunschweig, Germany}, pages = {95 -- 98}, publisher = {TU Braunschweig}, title = {{Reconstructing polygons from embedded straight skeletons}}, year = {2013}, } @inproceedings{2237, abstract = {We describe new extensions of the Vampire theorem prover for computing tree interpolants. These extensions generalize Craig interpolation in Vampire, and can also be used to derive sequence interpolants. We evaluated our implementation on a large number of examples over the theory of linear integer arithmetic and integer-indexed arrays, with and without quantifiers. When compared to other methods, our experiments show that some examples could only be solved by our implementation.}, author = {Blanc, Régis and Gupta, Ashutosh and Kovács, Laura and Kragl, Bernhard}, location = {Stellenbosch, South Africa}, pages = {173 -- 181}, publisher = {Springer}, title = {{Tree interpolation in Vampire}}, doi = {10.1007/978-3-642-45221-5_13}, volume = {8312}, year = {2013}, } @inproceedings{2238, abstract = {We study the problem of achieving a given value in Markov decision processes (MDPs) with several independent discounted reward objectives. We consider a generalised version of discounted reward objectives, in which the amount of discounting depends on the states visited and on the objective. This definition extends the usual definition of discounted reward, and allows to capture the systems in which the value of different commodities diminish at different and variable rates. We establish results for two prominent subclasses of the problem, namely state-discount models where the discount factors are only dependent on the state of the MDP (and independent of the objective), and reward-discount models where they are only dependent on the objective (but not on the state of the MDP). For the state-discount models we use a straightforward reduction to expected total reward and show that the problem whether a value is achievable can be solved in polynomial time. For the reward-discount model we show that memory and randomisation of the strategies are required, but nevertheless that the problem is decidable and it is sufficient to consider strategies which after a certain number of steps behave in a memoryless way. For the general case, we show that when restricted to graphs (i.e. MDPs with no randomisation), pure strategies and discount factors of the form 1/n where n is an integer, the problem is in PSPACE and finite memory suffices for achieving a given value. We also show that when the discount factors are not of the form 1/n, the memory required by a strategy can be infinite. }, author = {Chatterjee, Krishnendu and Forejt, Vojtěch and Wojtczak, Dominik}, location = {Stellenbosch, South Africa}, pages = {228 -- 242}, publisher = {Springer}, title = {{Multi-objective discounted reward verification in graphs and MDPs}}, doi = {10.1007/978-3-642-45221-5_17}, volume = {8312}, year = {2013}, } @inproceedings{2243, abstract = {We show that modal logic over universally first-order definable classes of transitive frames is decidable. More precisely, let K be an arbitrary class of transitive Kripke frames definable by a universal first-order sentence. We show that the global and finite global satisfiability problems of modal logic over K are decidable in NP, regardless of choice of K. We also show that the local satisfiability and the finite local satisfiability problems of modal logic over K are decidable in NEXPTIME.}, author = {Michaliszyn, Jakub and Otop, Jan}, location = {Torino, Italy}, pages = {563 -- 577}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Elementary modal logics over transitive structures}}, doi = {10.4230/LIPIcs.CSL.2013.563}, volume = {23}, year = {2013}, } @inproceedings{2244, abstract = {We consider two systems (α1,...,αm) and (β1,...,βn) of curves drawn on a compact two-dimensional surface ℳ with boundary. Each αi and each βj is either an arc meeting the boundary of ℳ at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to "untangle" the βj from the αi by a self-homeomorphism of ℳ; more precisely, we seek an homeomorphism φ: ℳ → ℳ fixing the boundary of ℳ pointwise such that the total number of crossings of the αi with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if ℳ is planar, i.e., a sphere with h ≥ 0 boundary components ("holes"), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface ℳ with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. }, author = {Matoušek, Jiří and Sedgwick, Eric and Tancer, Martin and Wagner, Uli}, location = {Bordeaux, France}, pages = {472 -- 483}, publisher = {Springer}, title = {{Untangling two systems of noncrossing curves}}, doi = {10.1007/978-3-319-03841-4_41}, volume = {8242}, year = {2013}, } @inproceedings{2259, abstract = {The learning with rounding (LWR) problem, introduced by Banerjee, Peikert and Rosen at EUROCRYPT ’12, is a variant of learning with errors (LWE), where one replaces random errors with deterministic rounding. The LWR problem was shown to be as hard as LWE for a setting of parameters where the modulus and modulus-to-error ratio are super-polynomial. In this work we resolve the main open problem and give a new reduction that works for a larger range of parameters, allowing for a polynomial modulus and modulus-to-error ratio. In particular, a smaller modulus gives us greater efficiency, and a smaller modulus-to-error ratio gives us greater security, which now follows from the worst-case hardness of GapSVP with polynomial (rather than super-polynomial) approximation factors. As a tool in the reduction, we show that there is a “lossy mode” for the LWR problem, in which LWR samples only reveal partial information about the secret. This property gives us several interesting new applications, including a proof that LWR remains secure with weakly random secrets of sufficient min-entropy, and very simple constructions of deterministic encryption, lossy trapdoor functions and reusable extractors. Our approach is inspired by a technique of Goldwasser et al. from ICS ’10, which implicitly showed the existence of a “lossy mode” for LWE. By refining this technique, we also improve on the parameters of that work to only requiring a polynomial (instead of super-polynomial) modulus and modulus-to-error ratio. }, author = {Alwen, Joel F and Krenn, Stephan and Pietrzak, Krzysztof Z and Wichs, Daniel}, location = {Santa Barbara, CA, United States}, number = {1}, pages = {57 -- 74}, publisher = {Springer}, title = {{Learning with rounding, revisited: New reduction properties and applications}}, doi = {10.1007/978-3-642-40041-4_4}, volume = {8042}, year = {2013}, } @inproceedings{2258, abstract = {In a digital signature scheme with message recovery, rather than transmitting the message m and its signature σ, a single enhanced signature τ is transmitted. The verifier is able to recover m from τ and at the same time verify its authenticity. The two most important parameters of such a scheme are its security and overhead |τ| − |m|. A simple argument shows that for any scheme with “n bits security” |τ| − |m| ≥ n, i.e., the overhead is lower bounded by the security parameter n. Currently, the best known constructions in the random oracle model are far from this lower bound requiring an overhead of n + logq h , where q h is the number of queries to the random oracle. In this paper we give a construction which basically matches the n bit lower bound. We propose a simple digital signature scheme with n + o(logq h ) bits overhead, where q h denotes the number of random oracle queries. Our construction works in two steps. First, we propose a signature scheme with message recovery having optimal overhead in a new ideal model, the random invertible function model. Second, we show that a four-round Feistel network with random oracles as round functions is tightly “public-indifferentiable” from a random invertible function. At the core of our indifferentiability proof is an almost tight upper bound for the expected number of edges of the densest “small” subgraph of a random Cayley graph, which may be of independent interest. }, author = {Kiltz, Eike and Pietrzak, Krzysztof Z and Szegedy, Mario}, location = {Santa Barbara, CA, United States}, pages = {571 -- 588}, publisher = {Springer}, title = {{Digital signatures with minimal overhead from indifferentiable random invertible functions}}, doi = {10.1007/978-3-642-40041-4_31}, volume = {8042}, year = {2013}, } @article{2256, abstract = {Linked (Open) Data - bibliographic data on the Semantic Web. Report of the Working Group on Linked Data to the plenary assembly of the Austrian Library Network (translation of the title). Linked Data stands for a certain approach to publishing data on the Web. The underlying idea is to harmonise heterogeneous data sources of different origin in order to improve their accessibility and interoperability, effectively making them queryable as a big distributed database. This report summarises relevant developments in Europe as well as the Linked Data Working Group‘s strategic and technical considerations regarding the publishing of the Austrian Library Network’s (OBV’s) bibliographic datasets. It concludes with the mutual agreement that the implementation of Linked Data principles within the OBV can only be taken into consideration accompanied by a discussion about the provision of the datasets under a free license.}, author = {Danowski, Patrick and Goldfarb, Doron and Schaffner, Verena and Seidler, Wolfram}, journal = {VÖB Mitteilungen}, number = {3/4}, pages = {559 -- 587}, publisher = {Verein Österreichischer Bibliothekarinnen und Bibliothekare}, title = {{Linked (Open) Data - Bibliographische Daten im Semantic Web}}, volume = {66}, year = {2013}, } @inproceedings{2260, abstract = {Direct Anonymous Attestation (DAA) is one of the most complex cryptographic protocols deployed in practice. It allows an embedded secure processor known as a Trusted Platform Module (TPM) to attest to the configuration of its host computer without violating the owner’s privacy. DAA has been standardized by the Trusted Computing Group and ISO/IEC. The security of the DAA standard and all existing schemes is analyzed in the random-oracle model. We provide the first constructions of DAA in the standard model, that is, without relying on random oracles. Our constructions use new building blocks, including the first efficient signatures of knowledge in the standard model, which have many applications beyond DAA. }, author = {Bernhard, David and Fuchsbauer, Georg and Ghadafi, Essam}, location = {Banff, AB, Canada}, pages = {518 -- 533}, publisher = {Springer}, title = {{Efficient signatures of knowledge and DAA in the standard model}}, doi = {10.1007/978-3-642-38980-1_33}, volume = {7954}, year = {2013}, } @article{2264, abstract = {Faithful progression through the cell cycle is crucial to the maintenance and developmental potential of stem cells. Here, we demonstrate that neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs) employ a zinc-finger transcription factor specificity protein 2 (Sp2) as a cell cycle regulator in two temporally and spatially distinct progenitor domains. Differential conditional deletion of Sp2 in early embryonic cerebral cortical progenitors, and perinatal olfactory bulb progenitors disrupted transitions through G1, G2 and M phases, whereas DNA synthesis appeared intact. Cell-autonomous function of Sp2 was identified by deletion of Sp2 using mosaic analysis with double markers, which clearly established that conditional Sp2-null NSCs and NPCs are M phase arrested in vivo. Importantly, conditional deletion of Sp2 led to a decline in the generation of NPCs and neurons in the developing and postnatal brains. Our findings implicate Sp2-dependent mechanisms as novel regulators of cell cycle progression, the absence of which disrupts neurogenesis in the embryonic and postnatal brain.}, author = {Liang, Huixuan and Xiao, Guanxi and Yin, Haifeng and Hippenmeyer, Simon and Horowitz, Jonathan and Ghashghaei, Troy}, journal = {Development}, number = {3}, pages = {552 -- 561}, publisher = {Company of Biologists}, title = {{Neural development is dependent on the function of specificity protein 2 in cell cycle progression}}, doi = {10.1242/dev.085621}, volume = {140}, year = {2013}, } @article{2269, abstract = {This paper presents a parallel, implementation-friendly analytic visibility method for triangular meshes. Together with an analytic filter convolution, it allows for a fully analytic solution to anti-aliased 3D mesh rendering on parallel hardware. Building on recent works in computational geometry, we present a new edge-triangle intersection algorithm and a novel method to complete the boundaries of all visible triangle regions after a hidden line elimination step. All stages of the method are embarrassingly parallel and easily implementable on parallel hardware. A GPU implementation is discussed and performance characteristics of the method are shown and compared to traditional sampling-based rendering methods.}, author = {Thomas Auzinger and Wimmer, Michael and Stefan Jeschke}, journal = {Computer Graphics Forum}, number = {124}, pages = {409 -- 418}, publisher = {Wiley-Blackwell}, title = {{Analytic Visibility on the GPU}}, doi = {DOI: 10.1111/cgf.12061}, volume = {32}, year = {2013}, } @inproceedings{2270, abstract = {Representation languages for coalitional games are a key research area in algorithmic game theory. There is an inher- ent tradeoff between how general a language is, allowing it to capture more elaborate games, and how hard it is computationally to optimize and solve such games. One prominent such language is the simple yet expressive Weighted Graph Games (WGGs) representation (Deng and Papadimitriou 1994), which maintains knowledge about synergies between agents in the form of an edge weighted graph. We consider the problem of finding the optimal coalition structure in WGGs. The agents in such games are vertices in a graph, and the value of a coalition is the sum of the weights of the edges present between coalition members. The optimal coalition structure is a partition of the agents to coalitions, that maximizes the sum of utilities obtained by the coalitions. We show that finding the optimal coalition structure is not only hard for general graphs, but is also intractable for restricted families such as planar graphs which are amenable for many other combinatorial problems. We then provide algorithms with constant factor approximations for planar, minorfree and bounded degree graphs.}, author = {Bachrach, Yoram and Kohli, Pushmeet and Kolmogorov, Vladimir and Zadimoghaddam, Morteza}, location = {Bellevue, WA, United States}, pages = {81--87}, publisher = {AAAI Press}, title = {{Optimal Coalition Structures in Cooperative Graph Games}}, year = {2013}, } @techreport{2273, abstract = {We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. We present such a generalization for the case of higher-order graphical models, and test it on several real-world problems with promising results.}, author = {Vladimir Kolmogorov}, publisher = {IST Austria}, title = {{Reweighted message passing revisited}}, year = {2013}, } @article{2278, abstract = {It is firmly established that interactions between neurons and glia are fundamental across species for the correct establishment of a functional brain. Here, we found that the glia of the Drosophila larval brain display an essential non-autonomous role during the development of the optic lobe. The optic lobe develops from neuroepithelial cells that proliferate by dividing symmetrically until they switch to asymmetric/differentiative divisions that generate neuroblasts. The proneural gene lethal of scute (l9sc) is transiently activated by the epidermal growth factor receptor (EGFR)-Ras signal transduction pathway at the leading edge of a proneural wave that sweeps from medial to lateral neuroepithelium, promoting this switch. This process is tightly regulated by the tissue-autonomous function within the neuroepithelium of multiple signaling pathways, including EGFR-Ras and Notch. This study shows that the Notch ligand Serrate (Ser) is expressed in the glia and it forms a complex in vivo with Notch and Canoe, which colocalize at the adherens junctions of neuroepithelial cells. This complex is crucial for interactions between glia and neuroepithelial cells during optic lobe development. Ser is tissue-autonomously required in the glia where it activates Notch to regulate its proliferation, and non-autonomously in the neuroepithelium where Ser induces Notch signaling to avoid the premature activation of the EGFR-Ras pathway and hence of L9sc. Interestingly, different Notch activity reporters showed very different expression patterns in the glia and in the neuroepithelium, suggesting the existence of tissue-specific factors that promote the expression of particular Notch target genes or/and a reporter response dependent on different thresholds of Notch signaling.}, author = {Pérez Gómez, Raquel and Slovakova, Jana and Rives Quinto, Noemí and Krejčí, Alena and Carmena, Ana}, journal = {Journal of Cell Science}, number = {21}, pages = {4873 -- 4884}, publisher = {Company of Biologists}, title = {{A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development}}, doi = {10.1242/jcs.125617}, volume = {126}, year = {2013}, } @inproceedings{2276, abstract = {The problem of minimizing the Potts energy function frequently occurs in computer vision applications. One way to tackle this NP-hard problem was proposed by Kovtun [19, 20]. It identifies a part of an optimal solution by running k maxflow computations, where k is the number of labels. The number of “labeled” pixels can be significant in some applications, e.g. 50-93% in our tests for stereo. We show how to reduce the runtime to O (log k) maxflow computations (or one parametric maxflow computation). Furthermore, the output of our algorithm allows to speed-up the subsequent alpha expansion for the unlabeled part, or can be used as it is for time-critical applications. To derive our technique, we generalize the algorithm of Felzenszwalb et al. [7] for Tree Metrics . We also show a connection to k-submodular functions from combinatorial optimization, and discuss k-submodular relaxations for general energy functions.}, author = {Gridchyn, Igor and Kolmogorov, Vladimir}, location = {Sydney, Australia}, pages = {2320 -- 2327}, publisher = {IEEE}, title = {{Potts model, parametric maxflow and k-submodular functions}}, doi = {10.1109/ICCV.2013.288}, year = {2013}, } @article{2280, abstract = {The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application-chromosome organization in the human cell nucleus-is discussed briefly, and some illustrative results are presented.}, author = {Uhler, Caroline and Wright, Stephen}, journal = {SIAM Review}, number = {4}, pages = {671 -- 706}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Packing ellipsoids with overlap}}, doi = {10.1137/120872309}, volume = {55}, year = {2013}, } @article{2287, abstract = {Negative frequency-dependent selection should result in equal sex ratios in large populations of dioecious flowering plants, but deviations from equality are commonly reported. A variety of ecological and genetic factors can explain biased sex ratios, although the mechanisms involved are not well understood. Most dioecious species are long-lived and/or clonal complicating efforts to identify stages during the life cycle when biases develop. We investigated the demographic correlates of sex-ratio variation in two chromosome races of Rumex hastatulus, an annual, wind-pollinated colonizer of open habitats from the southern USA. We examined sex ratios in 46 populations and evaluated the hypothesis that the proximity of males in the local mating environment, through its influence on gametophytic selection, is the primary cause of female-biased sex ratios. Female-biased sex ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62), with significant female bias in 89% of populations. Large, high-density populations had the highest proportion of females, whereas smaller, low-density populations had sex ratios closer to equality. Progeny sex ratios were more female biased when males were in closer proximity to females, a result consistent with the gametophytic selection hypothesis. Our results suggest that interactions between demographic and genetic factors are probably the main cause of female-biased sex ratios in R. hastatulus. The annual life cycle of this species may limit the scope for selection against males and may account for the weaker degree of bias in comparison with perennial Rumex species.}, author = {Pickup, Melinda and Barrett, Spencer}, journal = {Ecology and Evolution}, number = {3}, pages = {629 -- 639}, publisher = {Wiley-Blackwell}, title = {{The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant}}, doi = {10.1002/ece3.465}, volume = {3}, year = {2013}, } @article{2282, abstract = {Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly.}, author = {Campinho, Pedro and Behrndt, Martin and Ranft, Jonas and Risler, Thomas and Minc, Nicolas and Heisenberg, Carl-Philipp J}, journal = {Nature Cell Biology}, pages = {1405 -- 1414}, publisher = {Nature Publishing Group}, title = {{Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly}}, doi = {10.1038/ncb2869}, volume = {15}, year = {2013}, } @article{2283, abstract = {Pathogens exert a strong selection pressure on organisms to evolve effective immune defences. In addition to individual immunity, social organisms can act cooperatively to produce collective defences. In many ant species, queens have the option to found a colony alone or in groups with other, often unrelated, conspecifics. These associations are transient, usually lasting only as long as each queen benefits from the presence of others. In fact, once the first workers emerge, queens fight to the death for dominance. One potential advantage of co-founding may be that queens benefit from collective disease defences, such as mutual grooming, that act against common soil pathogens. We test this hypothesis by exposing single and co-founding queens to a fungal parasite, in order to assess whether queens in co-founding associations have improved survival. Surprisingly, co-foundresses exposed to the entomopathogenic fungus Metarhizium did not engage in cooperative disease defences, and consequently, we find no direct benefit of multiple queens on survival. However, an indirect benefit was observed, with parasite-exposed queens producing more brood when they co-founded, than when they were alone. We suggest this is due to a trade-off between reproduction and immunity. Additionally, we report an extraordinary ability of the queens to tolerate an infection for long periods after parasite exposure. Our study suggests that there are no social immunity benefits for co-founding ant queens, but that in parasite-rich environments, the presence of additional queens may nevertheless improve the chances of colony founding success.}, author = {Pull, Christopher and Hughes, William and Brown, Markus}, journal = {Naturwissenschaften}, number = {12}, pages = {1125 -- 1136}, publisher = {Springer}, title = {{Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger }}, doi = {10.1007/s00114-013-1115-5}, volume = {100}, year = {2013}, } @article{2286, abstract = {The spatiotemporal control of cell divisions is a key factor in epithelial morphogenesis and patterning. Mao et al (2013) now describe how differential rates of proliferation within the Drosophila wing disc epithelium give rise to anisotropic tissue tension in peripheral/proximal regions of the disc. Such global tissue tension anisotropy in turn determines the orientation of cell divisions by controlling epithelial cell elongation.}, author = {Campinho, Pedro and Heisenberg, Carl-Philipp J}, journal = {EMBO Journal}, number = {21}, pages = {2783 -- 2784}, publisher = {Wiley-Blackwell}, title = {{The force and effect of cell proliferation}}, doi = {10.1038/emboj.2013.225}, volume = {32}, year = {2013}, } @article{2289, abstract = {Formal verification aims to improve the quality of software by detecting errors before they do harm. At the basis of formal verification is the logical notion of correctness, which purports to capture whether or not a program behaves as desired. We suggest that the boolean partition of software into correct and incorrect programs falls short of the practical need to assess the behavior of software in a more nuanced fashion against multiple criteria. We therefore propose to introduce quantitative fitness measures for programs, specifically for measuring the function, performance, and robustness of reactive programs such as concurrent processes. This article describes the goals of the ERC Advanced Investigator Project QUAREM. The project aims to build and evaluate a theory of quantitative fitness measures for reactive models. Such a theory must strive to obtain quantitative generalizations of the paradigms that have been success stories in qualitative reactive modeling, such as compositionality, property-preserving abstraction and abstraction refinement, model checking, and synthesis. The theory will be evaluated not only in the context of software and hardware engineering, but also in the context of systems biology. In particular, we will use the quantitative reactive models and fitness measures developed in this project for testing hypotheses about the mechanisms behind data from biological experiments.}, author = {Henzinger, Thomas A}, journal = {Computer Science Research and Development}, number = {4}, pages = {331 -- 344}, publisher = {Springer}, title = {{Quantitative reactive modeling and verification}}, doi = {10.1007/s00450-013-0251-7}, volume = {28}, year = {2013}, } @article{2290, abstract = {The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development.}, author = {Boutté, Yohann and Jonsson, Kristoffer and Mcfarlane, Heather and Johnson, Errin and Gendre, Delphine and Swarup, Ranjan and Friml, Jirí and Samuels, Lacey and Robert, Stéphanie and Bhalerao, Rishikesh}, journal = {PNAS}, number = {40}, pages = {16259 -- 16264}, publisher = {National Academy of Sciences}, title = {{ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation}}, doi = {10.1073/pnas.1309057110}, volume = {110}, 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}, } @proceedings{2292, abstract = {This book constitutes the thoroughly refereed conference proceedings of the 38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013, held in Klosterneuburg, Austria, in August 2013. The 67 revised full papers presented together with six invited talks were carefully selected from 191 submissions. Topics covered include algorithmic game theory, algorithmic learning theory, algorithms and data structures, automata, formal languages, bioinformatics, complexity, computational geometry, computer-assisted reasoning, concurrency theory, databases and knowledge-based systems, foundations of computing, logic in computer science, models of computation, semantics and verification of programs, and theoretical issues in artificial intelligence.}, editor = {Chatterjee, Krishnendu and Sgall, Jiri}, isbn = {978-3-642-40312-5}, location = {Klosterneuburg, Austria}, pages = {VI -- 854}, publisher = {Springer}, title = {{Mathematical Foundations of Computer Science 2013}}, doi = {10.1007/978-3-642-40313-2}, volume = {8087}, year = {2013}, } @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{2291, abstract = {Cryptographic access control promises to offer easily distributed trust and broader applicability, while reducing reliance on low-level online monitors. Traditional implementations of cryptographic access control rely on simple cryptographic primitives whereas recent endeavors employ primitives with richer functionality and security guarantees. Worryingly, few of the existing cryptographic access-control schemes come with precise guarantees, the gap between the policy specification and the implementation being analyzed only informally, if at all. In this paper we begin addressing this shortcoming. Unlike prior work that targeted ad-hoc policy specification, we look at the well-established Role-Based Access Control (RBAC) model, as used in a typical file system. In short, we provide a precise syntax for a computational version of RBAC, offer rigorous definitions for cryptographic policy enforcement of a large class of RBAC security policies, and demonstrate that an implementation based on attribute-based encryption meets our security notions. We view our main contribution as being at the conceptual level. Although we work with RBAC for concreteness, our general methodology could guide future research for uses of cryptography in other access-control models. }, author = {Ferrara, Anna and Fuchsbauer, Georg and Warinschi, Bogdan}, location = {New Orleans, LA, United States}, pages = {115 -- 129}, publisher = {IEEE}, title = {{Cryptographically enforced RBAC}}, doi = {10.1109/CSF.2013.15}, year = {2013}, } @proceedings{2288, abstract = {This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms.}, editor = {Gupta, Ashutosh and Henzinger, Thomas A}, isbn = {978-3-642-40707-9}, location = {Klosterneuburg, Austria}, publisher = {Springer}, title = {{Computational Methods in Systems Biology}}, doi = {10.1007/978-3-642-40708-6}, volume = {8130}, 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{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}, } @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}, isbn = { 978-3-11-027634-3}, issn = {2191-3587}, publisher = {De Gruyter}, title = {{(Open) Linked Data in Bibliotheken}}, doi = {10.1515/9783110278736}, volume = {50}, year = {2013}, } @inproceedings{2301, abstract = {We describe the design and implementation of P, a domain-specific language to write asynchronous event driven code. P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to "close" the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving. The P language is designed so that a P program can be checked for responsiveness-the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhan-dled events. The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P.}, author = {Desai, Ankush and Gupta, Vivek and Jackson, Ethan and Qadeer, Shaz and Rajamani, Sriram and Zufferey, Damien}, booktitle = {Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation}, location = {Seattle, WA, United States}, pages = {321 -- 331}, publisher = {ACM}, title = {{P: Safe asynchronous event-driven programming}}, doi = {10.1145/2491956.2462184}, 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}, } @article{2303, abstract = {MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools.}, author = {Hippenmeyer, Simon}, journal = {Frontiers in Biology}, number = {6}, pages = {557 -- 568}, publisher = {Springer}, title = {{Dissection of gene function at clonal level using mosaic analysis with double markers}}, doi = {10.1007/s11515-013-1279-6}, volume = {8}, year = {2013}, } @article{2304, abstract = {This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter.}, author = {Pausinger, Florian}, journal = {Electronic Notes in Discrete Mathematics}, pages = {43 -- 50}, publisher = {Elsevier}, title = {{Van der Corput sequences and linear permutations}}, doi = {10.1016/j.endm.2013.07.008}, volume = {43}, 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{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}, } @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{2406, 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. We prove that, in the Gross-Pitaevskii limit, Bose Einstein condensation takes place in the whole parameter range considered. 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 unit interval.}, author = {Robert Seiringer and Yngvason, Jakob and Zagrebnov, Valentin A}, journal = {European Physical Journal: Special Topics}, number = {1}, pages = {103 -- 107}, publisher = {Springer}, title = {{Condensation of interacting bosons in a random potential}}, doi = {10.1140/epjst/e2013-01759-5}, volume = {217}, 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{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}, } @inbook{2413, abstract = {Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness.}, author = {Valderrama, Mario and Botella Soler, Vicente and Le Van Quyen, Michel}, booktitle = {Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain}, editor = {Meyer, Misha and Pesenson, Z.}, isbn = {9783527411986 }, publisher = {Wiley-VCH}, title = {{Neuronal oscillations scale up and scale down the brain dynamics }}, doi = {10.1002/9783527671632.ch08}, 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}, } @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{2443, abstract = {The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.}, author = {Simon, Sibu and Kubeš, Martin and Baster, Pawel and Robert, Stéphanie and Dobrev, Petre and Friml, Jirí and Petrášek, Jan and Zažímalová, Eva}, journal = {New Phytologist}, number = {4}, pages = {1034 -- 1048}, publisher = {Wiley}, title = {{Defining the selectivity of processes along the auxin response chain: A study using auxin analogues}}, doi = {10.1111/nph.12437}, volume = {200}, 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{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}, } @article{2449, abstract = {Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. }, author = {Nodzyński, Tomasz and Feraru, Murguel and Hirsch, Sibylle and De Rycke, Riet and Nicuales, Claudiu and Van Leene, Jelle and De Jaeger, Geert and Vanneste, Steffen and Friml, Jirí}, journal = {Molecular Plant}, number = {6}, pages = {1849 -- 1862}, publisher = {Cell Press}, title = {{Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis}}, doi = {10.1093/mp/sst044}, volume = {6}, year = {2013}, } @article{2452, abstract = {Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.}, author = {Barbez, Elke and Laňková, Martina and Pařezová, Markéta and Maizel, Alexis and Zažímalová, Eva and Petrášek, Jan and Jirí Friml and Kleine-Vehn, Jürgen}, journal = {BMC Plant Biology}, number = {1}, publisher = {BioMed Central}, title = {{Single-cell-based system to monitor carrier driven cellular auxin homeostasis}}, doi = {10.1186/1471-2229-13-20}, volume = {13}, year = {2013}, } @article{2450, abstract = {Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interactions. Here we use experimentation and network construction to elucidate the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants such as polaris (pls), we show experimentally that expression of both PIN1 and PIN2 significantly increases. This relationship is analyzed in the context of the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin, ethylene and cytokinin concentration decreases, approximately remains unchanged and increases, respectively. Experimental data are integrated into a hormonal crosstalk network through combination with information in literature. Network construction reveals that the regulation of both PIN1 and PIN2 is predominantly via ethylene signaling. In addition, it is deduced that the relationship between cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition to its regulation to auxin, ethylene, and PLS levels. We discuss how the network of hormones and genes coordinates plant growth by simultaneously regulating the activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk, root development, auxin flux, PIN proteins, PLS protein, signaling network}, author = {Liu, Junli and Menhi, Saher and Topping, Jennifer and Jirí Friml and Lindsey, Keith}, journal = {Frontiers in Plant Science}, number = {75}, publisher = {Frontiers Research Foundation}, title = {{Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development}}, doi = {10.3389/fpls.2013.00075}, volume = {4}, 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{2457, author = {Viaene, Tom and Delwiche, Charles and Rensing, Stefan and Friml, Jirí}, journal = {Trends in Plant Science}, number = {1}, pages = {5 -- 10}, publisher = {Cell Press}, title = {{Origin and evolution of PIN auxin transporters in the green lineage}}, doi = {10.1016/j.tplants.2012.08.009}, volume = {18}, year = {2013}, } @article{246, abstract = {Given an intersection of two quadrics X Pm1, with m > 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i).}, author = {Timothy Browning and Munshi, Ritabrata}, journal = {Compositio Mathematica}, number = {9}, pages = {1457 -- 1494}, publisher = {Cambridge University Press}, title = {{Rational points on singular intersections of quadrics}}, doi = {10.1112/S0010437X13007185}, volume = {149}, 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{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{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{247, abstract = {An improved estimate is provided for the number of Fq-rational points on a geometrically irreducible, projective, cubic hypersurface that is not equal to a cone.}, author = {Timothy Browning}, journal = {Canadian Mathematical Bulletin}, number = {3}, pages = {500 -- 502}, publisher = {Unknown}, title = {{The Lang-Weil estimate for cubic hypersurfaces}}, doi = {10.4153/CMB-2011-177-4}, volume = {56}, 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{2478, abstract = {Despite the pivotal functions of the NMDA receptor (NMDAR) for neural circuit development and synaptic plasticity, the molecular mechanisms underlying the dynamics of NMDAR trafficking are poorly understood. The cell adhesion molecule neuroligin-1 (NL1) modifies NMDAR-dependent synaptic transmission and synaptic plasticity, but it is unclear whether NL1 controls synaptic accumulation or function of the receptors. Here, we provide evidence that NL1 regulates the abundance of NMDARs at postsynaptic sites. This function relies on extracellular, NL1 isoform-specific sequences that facilitate biochemical interactions between NL1 and the NMDAR GluN1 subunit. Our work uncovers NL1 isoform-specific cisinteractions with ionotropic glutamate receptors as a key mechanism for controlling synaptic properties.}, author = {Budreck, Elaine C and Kwon, Oh-Bin and Jung, Jung-Hoon and Baudouin, Stéphane J and Thommen, Albert and Kim, Hye-Sun and Fukazawa, Yugo and Harumi Harada and Tabuchi, Katsuhiko and Ryuichi Shigemoto and Scheiffele, Peter and Kim, Joung-Hun}, journal = {PNAS}, number = {2}, pages = {725 -- 730}, publisher = {National Academy of Sciences}, title = {{Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling}}, doi = {10.1073/pnas.1214718110}, volume = {110}, 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}, } @article{251, abstract = {We study the density of varieties in a certain family which do not satisfy the Hasse principle. This work relies on results recently obtained by Colliot-Thélène [3].}, author = {de la Bretèche, Régis and Timothy Browning}, journal = {Journal de Theorie des Nombres de Bordeaux}, number = {1}, pages = {25 -- 44}, publisher = {Universite de Bordeaux I}, title = {{Counter examples to the Hasse principle among certain coflasque tori}}, doi = {10.5802/jtnb.857}, volume = {26}, 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}, } @article{2516, abstract = {We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes.}, author = {Lampert, Christoph and Nickisch, Hannes and Harmeling, Stefan}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {3}, pages = {453 -- 465}, publisher = {IEEE}, title = {{Attribute-based classification for zero-shot learning of object categories}}, doi = {10.1109/TPAMI.2013.140}, volume = {36}, 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{253, author = {Timothy Browning}, journal = {Mathematika}, number = {1}, pages = {101 -- 107}, publisher = {Unknown}, title = {{Counting rational points on cubic hypersurfaces: Corrigendum}}, doi = {10.1112/S0025579313000132}, volume = {60}, year = {2013}, } @article{2692, abstract = {The group III metabotropic glutamate (mGlu) receptors mGlu7 and mGlu8 are receiving increased attention as potential novel therapeutic targets for anxiety disorders. The effects mediated by these receptors appear to result from a complex interplay of facilitatory and inhibitory actions at different brain sites in the anxiety/fear circuits. To better understand the effect of mGlu7 and mGlu8 receptors on extinction of contextual fear and their critical sites of action in the fear networks, we focused on the amygdala. Direct injection into the basolateral complex of the amygdala of the mGlu7 receptor agonist AMN082 facilitated extinction, whereas the mGlu8 receptor agonist (S)-3,4-DCPG sustained freezing during the extinction acquisition trial. We also determined at the ultrastructural level the synaptic distribution of these receptors in the basal nucleus (BA) and intercalated cell clusters (ITCs) of the amygdala. Both areas are thought to exert key roles in fear extinction. We demonstrate that mGlu7 and mGlu8 receptors are located in different presynaptic terminals forming both asymmetric and symmetric synapses, and that they preferentially target neurons expressing mGlu1α receptors mostly located around ITCs. In addition we show that mGlu7 and mGlu8 receptors were segregated to different inputs to a significant extent. In particular, mGlu7a receptors were primarily onto glutamatergic afferents arising from the BA or midline thalamic nuclei, but not the medial prefrontal cortex (mPFC), as revealed by combined anterograde tracing and pre-embedding electron microscopy. On the other hand, mGlu8a showed a more restricted distribution in the BA and appeared absent from thalamic, mPFC and intrinsic inputs. This segregation of mGlu7 and mGlu8 receptors in different neuronal pathways of the fear circuit might explain the distinct effects on fear extinction training observed with mGlu7 and mGlu8 receptor agonists.}, author = {Dobi, Alice and Sartori, Simone B and Busti, Daniela and Van Der Putten, Herman V and Singewald, Nicolas and Ryuichi Shigemoto and Ferraguti, Francesco}, journal = {Neuropharmacology}, pages = {274 -- 289}, publisher = {Elsevier}, title = {{Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice}}, doi = {10.1016/j.neuropharm.2012.05.025}, volume = {66}, year = {2013}, } @article{2691, abstract = {P/Q-type voltage-dependent calcium channels play key roles in transmitter release, integration of dendritic signals, generation of dendritic spikes, and gene expression. High intracellular calcium concentration transient produced by these channels is restricted to tens to hundreds of nanometers from the channels. Therefore, precise localization of these channels along the plasma membrane was long sought to decipher how each neuronal cell function is controlled. Here, we analyzed the distribution of Cav2.1 subunit of the P/Q-type channel using highly sensitive SDS-digested freeze-fracture replica labeling in the rat cerebellar Purkinje cells. The labeling efficiency was such that the number of immunogold particles in each parallel fiber active zone was comparable to that of functional channels calculated from previous reports. Two distinct patterns of Cav2.1 distribution, scattered and clustered, were found in Purkinje cells. The scattered Cav2.1 had a somatodendritic gradient with the density of immunogold particles increasing 2.5-fold from soma to distal dendrites. The other population with 74-fold higher density than the scattered particles was found within clusters of intramembrane particles on the P-face of soma and primary dendrites. Both populations of Cav2.1 were found as early as P3 and increased in the second postnatal week to a mature level. Using double immunogold labeling, we found that virtually all of the Cav2.1 clusters were colocalized with two types of calcium-activated potassium channels, BK and SK2, with the nearest neighbor distance of 40∼nm. Calcium nanodomain created by the opening of Cav2.1 channels likely activates the two channels that limit the extent of depolarization.}, author = {Indriati, Dwi Wahyu and Kamasawa, Naomi and Matsui, Ko and Meredith, Andrea L and Watanabe, Masahiko and Ryuichi Shigemoto}, journal = {Journal of Neuroscience}, number = {8}, pages = {3668 -- 3678}, publisher = {Society for Neuroscience}, title = {{Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels}}, doi = {10.1523/JNEUROSCI.2921-12.2013}, volume = {33}, year = {2013}, } @article{2690, abstract = {Establishing the spatiotemporal concentration profile of neurotransmitter following synaptic vesicular release is essential for our understanding of inter-neuronal communication. Such profile is a determinant of synaptic strength, short-term plasticity and inter-synaptic crosstalk. Synaptically released glutamate has been suggested to reach a few millimolar in concentration and last for <1 ms. The synaptic cleft is often conceived as a single concentration compartment, whereas a huge gradient likely exists. Modelling studies have attempted to describe this gradient, but two key parameters, the number of glutamate in a vesicle (NGlu) and its diffusion coefficient (DGlu) in the extracellular space, remained unresolved. To determine this profile, the rat calyx of Held synapse at postnatal day 12-16 was studied where diffusion of glutamate occurs two-dimensionally and where quantification of AMPA receptor distribution on individual postsynaptic specialization on medial nucleus of the trapezoid body principal cells is possible using SDS-digested freeze-fracture replica labelling. To assess the performance of these receptors as glutamate sensors, a kinetic model of the receptors was constructed from outside-out patch recordings. From here, we simulated synaptic responses and compared them with the EPSC recordings. Combinations of NGlu and DGlu with an optimum of 7000 and 0.3 μm2 ms-1 reproduced the data, suggesting slow diffusion. Further simulations showed that a single vesicle does not saturate the synaptic receptors, and that glutamate spillover does not affect the conductance amplitude at this synapse. Using the estimated profile, we also evaluated how the number of multiple vesicle releases at individual active zones affects the amplitude of postsynaptic signals.}, author = {Budisantoso, Timotheus and Harumi Harada and Kamasawa, Naomi and Fukazawa, Yugo and Ryuichi Shigemoto and Matsui, Ko}, journal = {Journal of Physiology}, number = {1}, pages = {219 -- 239}, publisher = {Wiley-Blackwell}, title = {{Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held}}, doi = {10.1113/jphysiol.2012.241398}, volume = {591}, year = {2013}, } @article{2693, abstract = {Inhibitory parvalbumin-containing interneurons (PVIs) control neuronal discharge and support the generation of theta- and gammafrequency oscillations in cortical networks. Fast GABAergic input onto PVIs is crucial for their synchronization and oscillatory entrainment, but the role of metabotropic GABAB receptors (GABABRs) in mediating slow presynaptic and postsynaptic inhibition remains unknown. In this study, we have combined high-resolution immunoelectron microscopy, whole-cell patch-clamp recording, and computational modeling to investigate the subcellular distribution and effects of GABABRs and their postsynaptic effector Kir3 channels in rat hippocampal PVIs. Pre-embedding immunogold labeling revealed that the receptors and channels localize at high levels to the extrasynaptic membrane of parvalbumin-immunoreactive dendrites. Immunoreactivity forGABABRs was also present at lower levels on PVI axon terminals. Whole-cell recordings further showed that synaptically released GABA in response to extracellular stimulation evokes large GABABR-mediated slow IPSCs in perisomatic-targeting (PT) PVIs, but only small or no currents in dendrite-targeting (DT) PVIs. In contrast, paired recordings demonstrated that GABABR activation results in presynaptic inhibition at the output synapses of both PT and DT PVIs, but more strongly in the latter. Finally, computational analysis indicated that GABAB IPSCs can phasically modulate the discharge of PT interneurons at theta frequencies. In summary, our results show that GABABRs differentially mediate slow presynaptic and postsynaptic inhibition in PVIs and can contribute to the dynamic modulation of their activity during oscillations. Furthermore, these data provide evidence for a compartment-specific molecular divergence of hippocampal PVI subtypes, suggesting that activation of GABABRs may shift the balance between perisomatic and dendritic inhibition.}, author = {Booker, Sam A and Gross, Anna and Althof, Daniel and Ryuichi Shigemoto and Bettler, Bernhard and Frotscher, Michael and Hearing, Matthew C and Wickman, Kevin D and Watanabe, Masahiko and Kulik, Ákos and Vida, Imre}, journal = {Journal of Neuroscience}, number = {18}, pages = {7961 -- 7974}, publisher = {Society for Neuroscience}, title = {{Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons}}, doi = {10.1523/JNEUROSCI.1186-12.2013}, volume = {33}, 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}, } @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}, } @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}, } @inproceedings{2719, abstract = {Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation.}, author = {Paixao, Tiago and Barton, Nicholas H}, booktitle = {Proceedings of the 15th annual conference on Genetic and evolutionary computation}, location = {Amsterdam, Netherlands}, pages = {845 -- 852}, publisher = {ACM}, title = {{A variance decomposition approach to the analysis of genetic algorithms}}, doi = {10.1145/2463372.2463470}, 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}, } @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{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}, } @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}, }