@inproceedings{1601, abstract = {We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata.}, author = {Babiak, Tomáš and Blahoudek, František and Duret Lutz, Alexandre and Klein, Joachim and Kretinsky, Jan and Mueller, Daniel and Parker, David and Strejček, Jan}, location = {San Francisco, CA, United States}, pages = {479 -- 486}, publisher = {Springer}, title = {{The Hanoi omega-automata format}}, doi = {10.1007/978-3-319-21690-4_31}, volume = {9206}, year = {2015}, } @inproceedings{1605, abstract = {Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model.}, author = {Bogomolov, Sergiy and Schilling, Christian and Bartocci, Ezio and Batt, Grégory and Kong, Hui and Grosu, Radu}, location = {Haifa, Israel}, pages = {19 -- 35}, publisher = {Springer}, title = {{Abstraction-based parameter synthesis for multiaffine systems}}, doi = {10.1007/978-3-319-26287-1_2}, volume = {9434}, year = {2015}, } @inproceedings{1609, abstract = {The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Vardi, Moshe}, booktitle = {42nd International Colloquium}, isbn = {978-3-662-47665-9}, location = {Kyoto, Japan}, pages = {108 -- 120}, publisher = {Springer Nature}, title = {{The complexity of synthesis from probabilistic components}}, doi = {10.1007/978-3-662-47666-6_9}, volume = {9135}, year = {2015}, } @article{1615, abstract = {Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches.}, author = {Hammer, Matthieu and Krueger Burg, Dilja and Tuffy, Liam and Cooper, Benjamin and Taschenberger, Holger and Goswami, Sarit and Ehrenreich, Hannelore and Jonas, Peter M and Varoqueaux, Frederique and Rhee, Jeong and Brose, Nils}, journal = {Cell Reports}, number = {3}, pages = {516 -- 523}, publisher = {Cell Press}, title = {{Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism}}, doi = {10.1016/j.celrep.2015.09.011}, volume = {13}, year = {2015}, } @article{1614, abstract = {GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. }, author = {Strüber, Michael and Jonas, Peter M and Bartos, Marlene}, journal = {PNAS}, number = {4}, pages = {1220 -- 1225}, publisher = {National Academy of Sciences}, title = {{Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells}}, doi = {10.1073/pnas.1412996112}, volume = {112}, year = {2015}, } @article{1611, abstract = {Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue.}, author = {Whitfield, Jason and Zhang, William and Herde, Michel and Clifton, Ben and Radziejewski, Johanna and Janovjak, Harald L and Henneberger, Christian and Jackson, Colin}, journal = {Protein Science}, number = {9}, pages = {1412 -- 1422}, publisher = {Wiley}, title = {{Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction}}, doi = {10.1002/pro.2721}, volume = {24}, year = {2015}, } @article{1624, abstract = {Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions.}, author = {Pavlogiannis, Andreas and Chatterjee, Krishnendu and Adlam, Ben and Nowak, Martin}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Cellular cooperation with shift updating and repulsion}}, doi = {10.1038/srep17147}, volume = {5}, year = {2015}, } @article{1623, abstract = {Background Photosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible. Results We present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells. Conclusions The workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology. }, author = {Hammar, Petter and Angermayr, Andreas and Sjostrom, Staffan and Van Der Meer, Josefin and Hellingwerf, Klaas and Hudson, Elton and Joensson, Hakaan}, journal = {Biotechnology for Biofuels}, number = {1}, publisher = {BioMed Central}, title = {{Single-cell screening of photosynthetic growth and lactate production by cyanobacteria}}, doi = {10.1186/s13068-015-0380-2}, volume = {8}, year = {2015}, } @inproceedings{1628, abstract = {We propose a method for fabricating deformable objects with spatially varying elasticity using 3D printing. Using a single, relatively stiff printer material, our method designs an assembly of smallscale microstructures that have the effect of a softer material at the object scale, with properties depending on the microstructure used in each part of the object. We build on work in the area of metamaterials, using numerical optimization to design tiled microstructures with desired properties, but with the key difference that our method designs families of related structures that can be interpolated to smoothly vary the material properties over a wide range. To create an object with spatially varying elastic properties, we tile the object's interior with microstructures drawn from these families, generating a different microstructure for each cell using an efficient algorithm to select compatible structures for neighboring cells. We show results computed for both 2D and 3D objects, validating several 2D and 3D printed structures using standard material tests as well as demonstrating various example applications.}, author = {Schumacher, Christian and Bickel, Bernd and Rys, Jan and Marschner, Steve and Daraio, Chiara and Gross, Markus}, location = {Los Angeles, CA, USA}, number = {4}, publisher = {ACM}, title = {{Microstructures to control elasticity in 3D printing}}, doi = {10.1145/2766926}, volume = {34}, year = {2015}, } @inproceedings{1634, abstract = {Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart.}, author = {Da, Fang and Batty, Christopher and Wojtan, Christopher J and Grinspun, Eitan}, location = {Los Angeles, CA, United States}, number = {4}, publisher = {ACM}, title = {{Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams}}, doi = {10.1145/2767003}, volume = {34}, year = {2015}, } @inproceedings{1636, abstract = {Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem that appears in many areas of Computer Science. It can be equivalently stated as computing a homomorphism R→ΓΓ between two relational structures, e.g. between two directed graphs. Analyzing its complexity has been a prominent research direction, especially for the fixed template CSPs where the right side ΓΓ is fixed and the left side R is unconstrained. Far fewer results are known for the hybrid setting that restricts both sides simultaneously. It assumes that R belongs to a certain class of relational structures (called a structural restriction in this paper). We study which structural restrictions are effective, i.e. there exists a fixed template ΓΓ (from a certain class of languages) for which the problem is tractable when R is restricted, and NP-hard otherwise. We provide a characterization for structural restrictions that are closed under inverse homomorphisms. The criterion is based on the chromatic number of a relational structure defined in this paper; it generalizes the standard chromatic number of a graph. As our main tool, we use the algebraic machinery developed for fixed template CSPs. To apply it to our case, we introduce a new construction called a “lifted language”. We also give a characterization for structural restrictions corresponding to minor-closed families of graphs, extend results to certain Valued CSPs (namely conservative valued languages), and state implications for (valued) CSPs with ordered variables and for the maximum weight independent set problem on some restricted families of graphs.}, author = {Kolmogorov, Vladimir and Rolinek, Michal and Takhanov, Rustem}, booktitle = {26th International Symposium}, isbn = {978-3-662-48970-3}, location = {Nagoya, Japan}, pages = {566 -- 577}, publisher = {Springer Nature}, title = {{Effectiveness of structural restrictions for hybrid CSPs}}, doi = {10.1007/978-3-662-48971-0_48}, volume = {9472}, year = {2015}, } @inproceedings{1632, abstract = {This paper presents a liquid simulation technique that enforces the incompressibility condition using a stream function solve instead of a pressure projection. Previous methods have used stream function techniques for the simulation of detailed single-phase flows, but a formulation for liquid simulation has proved elusive in part due to the free surface boundary conditions. In this paper, we introduce a stream function approach to liquid simulations with novel boundary conditions for free surfaces, solid obstacles, and solid-fluid coupling. Although our approach increases the dimension of the linear system necessary to enforce incompressibility, it provides interesting and surprising benefits. First, the resulting flow is guaranteed to be divergence-free regardless of the accuracy of the solve. Second, our free-surface boundary conditions guarantee divergence-free motion even in the un-simulated air phase, which enables two-phase flow simulation by only computing a single phase. We implemented this method using a variant of FLIP simulation which only samples particles within a narrow band of the liquid surface, and we illustrate the effectiveness of our method for detailed two-phase flow simulations with complex boundaries, detailed bubble interactions, and two-way solid-fluid coupling.}, author = {Ando, Ryoichi and Thuerey, Nils and Wojtan, Christopher J}, location = {Los Angeles, CA, USA}, number = {4}, publisher = {ACM}, title = {{A stream function solver for liquid simulations}}, doi = {10.1145/2766935}, volume = {34}, year = {2015}, } @inproceedings{1630, abstract = {We present a method to learn and propagate shape placements in 2D polygonal scenes from a few examples provided by a user. The placement of a shape is modeled as an oriented bounding box. Simple geometric relationships between this bounding box and nearby scene polygons define a feature set for the placement. The feature sets of all example placements are then used to learn a probabilistic model over all possible placements and scenes. With this model, we can generate a new set of placements with similar geometric relationships in any given scene. We introduce extensions that enable propagation and generation of shapes in 3D scenes, as well as the application of a learned modeling session to large scenes without additional user interaction. These concepts allow us to generate complex scenes with thousands of objects with relatively little user interaction.}, author = {Guerrero, Paul and Jeschke, Stefan and Wimmer, Michael and Wonka, Peter}, location = {Los Angeles, CA, United States}, number = {4}, publisher = {ACM}, title = {{Learning shape placements by example}}, doi = {10.1145/2766933}, volume = {34}, year = {2015}, } @article{1640, abstract = {Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.}, author = {Šimášková, Mária and O'Brien, José and Khan-Djamei, Mamoona and Van Noorden, Giel and Ötvös, Krisztina and Vieten, Anne and De Clercq, Inge and Van Haperen, Johanna and Cuesta, Candela and Hoyerová, Klára and Vanneste, Steffen and Marhavy, Peter and Wabnik, Krzysztof T and Van Breusegem, Frank and Nowack, Moritz and Murphy, Angus and Friml, Jiřĺ and Weijers, Dolf and Beeckman, Tom and Benková, Eva}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Cytokinin response factors regulate PIN-FORMED auxin transporters}}, doi = {10.1038/ncomms9717}, volume = {6}, year = {2015}, } @article{1642, abstract = {The Hanani-Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this result to clustered graphs with two disjoint clusters, and show that a straightforward extension to flat clustered graphs with three or more disjoint clusters is not possible. For general clustered graphs we show a variant of the Hanani-Tutte theorem in the case when each cluster induces a connected subgraph. Di Battista and Frati proved that clustered planarity of embedded clustered graphs whose every face is incident to at most five vertices can be tested in polynomial time. We give a new and short proof of this result, using the matroid intersection algorithm.}, author = {Fulek, Radoslav and Kynčl, Jan and Malinovič, Igor and Pálvölgyi, Dömötör}, issn = {1077-8926}, journal = {Electronic Journal of Combinatorics}, number = {4}, publisher = {Electronic Journal of Combinatorics}, title = {{Clustered planarity testing revisited}}, doi = {10.37236/5002}, volume = {22}, year = {2015}, } @article{1639, abstract = {In this paper the optimal transport and the metamorphosis perspectives are combined. For a pair of given input images geodesic paths in the space of images are defined as minimizers of a resulting path energy. To this end, the underlying Riemannian metric measures the rate of transport cost and the rate of viscous dissipation. Furthermore, the model is capable to deal with strongly varying image contrast and explicitly allows for sources and sinks in the transport equations which are incorporated in the metric related to the metamorphosis approach by Trouvé and Younes. In the non-viscous case with source term existence of geodesic paths is proven in the space of measures. The proposed model is explored on the range from merely optimal transport to strongly dissipative dynamics. For this model a robust and effective variational time discretization of geodesic paths is proposed. This requires to minimize a discrete path energy consisting of a sum of consecutive image matching functionals. These functionals are defined on corresponding pairs of intensity functions and on associated pairwise matching deformations. Existence of time discrete geodesics is demonstrated. Furthermore, a finite element implementation is proposed and applied to instructive test cases and to real images. In the non-viscous case this is compared to the algorithm proposed by Benamou and Brenier including a discretization of the source term. Finally, the model is generalized to define discrete weighted barycentres with applications to textures and objects.}, author = {Maas, Jan and Rumpf, Martin and Schönlieb, Carola and Simon, Stefan}, journal = {ESAIM: Mathematical Modelling and Numerical Analysis}, number = {6}, pages = {1745 -- 1769}, publisher = {EDP Sciences}, title = {{A generalized model for optimal transport of images including dissipation and density modulation}}, doi = {10.1051/m2an/2015043}, volume = {49}, year = {2015}, } @inproceedings{1646, abstract = {A pseudorandom function (PRF) is a keyed function F : K × X → Y where, for a random key k ∈ K, the function F(k, ·) is indistinguishable from a uniformly random function, given black-box access. A key-homomorphic PRF has the additional feature that for any keys k, k' and any input x, we have F(k+k', x) = F(k, x)⊕F(k', x) for some group operations +,⊕ on K and Y, respectively. A constrained PRF for a family of setsS ⊆ P(X) has the property that, given any key k and set S ∈ S, one can efficiently compute a “constrained” key kS that enables evaluation of F(k, x) on all inputs x ∈ S, while the values F(k, x) for x /∈ S remain pseudorandom even given kS. In this paper we construct PRFs that are simultaneously constrained and key homomorphic, where the homomorphic property holds even for constrained keys. We first show that the multilinear map-based bit-fixing and circuit-constrained PRFs of Boneh and Waters (Asiacrypt 2013) can be modified to also be keyhomomorphic. We then show that the LWE-based key-homomorphic PRFs of Banerjee and Peikert (Crypto 2014) are essentially already prefix-constrained PRFs, using a (non-obvious) definition of constrained keys and associated group operation. Moreover, the constrained keys themselves are pseudorandom, and the constraining and evaluation functions can all be computed in low depth. As an application of key-homomorphic constrained PRFs,we construct a proxy re-encryption schemewith fine-grained access control. This scheme allows storing encrypted data on an untrusted server, where each file can be encrypted relative to some attributes, so that only parties whose constrained keys match the attributes can decrypt. Moreover, the server can re-key (arbitrary subsets of) the ciphertexts without learning anything about the plaintexts, thus permitting efficient and finegrained revocation.}, author = {Banerjee, Abishek and Fuchsbauer, Georg and Peikert, Chris and Pietrzak, Krzysztof Z and Stevens, Sophie}, booktitle = {12th Theory of Cryptography Conference}, isbn = {978-3-662-46496-0}, location = {Warsaw, Poland}, pages = {31 -- 60}, publisher = {Springer Nature}, title = {{Key-homomorphic constrained pseudorandom functions}}, doi = {10.1007/978-3-662-46497-7_2}, volume = {9015}, year = {2015}, } @inproceedings{1648, abstract = {Generalized Selective Decryption (GSD), introduced by Panjwani [TCC’07], is a game for a symmetric encryption scheme Enc that captures the difficulty of proving adaptive security of certain protocols, most notably the Logical Key Hierarchy (LKH) multicast encryption protocol. In the GSD game there are n keys k1,..., kn, which the adversary may adaptively corrupt (learn); moreover, it can ask for encryptions Encki (kj) of keys under other keys. The adversary’s task is to distinguish keys (which it cannot trivially compute) from random. Proving the hardness of GSD assuming only IND-CPA security of Enc is surprisingly hard. Using “complexity leveraging” loses a factor exponential in n, which makes the proof practically meaningless. We can think of the GSD game as building a graph on n vertices, where we add an edge i → j when the adversary asks for an encryption of kj under ki. If restricted to graphs of depth ℓ, Panjwani gave a reduction that loses only a factor exponential in ℓ (not n). To date, this is the only non-trivial result known for GSD. In this paper we give almost-polynomial reductions for large classes of graphs. Most importantly, we prove the security of the GSD game restricted to trees losing only a quasi-polynomial factor n3 log n+5. Trees are an important special case capturing real-world protocols like the LKH protocol. Our new bound improves upon Panjwani’s on some LKH variants proposed in the literature where the underlying tree is not balanced. Our proof builds on ideas from the “nested hybrids” technique recently introduced by Fuchsbauer et al. [Asiacrypt’14] for proving the adaptive security of constrained PRFs.}, author = {Fuchsbauer, Georg and Jafargholi, Zahra and Pietrzak, Krzysztof Z}, location = {Santa Barbara, CA, USA}, pages = {601 -- 620}, publisher = {Springer}, title = {{A quasipolynomial reduction for generalized selective decryption on trees}}, doi = {10.1007/978-3-662-47989-6_29}, volume = {9215}, year = {2015}, } @inproceedings{1649, abstract = {We extend a commitment scheme based on the learning with errors over rings (RLWE) problem, and present efficient companion zeroknowledge proofs of knowledge. Our scheme maps elements from the ring (or equivalently, n elements from }, author = {Benhamouda, Fabrice and Krenn, Stephan and Lyubashevsky, Vadim and Pietrzak, Krzysztof Z}, location = {Vienna, Austria}, pages = {305 -- 325}, publisher = {Springer}, title = {{Efficient zero-knowledge proofs for commitments from learning with errors over rings}}, doi = {10.1007/978-3-319-24174-6_16}, volume = {9326}, year = {2015}, } @inproceedings{1644, abstract = {Increasing the computational complexity of evaluating a hash function, both for the honest users as well as for an adversary, is a useful technique employed for example in password-based cryptographic schemes to impede brute-force attacks, and also in so-called proofs of work (used in protocols like Bitcoin) to show that a certain amount of computation was performed by a legitimate user. A natural approach to adjust the complexity of a hash function is to iterate it c times, for some parameter c, in the hope that any query to the scheme requires c evaluations of the underlying hash function. However, results by Dodis et al. (Crypto 2012) imply that plain iteration falls short of achieving this goal, and designing schemes which provably have such a desirable property remained an open problem. This paper formalizes explicitly what it means for a given scheme to amplify the query complexity of a hash function. In the random oracle model, the goal of a secure query-complexity amplifier (QCA) scheme is captured as transforming, in the sense of indifferentiability, a random oracle allowing R queries (for the adversary) into one provably allowing only r < R queries. Turned around, this means that making r queries to the scheme requires at least R queries to the actual random oracle. Second, a new scheme, called collision-free iteration, is proposed and proven to achieve c-fold QCA for both the honest parties and the adversary, for any fixed parameter c.}, author = {Demay, Grégory and Gazi, Peter and Maurer, Ueli and Tackmann, Björn}, location = {Lugano, Switzerland}, pages = {159 -- 180}, publisher = {Springer}, title = {{Query-complexity amplification for random oracles}}, doi = {10.1007/978-3-319-17470-9_10}, volume = {9063}, year = {2015}, } @inproceedings{1647, abstract = {Round-optimal blind signatures are notoriously hard to construct in the standard model, especially in the malicious-signer model, where blindness must hold under adversarially chosen keys. This is substantiated by several impossibility results. The only construction that can be termed theoretically efficient, by Garg and Gupta (Eurocrypt’14), requires complexity leveraging, inducing an exponential security loss. We present a construction of practically efficient round-optimal blind signatures in the standard model. It is conceptually simple and builds on the recent structure-preserving signatures on equivalence classes (SPSEQ) from Asiacrypt’14. While the traditional notion of blindness follows from standard assumptions, we prove blindness under adversarially chosen keys under an interactive variant of DDH. However, we neither require non-uniform assumptions nor complexity leveraging. We then show how to extend our construction to partially blind signatures and to blind signatures on message vectors, which yield a construction of one-show anonymous credentials à la “anonymous credentials light” (CCS’13) in the standard model. Furthermore, we give the first SPS-EQ construction under noninteractive assumptions and show how SPS-EQ schemes imply conventional structure-preserving signatures, which allows us to apply optimality results for the latter to SPS-EQ.}, author = {Fuchsbauer, Georg and Hanser, Christian and Slamanig, Daniel}, location = {Santa Barbara, CA, United States}, pages = {233 -- 253}, publisher = {Springer}, title = {{Practical round-optimal blind signatures in the standard model}}, doi = {10.1007/978-3-662-48000-7_12}, volume = {9216}, year = {2015}, } @inproceedings{1654, abstract = {HMAC and its variant NMAC are the most popular approaches to deriving a MAC (and more generally, a PRF) from a cryptographic hash function. Despite nearly two decades of research, their exact security still remains far from understood in many different contexts. Indeed, recent works have re-surfaced interest for {\em generic} attacks, i.e., attacks that treat the compression function of the underlying hash function as a black box. Generic security can be proved in a model where the underlying compression function is modeled as a random function -- yet, to date, the question of proving tight, non-trivial bounds on the generic security of HMAC/NMAC even as a PRF remains a challenging open question. In this paper, we ask the question of whether a small modification to HMAC and NMAC can allow us to exactly characterize the security of the resulting constructions, while only incurring little penalty with respect to efficiency. To this end, we present simple variants of NMAC and HMAC, for which we prove tight bounds on the generic PRF security, expressed in terms of numbers of construction and compression function queries necessary to break the construction. All of our constructions are obtained via a (near) {\em black-box} modification of NMAC and HMAC, which can be interpreted as an initial step of key-dependent message pre-processing. While our focus is on PRF security, a further attractive feature of our new constructions is that they clearly defeat all recent generic attacks against properties such as state recovery and universal forgery. These exploit properties of the so-called ``functional graph'' which are not directly accessible in our new constructions. }, author = {Gazi, Peter and Pietrzak, Krzysztof Z and Tessaro, Stefano}, location = {Auckland, New Zealand}, pages = {85 -- 109}, publisher = {Springer}, title = {{Generic security of NMAC and HMAC with input whitening}}, doi = {10.1007/978-3-662-48800-3_4}, volume = {9453}, year = {2015}, } @inproceedings{1650, abstract = {We consider the task of deriving a key with high HILL entropy (i.e., being computationally indistinguishable from a key with high min-entropy) from an unpredictable source. Previous to this work, the only known way to transform unpredictability into a key that was ϵ indistinguishable from having min-entropy was via pseudorandomness, for example by Goldreich-Levin (GL) hardcore bits. This approach has the inherent limitation that from a source with k bits of unpredictability entropy one can derive a key of length (and thus HILL entropy) at most k−2log(1/ϵ) bits. In many settings, e.g. when dealing with biometric data, such a 2log(1/ϵ) bit entropy loss in not an option. Our main technical contribution is a theorem that states that in the high entropy regime, unpredictability implies HILL entropy. Concretely, any variable K with |K|−d bits of unpredictability entropy has the same amount of so called metric entropy (against real-valued, deterministic distinguishers), which is known to imply the same amount of HILL entropy. The loss in circuit size in this argument is exponential in the entropy gap d, and thus this result only applies for small d (i.e., where the size of distinguishers considered is exponential in d). To overcome the above restriction, we investigate if it’s possible to first “condense” unpredictability entropy and make the entropy gap small. We show that any source with k bits of unpredictability can be condensed into a source of length k with k−3 bits of unpredictability entropy. Our condenser simply “abuses" the GL construction and derives a k bit key from a source with k bits of unpredicatibily. The original GL theorem implies nothing when extracting that many bits, but we show that in this regime, GL still behaves like a “condenser" for unpredictability. This result comes with two caveats (1) the loss in circuit size is exponential in k and (2) we require that the source we start with has no HILL entropy (equivalently, one can efficiently check if a guess is correct). We leave it as an intriguing open problem to overcome these restrictions or to prove they’re inherent.}, author = {Skórski, Maciej and Golovnev, Alexander and Pietrzak, Krzysztof Z}, location = {Kyoto, Japan}, pages = {1046 -- 1057}, publisher = {Springer}, title = {{Condensed unpredictability }}, doi = {10.1007/978-3-662-47672-7_85}, volume = {9134}, year = {2015}, } @inproceedings{1651, abstract = {Cryptographic e-cash allows off-line electronic transactions between a bank, users and merchants in a secure and anonymous fashion. A plethora of e-cash constructions has been proposed in the literature; however, these traditional e-cash schemes only allow coins to be transferred once between users and merchants. Ideally, we would like users to be able to transfer coins between each other multiple times before deposit, as happens with physical cash. “Transferable” e-cash schemes are the solution to this problem. Unfortunately, the currently proposed schemes are either completely impractical or do not achieve the desirable anonymity properties without compromises, such as assuming the existence of a trusted “judge” who can trace all coins and users in the system. This paper presents the first efficient and fully anonymous transferable e-cash scheme without any trusted third parties. We start by revising the security and anonymity properties of transferable e-cash to capture issues that were previously overlooked. For our construction we use the recently proposed malleable signatures by Chase et al. to allow the secure and anonymous transfer of coins, combined with a new efficient double-spending detection mechanism. Finally, we discuss an instantiation of our construction.}, author = {Baldimtsi, Foteini and Chase, Melissa and Fuchsbauer, Georg and Kohlweiss, Markulf}, booktitle = {Public-Key Cryptography - PKC 2015}, isbn = {978-3-662-46446-5}, location = {Gaithersburg, MD, United States}, pages = {101 -- 124}, publisher = {Springer}, title = {{Anonymous transferable e-cash}}, doi = {10.1007/978-3-662-46447-2_5}, volume = {9020}, year = {2015}, } @inproceedings{1652, abstract = {We develop new theoretical tools for proving lower-bounds on the (amortized) complexity of certain functions in models of parallel computation. We apply the tools to construct a class of functions with high amortized memory complexity in the parallel Random Oracle Model (pROM); a variant of the standard ROM allowing for batches of simultaneous queries. In particular we obtain a new, more robust, type of Memory-Hard Functions (MHF); a security primitive which has recently been gaining acceptance in practice as an effective means of countering brute-force attacks on security relevant functions. Along the way we also demonstrate an important shortcoming of previous definitions of MHFs and give a new definition addressing the problem. The tools we develop represent an adaptation of the powerful pebbling paradigm (initially introduced by Hewitt and Paterson [HP70] and Cook [Coo73]) to a simple and intuitive parallel setting. We define a simple pebbling game Gp over graphs which aims to abstract parallel computation in an intuitive way. As a conceptual contribution we define a measure of pebbling complexity for graphs called cumulative complexity (CC) and show how it overcomes a crucial shortcoming (in the parallel setting) exhibited by more traditional complexity measures used in the past. As a main technical contribution we give an explicit construction of a constant in-degree family of graphs whose CC in Gp approaches maximality to within a polylogarithmic factor for any graph of equal size (analogous to the graphs of Tarjan et. al. [PTC76, LT82] for sequential pebbling games). Finally, for a given graph G and related function fG, we derive a lower-bound on the amortized memory complexity of fG in the pROM in terms of the CC of G in the game Gp.}, author = {Alwen, Joel F and Serbinenko, Vladimir}, booktitle = {Proceedings of the 47th annual ACM symposium on Theory of computing}, location = {Portland, OR, United States}, pages = {595 -- 603}, publisher = {ACM}, title = {{High parallel complexity graphs and memory-hard functions}}, doi = {10.1145/2746539.2746622}, year = {2015}, } @inproceedings{1660, abstract = {We study the pattern frequency vector for runs in probabilistic Vector Addition Systems with States (pVASS). Intuitively, each configuration of a given pVASS is assigned one of finitely many patterns, and every run can thus be seen as an infinite sequence of these patterns. The pattern frequency vector assigns to each run the limit of pattern frequencies computed for longer and longer prefixes of the run. If the limit does not exist, then the vector is undefined. We show that for one-counter pVASS, the pattern frequency vector is defined and takes one of finitely many values for almost all runs. Further, these values and their associated probabilities can be approximated up to an arbitrarily small relative error in polynomial time. For stable two-counter pVASS, we show the same result, but we do not provide any upper complexity bound. As a byproduct of our study, we discover counterexamples falsifying some classical results about stochastic Petri nets published in the 80s.}, author = {Brázdil, Tomáš and Kiefer, Stefan and Kučera, Antonín and Novotny, Petr}, location = {Kyoto, Japan}, pages = {44 -- 55}, publisher = {IEEE}, title = {{Long-run average behaviour of probabilistic vector addition systems}}, doi = {10.1109/LICS.2015.15}, year = {2015}, } @article{1665, abstract = {Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome.}, author = {Landau, Dan and Tausch, Eugen and Taylor Weiner, Amaro and Stewart, Chip and Reiter, Johannes and Bahlo, Jasmin and Kluth, Sandra and Božić, Ivana and Lawrence, Michael and Böttcher, Sebastian and Carter, Scott and Cibulskis, Kristian and Mertens, Daniel and Sougnez, Carrie and Rosenberg, Mara and Hess, Julian and Edelmann, Jennifer and Kless, Sabrina and Kneba, Michael and Ritgen, Matthias and Fink, Anna and Fischer, Kirsten and Gabriel, Stacey and Lander, Eric and Nowak, Martin and Döhner, Hartmut and Hallek, Michael and Neuberg, Donna and Getz, Gad and Stilgenbauer, Stephan and Wu, Catherine}, journal = {Nature}, number = {7574}, pages = {525 -- 530}, publisher = {Nature Publishing Group}, title = {{Mutations driving CLL and their evolution in progression and relapse}}, doi = {10.1038/nature15395}, volume = {526}, year = {2015}, } @inproceedings{1667, abstract = {We consider parametric version of fixed-delay continuoustime Markov chains (or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay transitions are specified by parameters, rather than concrete values. Our goal is to synthesize values of these parameters that, for a given cost function, minimise expected total cost incurred before reaching a given set of target states. We show that under mild assumptions, optimal values of parameters can be effectively approximated using translation to a Markov decision process (MDP) whose actions correspond to discretized values of these parameters. To this end we identify and overcome several interesting phenomena arising in systems with fixed delays.}, author = {Brázdil, Tomáš and Korenčiak, L'Uboš and Krčál, Jan and Novotny, Petr and Řehák, Vojtěch}, location = {Madrid, Spain}, pages = {141 -- 159}, publisher = {Springer}, title = {{Optimizing performance of continuous-time stochastic systems using timeout synthesis}}, doi = {10.1007/978-3-319-22264-6_10}, volume = {9259}, year = {2015}, } @article{1664, abstract = {Over a century of research into the origin of turbulence in wall-bounded shear flows has resulted in a puzzling picture in which turbulence appears in a variety of different states competing with laminar background flow. At moderate flow speeds, turbulence is confined to localized patches; it is only at higher speeds that the entire flow becomes turbulent. The origin of the different states encountered during this transition, the front dynamics of the turbulent regions and the transformation to full turbulence have yet to be explained. By combining experiments, theory and computer simulations, here we uncover a bifurcation scenario that explains the transformation to fully turbulent pipe flow and describe the front dynamics of the different states encountered in the process. Key to resolving this problem is the interpretation of the flow as a bistable system with nonlinear propagation (advection) of turbulent fronts. These findings bridge the gap between our understanding of the onset of turbulence and fully turbulent flows.}, author = {Barkley, Dwight and Song, Baofang and Vasudevan, Mukund and Lemoult, Grégoire M and Avila, Marc and Hof, Björn}, journal = {Nature}, number = {7574}, pages = {550 -- 553}, publisher = {Nature Publishing Group}, title = {{The rise of fully turbulent flow}}, doi = {10.1038/nature15701}, volume = {526}, year = {2015}, } @inproceedings{1672, abstract = {Composable notions of incoercibility aim to forbid a coercer from using anything beyond the coerced parties’ inputs and outputs to catch them when they try to deceive him. Existing definitions are restricted to weak coercion types, and/or are not universally composable. Furthermore, they often make too strong assumptions on the knowledge of coerced parties—e.g., they assume they known the identities and/or the strategies of other coerced parties, or those of corrupted parties— which makes them unsuitable for applications of incoercibility such as e-voting, where colluding adversarial parties may attempt to coerce honest voters, e.g., by offering them money for a promised vote, and use their own view to check that the voter keeps his end of the bargain. In this work we put forward the first universally composable notion of incoercible multi-party computation, which satisfies the above intuition and does not assume collusions among coerced parties or knowledge of the corrupted set. We define natural notions of UC incoercibility corresponding to standard coercion-types, i.e., receipt-freeness and resistance to full-active coercion. Importantly, our suggested notion has the unique property that it builds on top of the well studied UC framework by Canetti instead of modifying it. This guarantees backwards compatibility, and allows us to inherit results from the rich UC literature. We then present MPC protocols which realize our notions of UC incoercibility given access to an arguably minimal setup—namely honestly generate tamper-proof hardware performing a very simple cryptographic operation—e.g., a smart card. This is, to our knowledge, the first proposed construction of an MPC protocol (for more than two parties) that is incoercibly secure and universally composable, and therefore the first construction of a universally composable receipt-free e-voting protocol.}, author = {Alwen, Joel F and Ostrovsky, Rafail and Zhou, Hongsheng and Zikas, Vassilis}, booktitle = {Advances in Cryptology - CRYPTO 2015}, isbn = {978-3-662-47999-5}, location = {Santa Barbara, CA, United States}, pages = {763 -- 780}, publisher = {Springer}, title = {{Incoercible multi-party computation and universally composable receipt-free voting}}, doi = {10.1007/978-3-662-48000-7_37}, volume = {9216}, year = {2015}, } @inproceedings{1669, abstract = {Computational notions of entropy (a.k.a. pseudoentropy) have found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The most important tools to argue about pseudoentropy are chain rules, which quantify by how much (in terms of quantity and quality) the pseudoentropy of a given random variable X decreases when conditioned on some other variable Z (think for example of X as a secret key and Z as information leaked by a side-channel). In this paper we give a very simple and modular proof of the chain rule for HILL pseudoentropy, improving best known parameters. Our version allows for increasing the acceptable length of leakage in applications up to a constant factor compared to the best previous bounds. As a contribution of independent interest, we provide a comprehensive study of all known versions of the chain rule, comparing their worst-case strength and limitations.}, author = {Pietrzak, Krzysztof Z and Skórski, Maciej}, location = {Guadalajara, Mexico}, pages = {81 -- 98}, publisher = {Springer}, title = {{The chain rule for HILL pseudoentropy, revisited}}, doi = {10.1007/978-3-319-22174-8_5}, volume = {9230}, year = {2015}, } @inproceedings{1671, abstract = {This paper studies the concrete security of PRFs and MACs obtained by keying hash functions based on the sponge paradigm. One such hash function is KECCAK, selected as NIST’s new SHA-3 standard. In contrast to other approaches like HMAC, the exact security of keyed sponges is not well understood. Indeed, recent security analyses delivered concrete security bounds which are far from existing attacks. This paper aims to close this gap. We prove (nearly) exact bounds on the concrete PRF security of keyed sponges using a random permutation. These bounds are tight for the most relevant ranges of parameters, i.e., for messages of length (roughly) l ≤ min{2n/4, 2r} blocks, where n is the state size and r is the desired output length; and for l ≤ q queries (to the construction or the underlying permutation). Moreover, we also improve standard-model bounds. As an intermediate step of independent interest, we prove tight bounds on the PRF security of the truncated CBC-MAC construction, which operates as plain CBC-MAC, but only returns a prefix of the output.}, author = {Gazi, Peter and Pietrzak, Krzysztof Z and Tessaro, Stefano}, location = {Santa Barbara, CA, United States}, pages = {368 -- 387}, publisher = {Springer}, title = {{The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC}}, doi = {10.1007/978-3-662-47989-6_18}, volume = {9215}, year = {2015}, } @article{1673, abstract = {When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement-that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two. }, author = {Adlam, Ben and Chatterjee, Krishnendu and Nowak, Martin}, journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences}, number = {2181}, publisher = {Royal Society of London}, title = {{Amplifiers of selection}}, doi = {10.1098/rspa.2015.0114}, volume = {471}, year = {2015}, } @inproceedings{1668, abstract = {We revisit the security (as a pseudorandom permutation) of cascading-based constructions for block-cipher key-length extension. Previous works typically considered the extreme case where the adversary is given the entire codebook of the construction, the only complexity measure being the number qe of queries to the underlying ideal block cipher, representing adversary’s secret-key-independent computation. Here, we initiate a systematic study of the more natural case of an adversary restricted to adaptively learning a number qc of plaintext/ciphertext pairs that is less than the entire codebook. For any such qc, we aim to determine the highest number of block-cipher queries qe the adversary can issue without being able to successfully distinguish the construction (under a secret key) from a random permutation. More concretely, we show the following results for key-length extension schemes using a block cipher with n-bit blocks and κ-bit keys: Plain cascades of length ℓ=2r+1 are secure whenever qcqre≪2r(κ+n), qc≪2κ and qe≪22κ. The bound for r=1 also applies to two-key triple encryption (as used within Triple DES). The r-round XOR-cascade is secure as long as qcqre≪2r(κ+n), matching an attack by Gaži (CRYPTO 2013). We fully characterize the security of Gaži and Tessaro’s two-call }, author = {Gazi, Peter and Lee, Jooyoung and Seurin, Yannick and Steinberger, John and Tessaro, Stefano}, location = {Istanbul, Turkey}, pages = {319 -- 341}, publisher = {Springer}, title = {{Relaxing full-codebook security: A refined analysis of key-length extension schemes}}, doi = {10.1007/978-3-662-48116-5_16}, volume = {9054}, year = {2015}, } @article{1674, abstract = {We consider N × N random matrices of the form H = W + V where W is a real symmetric Wigner matrix and V a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W and we choose V so that the eigenvalues of W and V are typically of the same order. For a large class of diagonal matrices V, we show that the rescaled distribution of the extremal eigenvalues is given by the Tracy-Widom distribution F1 in the limit of large N. Our proofs also apply to the complex Hermitian setting, i.e. when W is a complex Hermitian Wigner matrix.}, author = {Lee, Jioon and Schnelli, Kevin}, journal = {Reviews in Mathematical Physics}, number = {8}, publisher = {World Scientific Publishing}, title = {{Edge universality for deformed Wigner matrices}}, doi = {10.1142/S0129055X1550018X}, volume = {27}, year = {2015}, } @article{1679, author = {Lemoult, Grégoire M and Maier, Philipp and Hof, Björn}, journal = {Physics of Fluids}, number = {9}, publisher = {American Institute of Physics}, title = {{Taylor's Forest}}, doi = {10.1063/1.4930850}, volume = {27}, year = {2015}, } @article{1684, abstract = {Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa.}, author = {Vicoso, Beatriz and Bachtrog, Doris}, journal = {PLoS Biology}, number = {4}, publisher = {Public Library of Science}, title = {{Numerous transitions of sex chromosomes in Diptera}}, doi = {10.1371/journal.pbio.1002078}, volume = {13}, year = {2015}, } @article{1687, abstract = {Guided cell movement is essential for development and integrity of animals and crucially involved in cellular immune responses. Leukocytes are professional migratory cells that can navigate through most types of tissues and sense a wide range of directional cues. The responses of these cells to attractants have been mainly explored in tissue culture settings. How leukocytes make directional decisions in situ, within the challenging environment of a tissue maze, is less understood. Here we review recent advances in how leukocytes sense chemical cues in complex tissue settings and make links with paradigms of directed migration in development and Dictyostelium discoideum amoebae.}, author = {Sarris, Milka and Sixt, Michael K}, journal = {Current Opinion in Cell Biology}, number = {10}, pages = {93 -- 102}, publisher = {Elsevier}, title = {{Navigating in tissue mazes: Chemoattractant interpretation in complex environments}}, doi = {10.1016/j.ceb.2015.08.001}, volume = {36}, year = {2015}, } @inproceedings{1685, abstract = {Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3. Our techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest.}, author = {Cohen Addad, Vincent and De Mesmay, Arnaud N}, location = {Patras, Greece}, pages = {386 -- 398}, publisher = {Springer}, title = {{A fixed parameter tractable approximation scheme for the optimal cut graph of a surface}}, doi = {10.1007/978-3-662-48350-3_33}, volume = {9294}, year = {2015}, } @article{1688, abstract = {We estimate the selection constant in the following geometric selection theorem by Pach: For every positive integer d, there is a constant (Formula presented.) such that whenever (Formula presented.) are n-element subsets of (Formula presented.), we can find a point (Formula presented.) and subsets (Formula presented.) for every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices determined by (Formula presented.) simplices with one vertex in each Yi. We show a super-exponentially decreasing upper bound (Formula presented.). The ideas used in the proof of the upper bound also help us to prove Pach’s theorem with (Formula presented.), which is a lower bound doubly exponentially decreasing in d (up to some polynomial in the exponent). For comparison, Pach’s original approach yields a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem with (Formula presented.). In our construction for the upper bound, we use the fact that the minimum solid angle of every d-simplex is super-exponentially small. This fact was previously unknown and might be of independent interest. For the lower bound, we improve the ‘separation’ part of the argument by showing that in one of the key steps only d+1 separations are necessary, compared to 2d separations in the original proof. We also provide a measure version of Pach’s theorem.}, author = {Karasev, Roman and Kynčl, Jan and Paták, Pavel and Patakova, Zuzana and Tancer, Martin}, journal = {Discrete & Computational Geometry}, number = {3}, pages = {610 -- 636}, publisher = {Springer}, title = {{Bounds for Pach's selection theorem and for the minimum solid angle in a simplex}}, doi = {10.1007/s00454-015-9720-z}, volume = {54}, year = {2015}, } @article{1682, abstract = {We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f:K→ ℝn on a finite simplicial complex K and α > 0, it holds that each function g: K → ℝn such that ||g - f || ∞ < α, has a root in K. Via a reduction to the extension problem of maps into a sphere, we particularly show that this problem is decidable in polynomial time for every fixed n, assuming dimK ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction, we prove that the problem is undecidable when dim K > 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is simplexwise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings.}, author = {Franek, Peter and Krcál, Marek}, journal = {Journal of the ACM}, number = {4}, publisher = {ACM}, title = {{Robust satisfiability of systems of equations}}, doi = {10.1145/2751524}, volume = {62}, year = {2015}, } @article{1693, abstract = {Quantum interference between energetically close states is theoretically investigated, with the state structure being observed via laser spectroscopy. In this work, we focus on hyperfine states of selected hydrogenic muonic isotopes, and on how quantum interference affects the measured Lamb shift. The process of photon excitation and subsequent photon decay is implemented within the framework of nonrelativistic second-order perturbation theory. Due to its experimental interest, calculations are performed for muonic hydrogen, deuterium, and helium-3. We restrict our analysis to the case of photon scattering by incident linear polarized photons and the polarization of the scattered photons not being observed. We conclude that while quantum interference effects can be safely neglected in muonic hydrogen and helium-3, in the case of muonic deuterium there are resonances with close proximity, where quantum interference effects can induce shifts up to a few percent of the linewidth, assuming a pointlike detector. However, by taking into account the geometry of the setup used by the CREMA collaboration, this effect is reduced to less than 0.2% of the linewidth in all possible cases, which makes it irrelevant at the present level of accuracy. © 2015 American Physical Society.}, author = {Amaro, Pedro and Franke, Beatrice and Krauth, Julian and Diepold, Marc and Fratini, Filippo and Safari, Laleh and Machado, Jorge and Antognini, Aldo and Kottmann, Franz and Indelicato, Paul and Pohl, Randolf and Santos, José}, journal = {Physical Review A}, number = {2}, publisher = {American Physical Society}, title = {{Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3}}, doi = {10.1103/PhysRevA.92.022514}, volume = {92}, year = {2015}, } @article{1695, abstract = {We give a comprehensive introduction into a diagrammatic method that allows for the evaluation of Gutzwiller wave functions in finite spatial dimensions. We discuss in detail some numerical schemes that turned out to be useful in the real-space evaluation of the diagrams. The method is applied to the problem of d-wave superconductivity in a two-dimensional single-band Hubbard model. Here, we discuss in particular the role of long-range contributions in our diagrammatic expansion. We further reconsider our previous analysis on the kinetic energy gain in the superconducting state.}, author = {Kaczmarczyk, Jan and Schickling, Tobias and Bünemann, Jörg}, journal = {Physica Status Solidi (B): Basic Solid State Physics}, number = {9}, pages = {2059 -- 2071}, publisher = {Wiley}, title = {{Evaluation techniques for Gutzwiller wave functions in finite dimensions}}, doi = {10.1002/pssb.201552082}, volume = {252}, year = {2015}, } @article{1697, abstract = {Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits.}, author = {Marre, Olivier and Botella Soler, Vicente and Simmons, Kristina and Mora, Thierry and Tkacik, Gasper and Berry, Michael}, journal = {PLoS Computational Biology}, number = {7}, publisher = {Public Library of Science}, title = {{High accuracy decoding of dynamical motion from a large retinal population}}, doi = {10.1371/journal.pcbi.1004304}, volume = {11}, year = {2015}, } @article{1699, abstract = {By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.}, author = {Uecker, Hildegard and Setter, Derek and Hermisson, Joachim}, journal = {Journal of Mathematical Biology}, number = {7}, pages = {1523 -- 1580}, publisher = {Springer}, title = {{Adaptive gene introgression after secondary contact}}, doi = {10.1007/s00285-014-0802-y}, volume = {70}, year = {2015}, } @article{1696, abstract = {The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller wave function (GWF) is applied to the Anderson lattice model. This approach allows for a systematic evaluation of the expectation values with full Gutzwiller wave function in finite-dimensional systems. It introduces results extending in an essential manner those obtained by means of the standard Gutzwiller approximation (GA), which is variationally exact only in infinite dimensions. Within the DE-GWF approach we discuss the principal paramagnetic properties and their relevance to heavy-fermion systems. We demonstrate the formation of an effective, narrow f band originating from atomic f-electron states and subsequently interpret this behavior as a direct itineracy of f electrons; it represents a combined effect of both the hybridization and the correlations induced by the Coulomb repulsive interaction. Such a feature is absent on the level of GA, which is equivalent to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent narrow f band rationalizes the common assumption of such dispersion of f levels in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it is shown that the emerging f-electron direct itineracy leads in a natural manner to three physically distinct regimes within a single model that are frequently discussed for 4f- or 5f-electron compounds as separate model situations. We identify these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging correlated quantum liquid state are stressed.}, author = {Wysokiński, Marcin and Kaczmarczyk, Jan and Spałek, Jozef}, journal = {Physical Review B}, number = {12}, publisher = {American Physical Society}, title = {{Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states}}, doi = {10.1103/PhysRevB.92.125135}, volume = {92}, year = {2015}, } @article{1701, abstract = {The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance. }, author = {Tkacik, Gasper and Mora, Thierry and Marre, Olivier and Amodei, Dario and Palmer, Stephanie and Berry Ii, Michael and Bialek, William}, journal = {PNAS}, number = {37}, pages = {11508 -- 11513}, publisher = {National Academy of Sciences}, title = {{Thermodynamics and signatures of criticality in a network of neurons}}, doi = {10.1073/pnas.1514188112}, volume = {112}, year = {2015}, } @article{1698, abstract = {In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Multi-mean-payoff and multi-energy games replace individual weights by tuples, and the limit average (resp., running sum) of each coordinate must be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy games and show inter-reducibility of multi-mean-payoff and multi-energy games for finite-memory strategies. We improve the computational complexity for solving both classes with finite-memory strategies: we prove coNP-completeness improving the previous known EXPSPACE bound. For memoryless strategies, we show that deciding the existence of a winning strategy for the protagonist is NP-complete. We present the first solution of multi-mean-payoff games with infinite-memory strategies: we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf objectives are coNP-complete.}, author = {Velner, Yaron and Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A and Rabinovich, Alexander and Raskin, Jean}, journal = {Information and Computation}, number = {4}, pages = {177 -- 196}, publisher = {Elsevier}, title = {{The complexity of multi-mean-payoff and multi-energy games}}, doi = {10.1016/j.ic.2015.03.001}, volume = {241}, year = {2015}, } @article{1700, abstract = {We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms.}, author = {Van Loon, Erik and Katsnelson, Mikhail and Lemeshko, Mikhail}, journal = {Physical Review B}, number = {8}, publisher = {American Physical Society}, title = {{Ultralong-range order in the Fermi-Hubbard model with long-range interactions}}, doi = {10.1103/PhysRevB.92.081106}, volume = {92}, year = {2015}, } @article{1704, abstract = {Given a convex function (Formula presented.) and two hermitian matrices A and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative entropy defined by (Formula presented.). Among other things, they prove that the so-defined quantity is monotone if and only if (Formula presented.) is operator monotone. The monotonicity is then used to properly define (Formula presented.) for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional projections (Formula presented.) with (Formula presented.) strongly, the limit (Formula presented.) is shown to exist and to be independent of the sequence of projections (Formula presented.). The question whether this sequence converges to its "obvious" limit, namely (Formula presented.), has been left open. We answer this question in principle affirmatively and show that (Formula presented.). If the operators A and B are regular enough, that is (A − B), (Formula presented.) and (Formula presented.) are trace-class, the identity (Formula presented.) holds.}, author = {Deuchert, Andreas and Hainzl, Christian and Seiringer, Robert}, journal = {Letters in Mathematical Physics}, number = {10}, pages = {1449 -- 1466}, publisher = {Springer}, title = {{Note on a family of monotone quantum relative entropies}}, doi = {10.1007/s11005-015-0787-5}, volume = {105}, year = {2015}, } @inproceedings{1706, abstract = {We consider a problem of learning kernels for use in SVM classification in the multi-task and lifelong scenarios and provide generalization bounds on the error of a large margin classifier. Our results show that, under mild conditions on the family of kernels used for learning, solving several related tasks simultaneously is beneficial over single task learning. In particular, as the number of observed tasks grows, assuming that in the considered family of kernels there exists one that yields low approximation error on all tasks, the overhead associated with learning such a kernel vanishes and the complexity converges to that of learning when this good kernel is given to the learner.}, author = {Pentina, Anastasia and Ben David, Shai}, location = {Banff, AB, Canada}, pages = {194 -- 208}, publisher = {Springer}, title = {{Multi-task and lifelong learning of kernels}}, doi = {10.1007/978-3-319-24486-0_13}, volume = {9355}, year = {2015}, } @article{1712, abstract = {The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses.}, author = {Ratheesh, Aparna and Belyaeva, Vera and Siekhaus, Daria E}, journal = {Current Opinion in Cell Biology}, number = {10}, pages = {71 -- 79}, publisher = {Elsevier}, title = {{Drosophila immune cell migration and adhesion during embryonic development and larval immune responses}}, doi = {10.1016/j.ceb.2015.07.003}, volume = {36}, year = {2015}, } @article{1710, abstract = {We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞.}, author = {Akopyan, Arseniy and Plakhov, Alexander}, journal = {Society for Industrial and Applied Mathematics}, number = {4}, pages = {2754 -- 2769}, publisher = {SIAM}, title = {{Minimal resistance of curves under the single impact assumption}}, doi = {10.1137/140993843}, volume = {47}, year = {2015}, } @article{1730, abstract = {How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations.}, author = {Colin De Verdière, Éric and Hubard, Alfredo and De Mesmay, Arnaud N}, journal = {Discrete & Computational Geometry}, number = {3}, pages = {587 -- 620}, publisher = {Springer}, title = {{Discrete systolic inequalities and decompositions of triangulated surfaces}}, doi = {10.1007/s00454-015-9679-9}, volume = {53}, year = {2015}, } @article{1735, abstract = {This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations.}, author = {Ando, Ryoichi and Thürey, Nils and Wojtan, Christopher J}, journal = {Computer Graphics Forum}, number = {2}, pages = {473 -- 480}, publisher = {Wiley}, title = {{A dimension-reduced pressure solver for liquid simulations}}, doi = {10.1111/cgf.12576}, volume = {34}, year = {2015}, } @article{1789, abstract = {Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID.}, author = {Kuechler, Alma and Zink, Alexander and Wieland, Thomas and Lüdecke, Hermann and Cremer, Kirsten and Salviati, Leonardo and Magini, Pamela and Najafi, Kimia and Zweier, Christiane and Czeschik, Johanna and Aretz, Stefan and Endele, Sabine and Tamburrino, Federica and Pinato, Claudia and Clementi, Maurizio and Gundlach, Jasmin and Maylahn, Carina and Mazzanti, Laura and Wohlleber, Eva and Schwarzmayr, Thomas and Kariminejad, Roxana and Schlessinger, Avner and Wieczorek, Dagmar and Strom, Tim and Novarino, Gaia and Engels, Hartmut}, journal = {European Journal of Human Genetics}, number = {6}, pages = {753 -- 760}, publisher = {Nature Publishing Group}, title = {{Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome}}, doi = {10.1038/ejhg.2014.165}, volume = {23}, year = {2015}, } @article{1804, abstract = {It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control.}, author = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Transition to turbulence in Taylor-Couette ferrofluidic flow}}, doi = {10.1038/srep10781}, volume = {5}, year = {2015}, } @article{1807, abstract = {We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.}, author = {Goldman, Michael and Royo-Letelier, Jimena}, journal = {ESAIM - Control, Optimisation and Calculus of Variations}, number = {3}, pages = {603 -- 624}, publisher = {EDP Sciences}, title = {{Sharp interface limit for two components Bose-Einstein condensates}}, doi = {10.1051/cocv/2014040}, volume = {21}, year = {2015}, } @article{1810, abstract = {Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.}, author = {Bollenbach, Mark Tobias}, journal = {Current Opinion in Microbiology}, pages = {1 -- 9}, publisher = {Elsevier}, title = {{Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution}}, doi = {10.1016/j.mib.2015.05.008}, volume = {27}, year = {2015}, } @article{1812, abstract = {We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules. }, author = {Lahrz, Martin and Lemeshko, Mikhail and Mathey, Ludwig}, journal = {New Journal of Physics}, number = {4}, publisher = {IOP Publishing Ltd.}, title = {{Exotic roton excitations in quadrupolar Bose–Einstein condensates }}, doi = {10.1088/1367-2630/17/4/045005}, volume = {17}, year = {2015}, } @article{1811, abstract = {Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.}, author = {Safari, Laleh and Santos, José and Amaro, Pedro and Jänkälä, Kari and Fratini, Filippo}, journal = {Journal of Mathematical Physics}, number = {5}, publisher = {American Institute of Physics}, title = {{Analytical evaluation of atomic form factors: Application to Rayleigh scattering}}, doi = {10.1063/1.4921227}, volume = {56}, year = {2015}, } @article{1813, abstract = {We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.}, author = {Schmidt, Richard and Lemeshko, Mikhail}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{Rotation of quantum impurities in the presence of a many-body environment}}, doi = {10.1103/PhysRevLett.114.203001}, volume = {114}, year = {2015}, } @article{1817, abstract = {Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. }, author = {Porazinski, Sean and Wang, Huijia and Asaoka, Yoichi and Behrndt, Martin and Miyamoto, Tatsuo and Morita, Hitoshi and Hata, Shoji and Sasaki, Takashi and Krens, Gabriel and Osada, Yumi and Asaka, Satoshi and Momoi, Akihiro and Linton, Sarah and Miesfeld, Joel and Link, Brian and Senga, Takeshi and Castillo Morales, Atahualpa and Urrutia, Araxi and Shimizu, Nobuyoshi and Nagase, Hideaki and Matsuura, Shinya and Bagby, Stefan and Kondoh, Hisato and Nishina, Hiroshi and Heisenberg, Carl-Philipp J and Furutani Seiki, Makoto}, journal = {Nature}, number = {7551}, pages = {217 -- 221}, publisher = {Nature Publishing Group}, title = {{YAP is essential for tissue tension to ensure vertebrate 3D body shape}}, doi = {10.1038/nature14215}, volume = {521}, year = {2015}, } @inproceedings{1820, abstract = {We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.}, author = {Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Raghav and Kanodia, Ayush}, booktitle = {Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence }, location = {Austin, TX, USA}, pages = {3496--3502}, publisher = {AAAI Press}, title = {{Optimal cost almost-sure reachability in POMDPs}}, volume = {5}, year = {2015}, } @article{1814, abstract = {We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.}, author = {Jeschke, Stefan and Wojtan, Christopher J}, journal = {ACM Transactions on Graphics}, number = {3}, publisher = {ACM}, title = {{Water wave animation via wavefront parameter interpolation}}, doi = {10.1145/2714572}, volume = {34}, year = {2015}, } @article{1818, abstract = {Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.}, author = {Polechova, Jitka and Barton, Nicholas H}, journal = {PNAS}, number = {20}, pages = {6401 -- 6406}, publisher = {National Academy of Sciences}, title = {{Limits to adaptation along environmental gradients}}, doi = {10.1073/pnas.1421515112}, volume = {112}, year = {2015}, } @article{1823, abstract = {Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways.}, author = {Chevereau, Guillaume and Bollenbach, Mark Tobias}, journal = {Molecular Systems Biology}, number = {4}, publisher = {Nature Publishing Group}, title = {{Systematic discovery of drug interaction mechanisms}}, doi = {10.15252/msb.20156098}, volume = {11}, year = {2015}, } @article{1824, abstract = {Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates.}, author = {Knebel, Johannes and Weber, Markus and Krüger, Torben H and Frey, Erwin}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Evolutionary games of condensates in coupled birth-death processes}}, doi = {10.1038/ncomms7977}, volume = {6}, year = {2015}, } @article{1831, abstract = {This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research.}, author = {Kappeler, Peter and Cremer, Sylvia and Nunn, Charles}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1669}, publisher = {Royal Society}, title = {{Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies}}, doi = {10.1098/rstb.2014.0116}, volume = {370}, year = {2015}, } @article{1828, abstract = {We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory.}, author = {Akopyan, Arseniy and Pirogov, Sergey and Rybko, Aleksandr}, journal = {Journal of Statistical Physics}, number = {1}, pages = {163 -- 167}, publisher = {Springer}, title = {{Invariant measures of genetic recombination process}}, doi = {10.1007/s10955-015-1238-5}, volume = {160}, year = {2015}, } @inproceedings{1838, abstract = {Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples.}, author = {Bloem, Roderick and Chatterjee, Krishnendu and Jacobs, Swen and Könighofer, Robert}, location = {London, United Kingdom}, pages = {517 -- 532}, publisher = {Springer}, title = {{Assume-guarantee synthesis for concurrent reactive programs with partial information}}, doi = {10.1007/978-3-662-46681-0_50}, volume = {9035}, year = {2015}, } @inproceedings{1839, abstract = {We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies.}, author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín}, location = {London, United Kingdom}, pages = {181 -- 187}, publisher = {Springer}, title = {{Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives}}, doi = {10.1007/978-3-662-46681-0_12}, volume = {9035}, year = {2015}, } @article{1837, abstract = {Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.}, author = {Kühnen, Jakob and Braunshier, P and Schwegel, M and Kuhlmann, Hendrik and Hof, Björn}, journal = {Journal of Fluid Mechanics}, number = {5}, publisher = {Cambridge University Press}, title = {{Subcritical versus supercritical transition to turbulence in curved pipes}}, doi = {10.1017/jfm.2015.184}, volume = {770}, year = {2015}, } @article{1848, abstract = {The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis.}, author = {Schwamb, Bettina and Pick, Robert and Fernández, Sara and Völp, Kirsten and Heering, Jan and Dötsch, Volker and Bösser, Susanne and Jung, Jennifer and Beinoravičiute Kellner, Rasa and Wesely, Josephine and Zörnig, Inka and Hammerschmidt, Matthias and Nowak, Matthias and Penzel, Roland and Zatloukal, Kurt and Joos, Stefan and Rieker, Ralf and Agaimy, Abbas and Söder, Stephan and Reid Lombardo, Kmarie and Kendrick, Michael and Bardsley, Michael and Hayashi, Yujiro and Asuzu, David and Syed, Sabriya and Ördög, Tamás and Zörnig, Martin}, journal = {International Journal of Cancer}, number = {6}, pages = {1318 -- 1329}, publisher = {Wiley}, title = {{FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors}}, doi = {10.1002/ijc.29498}, volume = {137}, year = {2015}, } @article{1846, abstract = {Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS.}, author = {Beneš, Nikola and Kretinsky, Jan and Larsen, Kim and Möller, Mikael and Sickert, Salomon and Srba, Jiří}, journal = {Acta Informatica}, number = {2-3}, pages = {269 -- 297}, publisher = {Springer}, title = {{Refinement checking on parametric modal transition systems}}, doi = {10.1007/s00236-015-0215-4}, volume = {52}, year = {2015}, } @article{1845, abstract = {Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression.}, author = {Vandael, David H and Espinoza Martinez, Claudia and Jonas, Peter M}, journal = {Neuron}, number = {6}, pages = {1149 -- 1151}, publisher = {Elsevier}, title = {{Excitement about inhibitory presynaptic terminals}}, doi = {10.1016/j.neuron.2015.03.006}, volume = {85}, year = {2015}, } @article{1840, abstract = {In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.}, author = {Geiger, Bernhard and Petrov, Tatjana and Kubin, Gernot and Koeppl, Heinz}, issn = {0018-9286}, journal = {IEEE Transactions on Automatic Control}, number = {4}, pages = {1010 -- 1022}, publisher = {IEEE}, title = {{Optimal Kullback-Leibler aggregation via information bottleneck}}, doi = {10.1109/TAC.2014.2364971}, volume = {60}, year = {2015}, } @article{1841, abstract = {We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results.}, author = {Kolmogorov, Vladimir}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {5}, pages = {919 -- 930}, publisher = {IEEE}, title = {{A new look at reweighted message passing}}, doi = {10.1109/TPAMI.2014.2363465}, volume = {37}, year = {2015}, } @article{1850, abstract = {Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.}, author = {Novak, Sebastian and Cremer, Sylvia}, journal = {Journal of Theoretical Biology}, number = {5}, pages = {54 -- 64}, publisher = {Elsevier}, title = {{Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates}}, doi = {10.1016/j.jtbi.2015.02.018}, volume = {372}, year = {2015}, } @article{1851, abstract = {We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them.}, author = {Priklopil, Tadeas and Kisdi, Eva and Gyllenberg, Mats}, issn = {1558-5646}, journal = {Evolution}, number = {4}, pages = {1015 -- 1026}, publisher = {Wiley}, title = {{Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating}}, doi = {10.1111/evo.12618}, volume = {69}, year = {2015}, } @inproceedings{1859, abstract = {Structural support vector machines (SSVMs) are amongst the best performing models for structured computer vision tasks, such as semantic image segmentation or human pose estimation. Training SSVMs, however, is computationally costly, because it requires repeated calls to a structured prediction subroutine (called \emph{max-oracle}), which has to solve an optimization problem itself, e.g. a graph cut. In this work, we introduce a new algorithm for SSVM training that is more efficient than earlier techniques when the max-oracle is computationally expensive, as it is frequently the case in computer vision tasks. The main idea is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm with efficient hyperplane caching, and (ii) use an automatic selection rule for deciding whether to call the exact max-oracle or to rely on an approximate one based on the cached hyperplanes. We show experimentally that this strategy leads to faster convergence to the optimum with respect to the number of requires oracle calls, and that this translates into faster convergence with respect to the total runtime when the max-oracle is slow compared to the other steps of the algorithm. }, author = {Shah, Neel and Kolmogorov, Vladimir and Lampert, Christoph}, location = {Boston, MA, USA}, pages = {2737 -- 2745}, publisher = {IEEE}, title = {{A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle}}, doi = {10.1109/CVPR.2015.7298890}, year = {2015}, } @inproceedings{1860, abstract = {Classifiers for object categorization are usually evaluated by their accuracy on a set of i.i.d. test examples. This provides us with an estimate of the expected error when applying the classifiers to a single new image. In real application, however, classifiers are rarely only used for a single image and then discarded. Instead, they are applied sequentially to many images, and these are typically not i.i.d. samples from a fixed data distribution, but they carry dependencies and their class distribution varies over time. In this work, we argue that the phenomenon of correlated data at prediction time is not a nuisance, but a blessing in disguise. We describe a probabilistic method for adapting classifiers at prediction time without having to retrain them. We also introduce a framework for creating realistically distributed image sequences, which offers a way to benchmark classifier adaptation methods, such as the one we propose. Experiments on the ILSVRC2010 and ILSVRC2012 datasets show that adapting object classification systems at prediction time can significantly reduce their error rate, even with no additional human feedback.}, author = {Royer, Amélie and Lampert, Christoph}, location = {Boston, MA, United States}, pages = {1401 -- 1409}, publisher = {IEEE}, title = {{Classifier adaptation at prediction time}}, doi = {10.1109/CVPR.2015.7298746}, year = {2015}, } @inproceedings{1858, abstract = {We study the problem of predicting the future, though only in the probabilistic sense of estimating a future state of a time-varying probability distribution. This is not only an interesting academic problem, but solving this extrapolation problem also has many practical application, e.g. for training classifiers that have to operate under time-varying conditions. Our main contribution is a method for predicting the next step of the time-varying distribution from a given sequence of sample sets from earlier time steps. For this we rely on two recent machine learning techniques: embedding probability distributions into a reproducing kernel Hilbert space, and learning operators by vector-valued regression. We illustrate the working principles and the practical usefulness of our method by experiments on synthetic and real data. We also highlight an exemplary application: training a classifier in a domain adaptation setting without having access to examples from the test time distribution at training time.}, author = {Lampert, Christoph}, location = {Boston, MA, United States}, pages = {942 -- 950}, publisher = {IEEE}, title = {{Predicting the future behavior of a time-varying probability distribution}}, doi = {10.1109/CVPR.2015.7298696}, year = {2015}, } @inproceedings{1857, abstract = {Sharing information between multiple tasks enables algorithms to achieve good generalization performance even from small amounts of training data. However, in a realistic scenario of multi-task learning not all tasks are equally related to each other, hence it could be advantageous to transfer information only between the most related tasks. In this work we propose an approach that processes multiple tasks in a sequence with sharing between subsequent tasks instead of solving all tasks jointly. Subsequently, we address the question of curriculum learning of tasks, i.e. finding the best order of tasks to be learned. Our approach is based on a generalization bound criterion for choosing the task order that optimizes the average expected classification performance over all tasks. Our experimental results show that learning multiple related tasks sequentially can be more effective than learning them jointly, the order in which tasks are being solved affects the overall performance, and that our model is able to automatically discover the favourable order of tasks. }, author = {Pentina, Anastasia and Sharmanska, Viktoriia and Lampert, Christoph}, location = {Boston, MA, United States}, pages = {5492 -- 5500}, publisher = {IEEE}, title = {{Curriculum learning of multiple tasks}}, doi = {10.1109/CVPR.2015.7299188}, year = {2015}, } @article{1864, abstract = {The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive regime, a universal power law behaviour for the correlation functions of the mesoscopic eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013), we prove these formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013) we introduced a diagrammatic approach and presented robust estimates on general diagrams under certain simplifying assumptions. In this paper, we remove these assumptions by giving a general estimate of the subleading diagrams. We also give a precise analysis of the leading diagrams which give rise to the Altschuler–Shklovskii power laws. Moreover, we introduce a family of general random band matrices which interpolates between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track the transition for the mesoscopic density–density correlation. Finally, we address the higher-order correlation functions by proving that they behave asymptotically according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii formulas. }, author = {Erdös, László and Knowles, Antti}, journal = {Annales Henri Poincare}, number = {3}, pages = {709 -- 799}, publisher = {Springer}, title = {{The Altshuler–Shklovskii formulas for random band matrices II: The general case}}, doi = {10.1007/s00023-014-0333-5}, volume = {16}, year = {2015}, } @article{1871, abstract = {The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.}, author = {Grones, Peter and Friml, Jirí}, journal = {Journal of Cell Science}, number = {1}, pages = {1 -- 7}, publisher = {Company of Biologists}, title = {{Auxin transporters and binding proteins at a glance}}, doi = {10.1242/jcs.159418}, volume = {128}, year = {2015}, } @article{1873, abstract = {We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with every transition, and the payoff of an infinite path is the long-run average of the rewards. We consider two types of path constraints: (i) a quantitative constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples.}, author = {Chatterjee, Krishnendu and Chmelik, Martin}, journal = {Artificial Intelligence}, pages = {46 -- 72}, publisher = {Elsevier}, title = {{POMDPs under probabilistic semantics}}, doi = {10.1016/j.artint.2014.12.009}, volume = {221}, year = {2015}, } @article{1879, abstract = {When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.}, author = {Kremer, A and Lippens, Stefaan and Bartunkova, Sonia and Asselbergh, Bob and Blanpain, Cendric and Fendrych, Matyas and Goossens, A and Holt, Matthew and Janssens, Sophie and Krols, Michiel and Larsimont, Jean and Mc Guire, Conor and Nowack, Moritz and Saelens, Xavier and Schertel, Andreas and Schepens, B and Slezak, M and Timmerman, Vincent and Theunis, Clara and Van Brempt, Ronald and Visser, Y and Guérin, Christophe}, journal = {Journal of Microscopy}, number = {2}, pages = {80 -- 96}, publisher = {Wiley-Blackwell}, title = {{Developing 3D SEM in a broad biological context}}, doi = {10.1111/jmi.12211}, volume = {259}, year = {2015}, } @article{1880, abstract = {We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder}, author = {Könenberg, Martin and Moser, Thomas and Seiringer, Robert and Yngvason, Jakob}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Superfluid behavior of a Bose-Einstein condensate in a random potential}}, doi = {10.1088/1367-2630/17/1/013022}, volume = {17}, year = {2015}, } @inproceedings{1882, abstract = {We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations.}, author = {Fahrenberg, Uli and Kretinsky, Jan and Legay, Axel and Traonouez, Louis}, location = {Bertinoro, Italy}, pages = {306 -- 324}, publisher = {Springer}, title = {{Compositionality for quantitative specifications}}, doi = {10.1007/978-3-319-15317-9_19}, volume = {8997}, year = {2015}, } @article{1883, abstract = {We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point. }, author = {Keller-Schmidt, Stephanie and Tugrul, Murat and Eguíluz, Víctor and Hernandez Garcia, Emilio and Klemm, Konstantin}, journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics}, number = {2}, publisher = {American Institute of Physics}, title = {{Anomalous scaling in an age-dependent branching model}}, doi = {10.1103/PhysRevE.91.022803}, volume = {91}, year = {2015}, } @article{1885, abstract = {The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. }, author = {Tkacik, Gasper and Dubuis, Julien and Petkova, Mariela and Gregor, Thomas}, journal = {Genetics}, number = {1}, pages = {39 -- 59}, publisher = {Genetics Society of America}, title = {{Positional information, positional error, and readout precision in morphogenesis: A mathematical framework}}, doi = {10.1534/genetics.114.171850}, volume = {199}, year = {2015}, } @article{1940, abstract = {We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.}, author = {Sokolowski, Thomas R and Tkacik, Gasper}, journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics}, number = {6}, publisher = {American Institute of Physics}, title = {{Optimizing information flow in small genetic networks. IV. Spatial coupling}}, doi = {10.1103/PhysRevE.91.062710}, volume = {91}, year = {2015}, } @inproceedings{1992, abstract = {We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings. We claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising. In the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula.}, author = {Gupta, Ashutosh and Henzinger, Thomas A and Radhakrishna, Arjun and Samanta, Roopsha and Tarrach, Thorsten}, isbn = {978-1-4503-3300-9}, location = {Mumbai, India}, pages = {433 -- 444}, publisher = {ACM}, title = {{Succinct representation of concurrent trace sets}}, doi = {10.1145/2676726.2677008}, year = {2015}, } @article{1997, abstract = {We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials.}, author = {Noren, Patrik}, journal = {Journal of Symbolic Computation}, number = {May-June}, pages = {285 -- 296}, publisher = {Elsevier}, title = {{The three-state toric homogeneous Markov chain model has Markov degree two}}, doi = {10.1016/j.jsc.2014.09.014}, volume = {68/Part 2}, year = {2015}, } @article{2008, abstract = {The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package.}, author = {Klimova, Anna and Rudas, Tamás}, journal = {Scandinavian Journal of Statistics}, number = {3}, pages = {832 -- 847}, publisher = {Wiley}, title = {{Iterative scaling in curved exponential families}}, doi = {10.1111/sjos.12139}, volume = {42}, year = {2015}, } @article{2006, abstract = {The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. }, author = {Hein, Nicolas and Hillar, Christopher and Martin Del Campo Sanchez, Abraham and Sottile, Frank and Teitler, Zach}, journal = {Experimental Mathematics}, number = {3}, pages = {261 -- 269}, publisher = {Taylor & Francis}, title = {{The monotone secant conjecture in the real Schubert calculus}}, doi = {10.1080/10586458.2014.980044}, volume = {24}, year = {2015}, } @article{2014, abstract = {The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association.}, author = {Klimova, Anna and Uhler, Caroline and Rudas, Tamás}, journal = {Computational Statistics & Data Analysis}, number = {7}, pages = {57 -- 72}, publisher = {Elsevier}, title = {{Faithfulness and learning hypergraphs from discrete distributions}}, doi = {10.1016/j.csda.2015.01.017}, volume = {87}, year = {2015}, } @article{2025, abstract = {Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.}, author = {Kawada, Daiki and Kobayashi, Hiromu and Tomita, Tsuyoshi and Nakata, Eisuke and Nagano, Makoto and Siekhaus, Daria E and Toshima, Junko and Toshimaa, Jiro}, journal = {Biochimica et Biophysica Acta - Molecular Cell Research}, number = {1}, pages = {144 -- 156}, publisher = {Elsevier}, title = {{The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins}}, doi = {10.1016/j.bbamcr.2014.10.009}, volume = {1853}, year = {2015}, } @article{2030, abstract = {A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.}, author = {Shi, Liang and Rampp, Markus and Hof, Björn and Avila, Marc}, journal = {Computers and Fluids}, number = {1}, pages = {1 -- 11}, publisher = {Elsevier}, title = {{A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow}}, doi = {10.1016/j.compfluid.2014.09.021}, volume = {106}, year = {2015}, }