@article{2169,
author = {Barton, Nicholas H and Novak, Sebastian and Paixao, Tiago},
journal = {PNAS},
number = {29},
pages = {10398 -- 10399},
publisher = {National Academy of Sciences},
title = {{Diverse forms of selection in evolution and computer science}},
doi = {10.1073/pnas.1410107111},
volume = {111},
year = {2014},
}
@inproceedings{2171,
abstract = {We present LS-CRF, a new method for training cyclic Conditional Random Fields (CRFs) from large datasets that is inspired by classical closed-form expressions for the maximum likelihood parameters of a generative graphical model with tree topology. Training a CRF with LS-CRF requires only solving a set of independent regression problems, each of which can be solved efficiently in closed form or by an iterative solver. This makes LS-CRF orders of magnitude faster than classical CRF training based on probabilistic inference, and at the same time more flexible and easier to implement than other approximate techniques, such as pseudolikelihood or piecewise training. We apply LS-CRF to the task of semantic image segmentation, showing that it achieves on par accuracy to other training techniques at higher speed, thereby allowing efficient CRF training from very large training sets. For example, training a linearly parameterized pairwise CRF on 150,000 images requires less than one hour on a modern workstation.},
author = {Kolesnikov, Alexander and Guillaumin, Matthieu and Ferrari, Vittorio and Lampert, Christoph},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
editor = {Fleet, David and Pajdla, Tomas and Schiele, Bernt and Tuytelaars, Tinne},
location = {Zurich, Switzerland},
number = {PART 3},
pages = {550 -- 565},
publisher = {Springer},
title = {{Closed-form approximate CRF training for scalable image segmentation}},
doi = {10.1007/978-3-319-10578-9_36},
volume = {8691},
year = {2014},
}
@article{2183,
abstract = {We describe a simple adaptive network of coupled chaotic maps. The network reaches a stationary state (frozen topology) for all values of the coupling parameter, although the dynamics of the maps at the nodes of the network can be nontrivial. The structure of the network shows interesting hierarchical properties and in certain parameter regions the dynamics is polysynchronous: Nodes can be divided in differently synchronized classes but, contrary to cluster synchronization, nodes in the same class need not be connected to each other. These complicated synchrony patterns have been conjectured to play roles in systems biology and circuits. The adaptive system we study describes ways whereby this behavior can evolve from undifferentiated nodes.},
author = {Botella Soler, Vicente and Glendinning, Paul},
journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
number = {6},
publisher = {American Institute of Physics},
title = {{Hierarchy and polysynchrony in an adaptive network }},
doi = {10.1103/PhysRevE.89.062809 },
volume = {89},
year = {2014},
}
@article{2188,
abstract = {Although plant and animal cells use a similar core mechanism to deliver proteins to the plasma membrane, their different lifestyle, body organization and specific cell structures resulted in the acquisition of regulatory mechanisms that vary in the two kingdoms. In particular, cell polarity regulators do not seem to be conserved, because genes encoding key components are absent in plant genomes. In plants, the broad knowledge on polarity derives from the study of auxin transporters, the PIN-FORMED proteins, in the model plant Arabidopsis thaliana. In animals, much information is provided from the study of polarity in epithelial cells that exhibit basolateral and luminal apical polarities, separated by tight junctions. In this review, we summarize the similarities and differences of the polarization mechanisms between plants and animals and survey the main genetic approaches that have been used to characterize new genes involved in polarity establishment in plants, including the frequently used forward and reverse genetics screens as well as a novel chemical genetics approach that is expected to overcome the limitation of classical genetics methods.},
author = {Kania, Urszula and Fendrych, Matyas and Friml, Jiřĺ},
journal = {Open Biology},
number = {APRIL},
publisher = {Royal Society},
title = {{Polar delivery in plants; commonalities and differences to animal epithelial cells}},
doi = {10.1098/rsob.140017},
volume = {4},
year = {2014},
}
@article{2208,
abstract = {We propose to detect quadrupole interactions of neutral ultracold atoms via their induced mean-field shift. We consider a Mott insulator state of spin-polarized atoms in a two-dimensional optical square lattice. The quadrupole moments of the atoms are aligned by an external magnetic field. As the alignment angle is varied, the mean-field shift shows a characteristic angular dependence, which constitutes the defining signature of the quadrupole interaction. For the 3P2 states of Yb and Sr atoms, we find a frequency shift of the order of tens of Hertz, which can be realistically detected in experiment with current technology. We compare our results to the mean-field shift of a spin-polarized quasi-two-dimensional Fermi gas in continuum. },
author = {Lahrz, Martin and Lemeshko, Mikhail and Sengstock, Klaus and Becker, Christoph and Mathey, Ludwig},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {4},
publisher = {American Physical Society},
title = {{Detecting quadrupole interactions in ultracold Fermi gases}},
doi = {10.1103/PhysRevA.89.043616},
volume = {89},
year = {2014},
}
@article{2246,
abstract = {Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth. },
author = {Grinshpun, Andrey and Phalitnonkiat, Pakawat and Rubin, Sasha and Tarfulea, Andrei},
issn = {03043975},
journal = {Theoretical Computer Science},
pages = {73 -- 91},
publisher = {Elsevier},
title = {{Alternating traps in Muller and parity games}},
doi = {10.1016/j.tcs.2013.11.032},
volume = {521},
year = {2014},
}
@article{3263,
abstract = {Adaptation in the retina is thought to optimize the encoding of natural light signals into sequences of spikes sent to the brain. While adaptive changes in retinal processing to the variations of the mean luminance level and second-order stimulus statistics have been documented before, no such measurements have been performed when higher-order moments of the light distribution change. We therefore measured the ganglion cell responses in the tiger salamander retina to controlled changes in the second (contrast), third (skew) and fourth (kurtosis) moments of the light intensity distribution of spatially uniform temporally independent stimuli. The skew and kurtosis of the stimuli were chosen to cover the range observed in natural scenes. We quantified adaptation in ganglion cells by studying linear-nonlinear models that capture well the retinal encoding properties across all stimuli. We found that the encoding properties of retinal ganglion cells change only marginally when higher-order statistics change, compared to the changes observed in response to the variation in contrast. By analyzing optimal coding in LN-type models, we showed that neurons can maintain a high information rate without large dynamic adaptation to changes in skew or kurtosis. This is because, for uncorrelated stimuli, spatio-temporal summation within the receptive field averages away non-gaussian aspects of the light intensity distribution.},
author = {Tkacik, Gasper and Ghosh, Anandamohan and Schneidman, Elad and Segev, Ronen},
journal = {PLoS One},
number = {1},
publisher = {Public Library of Science},
title = {{Adaptation to changes in higher-order stimulus statistics in the salamander retina}},
doi = {10.1371/journal.pone.0085841},
volume = {9},
year = {2014},
}
@inproceedings{775,
abstract = {The long-lived renaming problem appears in shared-memory systems where a set of threads need to register and deregister frequently from the computation, while concurrent operations scan the set of currently registered threads. Instances of this problem show up in concurrent implementations of transactional memory, flat combining, thread barriers, and memory reclamation schemes for lock-free data structures. In this paper, we analyze a randomized solution for long-lived renaming. The algorithmic technique we consider, called the Level Array, has previously been used for hashing and one-shot (single-use) renaming. Our main contribution is to prove that, in long-lived executions, where processes may register and deregister polynomially many times, the technique guarantees constant steps on average and O (log log n) steps with high probability for registering, unit cost for deregistering, and O (n) steps for collect queries, where n is an upper bound on the number of processes that may be active at any point in time. We also show that the algorithm has the surprising property that it is self-healing: under reasonable assumptions on the schedule, operations running while the data structure is in a degraded state implicitly help the data structure re-balance itself. This subtle mechanism obviates the need for expensive periodic rebuilding procedures. Our benchmarks validate this approach, showing that, for typical use parameters, the average number of steps a process takes to register is less than two and the worst-case number of steps is bounded by six, even in executions with billions of operations. We contrast this with other randomized implementations, whose worst-case behavior we show to be unreliable, and with deterministic implementations, whose cost is linear in n.},
author = {Alistarh, Dan and Kopinsky, Justin and Matveev, Alexander and Shavit, Nir N},
pages = {348 -- 357},
publisher = {IEEE},
title = {{The levelarray: A fast, practical long-lived renaming algorithm}},
doi = {10.1109/ICDCS.2014.43},
year = {2014},
}
@article{97,
abstract = {The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm).},
author = {Higginbotham, Andrew P and Kuemmeth, Ferdinand and Larsen, Thorvald and Fitzpatrick, Mattias and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles},
journal = {APS Physics, Physical Review Letters},
number = {21},
publisher = {American Physical Society},
title = {{Antilocalization of coulomb blockade in a Ge/Si nanowire}},
doi = {10.1103/PhysRevLett.112.216806},
volume = {112},
year = {2014},
}
@article{977,
abstract = {We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems.},
author = {Maksym Serbyn and Knap, Michael J and Gopalakrishnan, Sarang and Papić, Zlatko and Yao, Norman Y and Laumann, Chris R and Abanin, Dmitry A and Lukin, Mikhail D and Demler, Eugene A},
journal = {Physical Review Letters},
number = {14},
publisher = {American Physical Society},
title = {{Interferometric probes of many-body localization}},
doi = {10.1103/PhysRevLett.113.147204},
volume = {113},
year = {2014},
}
@article{1375,
abstract = {We consider directed graphs where each edge is labeled with an integer weight and study the fundamental algorithmic question of computing the value of a cycle with minimum mean weight. Our contributions are twofold: (1) First we show that the algorithmic question is reducible to the problem of a logarithmic number of min-plus matrix multiplications of n×n-matrices, where n is the number of vertices of the graph. (2) Second, when the weights are nonnegative, we present the first (1+ε)-approximation algorithm for the problem and the running time of our algorithm is Õ(nωlog3(nW/ε)/ε),1 where O(nω) is the time required for the classic n×n-matrix multiplication and W is the maximum value of the weights. With an additional O(log(nW/ε)) factor in space a cycle with approximately optimal weight can be computed within the same time bound.},
author = {Chatterjee, Krishnendu and Henzinger, Monika and Krinninger, Sebastian and Loitzenbauer, Veronika and Raskin, Michael},
journal = {Theoretical Computer Science},
number = {C},
pages = {104 -- 116},
publisher = {Elsevier},
title = {{Approximating the minimum cycle mean}},
doi = {10.1016/j.tcs.2014.06.031},
volume = {547},
year = {2014},
}
@article{2234,
abstract = {We study Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) functions. We consider two different objectives, namely, expectation and satisfaction objectives. Given an MDP with κ limit-average functions, in the expectation objective the goal is to maximize the expected limit-average value, and in the satisfaction objective the goal is to maximize the probability of runs such that the limit-average value stays above a given vector. We show that under the expectation objective, in contrast to the case of one limit-average function, both randomization and memory are necessary for strategies even for ε-approximation, and that finite-memory randomized strategies are sufficient for achieving Pareto optimal values. Under the satisfaction objective, in contrast to the case of one limit-average function, infinite memory is necessary for strategies achieving a specific value (i.e. randomized finite-memory strategies are not sufficient), whereas memoryless randomized strategies are sufficient for ε-approximation, for all ε > 0. We further prove that the decision problems for both expectation and satisfaction objectives can be solved in polynomial time and the trade-off curve (Pareto curve) can be ε-approximated in time polynomial in the size of the MDP and 1/ε, and exponential in the number of limit-average functions, for all ε > 0. Our analysis also reveals flaws in previous work for MDPs with multiple mean-payoff functions under the expectation objective, corrects the flaws, and allows us to obtain improved results.},
author = {Brázdil, Tomáš and Brožek, Václav and Chatterjee, Krishnendu and Forejt, Vojtěch and Kučera, Antonín},
issn = {18605974},
journal = {Logical Methods in Computer Science},
number = {1},
publisher = {International Federation of Computational Logic},
title = {{Markov decision processes with multiple long-run average objectives}},
doi = {10.2168/LMCS-10(1:13)2014},
volume = {10},
year = {2014},
}
@inproceedings{2190,
abstract = {We present a new algorithm to construct a (generalized) deterministic Rabin automaton for an LTL formula φ. The automaton is the product of a master automaton and an array of slave automata, one for each G-subformula of φ. The slave automaton for G ψ is in charge of recognizing whether FG ψ holds. As opposed to standard determinization procedures, the states of all our automata have a clear logical structure, which allows for various optimizations. Our construction subsumes former algorithms for fragments of LTL. Experimental results show improvement in the sizes of the resulting automata compared to existing methods.},
author = {Esparza, Javier and Kretinsky, Jan},
pages = {192 -- 208},
publisher = {Springer},
title = {{From LTL to deterministic automata: A safraless compositional approach}},
doi = {10.1007/978-3-319-08867-9_13},
volume = {8559},
year = {2014},
}
@article{535,
abstract = {Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help.},
author = {Chatterjee, Krishnendu and Henzinger, Monika and Krinninger, Sebastian and Nanongkai, Danupon},
journal = {Algorithmica},
number = {3},
pages = {457 -- 492},
publisher = {Springer},
title = {{Polynomial time algorithms for energy games with special weight structures}},
doi = {10.1007/s00453-013-9843-7},
volume = {70},
year = {2014},
}
@inproceedings{2905,
abstract = {Persistent homology is a recent grandchild of homology that has found use in
science and engineering as well as in mathematics. This paper surveys the method as well
as the applications, neglecting completeness in favor of highlighting ideas and directions.},
author = {Edelsbrunner, Herbert and Morozovy, Dmitriy},
location = {Kraków, Poland},
pages = {31 -- 50},
publisher = {European Mathematical Society Publishing House},
title = {{Persistent homology: Theory and practice}},
doi = {10.4171/120-1/3},
year = {2014},
}
@article{1926,
abstract = {We consider cross products of finite graphs with a class of trees that have arbitrarily but finitely long line segments, such as the Fibonacci tree. Such cross products are called tree-strips. We prove that for small disorder random Schrödinger operators on such tree-strips have purely absolutely continuous spectrum in a certain set.},
author = {Sadel, Christian},
journal = {Mathematical Physics, Analysis and Geometry},
number = {3-4},
pages = {409 -- 440},
publisher = {Springer},
title = {{Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips}},
doi = {10.1007/s11040-014-9163-4},
volume = {17},
year = {2014},
}
@article{1899,
abstract = {Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation.},
author = {Williams, Scott and Ratliff, Lyndsay and Postiglione, Maria P and Knoblich, Juergen and Fuchs, Elaine},
journal = {Nature Cell Biology},
number = {8},
pages = {758 -- 769},
publisher = {Nature Publishing Group},
title = {{Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN}},
doi = {10.1038/ncb3001},
volume = {16},
year = {2014},
}
@article{2253,
abstract = {Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation.},
author = {Bailly, Aurélien and Wang, Bangjun and Zwiewka, Marta and Pollmann, Stephan and Schenck, Daniel and Lüthen, Hartwig and Schulz, Alexander and Friml, Jirí and Geisler, Markus},
issn = {09607412},
journal = {Plant Journal},
number = {1},
pages = {108 -- 118},
publisher = {Wiley-Blackwell},
title = {{Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth}},
doi = {10.1111/tpj.12369},
volume = {77},
year = {2014},
}
@article{1629,
abstract = {We propose a method for propagating edit operations in 2D vector graphics, based on geometric relationship functions. These functions quantify the geometric relationship of a point to a polygon, such as the distance to the boundary or the direction to the closest corner vertex. The level sets of the relationship functions describe points with the same relationship to a polygon. For a given query point, we first determine a set of relationships to local features, construct all level sets for these relationships, and accumulate them. The maxima of the resulting distribution are points with similar geometric relationships. We show extensions to handle mirror symmetries, and discuss the use of relationship functions as local coordinate systems. Our method can be applied, for example, to interactive floorplan editing, and it is especially useful for large layouts, where individual edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds of objects by propagating relatively few edit operations.},
author = {Guerrero, Paul and Jeschke, Stefan and Wimmer, Michael and Wonka, Peter},
journal = {ACM Transactions on Graphics},
number = {2},
publisher = {ACM},
title = {{Edit propagation using geometric relationship functions}},
doi = {10.1145/2591010},
volume = {33},
year = {2014},
}
@inproceedings{1643,
abstract = {We extend the notion of verifiable random functions (VRF) to constrained VRFs, which generalize the concept of constrained pseudorandom functions, put forward by Boneh and Waters (Asiacrypt’13), and independently by Kiayias et al. (CCS’13) and Boyle et al. (PKC’14), who call them delegatable PRFs and functional PRFs, respectively. In a standard VRF the secret key sk allows one to evaluate a pseudorandom function at any point of its domain; in addition, it enables computation of a non-interactive proof that the function value was computed correctly. In a constrained VRF from the key sk one can derive constrained keys skS for subsets S of the domain, which allow computation of function values and proofs only at points in S. After formally defining constrained VRFs, we derive instantiations from the multilinear-maps-based constrained PRFs by Boneh and Waters, yielding a VRF with constrained keys for any set that can be decided by a polynomial-size circuit. Our VRFs have the same function values as the Boneh-Waters PRFs and are proved secure under the same hardness assumption, showing that verifiability comes at no cost. Constrained (functional) VRFs were stated as an open problem by Boyle et al.},
author = {Fuchsbauer, Georg},
booktitle = {SCN 2014},
editor = {Abdalla, Michel and De Prisco, Roberto},
location = {Amalfi, Italy},
pages = {95 -- 114},
publisher = {Springer},
title = {{Constrained Verifiable Random Functions }},
doi = {10.1007/978-3-319-10879-7_7},
volume = {8642},
year = {2014},
}
@article{1876,
abstract = {We study densities of functionals over uniformly bounded triangulations of a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay triangulation if this is the case for finite sets.},
author = {Dolbilin, Nikolai and Edelsbrunner, Herbert and Glazyrin, Alexey and Musin, Oleg},
journal = {Moscow Mathematical Journal},
number = {3},
pages = {491 -- 504},
publisher = {Independent University of Moscow},
title = {{Functionals on triangulations of delaunay sets}},
volume = {14},
year = {2014},
}
@article{1890,
abstract = {To search for a target in a complex environment is an everyday behavior that ends with finding the target. When we search for two identical targets, however, we must continue the search after finding the first target and memorize its location. We used fixation-related potentials to investigate the neural correlates of different stages of the search, that is, before and after finding the first target. Having found the first target influenced subsequent distractor processing. Compared to distractor fixations before the first target fixation, a negative shift was observed for three subsequent distractor fixations. These results suggest that processing a target in continued search modulates the brain's response, either transiently by reflecting temporary working memory processes or permanently by reflecting working memory retention.},
author = {Körner, Christof and Braunstein, Verena and Stangl, Matthias and Schlögl, Alois and Neuper, Christa and Ischebeck, Anja},
journal = {Psychophysiology},
number = {4},
pages = {385 -- 395},
publisher = {Wiley-Blackwell},
title = {{Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection}},
doi = {10.1111/psyp.12062},
volume = {51},
year = {2014},
}
@article{1895,
abstract = {Major histocompatibility complex class I (MHCI) molecules were recently identified as novel regulators of synaptic plasticity. These molecules are expressed in various brain areas, especially in regions undergoing activity-dependent synaptic plasticity, but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin, which causes lack of cell surface expression of MHCI. First, we confirmed that MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin knock-out mice lacking cell surface expression of MHCI. We found that low frequency stimulation induced long-term depression in wild-type but not knock-out mice, whereas high frequency stimulation induced long-term potentiation in both genotypes, with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related behavior. Using this model, we analyzed the density of total AMPA receptors and their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture replica labeling. After repeated cocaine exposure, the density of GluR1 was increased, but there was no change in total AMPA receptors and GluR2 levels in wildtype mice. In contrast, following repeated cocaine exposure, increased densities of total AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results indicate that functional deficiency of MHCI enhances synaptic potentiation, induced by electrical and pharmacological stimulation.},
author = {Edamura, Mitsuhiro and Murakami, Gen and Meng, Hongrui and Itakura, Makoto and Shigemoto, Ryuichi and Fukuda, Atsuo and Nakahara, Daiichiro},
journal = {PLoS One},
number = {9},
publisher = {Public Library of Science},
title = {{Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice}},
doi = {10.1371/journal.pone.0107099},
volume = {9},
year = {2014},
}
@article{1908,
abstract = {In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations.},
author = {Weissman, Daniel and Hallatschek, Oskar},
journal = {Genetics},
number = {4},
pages = {1167 -- 1183},
publisher = {Genetics Society of America},
title = {{The rate of adaptation in large sexual populations with linear chromosomes}},
doi = {10.1534/genetics.113.160705},
volume = {196},
year = {2014},
}
@article{1852,
abstract = {To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner.},
author = {Sassi, Massimiliano and Ali, Olivier and Boudon, Frédéric and Cloarec, Gladys and Abad, Ursula and Cellier, Coralie and Chen, Xu and Gilles, Benjamin and Milani, Pascale and Friml, Jirí and Vernoux, Teva and Godin, Christophe and Hamant, Olivier and Traas, Jan},
journal = {Current Biology},
number = {19},
pages = {2335 -- 2342},
publisher = {Cell Press},
title = {{An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis}},
doi = {10.1016/j.cub.2014.08.036},
volume = {24},
year = {2014},
}
@article{1821,
abstract = {We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end.},
author = {Seiringer, Robert},
journal = {Journal of Mathematical Physics},
number = {7},
publisher = {American Institute of Physics},
title = {{Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation}},
doi = {10.1063/1.4881536},
volume = {55},
year = {2014},
}
@article{1996,
abstract = {Auxin polar transport, local maxima, and gradients have become an importantmodel system for studying self-organization. Auxin distribution is regulated by auxin-dependent positive feedback loops that are not well-understood at the molecular level. Previously, we showed the involvement of the RHO of Plants (ROP) effector INTERACTOR of CONSTITUTIVELY active ROP 1 (ICR1) in regulation of auxin transport and that ICR1 levels are posttranscriptionally repressed at the site of maximum auxin accumulation at the root tip. Here, we show that bimodal regulation of ICR1 levels by auxin is essential for regulating formation of auxin local maxima and gradients. ICR1 levels increase concomitant with increase in auxin response in lateral root primordia, cotyledon tips, and provascular tissues. However, in the embryo hypophysis and root meristem, when auxin exceeds critical levels, ICR1 is rapidly destabilized by an SCF(TIR1/AFB) [SKP, Cullin, F-box (transport inhibitor response 1/auxin signaling F-box protein)]-dependent auxin signaling mechanism. Furthermore, ectopic expression of ICR1 in the embryo hypophysis resulted in reduction of auxin accumulation and concomitant root growth arrest. ICR1 disappeared during root regeneration and lateral root initiation concomitantly with the formation of a local auxin maximum in response to external auxin treatments and transiently after gravitropic stimulation. Destabilization of ICR1 was impaired after inhibition of auxin transport and signaling, proteasome function, and protein synthesis. A mathematical model based on these findings shows that an in vivo-like auxin distribution, rootward auxin flux, and shootward reflux can be simulated without assuming preexisting tissue polarity. Our experimental results and mathematical modeling indicate that regulation of auxin distribution is tightly associated with auxin-dependent ICR1 levels.},
author = {Hazak, Ora and Obolski, Uri and Prat, Tomas and Friml, Jiří and Hadany, Lilach and Yalovsky, Shaul},
journal = {PNAS},
number = {50},
pages = {E5471 -- E5479},
publisher = {National Academy of Sciences},
title = {{Bimodal regulation of ICR1 levels generates self-organizing auxin distribution}},
doi = {10.1073/pnas.1413918111},
volume = {111},
year = {2014},
}
@inproceedings{1927,
abstract = {Constrained pseudorandom functions have recently been introduced independently by Boneh and Waters (Asiacrypt’13), Kiayias et al. (CCS’13), and Boyle et al. (PKC’14). In a standard pseudorandom function (PRF) a key k is used to evaluate the PRF on all inputs in the domain. Constrained PRFs additionally offer the functionality to delegate “constrained” keys kS which allow to evaluate the PRF only on a subset S of the domain. The three above-mentioned papers all show that the classical GGM construction (J.ACM’86) of a PRF from a pseudorandom generator (PRG) directly yields a constrained PRF where one can compute constrained keys to evaluate the PRF on all inputs with a given prefix. This constrained PRF has already found many interesting applications. Unfortunately, the existing security proofs only show selective security (by a reduction to the security of the underlying PRG). To achieve full security, one has to use complexity leveraging, which loses an exponential factor 2N in security, where N is the input length. The first contribution of this paper is a new reduction that only loses a quasipolynomial factor qlog N, where q is the number of adversarial queries. For this we develop a new proof technique which constructs a distinguisher by interleaving simple guessing steps and hybrid arguments a small number of times. This approach might be of interest also in other contexts where currently the only technique to achieve full security is complexity leveraging. Our second contribution is concerned with another constrained PRF, due to Boneh and Waters, which allows for constrained keys for the more general class of bit-fixing functions. Their security proof also suffers from a 2N loss, which we show is inherent. We construct a meta-reduction which shows that any “simple” reduction of full security from a noninteractive hardness assumption must incur an exponential security loss.},
author = {Georg Fuchsbauer and Konstantinov, Momchil and Krzysztof Pietrzak and Rao, Vanishree},
pages = {173 -- 192},
publisher = {Springer},
title = {{Adaptive security of constrained PRFs}},
doi = {10.1145/2591796.2591825},
volume = {8874},
year = {2014},
}
@article{2021,
abstract = {Neurotrophins regulate diverse aspects of neuronal development and plasticity, but their precise in vivo functions during neural circuit assembly in the central brain remain unclear. We show that the neurotrophin receptor tropomyosin-related kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3) from cerebellar granule cells, which provide major afferent input to developing Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development.},
author = {William, Joo and Hippenmeyer, Simon and Luo, Liqun},
journal = {Science},
number = {6209},
pages = {626 -- 629},
publisher = {American Association for the Advancement of Science},
title = {{Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling}},
doi = {10.1126/science.1258996},
volume = {346},
year = {2014},
}
@article{2002,
abstract = {Oriens-lacunosum moleculare (O-LM) interneurons in the CA1 region of the hippocampus play a key role in feedback inhibition and in the control of network activity. However, how these cells are efficiently activated in the network remains unclear. To address this question, I performed recordings from CA1 pyramidal neuron axons, the presynaptic fibers that provide feedback innervation of these interneurons. Two forms of axonal action potential (AP) modulation were identified. First, repetitive stimulation resulted in activity-dependent AP broadening. Broadening showed fast onset, with marked changes in AP shape following a single AP. Second, tonic depolarization in CA1 pyramidal neuron somata induced AP broadening in the axon, and depolarization-induced broadening summated with activity-dependent broadening. Outsideout patch recordings from CA1 pyramidal neuron axons revealed a high density of a-dendrotoxin (α-DTX)-sensitive, inactivating K+ channels, suggesting that K+ channel inactivation mechanistically contributes to AP broadening. To examine the functional consequences of axonal AP modulation for synaptic transmission, I performed paired recordings between synaptically connected CA1 pyramidal neurons and O-LM interneurons. CA1 pyramidal neuron-O-LM interneuron excitatory postsynaptic currents (EPSCs) showed facilitation during both repetitive stimulation and tonic depolarization of the presynaptic neuron. Both effects were mimicked and occluded by α-DTX, suggesting that they were mediated by K+ channel inactivation. Therefore, axonal AP modulation can greatly facilitate the activation of O-LM interneurons. In conclusion, modulation of AP shape in CA1 pyramidal neuron axons substantially enhances the efficacy of principal neuron-interneuron synapses, promoting the activation of O-LM interneurons in recurrent inhibitory microcircuits.},
author = {Kim, Sooyun},
journal = {PLoS One},
number = {11},
publisher = {Public Library of Science},
title = {{Action potential modulation in CA1 pyramidal neuron axons facilitates OLM interneuron activation in recurrent inhibitory microcircuits of rat hippocampus}},
doi = {10.1371/journal.pone.0113124},
volume = {9},
year = {2014},
}
@misc{2007,
author = {Anna Klimova and Rudas, Tamás},
publisher = {The Comprehensive R Archive Network},
title = {{gIPFrm: Generalized iterative proportional fitting for relational models}},
year = {2014},
}
@inproceedings{2033,
abstract = {The learning with privileged information setting has recently attracted a lot of attention within the machine learning community, as it allows the integration of additional knowledge into the training process of a classifier, even when this comes in the form of a data modality that is not available at test time. Here, we show that privileged information can naturally be treated as noise in the latent function of a Gaussian process classifier (GPC). That is, in contrast to the standard GPC setting, the latent function is not just a nuisance but a feature: it becomes a natural measure of confidence about the training data by modulating the slope of the GPC probit likelihood function. Extensive experiments on public datasets show that the proposed GPC method using privileged noise, called GPC+, improves over a standard GPC without privileged knowledge, and also over the current state-of-the-art SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep learning methods can be compressed as privileged information.},
author = {Hernandez Lobato, Daniel and Sharmanska, Viktoriia and Kersting, Kristian and Lampert, Christoph and Quadrianto, Novi},
booktitle = {Advances in Neural Information Processing Systems},
location = {Montreal, Canada},
number = {January},
pages = {837--845},
publisher = {Neural Information Processing Systems},
title = {{Mind the nuisance: Gaussian process classification using privileged noise}},
volume = {1},
year = {2014},
}
@article{2019,
abstract = {We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory.},
author = {Erdös, László and Schröder, Dominik J},
journal = {Mathematical Physics, Analysis and Geometry},
number = {3-4},
pages = {441 -- 464},
publisher = {Springer},
title = {{Phase transition in the density of states of quantum spin glasses}},
doi = {10.1007/s11040-014-9164-3},
volume = {17},
year = {2014},
}
@article{2040,
abstract = {Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. },
author = {Kicheva, Anna and Bollenbach, Mark Tobias and Ribeiro, Ana and Pérez Valle, Helena and Lovell Badge, Robin and Episkopou, Vasso and Briscoe, James},
journal = {Science},
number = {6204},
publisher = {American Association for the Advancement of Science},
title = {{Coordination of progenitor specification and growth in mouse and chick spinal cord}},
doi = {10.1126/science.1254927},
volume = {345},
year = {2014},
}
@inproceedings{2045,
abstract = {We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest.},
author = {Dachman Soled, Dana and Fuchsbauer, Georg and Mohassel, Payman and O’Neill, Adam},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
editor = {Krawczyk, Hugo},
location = {Buenos Aires, Argentina},
pages = {329 -- 344},
publisher = {Springer},
title = {{Enhanced chosen-ciphertext security and applications}},
doi = {10.1007/978-3-642-54631-0_19},
volume = {8383},
year = {2014},
}
@article{2064,
abstract = {We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses.},
author = {Rubio, Maía and Fukazawa, Yugo and Kamasawa, Naomi and Clarkson, Cheryl and Molnár, Elek and Shigemoto, Ryuichi},
journal = {Journal of Comparative Neurology},
number = {18},
pages = {4023 -- 4042},
publisher = {Wiley-Blackwell},
title = {{Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus}},
doi = {10.1002/cne.23654},
volume = {522},
year = {2014},
}
@inproceedings{2057,
abstract = {In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark.},
author = {Morvant, Emilie and Habrard, Amaury and Ayache, Stéphane},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
location = {Joensuu, Finland},
pages = {153 -- 162},
publisher = {Springer},
title = {{Majority vote of diverse classifiers for late fusion}},
doi = {10.1007/978-3-662-44415-3_16},
volume = {8621},
year = {2014},
}
@article{2184,
abstract = {Given topological spaces X,Y, a fundamental problem of algebraic topology is understanding the structure of all continuous maps X→ Y. We consider a computational version, where X,Y are given as finite simplicial complexes, and the goal is to compute [X,Y], that is, all homotopy classes of suchmaps.We solve this problem in the stable range, where for some d ≥ 2, we have dim X ≤ 2d-2 and Y is (d-1)-connected; in particular, Y can be the d-dimensional sphere Sd. The algorithm combines classical tools and ideas from homotopy theory (obstruction theory, Postnikov systems, and simplicial sets) with algorithmic tools from effective algebraic topology (locally effective simplicial sets and objects with effective homology). In contrast, [X,Y] is known to be uncomputable for general X,Y, since for X = S1 it includes a well known undecidable problem: testing triviality of the fundamental group of Y. In follow-up papers, the algorithm is shown to run in polynomial time for d fixed, and extended to other problems, such as the extension problem, where we are given a subspace A ⊂ X and a map A→ Y and ask whether it extends to a map X → Y, or computing the Z2-index-everything in the stable range. Outside the stable range, the extension problem is undecidable.},
author = {Čadek, Martin and Krcál, Marek and Matoušek, Jiří and Sergeraert, Francis and Vokřínek, Lukáš and Wagner, Uli},
journal = {Journal of the ACM},
number = {3},
publisher = {ACM},
title = {{Computing all maps into a sphere}},
doi = {10.1145/2597629},
volume = {61},
year = {2014},
}
@inproceedings{2153,
abstract = {We define a simple, explicit map sending a morphism f : M → N of pointwise finite dimensional persistence modules to a matching between the barcodes of M and N. Our main result is that, in a precise sense, the quality of this matching is tightly controlled by the lengths of the longest intervals in the barcodes of ker f and coker f . As an immediate corollary, we obtain a new proof of the algebraic stability theorem for persistence barcodes [5, 9], a fundamental result in the theory of persistent homology. In contrast to previous proofs, ours shows explicitly how a δ-interleaving morphism between two persistence modules induces a δ-matching between the barcodes of the two modules. Our main result also specializes to a structure theorem for submodules and quotients of persistence modules. Copyright is held by the owner/author(s).},
author = {Bauer, Ulrich and Lesnick, Michael},
booktitle = {Proceedings of the Annual Symposium on Computational Geometry},
location = {Kyoto, Japan},
pages = {355 -- 364},
publisher = {ACM},
title = {{Induced matchings of barcodes and the algebraic stability of persistence}},
doi = {10.1145/2582112.2582168},
year = {2014},
}
@article{2165,
abstract = {In machine learning, the domain adaptation problem arrives when the test (tar-get) and the train (source) data are generated from different distributions. A key applied issue is thus the design of algorithms able to generalize on a new distribution, for which we have no label information. We focus on learning classification models defined as a weighted majority vote over a set of real-valued functions. In this context, Germain et al. (2013) have shown that a measure of disagreement between these functions is crucial to control. The core of this measure is a theoretical bound—the C-bound (Lacasse et al., 2007)—which involves the disagreement and leads to a well performing majority vote learn-ing algorithm in usual non-adaptative supervised setting: MinCq. In this work,we propose a framework to extend MinCq to a domain adaptation scenario.This procedure takes advantage of the recent perturbed variation divergence between distributions proposed by Harel and Mannor (2012). Justified by a theoretical bound on the target risk of the vote, we provide to MinCq a tar-get sample labeled thanks to a perturbed variation-based self-labeling focused on the regions where the source and target marginals appear similar. We also study the influence of our self-labeling, from which we deduce an original process for tuning the hyperparameters. Finally, our framework called PV-MinCq shows very promising results on a rotation and translation synthetic problem.},
author = {Morvant, Emilie},
journal = {Pattern Recognition Letters},
pages = {37--43},
publisher = {Elsevier},
title = {{Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling}},
doi = {10.1016/j.patrec.2014.08.013},
volume = {51},
year = {2014},
}
@inproceedings{2160,
abstract = {Transfer learning has received a lot of attention in the machine learning community over the last years, and several effective algorithms have been developed. However, relatively little is known about their theoretical properties, especially in the setting of lifelong learning, where the goal is to transfer information to tasks for which no data have been observed so far. In this work we study lifelong learning from a theoretical perspective. Our main result is a PAC-Bayesian generalization bound that offers a unified view on existing paradigms for transfer learning, such as the transfer of parameters or the transfer of low-dimensional representations. We also use the bound to derive two principled lifelong learning algorithms, and we show that these yield results comparable with existing methods.},
author = {Pentina, Anastasia and Lampert, Christoph},
editor = {Xing, Eric and Jebara, Tony},
location = {Beijing, China},
pages = {991 -- 999},
publisher = {Omnipress},
title = {{A PAC-Bayesian bound for Lifelong Learning}},
volume = {32},
year = {2014},
}
@article{2158,
abstract = {Directional guidance of migrating cells is relatively well explored in the reductionist setting of cell culture experiments. Here spatial gradients of chemical cues as well as gradients of mechanical substrate characteristics prove sufficient to attract single cells as well as their collectives. How such gradients present and act in the context of an organism is far less clear. Here we review recent advances in understanding how guidance cues emerge and operate in the physiological context.},
author = {Majumdar, Ritankar and Sixt, Michael K and Parent, Carole},
journal = {Current Opinion in Cell Biology},
number = {1},
pages = {33 -- 40},
publisher = {Elsevier},
title = {{New paradigms in the establishment and maintenance of gradients during directed cell migration}},
doi = {10.1016/j.ceb.2014.05.010},
volume = {30},
year = {2014},
}
@article{2223,
abstract = {Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes.},
author = {Tanaka, Hirokazu and Nodzyński, Tomasz and Kitakura, Saeko and Feraru, Mugurel and Sasabe, Michiko and Ishikawa, Tomomi and Kleine Vehn, Jürgen and Kakimoto, Tatsuo and Friml, Jirí},
issn = {00320781},
journal = {Plant and Cell Physiology},
number = {4},
pages = {737 -- 749},
publisher = {Oxford University Press},
title = {{BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis}},
doi = {10.1093/pcp/pct196},
volume = {55},
year = {2014},
}
@article{2230,
abstract = {Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.},
author = {Guzmán, José and Schlögl, Alois and Schmidt Hieber, Christoph},
issn = {16625196},
journal = {Frontiers in Neuroinformatics},
number = {FEB},
publisher = {Frontiers Research Foundation},
title = {{Stimfit: Quantifying electrophysiological data with Python}},
doi = {10.3389/fninf.2014.00016},
volume = {8},
year = {2014},
}
@article{2235,
abstract = {Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators.},
author = {Fürst, Matthias and Mcmahon, Dino and Osborne, Juliet and Paxton, Robert and Brown, Mark},
issn = {00280836},
journal = {Nature},
number = {7488},
pages = {364 -- 366},
publisher = {Nature Publishing Group},
title = {{Disease associations between honeybees and bumblebees as a threat to wild pollinators}},
doi = {10.1038/nature12977},
volume = {506},
year = {2014},
}
@article{2261,
abstract = {To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.},
author = {Zhu, Fangfang and Gamboa, Matthew and Farruggio, Alfonso and Hippenmeyer, Simon and Tasic, Bosiljka and Schüle, Birgitt and Chen Tsai, Yanru and Calos, Michele},
journal = {Nucleic Acids Research},
number = {5},
publisher = {Oxford University Press},
title = {{DICE, an efficient system for iterative genomic editing in human pluripotent stem cells}},
doi = {10.1093/nar/gkt1290},
volume = {42},
year = {2014},
}
@article{2285,
abstract = {GABAergic inhibitory interneurons control fundamental aspects of neuronal network function. Their functional roles are assumed to be defined by the identity of their input synapses, the architecture of their dendritic tree, the passive and active membrane properties and finally the nature of their postsynaptic targets. Indeed, interneurons display a high degree of morphological and physiological heterogeneity. However, whether their morphological and physiological characteristics are correlated and whether interneuron diversity can be described by a continuum of GABAergic cell types or by distinct classes has remained unclear. Here we perform a detailed morphological and physiological characterization of GABAergic cells in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased and efficient sampling and classification we used knock-in mice expressing the enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive neurons and performed cluster analysis. We identified five interneuron classes, each of them characterized by a distinct set of anatomical and physiological parameters. Cross-correlation analysis further revealed a direct relation between morphological and physiological properties indicating that dentate gyrus interneurons fall into functionally distinct classes which may differentially control neuronal network activity.},
author = {Hosp, Jonas and Strüber, Michael and Yanagawa, Yuchio and Obata, Kunihiko and Vida, Imre and Jonas, Peter M and Bartos, Marlene},
journal = {Hippocampus},
number = {2},
pages = {189 -- 203},
publisher = {Wiley-Blackwell},
title = {{Morpho-physiological criteria divide dentate gyrus interneurons into classes}},
doi = {10.1002/hipo.22214},
volume = {23},
year = {2014},
}
@misc{5417,
abstract = {We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M'within distance ρ from M satisfy (or violate)φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata.
The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification.
We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved.
We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging.
We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.},
author = {Henzinger, Thomas A and Otop, Jan},
issn = {2664-1690},
pages = {14},
publisher = {IST Austria},
title = {{From model checking to model measuring}},
doi = {10.15479/AT:IST-2014-172-v1-1},
year = {2014},
}
@article{6124,
abstract = {Despite the importance of G-protein coupled receptors (GPCRs) their biogenesis is poorly understood. Like vertebrates, C. elegans uses a large family of GPCRs as chemoreceptors. A subset of these receptors, such as ODR-10, requires the odr-4 and odr-8 genes to be appropriately localized to sensory cilia. The odr-4 gene encodes a conserved tail-anchored transmembrane protein; the molecular identity of odr-8 is unknown. Here, we show that odr-8 encodes the C. elegans ortholog of Ufm1-specific protease 2 (UfSP2). UfSPs are cysteine proteases identified biochemically by their ability to liberate the ubiquitin-like modifier Ufm1 from its pro-form and protein conjugates. ODR-8/UfSP2 and ODR-4 are expressed in the same set of twelve chemosensory neurons, and physically interact at the ER membrane. ODR-4 also binds ODR-10, suggesting that an ODR-4/ODR-8 complex promotes GPCR folding, maturation, or export from the ER. The physical interaction between human ODR4 and UfSP2 suggests that this complex's role in GPCR biogenesis may be evolutionarily conserved. Unexpectedly, mutant versions of ODR-8/UfSP2 lacking catalytic residues required for protease activity can rescue all odr-8 mutant phenotypes tested. Moreover, deleting C. elegans ufm-1 does not alter chemoreceptor traffic to cilia, either in wild type or in odr-8 mutants. Thus, UfSP2 proteins have protease- and Ufm1-independent functions in GPCR biogenesis.},
author = {Chen, Changchun and Itakura, Eisuke and Weber, Katherine P. and Hegde, Ramanujan S. and de Bono, Mario},
issn = {1553-7404},
journal = {PLoS Genetics},
number = {3},
publisher = {Public Library of Science (PLoS)},
title = {{An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism}},
doi = {10.1371/journal.pgen.1004082},
volume = {10},
year = {2014},
}
@article{6319,
abstract = {Nous étudions le comportement asymptotique du nombre de variétés dans une certaine classe ne satisfaisant pas le principe de Hasse. Cette étude repose sur des résultats récemmentobtenus par Colliot-Thélène.},
author = {Bretèche, Régis de la and Browning, Timothy D},
issn = {1246-7405},
journal = {Journal de Théorie des Nombres de Bordeaux},
number = {1},
pages = {25--44},
publisher = {Cellule MathDoc/CEDRAM},
title = {{Contre-exemples au principe de Hasse pour certains tores coflasques}},
doi = {10.5802/jtnb.857},
volume = {26},
year = {2014},
}
@article{7071,
abstract = {Spin and orbital quantum numbers play a key role in the physics of Mott insulators, but in most systems they are connected only indirectly—via the Pauli exclusion principle and the Coulomb interaction. Iridium-based oxides (iridates) introduce strong spin–orbit coupling directly, such that these numbers become entwined together and the Mott physics attains a strong orbital character. In the layered honeycomb iridates this is thought to generate highly spin–anisotropic magnetic interactions, coupling the spin to a given spatial direction of exchange and leading to strongly frustrated magnetism. Here we report a new iridate structure that has the same local connectivity as the layered honeycomb and exhibits striking evidence for highly spin–anisotropic exchange. The basic structural units of this material suggest that a new family of three-dimensional structures could exist, the ‘harmonic honeycomb’ iridates, of which the present compound is the first example.},
author = {Modic, Kimberly A and Smidt, Tess E. and Kimchi, Itamar and Breznay, Nicholas P. and Biffin, Alun and Choi, Sungkyun and Johnson, Roger D. and Coldea, Radu and Watkins-Curry, Pilanda and McCandless, Gregory T. and Chan, Julia Y. and Gandara, Felipe and Islam, Z. and Vishwanath, Ashvin and Shekhter, Arkady and McDonald, Ross D. and Analytis, James G.},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
title = {{Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate}},
doi = {10.1038/ncomms5203},
volume = {5},
year = {2014},
}
@techreport{7038,
author = {Huszár, Kristóf and Rolinek, Michal},
pages = {5},
publisher = {IST Austria},
title = {{Playful Math - An introduction to mathematical games}},
year = {2014},
}
@article{978,
abstract = {The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications.},
author = {Zeljkovic, Ilija and Okada, Yoshinori and Huang, Chengyi and Sankar, Raman and Walkup, Daniel and Zhou, Wenwen and Maksym Serbyn and Chou, Fangcheng and Tsai, Wei-Feng and Lin, Hsin and Bansil, Arun and Fu, Liang and Hasan, Md Z and Madhavan, Vidya},
journal = {Nature Physics},
number = {8},
pages = {572 -- 577},
publisher = {Nature Publishing Group},
title = {{Mapping the unconventional orbital texture in topological crystalline insulators}},
doi = {10.1038/nphys3012},
volume = {10},
year = {2014},
}
@article{98,
abstract = {Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.},
author = {Higginbotham, Andrew P and Larsen, Thorvald and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles and Kuemmeth, Ferdinand},
journal = {Nano Letters},
number = {6},
pages = {3582 -- 3586},
publisher = {American Chemical Society},
title = {{Hole spin coherence in a Ge/Si heterostructure nanowire}},
doi = {10.1021/nl501242b},
volume = {14},
year = {2014},
}
@article{980,
abstract = {Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization.},
author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {17},
publisher = {American Physical Society},
title = {{Quantum quenches in the many-body localized phase}},
doi = {10.1103/PhysRevB.90.174302},
volume = {90},
year = {2014},
}
@article{2254,
abstract = {Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus.},
author = {Pernia-Andrade, Alejandro and Jonas, Peter M},
issn = {08966273},
journal = {Neuron},
number = {1},
pages = {140 -- 152},
publisher = {Elsevier},
title = {{Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations}},
doi = {10.1016/j.neuron.2013.09.046},
volume = {81},
year = {2014},
}
@article{2228,
abstract = {Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing.},
author = {Hu, Hua and Jonas, Peter M},
issn = {10976256},
journal = {Nature Neuroscience},
number = {5},
pages = {686--693},
publisher = {Nature Publishing Group},
title = {{A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons}},
doi = {10.1038/nn.3678},
volume = {17},
year = {2014},
}
@article{2716,
abstract = {Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω ω -regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on vector addition systems with states. Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts.},
author = {Chatterjee, Krishnendu and Randour, Mickael and Raskin, Jean},
journal = {Acta Informatica},
number = {3-4},
pages = {129 -- 163},
publisher = {Springer},
title = {{Strategy synthesis for multi-dimensional quantitative objectives}},
doi = {10.1007/s00236-013-0182-6},
volume = {51},
year = {2014},
}
@article{2038,
abstract = {Recently, there has been an effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions. At the heart of quantitative objectives lies the accumulation of values along a computation. It is often the accumulated sum, as with energy objectives, or the accumulated average, as with mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point in time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire infinite computation. We study the border of decidability for such quantitative extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with both prefix-accumulation assertions, or extending LTL with both path-accumulation assertions, results in temporal logics whose model-checking problem is decidable. Moreover, the prefix-accumulation assertions may be generalized with "controlled accumulation," allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that this branching-time logic is, in a sense, the maximal logic with one or both of the prefix-accumulation assertions that permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL, makes the problem undecidable.},
author = {Boker, Udi and Chatterjee, Krishnendu and Henzinger, Thomas A and Kupferman, Orna},
journal = {ACM Transactions on Computational Logic (TOCL)},
number = {4},
publisher = {ACM},
title = {{Temporal specifications with accumulative values}},
doi = {10.1145/2629686},
volume = {15},
year = {2014},
}
@inproceedings{2189,
abstract = {En apprentissage automatique, nous parlons d'adaptation de domaine lorsque les données de test (cibles) et d'apprentissage (sources) sont générées selon différentes distributions. Nous devons donc développer des algorithmes de classification capables de s'adapter à une nouvelle distribution, pour laquelle aucune information sur les étiquettes n'est disponible. Nous attaquons cette problématique sous l'angle de l'approche PAC-Bayésienne qui se focalise sur l'apprentissage de modèles définis comme des votes de majorité sur un ensemble de fonctions. Dans ce contexte, nous introduisons PV-MinCq une version adaptative de l'algorithme (non adaptatif) MinCq. PV-MinCq suit le principe suivant. Nous transférons les étiquettes sources aux points cibles proches pour ensuite appliquer MinCq sur l'échantillon cible ``auto-étiqueté'' (justifié par une borne théorique). Plus précisément, nous définissons un auto-étiquetage non itératif qui se focalise dans les régions où les distributions marginales source et cible sont les plus similaires. Dans un second temps, nous étudions l'influence de notre auto-étiquetage pour en déduire une procédure de validation des hyperparamètres. Finalement, notre approche montre des résultats empiriques prometteurs.},
author = {Morvant, Emilie},
location = {Saint-Etienne, France},
pages = {49--58},
publisher = {Elsevier},
title = {{Adaptation de domaine de vote de majorité par auto-étiquetage non itératif}},
volume = {1},
year = {2014},
}
@inproceedings{1516,
abstract = {We present a rigorous derivation of the BCS gap equation for superfluid fermionic gases with point interactions. Our starting point is the BCS energy functional, whose minimizer we investigate in the limit when the range of the interaction potential goes to zero.
},
author = {Bräunlich, Gerhard and Hainzl, Christian and Seiringer, Robert},
booktitle = {Proceedings of the QMath12 Conference},
location = {Berlin, Germany},
pages = {127 -- 137},
publisher = {World Scientific Publishing},
title = {{On the BCS gap equation for superfluid fermionic gases}},
doi = {10.1142/9789814618144_0007 },
year = {2014},
}
@article{2083,
abstract = {Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.},
author = {Lagator, Mato and Morgan, Andrew and Neve, Paul and Colegrave, Nick},
journal = {Evolution},
number = {8},
pages = {2296 -- 2305},
publisher = {Wiley},
title = {{Role of sex and migration in adaptation to sink environments}},
doi = {10.1111/evo.12440},
volume = {68},
year = {2014},
}
@article{119,
abstract = {Observations of flowing granular matter have suggested that same-material tribocharging depends on particle size, typically rendering large grains positive and small ones negative. Models assuming the transfer of trapped electrons can account for this trend, but have not been validated. Tracking individual grains in an electric field, we show quantitatively that charge is transferred based on size between materially identical grains. However, the surface density of trapped electrons, measured independently by thermoluminescence techniques, is orders of magnitude too small to account for the scale of charge transferred. This reveals that trapped electrons are not a necessary ingredient for same-material tribocharging.},
author = {Waitukaitis, Scott R and Lee, Victor and Pierson, James and Forman, Steven and Jaeger, Heinrich},
journal = {APS Physics, Physical Review Letters},
number = {21},
publisher = {American Physical Society},
title = {{Size-dependent same-material tribocharging in insulating grains}},
doi = {10.1103/PhysRevLett.112.218001},
volume = {112},
year = {2014},
}
@inproceedings{1702,
abstract = {In this paper we present INTERHORN, a solver for recursion-free Horn clauses. The main application domain of INTERHORN lies in solving interpolation problems arising in software verification. We show how a range of interpolation problems, including path, transition, nested, state/transition and well-founded interpolation can be handled directly by INTERHORN. By detailing these interpolation problems and their Horn clause representations, we hope to encourage the emergence of a common back-end interpolation interface useful for diverse verification tools.},
author = {Gupta, Ashutosh and Popeea, Corneliu and Rybalchenko, Andrey},
booktitle = {Electronic Proceedings in Theoretical Computer Science, EPTCS},
location = {Vienna, Austria},
pages = {31 -- 38},
publisher = {Open Publishing},
title = {{Generalised interpolation by solving recursion free-horn clauses}},
doi = {10.4204/EPTCS.169.5},
volume = {169},
year = {2014},
}
@article{1889,
abstract = {We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity.},
author = {Bräunlich, Gerhard and Hainzl, Christian and Seiringer, Robert},
journal = {Reviews in Mathematical Physics},
number = {7},
publisher = {World Scientific Publishing},
title = {{Translation-invariant quasi-free states for fermionic systems and the BCS approximation}},
doi = {10.1142/S0129055X14500123},
volume = {26},
year = {2014},
}
@article{1896,
abstract = {Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.},
author = {Kollár, Richard and Bod'ová, Katarína and Nosek, Jozef and Tomáška, Ľubomír},
journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
number = {3},
publisher = {American Institute of Physics},
title = {{Mathematical model of alternative mechanism of telomere length maintenance}},
doi = {10.1103/PhysRevE.89.032701},
volume = {89},
year = {2014},
}
@article{1923,
abstract = {We derive the equations for a thin, axisymmetric elastic shell subjected to an internal active stress giving rise to active tension and moments within the shell. We discuss the stability of a cylindrical elastic shell and its response to a localized change in internal active stress. This description is relevant to describe the cellular actomyosin cortex, a thin shell at the cell surface behaving elastically at a short timescale and subjected to active internal forces arising from myosin molecular motor activity. We show that the recent observations of cell deformation following detachment of adherent cells (Maître J-L et al 2012 Science 338 253-6) are well accounted for by this mechanical description. The actin cortex elastic and bending moduli can be obtained from a quantitative analysis of cell shapes observed in these experiments. Our approach thus provides a non-invasive, imaging-based method for the extraction of cellular physical parameters.},
author = {Berthoumieux, Hélène and Maître, Jean-Léon and Heisenberg, Carl-Philipp J and Paluch, Ewa and Julicher, Frank and Salbreux, Guillaume},
journal = {New Journal of Physics},
publisher = {IOP Publishing Ltd.},
title = {{Active elastic thin shell theory for cellular deformations}},
doi = {10.1088/1367-2630/16/6/065005},
volume = {16},
year = {2014},
}
@article{1935,
abstract = {We consider Ising models in d = 2 and d = 3 dimensions with nearest neighbor ferromagnetic and long-range antiferromagnetic interactions, the latter decaying as (distance)-p, p > 2d, at large distances. If the strength J of the ferromagnetic interaction is larger than a critical value J c, then the ground state is homogeneous. It has been conjectured that when J is smaller than but close to J c, the ground state is periodic and striped, with stripes of constant width h = h(J), and h → ∞ as J → Jc -. (In d = 3 stripes mean slabs, not columns.) Here we rigorously prove that, if we normalize the energy in such a way that the energy of the homogeneous state is zero, then the ratio e 0(J)/e S(J) tends to 1 as J → Jc -, with e S(J) being the energy per site of the optimal periodic striped/slabbed state and e 0(J) the actual ground state energy per site of the system. Our proof comes with explicit bounds on the difference e 0(J)-e S(J) at small but positive J c-J, and also shows that in this parameter range the ground state is striped/slabbed in a certain sense: namely, if one looks at a randomly chosen window, of suitable size ℓ (very large compared to the optimal stripe size h(J)), one finds a striped/slabbed state with high probability.},
author = {Giuliani, Alessandro and Lieb, Élliott and Seiringer, Robert},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {333 -- 350},
publisher = {Springer},
title = {{Formation of stripes and slabs near the ferromagnetic transition}},
doi = {10.1007/s00220-014-1923-2},
volume = {331},
year = {2014},
}
@article{1904,
abstract = {We prove a Strichartz inequality for a system of orthonormal functions, with an optimal behavior of the constant in the limit of a large number of functions. The estimate generalizes the usual Strichartz inequality, in the same fashion as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application, we consider the Schrödinger equation with a time-dependent potential and we show the existence of the wave operator in Schatten spaces.},
author = {Frank, Rupert and Lewin, Mathieu and Lieb, Élliott and Seiringer, Robert},
journal = {Journal of the European Mathematical Society},
number = {7},
pages = {1507 -- 1526},
publisher = {European Mathematical Society},
title = {{Strichartz inequality for orthonormal functions}},
doi = {10.4171/JEMS/467},
volume = {16},
year = {2014},
}
@article{1909,
abstract = {Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.},
author = {Ezard, Thomas and Prizak, Roshan and Hoyle, Rebecca},
journal = {Functional Ecology},
number = {3},
pages = {693 -- 701},
publisher = {Wiley-Blackwell},
title = {{The fitness costs of adaptation via phenotypic plasticity and maternal effects}},
doi = {10.1111/1365-2435.12207},
volume = {28},
year = {2014},
}
@article{2041,
abstract = {The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time.},
author = {Jonas, Peter M and Lisman, John},
journal = {Frontiers in Neural Circuits},
publisher = {Frontiers Research Foundation},
title = {{Structure, function and plasticity of hippocampal dentate gyrus microcircuits}},
doi = {10.3389/fncir.2014.00107},
volume = {8},
year = {2014},
}
@inproceedings{2046,
abstract = {We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications.},
author = {Bellare, Mihir and Fuchsbauer, Georg},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
editor = {Krawczyk, Hugo},
location = {Buenos Aires, Argentina},
pages = {520 -- 537},
publisher = {Springer},
title = {{Policy-based signatures}},
doi = {10.1007/978-3-642-54631-0_30},
volume = {8383},
year = {2014},
}
@inproceedings{2058,
abstract = {We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations.},
author = {Raveendran, Karthik and Wojtan, Christopher J and Thuerey, Nils and Türk, Greg},
booktitle = {ACM Transactions on Graphics},
location = {Vancouver, Canada},
number = {4},
publisher = {ACM},
title = {{Blending liquids}},
doi = {10.1145/2601097.2601126},
volume = {33},
year = {2014},
}
@article{2022,
abstract = {Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical neurons. To gain insight into the patterns of RGP division and neuron production, we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using Mosaic Analysis with Double Markers, which provides single-cell resolution of progenitor division patterns and potential in vivo. We found that RGPs progress through a coherent program in which their proliferative potential diminishes in a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce ∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary output in neuronal production. Removal of OTX1, a transcription factor transiently expressed in RGPs, results in both deep- and superficial-layer neuron loss and a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to produce glia. These results suggest that progenitor behavior and histogenesis in the mammalian neocortex conform to a remarkably orderly and deterministic program.},
author = {Gao, Peng and Postiglione, Maria P and Krieger, Teresa and Hernandez, Luisirene and Wang, Chao and Han, Zhi and Streicher, Carmen and Papusheva, Ekaterina and Insolera, Ryan and Chugh, Kritika and Kodish, Oren and Huang, Kun and Simons, Benjamin and Luo, Liqun and Hippenmeyer, Simon and Shi, Song},
journal = {Cell},
number = {4},
pages = {775 -- 788},
publisher = {Cell Press},
title = {{Deterministic progenitor behavior and unitary production of neurons in the neocortex}},
doi = {10.1016/j.cell.2014.10.027},
volume = {159},
year = {2014},
}
@inproceedings{2173,
abstract = {In this work we introduce a new approach to co-classification, i.e. the task of jointly classifying multiple, otherwise independent, data samples. The method we present, named CoConut, is based on the idea of adding a regularizer in the label space to encode certain priors on the resulting labelings. A regularizer that encourages labelings that are smooth across the test set, for instance, can be seen as a test-time variant of the cluster assumption, which has been proven useful at training time in semi-supervised learning. A regularizer that introduces a preference for certain class proportions can be regarded as a prior distribution on the class labels. CoConut can build on existing classifiers without making any assumptions on how they were obtained and without the need to re-train them. The use of a regularizer adds a new level of flexibility. It allows the integration of potentially new information at test time, even in other modalities than what the classifiers were trained on. We evaluate our framework on six datasets, reporting a clear performance gain in classification accuracy compared to the standard classification setup that predicts labels for each test sample separately.
},
author = {Khamis, Sameh and Lampert, Christoph},
booktitle = {Proceedings of the British Machine Vision Conference 2014},
location = {Nottingham, UK},
publisher = {BMVA Press},
title = {{CoConut: Co-classification with output space regularization}},
year = {2014},
}
@article{2178,
abstract = {We consider the three-state toric homogeneous Markov chain model (THMC) without loops and initial parameters. At time T, the size of the design matrix is 6 × 3 · 2T-1 and the convex hull of its columns is the model polytope. We study the behavior of this polytope for T ≥ 3 and we show that it is defined by 24 facets for all T ≥ 5. Moreover, we give a complete description of these facets. From this, we deduce that the toric ideal associated with the design matrix is generated by binomials of degree at most 6. Our proof is based on a result due to Sturmfels, who gave a bound on the degree of the generators of a toric ideal, provided the normality of the corresponding toric variety. In our setting, we established the normality of the toric variety associated to the THMC model by studying the geometric properties of the model polytope.},
author = {Haws, David and Martin Del Campo Sanchez, Abraham and Takemura, Akimichi and Yoshida, Ruriko},
journal = {Beitrage zur Algebra und Geometrie},
number = {1},
pages = {161 -- 188},
publisher = {Springer},
title = {{Markov degree of the three-state toric homogeneous Markov chain model}},
doi = {10.1007/s13366-013-0178-y},
volume = {55},
year = {2014},
}
@article{2180,
abstract = {Weighted majority votes allow one to combine the output of several classifiers or voters. MinCq is a recent algorithm for optimizing the weight of each voter based on the minimization of a theoretical bound over the risk of the vote with elegant PAC-Bayesian generalization guarantees. However, while it has demonstrated good performance when combining weak classifiers, MinCq cannot make use of the useful a priori knowledge that one may have when using a mixture of weak and strong voters. In this paper, we propose P-MinCq, an extension of MinCq that can incorporate such knowledge in the form of a constraint over the distribution of the weights, along with general proofs of convergence that stand in the sample compression setting for data-dependent voters. The approach is applied to a vote of k-NN classifiers with a specific modeling of the voters' performance. P-MinCq significantly outperforms the classic k-NN classifier, a symmetric NN and MinCq using the same voters. We show that it is also competitive with LMNN, a popular metric learning algorithm, and that combining both approaches further reduces the error.},
author = {Bellet, Aurélien and Habrard, Amaury and Morvant, Emilie and Sebban, Marc},
journal = {Machine Learning},
number = {1-2},
pages = {129 -- 154},
publisher = {Springer},
title = {{Learning a priori constrained weighted majority votes}},
doi = {10.1007/s10994-014-5462-z},
volume = {97},
year = {2014},
}
@inproceedings{2185,
abstract = {We revisit the classical problem of converting an imperfect source of randomness into a usable cryptographic key. Assume that we have some cryptographic application P that expects a uniformly random m-bit key R and ensures that the best attack (in some complexity class) against P(R) has success probability at most δ. Our goal is to design a key-derivation function (KDF) h that converts any random source X of min-entropy k into a sufficiently "good" key h(X), guaranteeing that P(h(X)) has comparable security δ′ which is 'close' to δ. Seeded randomness extractors provide a generic way to solve this problem for all applications P, with resulting security δ′ = O(δ), provided that we start with entropy k ≥ m + 2 log (1/δ) - O(1). By a result of Radhakrishnan and Ta-Shma, this bound on k (called the "RT-bound") is also known to be tight in general. Unfortunately, in many situations the loss of 2 log (1/δ) bits of entropy is unacceptable. This motivates the study KDFs with less entropy waste by placing some restrictions on the source X or the application P. In this work we obtain the following new positive and negative results in this regard: - Efficient samplability of the source X does not help beat the RT-bound for general applications. This resolves the SRT (samplable RT) conjecture of Dachman-Soled et al. [DGKM12] in the affirmative, and also shows that the existence of computationally-secure extractors beating the RT-bound implies the existence of one-way functions. - We continue in the line of work initiated by Barak et al. [BDK+11] and construct new information-theoretic KDFs which beat the RT-bound for large but restricted classes of applications. Specifically, we design efficient KDFs that work for all unpredictability applications P (e.g., signatures, MACs, one-way functions, etc.) and can either: (1) extract all of the entropy k = m with a very modest security loss δ′ = O(δ·log (1/δ)), or alternatively, (2) achieve essentially optimal security δ′ = O(δ) with a very modest entropy loss k ≥ m + loglog (1/δ). In comparison, the best prior results from [BDK+11] for this class of applications would only guarantee δ′ = O(√δ) when k = m, and would need k ≥ m + log (1/δ) to get δ′ = O(δ). - The weaker bounds of [BDK+11] hold for a larger class of so-called "square- friendly" applications (which includes all unpredictability, but also some important indistinguishability, applications). Unfortunately, we show that these weaker bounds are tight for the larger class of applications. - We abstract out a clean, information-theoretic notion of (k,δ,δ′)- unpredictability extractors, which guarantee "induced" security δ′ for any δ-secure unpredictability application P, and characterize the parameters achievable for such unpredictability extractors. Of independent interest, we also relate this notion to the previously-known notion of (min-entropy) condensers, and improve the state-of-the-art parameters for such condensers.},
author = {Dodis, Yevgeniy and Pietrzak, Krzysztof Z and Wichs, Daniel},
editor = {Nguyen, Phong and Oswald, Elisabeth},
location = {Copenhagen, Denmark},
pages = {93 -- 110},
publisher = {Springer},
title = {{Key derivation without entropy waste}},
doi = {10.1007/978-3-642-55220-5_6},
volume = {8441},
year = {2014},
}
@article{2154,
abstract = {A result of Boros and Füredi (d = 2) and of Bárány (arbitrary d) asserts that for every d there exists cd > 0 such that for every n-point set P ⊂ ℝd, some point of ℝd is covered by at least (Formula presented.) of the d-simplices spanned by the points of P. The largest possible value of cd has been the subject of ongoing research. Recently Gromov improved the existing lower bounds considerably by introducing a new, topological proof method. We provide an exposition of the combinatorial component of Gromov's approach, in terms accessible to combinatorialists and discrete geometers, and we investigate the limits of his method. In particular, we give tighter bounds on the cofilling profiles for the (n - 1)-simplex. These bounds yield a minor improvement over Gromov's lower bounds on cd for large d, but they also show that the room for further improvement through the cofilling profiles alone is quite small. We also prove a slightly better lower bound for c3 by an approach using an additional structure besides the cofilling profiles. We formulate a combinatorial extremal problem whose solution might perhaps lead to a tight lower bound for cd.},
author = {Matoušek, Jiří and Wagner, Uli},
journal = {Discrete & Computational Geometry},
number = {1},
pages = {1 -- 33},
publisher = {Springer},
title = {{On Gromov's method of selecting heavily covered points}},
doi = {10.1007/s00454-014-9584-7},
volume = {52},
year = {2014},
}
@inproceedings{2159,
abstract = {Motivated by topological Tverberg-type problems, we consider multiple (double, triple, and higher multiplicity) selfintersection points of maps from finite simplicial complexes (compact polyhedra) into ℝd and study conditions under which such multiple points can be eliminated. The most classical case is that of embeddings (i.e., maps without double points) of a κ-dimensional complex K into ℝ2κ. For this problem, the work of van Kampen, Shapiro, and Wu provides an efficiently testable necessary condition for embeddability (namely, vanishing of the van Kampen ob-struction). For κ ≥ 3, the condition is also sufficient, and yields a polynomial-time algorithm for deciding embeddability: One starts with an arbitrary map f : K→ℝ2κ, which generically has finitely many double points; if k ≥ 3 and if the obstruction vanishes then one can successively remove these double points by local modifications of the map f. One of the main tools is the famous Whitney trick that permits eliminating pairs of double points of opposite intersection sign. We are interested in generalizing this approach to intersection points of higher multiplicity. We call a point y 2 ℝd an r-fold Tverberg point of a map f : Kκ →ℝd if y lies in the intersection f(σ1)∩. ∩f(σr) of the images of r pairwise disjoint simplices of K. The analogue of (non-)embeddability that we study is the problem Tverbergκ r→d: Given a κ-dimensional complex K, does it satisfy a Tverberg-type theorem with parameters r and d, i.e., does every map f : K κ → ℝd have an r-fold Tverberg point? Here, we show that for fixed r, κ and d of the form d = rm and k = (r-1)m, m ≥ 3, there is a polynomial-time algorithm for deciding this (based on the vanishing of a cohomological obstruction, as in the case of embeddings). Our main tool is an r-fold analogue of the Whitney trick: Given r pairwise disjoint simplices of K such that the intersection of their images contains two r-fold Tverberg points y+ and y- of opposite intersection sign, we can eliminate y+ and y- by a local isotopy of f. In a subsequent paper, we plan to develop this further and present a generalization of the classical Haeiger-Weber Theorem (which yields a necessary and sufficient condition for embeddability of κ-complexes into ℝd for a wider range of dimensions) to intersection points of higher multiplicity.},
author = {Mabillard, Isaac and Wagner, Uli},
booktitle = {Proceedings of the Annual Symposium on Computational Geometry},
location = {Kyoto, Japan},
pages = {171 -- 180},
publisher = {ACM},
title = {{Eliminating Tverberg points, I. An analogue of the Whitney trick}},
doi = {10.1145/2582112.2582134},
year = {2014},
}
@article{2231,
abstract = {Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail.},
author = {Rieckh, Georg and Tkacik, Gasper},
issn = {00063495},
journal = {Biophysical Journal},
number = {5},
pages = {1194 -- 1204},
publisher = {Biophysical Society},
title = {{Noise and information transmission in promoters with multiple internal states}},
doi = {10.1016/j.bpj.2014.01.014},
volume = {106},
year = {2014},
}
@inproceedings{2236,
abstract = {Consider a joint distribution (X,A) on a set. We show that for any family of distinguishers, there exists a simulator such that 1 no function in can distinguish (X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient than the functions in. For the most interesting settings of the parameters (in particular, the cryptographic case where X has superlogarithmic min-entropy, ε > 0 is negligible and consists of circuits of polynomial size), we can make the simulator h deterministic. As an illustrative application of our theorem, we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09. Our proof is simpler and quantitatively much better than the original proof using the dense model theorem, giving meaningful security guarantees if instantiated with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and Pass gave an interactive variant of our main theorem, and used it to investigate weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version of our theorem using their new uniform min-max theorem.},
author = {Jetchev, Dimitar and Pietrzak, Krzysztof Z},
editor = {Lindell, Yehuda},
isbn = {978-364254241-1},
location = {San Diego, USA},
pages = {566 -- 590},
publisher = {Springer},
title = {{How to fake auxiliary input}},
doi = {10.1007/978-3-642-54242-8_24},
volume = {8349},
year = {2014},
}
@article{2250,
abstract = {The genome sequences of new viruses often contain many "orphan" or "taxon-specific" proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as "genus specific" by BLAST. More powerful methods developed recently, such as HHblits or HHpred (available through web-based, user-friendly interfaces), could detect distant homologs of a quarter of these proteins, suggesting that these methods should be used to annotate viral genomes. In-depth manual analyses of a subset of the remaining sequences, guided by contextual information such as taxonomy, gene order, or domain cooccurrence, identified distant homologs of another third. Thus, a combination of powerful automated methods and manual analyses can uncover distant homologs of many proteins thought to be orphans. We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses. As an application, we reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We could identify homologs of most of its proteins thought to be orphans; in each case, identifying homologs provided functional clues. We discovered that CBPV encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase; a putative membrane protein, SP24, with homologs in unrelated insect viruses and insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses, blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found in negeviruses. SP24 and ORF2 are probably major structural components of the virionsd.},
author = {Kuchibhatla, Durga and Sherman, Westley and Chung, Betty and Cook, Shelley and Schneider, Georg and Eisenhaber, Birgit and Karlin, David},
issn = {0022538X},
journal = {Journal of Virology},
number = {1},
pages = {10 -- 20},
publisher = {ASM},
title = {{Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins}},
doi = {10.1128/JVI.02595-13},
volume = {88},
year = {2014},
}
@article{2407,
abstract = {Two definitions of the effective mass of a particle interacting with a quantum field, such as a polaron, are considered and shown to be equal in models similar to the Fröhlich polaron model. These are: 1. the mass defined by the low momentum energy E(P)≈E(0)+P2/2 M of the translation invariant system constrained to have momentum P and 2. the mass M of a simple particle in an arbitrary slowly varying external potential, V, described by the nonrelativistic Schrödinger equation, whose ground state energy equals that of the combined particle/field system in a bound state in the same V.},
author = {Lieb, Élliott and Seiringer, Robert},
journal = {Journal of Statistical Physics},
number = {1-2},
pages = {51 -- 57},
publisher = {Springer},
title = {{Equivalence of two definitions of the effective mass of a polaron}},
doi = {10.1007/s10955-013-0791-z},
volume = {154},
year = {2014},
}
@article{2281,
abstract = {We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential.},
author = {Guo, Yujin and Seiringer, Robert},
journal = {Letters in Mathematical Physics},
number = {2},
pages = {141 -- 156},
publisher = {Springer},
title = {{On the mass concentration for Bose-Einstein condensates with attractive interactions}},
doi = {10.1007/s11005-013-0667-9},
volume = {104},
year = {2014},
}
@article{537,
abstract = {Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.},
author = {Prizak, Roshan and Ezard, Thomas and Hoyle, Rebecca},
journal = {Ecology and Evolution},
number = {15},
pages = {3139 -- 3145},
publisher = {Wiley-Blackwell},
title = {{Fitness consequences of maternal and grandmaternal effects}},
doi = {10.1002/ece3.1150},
volume = {4},
year = {2014},
}
@misc{5420,
abstract = {We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus},
issn = {2664-1690},
pages = {49},
publisher = {IST Austria},
title = {{The value 1 problem for concurrent mean-payoff games}},
doi = {10.15479/AT:IST-2014-191-v1-1},
year = {2014},
}
@inproceedings{6740,
abstract = {We describe coding techniques that achieve the capacity of a discrete memoryless asymmetric channel. To do so, we discuss how recent advances in coding for symmetric channels yield more efficient solutions also for the asymmetric case. In more detail, we consider three basic approaches. The first one is Gallager's scheme that concatenates a linear code with a non-linear mapper, in order to bias the input distribution. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Further, we derive a scaling law between the gap to capacity, the cardinality of channel input and output alphabets, and the required size of the mapper. The second one is an integrated approach in which the coding scheme is used both for source coding, in order to create codewords with the capacity-achieving distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third approach is based on an idea due to Böcherer and Mathar and separates completely the two tasks of source coding and channel coding by “chaining” together several codewords. We prove that we can combine any suitable source code with any suitable channel code in order to provide optimal schemes for asymmetric channels. In particular, polar codes and spatially coupled codes fulfill the required conditions.},
author = {Mondelli, Marco and Urbanke, Rudiger and Hassani, Hamed},
booktitle = {52nd Annual Allerton Conference on Communication, Control, and Computing},
location = {Monticello, IL, United States},
pages = {789--796},
publisher = {IEEE},
title = {{How to achieve the capacity of asymmetric channels}},
doi = {10.1109/allerton.2014.7028535},
year = {2014},
}
@inproceedings{772,
abstract = {Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. While obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most non-blocking commercial code is only lock-free. This paper suggests a simple solution to this problem. We show that, for a large class of lock-free algorithms, under scheduling conditions which approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can keep on designing simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes with the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1, but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst case adversary, in a stochastic model capturing their expected asymptotic behavior.},
author = {Alistarh, Dan and Censor-Hillel, Keren and Shavit, Nir N},
pages = {714 -- 723},
publisher = {ACM},
title = {{Are lock-free concurrent algorithms practically wait-free?}},
doi = {10.1145/2591796.2591836},
year = {2014},
}
@article{979,
abstract = {In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators.},
author = {Maksym Serbyn and Fu, Liang},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {3},
publisher = {American Physical Society},
title = {{Symmetry breaking and Landau quantization in topological crystalline insulators}},
doi = {10.1103/PhysRevB.90.035402},
volume = {90},
year = {2014},
}
@inproceedings{1872,
abstract = {Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover.},
author = {Gupta, Ashutosh and Kovács, Laura and Kragl, Bernhard and Voronkov, Andrei},
booktitle = {ATVA 2014},
editor = {Cassez, Franck and Raskin, Jean-François},
location = {Sydney, Australia},
pages = {185 -- 200},
publisher = {Springer},
title = {{Extensional crisis and proving identity}},
doi = {10.1007/978-3-319-11936-6_14},
volume = {8837},
year = {2014},
}
@inproceedings{2027,
abstract = {We present a general framework for applying machine-learning algorithms to the verification of Markov decision processes (MDPs). The primary goal of these techniques is to improve performance by avoiding an exhaustive exploration of the state space. Our framework focuses on probabilistic reachability, which is a core property for verification, and is illustrated through two distinct instantiations. The first assumes that full knowledge of the MDP is available, and performs a heuristic-driven partial exploration of the model, yielding precise lower and upper bounds on the required probability. The second tackles the case where we may only sample the MDP, and yields probabilistic guarantees, again in terms of both the lower and upper bounds, which provides efficient stopping criteria for the approximation. The latter is the first extension of statistical model checking for unbounded properties inMDPs. In contrast with other related techniques, our approach is not restricted to time-bounded (finite-horizon) or discounted properties, nor does it assume any particular properties of the MDP. We also show how our methods extend to LTL objectives. We present experimental results showing the performance of our framework on several examples.},
author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Chmelik, Martin and Forejt, Vojtěch and Kretinsky, Jan and Kwiatkowska, Marta and Parker, David and Ujma, Mateusz},
booktitle = { Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
editor = {Cassez, Franck and Raskin, Jean-François},
location = {Sydney, Australia},
pages = {98 -- 114},
publisher = {Society of Industrial and Applied Mathematics},
title = {{Verification of markov decision processes using learning algorithms}},
doi = {10.1007/978-3-319-11936-6_8},
volume = {8837},
year = {2014},
}
@article{2229,
abstract = {The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose "microdomain" coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity.},
author = {Vyleta, Nicholas and Jonas, Peter M},
issn = {00368075},
journal = {Science},
number = {6171},
pages = {665 -- 670},
publisher = {American Association for the Advancement of Science},
title = {{Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse}},
doi = {10.1126/science.1244811},
volume = {343},
year = {2014},
}
@article{2039,
abstract = {A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time.},
author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Adlam, Ben and Nowak, Martin},
journal = {PLoS Computational Biology},
number = {9},
publisher = {Public Library of Science},
title = {{The time scale of evolutionary innovation}},
doi = {10.1371/journal.pcbi.1003818},
volume = {10},
year = {2014},
}
@inproceedings{2053,
abstract = {In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems.},
author = {Hermanns, Holger and Krčál, Jan and Kretinsky, Jan},
booktitle = {Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)},
editor = {Baldan, Paolo and Gorla, Daniele},
location = {Rome, Italy},
pages = {249 -- 265},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Probabilistic bisimulation: Naturally on distributions}},
doi = {10.1007/978-3-662-44584-6_18},
volume = {8704},
year = {2014},
}
@article{1916,
abstract = {Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease.},
author = {Novarino, Gaia and Fenstermaker, Ali and Zaki, Maha and Hofree, Matan and Silhavy, Jennifer and Heiberg, Andrew and Abdellateef, Mostafa and Rosti, Başak and Scott, Eric and Mansour, Lobna and Masri, Amira and Kayserili, Hülya and Al Aama, Jumana and Abdel Salam, Ghada and Karminejad, Ariana and Kara, Majdi and Kara, Bülent and Bozorgmehri, Bita and Ben Omran, Tawfeg and Mojahedi, Faezeh and Mahmoud, Iman and Bouslam, Naïma and Bouhouche, Ahmed and Benomar, Ali and Hanein, Sylvain and Raymond, Laure and Forlani, Sylvie and Mascaro, Massimo and Selim, Laila and Shehata, Nabil and Al Allawi, Nasir and Bindu, Parayil and Azam, Matloob and Günel, Murat and Caglayan, Ahmet and Bilgüvar, Kaya and Tolun, Aslihan and Issa, Mahmoud and Schroth, Jana and Spencer, Emily and Rosti, Rasim and Akizu, Naiara and Vaux, Keith and Johansen, Anide and Koh, Alice and Megahed, Hisham and Dürr, Alexandra and Brice, Alexis and Stévanin, Giovanni and Gabriel, Stacy and Ideker, Trey and Gleeson, Joseph},
journal = {Science},
number = {6170},
pages = {506 -- 511},
publisher = {American Association for the Advancement of Science},
title = {{Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders}},
doi = {10.1126/science.1247363},
volume = {343},
year = {2014},
}
@inproceedings{8044,
author = {Seiringer, Robert},
booktitle = {Proceeding of the International Congress of Mathematicans, ICM 2014},
isbn = {9788961058063},
location = {Seoul, South Korea},
pages = {1175--1194},
title = {{Structure of the excitation spectrum for many-body quantum systems}},
volume = {3},
year = {2014},
}
@article{1816,
abstract = {Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques.},
author = {Huber, Stefan and Held, Martin and Meerwald, Peter and Kwitt, Roland},
journal = {International Journal of Computational Geometry and Applications},
number = {1},
pages = {61 -- 86},
publisher = {World Scientific Publishing},
title = {{Topology-preserving watermarking of vector graphics}},
doi = {10.1142/S0218195914500034},
volume = {24},
year = {2014},
}
@article{1842,
abstract = {We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices.},
author = {Cibulka, Josef and Gao, Pu and Krcál, Marek and Valla, Tomáš and Valtr, Pavel},
journal = {Discrete & Computational Geometry},
number = {1},
pages = {64 -- 79},
publisher = {Springer},
title = {{On the geometric ramsey number of outerplanar graphs}},
doi = {10.1007/s00454-014-9646-x},
volume = {53},
year = {2014},
}
@article{1892,
abstract = {Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in Lamprologus callipterus.},
author = {Ocana, Sabine and Meidl, Patrick and Bonfils, Danielle and Taborsky, Michael},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1794},
publisher = {Royal Society, The},
title = {{Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids}},
doi = {10.1098/rspb.2014.0253},
volume = {281},
year = {2014},
}