@article{8427,
abstract = {We show that any sufficiently (finitely) smooth ℤ₂-symmetric strictly convex domain sufficiently close to a circle is dynamically spectrally rigid; i.e., all deformations among domains in the same class that preserve the length of all periodic orbits of the associated billiard flow must necessarily be isometric deformations. This gives a partial answer to a question of P. Sarnak.},
author = {De Simoi, Jacopo and Kaloshin, Vadim and Wei, Qiaoling},
issn = {0003-486X},
journal = {Annals of Mathematics},
number = {1},
pages = {277--314},
publisher = {Annals of Mathematics},
title = {{Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle}},
doi = {10.4007/annals.2017.186.1.7},
volume = {186},
year = {2017},
}
@article{169,
abstract = {We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman sums leads to an optimal covering exponent for S3.},
author = {Browning, Timothy D and Kumaraswamy, Vinay and Steiner, Rapael},
journal = {International Mathematics Research Notices},
publisher = {Oxford University Press},
title = {{Twisted Linnik implies optimal covering exponent for S3}},
doi = {10.1093/imrn/rnx116},
year = {2017},
}
@article{172,
abstract = {We study strong approximation for some algebraic varieties over ℚ which are defined using norm forms. This allows us to confirm a special case of a conjecture due to Harpaz and Wittenberg.},
author = {Browning, Timothy D and Schindler, Damaris},
journal = {International Mathematics Research Notices},
publisher = {Oxford University Press},
title = {{Strong approximation and a conjecture of Harpaz and Wittenberg}},
doi = {10.1093/imrn/rnx252},
year = {2017},
}
@article{2016,
abstract = {The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.},
author = {Martin Del Campo Sanchez, Abraham and Cepeda Humerez, Sarah A and Uhler, Caroline},
issn = {03036898},
journal = {Scandinavian Journal of Statistics},
number = {2},
pages = {285 -- 306},
publisher = {Wiley-Blackwell},
title = {{Exact goodness-of-fit testing for the Ising model}},
doi = {10.1111/sjos.12251},
volume = {44},
year = {2017},
}
@phdthesis{202,
abstract = {Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.},
author = {Pleska, Maros},
pages = {126},
publisher = {IST Austria},
title = {{Biology of restriction-modification systems at the single-cell and population level}},
doi = {10.15479/AT:ISTA:th_916},
year = {2017},
}
@article{716,
abstract = {Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.},
author = {Chatterjee, Krishnendu and Velner, Yaron},
issn = {00045411},
journal = {Journal of the ACM},
number = {5},
pages = {34},
publisher = {ACM},
title = {{The complexity of mean-payoff pushdown games}},
doi = {10.1145/3121408},
volume = {64},
year = {2017},
}
@misc{7163,
abstract = {The de novo genome assemblies generated for this study, and the associated metadata.},
author = {Fraisse, Christelle},
publisher = {IST Austria},
title = {{Supplementary Files for "The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W"}},
doi = {10.15479/AT:ISTA:7163},
year = {2017},
}
@article{717,
abstract = {We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard.},
author = {Chatterjee, Krishnendu and Velner, Yaron},
journal = {Journal of Computer and System Sciences},
pages = {236 -- 259},
publisher = {Academic Press},
title = {{Hyperplane separation technique for multidimensional mean-payoff games}},
doi = {10.1016/j.jcss.2017.04.005},
volume = {88},
year = {2017},
}
@article{718,
abstract = {Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4.},
author = {Edelsbrunner, Herbert and Nikitenko, Anton and Reitzner, Matthias},
issn = {00018678},
journal = {Advances in Applied Probability},
number = {3},
pages = {745 -- 767},
publisher = {Cambridge University Press},
title = {{Expected sizes of poisson Delaunay mosaics and their discrete Morse functions}},
doi = {10.1017/apr.2017.20},
volume = {49},
year = {2017},
}
@article{720,
abstract = {Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.},
author = {Humplik, Jan and Tkacik, Gasper},
issn = {1553734X},
journal = {PLoS Computational Biology},
number = {9},
publisher = {Public Library of Science},
title = {{Probabilistic models for neural populations that naturally capture global coupling and criticality}},
doi = {10.1371/journal.pcbi.1005763},
volume = {13},
year = {2017},
}
@article{721,
abstract = {Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur.},
author = {Ajanki, Oskari H and Krüger, Torben H and Erdös, László},
issn = {00103640},
journal = {Communications on Pure and Applied Mathematics},
number = {9},
pages = {1672 -- 1705},
publisher = {Wiley-Blackwell},
title = {{Singularities of solutions to quadratic vector equations on the complex upper half plane}},
doi = {10.1002/cpa.21639},
volume = {70},
year = {2017},
}
@article{722,
abstract = {Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises.},
author = {Morris, Emily and Griffiths, Marcus and Golebiowska, Agata and Mairhofer, Stefan and Burr Hersey, Jasmine and Goh, Tatsuaki and Von Wangenheim, Daniel and Atkinson, Brian and Sturrock, Craig and Lynch, Jonathan and Vissenberg, Kris and Ritz, Karl and Wells, Darren and Mooney, Sacha and Bennett, Malcolm},
issn = {09609822},
journal = {Current Biology},
number = {17},
pages = {R919 -- R930},
publisher = {Cell Press},
title = {{Shaping 3D root system architecture}},
doi = {10.1016/j.cub.2017.06.043},
volume = {27},
year = {2017},
}
@article{724,
abstract = {We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic.},
author = {Hetterich, Daniel and Serbyn, Maksym and Domínguez, Fernando and Pollmann, Frank and Trauzettel, Björn},
issn = {24699950},
journal = {Physical Review B},
number = {10},
publisher = {American Physical Society},
title = {{Noninteracting central site model localization and logarithmic entanglement growth}},
doi = {10.1103/PhysRevB.96.104203},
volume = {96},
year = {2017},
}
@article{725,
abstract = {Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.},
author = {Harpaz, Roy and Tkacik, Gasper and Schneidman, Elad},
issn = {00278424},
journal = {PNAS},
number = {38},
pages = {10149 -- 10154},
publisher = {National Academy of Sciences},
title = {{Discrete modes of social information processing predict individual behavior of fish in a group}},
doi = {10.1073/pnas.1703817114},
volume = {114},
year = {2017},
}
@article{726,
abstract = {The morphogenesis of branched organs remains a subject of abiding interest. Although much is known about the underlying signaling pathways, it remains unclear how macroscopic features of branched organs, including their size, network topology, and spatial patterning, are encoded. Here, we show that, in mouse mammary gland, kidney, and human prostate, these features can be explained quantitatively within a single unifying framework of branching and annihilating random walks. Based on quantitative analyses of large-scale organ reconstructions and proliferation kinetics measurements, we propose that morphogenesis follows from the proliferative activity of equipotent tips that stochastically branch and randomly explore their environment but compete neutrally for space, becoming proliferatively inactive when in proximity with neighboring ducts. These results show that complex branched epithelial structures develop as a self-organized process, reliant upon a strikingly simple but generic rule, without recourse to a rigid and deterministic sequence of genetically programmed events.},
author = {Hannezo, Edouard B and Scheele, Colinda and Moad, Mohammad and Drogo, Nicholas and Heer, Rakesh and Sampogna, Rosemary and Van Rheenen, Jacco and Simons, Benjamin},
issn = {00928674},
journal = {Cell},
number = {1},
pages = {242 -- 255},
publisher = {Cell Press},
title = {{A unifying theory of branching morphogenesis}},
doi = {10.1016/j.cell.2017.08.026},
volume = {171},
year = {2017},
}
@article{7289,
abstract = {Aprotic sodium–O2 batteries require the reversible formation/dissolution of sodium superoxide (NaO2) on cycling. Poor cycle life has been associated with parasitic chemistry caused by the reactivity of electrolyte and electrode with NaO2, a strong nucleophile and base. Its reactivity can, however, not consistently explain the side reactions and irreversibility. Herein we show that singlet oxygen (1O2) forms at all stages of cycling and that it is a main driver for parasitic chemistry. It was detected in‐ and ex‐situ via a 1O2 trap that selectively and rapidly forms a stable adduct with 1O2. The 1O2 formation mechanism involves proton‐mediated superoxide disproportionation on discharge, rest, and charge below ca. 3.3 V, and direct electrochemical 1O2 evolution above ca. 3.3 V. Trace water, which is needed for high capacities also drives parasitic chemistry. Controlling the highly reactive singlet oxygen is thus crucial for achieving highly reversible cell operation.},
author = {Schafzahl, Lukas and Mahne, Nika and Schafzahl, Bettina and Wilkening, Martin and Slugovc, Christian and Borisov, Sergey M. and Freunberger, Stefan Alexander},
issn = {1433-7851},
journal = {Angewandte Chemie International Edition},
number = {49},
pages = {15728--15732},
publisher = {Wiley},
title = {{Singlet oxygen during cycling of the aprotic sodium-O2 battery}},
doi = {10.1002/anie.201709351},
volume = {56},
year = {2017},
}
@article{7290,
abstract = {We report a family of Pt and Pd benzoporphyrin dyes with versatile photophysical properties and easy access from cheap and abundant chemicals. Attaching 4 or 8 alkylsulfone groups onto a meso-tetraphenyltetrabenzoporphyrin (TPTBP) macrocylcle renders the dyes highly soluble in organic solvents, photostable, and electron-deficient with the redox potential raised up to 0.65 V versus the parent porphyrin. The new dyes intensively absorb in the blue (Soret band, 440–480 nm) and in the red (Q-band, 620–650 nm) parts of the electromagnetic spectrum and show bright phosphorescence at room-temperature in the NIR with quantum yields up to 30% in solution. The small singlet–triplet energy gap yields unusually efficient thermally activated delayed fluorescence (TADF) at elevated temperatures in solution and in polymeric matrices with quantum yields as high as 27% at 120 °C, which is remarkable for benzoporphyrins. Apart from oxygen sensing, these properties enable unprecedented simultaneous, self-referenced oxygen and temperature sensing with a single indicator dye: whereas oxygen can be determined either via the decay time of phosphorescence or TADF, the temperature is accessed via the ratio of the two emissions. Moreover, the dyes are efficient sensitizers for triplet–triplet annihilation (TTA)-based upconversion making possible longer sensitization wavelength than the conventional benzoporphyrin complexes. The Pt-octa-sulfone dye also features interesting semireversible transformation in basic media, which generates new NIR absorbing species.},
author = {Zach, Peter W. and Freunberger, Stefan Alexander and Klimant, Ingo and Borisov, Sergey M.},
issn = {1944-8252},
journal = {ACS Applied Materials & Interfaces},
number = {43},
pages = {38008--38023},
publisher = {ACS},
title = {{Electron-deficient near-infrared Pt(II) and Pd(II) benzoporphyrins with dual phosphorescence and unusually efficient thermally activated delayed fluorescence: First demonstration of simultaneous oxygen and temperature sensing with a single emitter}},
doi = {10.1021/acsami.7b10669},
volume = {9},
year = {2017},
}
@article{7292,
abstract = {Rechargeable Li–O2 batteries have amongst the highest formal energy and could store significantly more energy than other rechargeable batteries in practice if at least a large part of their promise could be realized. Realization, however, still faces many challenges than can only be overcome by fundamental understanding of the processes taking place. Here, we review recent advances in understanding the chemistry of the Li–O2 cathode and provide a perspective on dominant research needs. We put particular emphasis on issues that are often grossly misunderstood: realistic performance metrics and their reporting as well as identifying reversibility and quantitative measures to do so. Parasitic reactions are the prime obstacle for reversible cell operation and have recently been identified to be predominantly caused by singlet oxygen and not by reduced oxygen species as thought before. We discuss the far reaching implications of this finding on electrolyte and cathode stability, electrocatalysis, and future research needs.},
author = {Mahne, Nika and Fontaine, Olivier and Thotiyl, Musthafa Ottakam and Wilkening, Martin and Freunberger, Stefan Alexander},
issn = {2041-6539},
journal = {Chemical Science},
number = {10},
pages = {6716--6729},
publisher = {RSC},
title = {{Mechanism and performance of lithium–oxygen batteries – a perspective}},
doi = {10.1039/c7sc02519j},
volume = {8},
year = {2017},
}
@article{732,
abstract = {Background: Social insects form densely crowded societies in environments with high pathogen loads, but have evolved collective defences that mitigate the impact of disease. However, colony-founding queens lack this protection and suffer high rates of mortality. The impact of pathogens may be exacerbated in species where queens found colonies together, as healthy individuals may contract pathogens from infectious co-founders. Therefore, we tested whether ant queens avoid founding colonies with pathogen-exposed conspecifics and how they might limit disease transmission from infectious individuals. Results: Using Lasius Niger queens and a naturally infecting fungal pathogen Metarhizium brunneum, we observed that queens were equally likely to found colonies with another pathogen-exposed or sham-treated queen. However, when one queen died, the surviving individual performed biting, burial and removal of the corpse. These undertaking behaviours were performed prophylactically, i.e. targeted equally towards non-infected and infected corpses, as well as carried out before infected corpses became infectious. Biting and burial reduced the risk of the queens contracting and dying from disease from an infectious corpse of a dead co-foundress. Conclusions: We show that co-founding ant queens express undertaking behaviours that, in mature colonies, are performed exclusively by workers. Such infection avoidance behaviours act before the queens can contract the disease and will therefore improve the overall chance of colony founding success in ant queens.},
author = {Pull, Christopher and Cremer, Sylvia},
issn = {14712148},
journal = {BMC Evolutionary Biology},
number = {1},
publisher = {BioMed Central},
title = {{Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour}},
doi = {10.1186/s12862-017-1062-4},
volume = {17},
year = {2017},
}
@article{733,
abstract = {Let A and B be two N by N deterministic Hermitian matrices and let U be an N by N Haar distributed unitary matrix. It is well known that the spectral distribution of the sum H = A + UBU∗ converges weakly to the free additive convolution of the spectral distributions of A and B, as N tends to infinity. We establish the optimal convergence rate in the bulk of the spectrum.},
author = {Bao, Zhigang and Erdös, László and Schnelli, Kevin},
journal = {Advances in Mathematics},
pages = {251 -- 291},
publisher = {Academic Press},
title = {{Convergence rate for spectral distribution of addition of random matrices}},
doi = {10.1016/j.aim.2017.08.028},
volume = {319},
year = {2017},
}
@article{734,
abstract = {Social insect societies are long-standing models for understanding social behaviour and evolution. Unlike other advanced biological societies (such as the multicellular body), the component parts of social insect societies can be easily deconstructed and manipulated. Recent methodological and theoretical innovations have exploited this trait to address an expanded range of biological questions. We illustrate the broadening range of biological insight coming from social insect biology with four examples. These new frontiers promote open-minded, interdisciplinary exploration of one of the richest and most complex of biological phenomena: sociality.},
author = {Kennedy, Patrick and Baron, Gemma and Qiu, Bitao and Freitak, Dalial and Helantera, Heikki and Hunt, Edmund and Manfredini, Fabio and O'Shea Wheller, Thomas and Patalano, Solenn and Pull, Christopher and Sasaki, Takao and Taylor, Daisy and Wyatt, Christopher and Sumner, Seirian},
issn = {01695347},
journal = {Trends in Ecology and Evolution},
number = {11},
pages = {861 -- 872},
publisher = {Cell Press},
title = {{Deconstructing superorganisms and societies to address big questions in biology}},
doi = {10.1016/j.tree.2017.08.004},
volume = {32},
year = {2017},
}
@article{736,
abstract = {The neurotransmitter receptor subtype, number, density, and distribution relative to the location of transmitter release sites are key determinants of signal transmission. AMPA-type ionotropic glutamate receptors (AMPARs) containing GluA3 and GluA4 subunits are prominently expressed in subsets of neurons capable of firing action potentials at high frequencies, such as auditory relay neurons. The auditory nerve (AN) forms glutamatergic synapses on two types of relay neurons, bushy cells (BCs) and fusiform cells (FCs) of the cochlear nucleus. AN-BC and AN-FC synapses have distinct kinetics; thus, we investigated whether the number, density, and localization of GluA3 and GluA4 subunits in these synapses are differentially organized using quantitative freeze-fracture replica immunogold labeling. We identify a positive correlation between the number of AMPARs and the size of AN-BC and AN-FC synapses. Both types of AN synapses have similar numbers of AMPARs; however, the AN-BC have a higher density of AMPARs than AN-FC synapses, because the AN-BC synapses are smaller. A higher number and density of GluA3 subunits are observed at AN-BC synapses, whereas a higher number and density of GluA4 subunits are observed at AN-FC synapses. The intrasynaptic distribution of immunogold labeling revealed that AMPAR subunits, particularly GluA3, are concentrated at the center of the AN-BC synapses. The central distribution of AMPARs is absent in GluA3-knockout mice, and gold particles are evenly distributed along the postsynaptic density. GluA4 gold labeling was homogenously distributed along both synapse types. Thus, GluA3 and GluA4 subunits are distributed at AN synapses in a target-cell-dependent manner.},
author = {Rubio, María and Matsui, Ko and Fukazawa, Yugo and Kamasawa, Naomi and Harada, Harumi and Itakura, Makoto and Molnár, Elek and Abe, Manabu and Sakimura, Kenji and Shigemoto, Ryuichi},
issn = {18632653},
journal = {Brain Structure and Function},
number = {8},
pages = {3375 -- 3393},
publisher = {Springer},
title = {{The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells}},
doi = {10.1007/s00429-017-1408-0},
volume = {222},
year = {2017},
}
@article{7360,
abstract = {Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.},
author = {Smole, Anže and Lainšček, Duško and Bezeljak, Urban and Horvat, Simon and Jerala, Roman},
issn = {1525-0016},
journal = {Molecular Therapy},
number = {1},
pages = {102--119},
publisher = {Elsevier},
title = {{A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation}},
doi = {10.1016/j.ymthe.2016.10.005},
volume = {25},
year = {2017},
}
@article{739,
abstract = {We study the norm approximation to the Schrödinger dynamics of N bosons in with an interaction potential of the form . Assuming that in the initial state the particles outside of the condensate form a quasi-free state with finite kinetic energy, we show that in the large N limit, the fluctuations around the condensate can be effectively described using Bogoliubov approximation for all . The range of β is expected to be optimal for this large class of initial states.},
author = {Nam, Phan and Napiórkowski, Marcin M},
issn = {00217824},
journal = {Journal de Mathématiques Pures et Appliquées},
number = {5},
pages = {662 -- 688},
publisher = {Elsevier},
title = {{A note on the validity of Bogoliubov correction to mean field dynamics}},
doi = {10.1016/j.matpur.2017.05.013},
volume = {108},
year = {2017},
}
@article{740,
abstract = {Developments in bioengineering and molecular biology have introduced a palette of genetically encoded probes for identification of specific cell populations in electron microscopy. These probes can be targeted to distinct cellular compartments, rendering them electron dense through a subsequent chemical reaction. These electron densities strongly increase the local contrast in samples prepared for electron microscopy, allowing three major advances in ultrastructural mapping of circuits: genetic identification of circuit components, targeted imaging of regions of interest and automated analysis of the tagged circuits. Together, the gains from these advances can decrease the time required for the analysis of targeted circuit motifs by over two orders of magnitude. These genetic encoded tags for electron microscopy promise to simplify the analysis of circuit motifs and become a central tool for structure‐function studies of synaptic connections in the brain. We review the current state‐of‐the‐art with an emphasis on connectomics, the quantitative analysis of neuronal structures and motifs.},
author = {Shigemoto, Ryuichi and Jösch, Maximilian A},
issn = {17597684},
journal = {WIREs Developmental Biology},
number = {6},
publisher = {Wiley-Blackwell},
title = {{The genetic encoded toolbox for electron microscopy and connectomics}},
doi = {10.1002/wdev.288},
volume = {6},
year = {2017},
}
@article{741,
abstract = {We prove that a system of N fermions interacting with an additional particle via point interactions is stable if the ratio of the mass of the additional particle to the one of the fermions is larger than some critical m*. The value of m* is independent of N and turns out to be less than 1. This fact has important implications for the stability of the unitary Fermi gas. We also characterize the domain of the Hamiltonian of this model, and establish the validity of the Tan relations for all wave functions in the domain.},
author = {Moser, Thomas and Seiringer, Robert},
issn = {00103616},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {329 -- 355},
publisher = {Springer},
title = {{Stability of a fermionic N+1 particle system with point interactions}},
doi = {10.1007/s00220-017-2980-0},
volume = {356},
year = {2017},
}
@article{744,
abstract = {In evolutionary game theory interactions between individuals are often assumed obligatory. However, in many real-life situations, individuals can decide to opt out of an interaction depending on the information they have about the opponent. We consider a simple evolutionary game theoretic model to study such a scenario, where at each encounter between two individuals the type of the opponent (cooperator/defector) is known with some probability, and where each individual either accepts or opts out of the interaction. If the type of the opponent is unknown, a trustful individual accepts the interaction, whereas a suspicious individual opts out of the interaction. If either of the two individuals opt out both individuals remain without an interaction. We show that in the prisoners dilemma optional interactions along with suspicious behaviour facilitates the emergence of trustful cooperation.},
author = {Priklopil, Tadeas and Chatterjee, Krishnendu and Nowak, Martin},
issn = {00225193},
journal = { Journal of Theoretical Biology},
pages = {64 -- 72},
publisher = {Elsevier},
title = {{Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma}},
doi = {10.1016/j.jtbi.2017.08.025},
volume = {433},
year = {2017},
}
@article{745,
abstract = {Fluid flows in nature and applications are frequently subject to periodic velocity modulations. Surprisingly, even for the generic case of flow through a straight pipe, there is little consensus regarding the influence of pulsation on the transition threshold to turbulence: while most studies predict a monotonically increasing threshold with pulsation frequency (i.e. Womersley number, ), others observe a decreasing threshold for identical parameters and only observe an increasing threshold at low . In the present study we apply recent advances in the understanding of transition in steady shear flows to pulsating pipe flow. For moderate pulsation amplitudes we find that the first instability encountered is subcritical (i.e. requiring finite amplitude disturbances) and gives rise to localized patches of turbulence ('puffs') analogous to steady pipe flow. By monitoring the impact of pulsation on the lifetime of turbulence we map the onset of turbulence in parameter space. Transition in pulsatile flow can be separated into three regimes. At small Womersley numbers the dynamics is dominated by the decay turbulence suffers during the slower part of the cycle and hence transition is delayed significantly. As shown in this regime thresholds closely agree with estimates based on a quasi-steady flow assumption only taking puff decay rates into account. The transition point predicted in the zero limit equals to the critical point for steady pipe flow offset by the oscillation Reynolds number (i.e. the dimensionless oscillation amplitude). In the high frequency limit on the other hand, puff lifetimes are identical to those in steady pipe flow and hence the transition threshold appears to be unaffected by flow pulsation. In the intermediate frequency regime the transition threshold sharply drops (with increasing ) from the decay dominated (quasi-steady) threshold to the steady pipe flow level.},
author = {Xu, Duo and Warnecke, Sascha and Song, Baofang and Ma, Xingyu and Hof, Björn},
issn = {00221120},
journal = {Journal of Fluid Mechanics},
pages = {418 -- 432},
publisher = {Cambridge University Press},
title = {{Transition to turbulence in pulsating pipe flow}},
doi = {10.1017/jfm.2017.620},
volume = {831},
year = {2017},
}
@article{746,
abstract = {Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored. Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5 cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function, and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using single-molecule tracking, we found that mGluR5 was significantly more mobile at synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression, and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes of FXS, unveiling novel targets for mGluR5-based therapeutics.},
author = {Aloisi, Elisabetta and Le Corf, Katy and Dupuis, Julien and Zhang, Pei and Ginger, Melanie and Labrousse, Virginie and Spatuzza, Michela and Georg Haberl, Matthias and Costa, Lara and Shigemoto, Ryuichi and Tappe Theodor, Anke and Drago, Fillippo and Vincenzo Piazza, Pier and Mulle, Christophe and Groc, Laurent and Ciranna, Lucia and Catania, Maria and Frick, Andreas},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice}},
doi = {10.1038/s41467-017-01191-2},
volume = {8},
year = {2017},
}
@article{747,
abstract = {Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts multiple effects via B1 and B2 receptor activation. In the cardiovascular system, bradykinin has cardioprotective and vasodilator properties. We investigated the effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for the parasympathetic cardiac regulation. BK produced a dose-dependent increase in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist, but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate, antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase, while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons, which was prevented by the B2 receptor antagonist. In vivo studies indicate that microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic reticulum, and membrane depolarization; these effects are translated in vivo by bradycardia.},
author = {Brǎiloiu, Eugen and Mcguire, Matthew and Shuler, Shadaria and Deliu, Elena and Barr, Jeffrey and Abood, Mary and Brailoiu, Gabriela},
issn = {03064522},
journal = {Neuroscience},
pages = {23 -- 32},
publisher = {Elsevier},
title = {{Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus}},
doi = {10.1016/j.neuroscience.2017.09.034},
volume = {365},
year = {2017},
}
@article{749,
abstract = {Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, Syt7 is strongly expressed in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. To resolve this apparent contradiction, we examined the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment, and facilitation. In combination, these three effects ensure efficient transmitter release during high-frequency activity and guarantee frequency independence of inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency of high-frequency inhibitory synaptic transmission},
author = {Chen, Chong and Satterfield, Rachel and Young, Samuel and Jonas, Peter M},
issn = {22111247},
journal = {Cell Reports},
number = {8},
pages = {2082 -- 2089},
publisher = {Cell Press},
title = {{Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses}},
doi = {10.1016/j.celrep.2017.10.122},
volume = {21},
year = {2017},
}
@article{751,
abstract = {The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components.},
author = {Matsubayashi, Yutaka and Louani, Adam and Dragu, Anca and Sanchez Sanchez, Besaiz and Serna Morales, Eduardo and Yolland, Lawrence and György, Attila and Vizcay, Gema and Fleck, Roland and Heddleston, John and Chew, Teng and Siekhaus, Daria E and Stramer, Brian},
issn = {09609822},
journal = {Current Biology},
number = {22},
pages = {3526 -- 3534e.4},
publisher = {Cell Press},
title = {{A moving source of matrix components is essential for De Novo basement membrane formation}},
doi = {10.1016/j.cub.2017.10.001},
volume = {27},
year = {2017},
}
@article{7733,
abstract = {Sections
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Abstract
Background: Gene discovery has provided remarkable biological insights into amyotrophic lateral sclerosis (ALS). One challenge for clinical application of genetic testing is critical evaluation of the significance of reported variants.
Methods: We use whole exome sequencing (WES) to develop a clinically relevant approach to identify a subset of ALS patients harboring likely pathogenic mutations. In parallel, we assess if DNA methylation can be used to screen for pathogenicity of novel variants since a methylation signature has been shown to associate with the pathogenic C9orf72 expansion, but has not been explored for other ALS mutations. Australian patients identified with ALS‐relevant variants were cross‐checked with population databases and case reports to critically assess whether they were “likely causal,” “uncertain significance,” or “unlikely causal.”
Results: Published ALS variants were identified in >10% of patients; however, in only 3% of patients (4/120) could these be confidently considered pathogenic (in SOD1 and TARDBP). We found no evidence for a differential DNA methylation signature in these mutation carriers.
Conclusions: The use of WES in a typical ALS clinic demonstrates a critical approach to variant assessment with the capability to combine cohorts to enhance the largely unknown genetic basis of ALS.},
author = {Garton, Fleur C. and Benyamin, Beben and Zhao, Qiongyi and Liu, Zhijun and Gratten, Jacob and Henders, Anjali K. and Zhang, Zong-Hong and Edson, Janette and Furlong, Sarah and Morgan, Sarah and Heggie, Susan and Thorpe, Kathryn and Pfluger, Casey and Mather, Karen A. and Sachdev, Perminder S. and McRae, Allan F. and Robinson, Matthew Richard and Shah, Sonia and Visscher, Peter M. and Mangelsdorf, Marie and Henderson, Robert D. and Wray, Naomi R. and McCombe, Pamela A.},
issn = {2324-9269},
journal = {Molecular Genetics & Genomic Medicine},
number = {4},
pages = {418--428},
publisher = {Wiley},
title = {{Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort}},
doi = {10.1002/mgg3.302},
volume = {5},
year = {2017},
}
@article{7755,
abstract = {We give a bird's-eye view of the plastic deformation of crystals aimed at the statistical physics community, as well as a broad introduction to the statistical theories of forced rigid systems aimed at the plasticity community. Memory effects in magnets, spin glasses, charge density waves, and dilute colloidal suspensions are discussed in relation to the onset of plastic yielding in crystals. Dislocation avalanches and complex dislocation tangles are discussed via a brief introduction to the renormalization group and scaling. Analogies to emergent scale invariance in fracture, jamming, coarsening, and a variety of depinning transitions are explored. Dislocation dynamics in crystals challenge nonequilibrium statistical physics. Statistical physics provides both cautionary tales of subtle memory effects in nonequilibrium systems and systematic tools designed to address complex scale-invariant behavior on multiple length scales and timescales.},
author = {Sethna, James P. and Bierbaum, Matthew K. and Dahmen, Karin A. and Goodrich, Carl Peter and Greer, Julia R. and Hayden, Lorien X. and Kent-Dobias, Jaron P. and Lee, Edward D. and Liarte, Danilo B. and Ni, Xiaoyue and Quinn, Katherine N. and Raju, Archishman and Rocklin, D. Zeb and Shekhawat, Ashivni and Zapperi, Stefano},
issn = {1531-7331},
journal = {Annual Review of Materials Research},
pages = {217--246},
publisher = {Annual Reviews},
title = {{Deformation of crystals: Connections with statistical physics}},
doi = {10.1146/annurev-matsci-070115-032036},
volume = {47},
year = {2017},
}
@inproceedings{787,
abstract = {Population protocols are a popular model of distributed computing, in which randomly-interacting agents with little computational power cooperate to jointly perform computational tasks. Inspired by developments in molecular computation, and in particular DNA computing, recent algorithmic work has focused on the complexity of solving simple yet fundamental tasks in the population model, such as leader election (which requires convergence to a single agent in a special "leader" state), and majority (in which agents must converge to a decision as to which of two possible initial states had higher initial count). Known results point towards an inherent trade-off between the time complexity of such algorithms, and the space complexity, i.e. size of the memory available to each agent. In this paper, we explore this trade-off and provide new upper and lower bounds for majority and leader election. First, we prove a unified lower bound, which relates the space available per node with the time complexity achievable by a protocol: for instance, our result implies that any protocol solving either of these tasks for n agents using O(log log n) states must take (n=polylogn) expected time. This is the first result to characterize time complexity for protocols which employ super-constant number of states per node, and proves that fast, poly-logarithmic running times require protocols to have relatively large space costs. On the positive side, we give algorithms showing that fast, poly-logarithmic convergence time can be achieved using O(log2 n) space per node, in the case of both tasks. Overall, our results highlight a time complexity separation between O(log log n) and (log2 n) state space size for both majority and leader election in population protocols, and introduce new techniques, which should be applicable more broadly.},
author = {Alistarh, Dan-Adrian and Aspnes, James and Eisenstat, David and Rivest, Ronald and Gelashvili, Rati},
pages = {2560 -- 2579},
publisher = {SIAM},
title = {{Time-space trade-offs in population protocols}},
doi = {doi.org/10.1137/1.9781611974782.169},
year = {2017},
}
@inproceedings{788,
abstract = {In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical algorithms must be designed with an appropriate error model in mind. Here we consider the model of chemical reaction networks that preserve molecular count (population protocols), and ask whether computation can be made robust to a natural model of unintended “leak” reactions. Our definition of leak is motivated by both the particular spurious behavior seen when implementing chemical reaction networks with DNA strand displacement cascades, as well as the unavoidable side reactions in any implementation due to the basic laws of chemistry. We develop a new “Robust Detection” algorithm for the problem of fast (logarithmic time) single molecule detection, and prove that it is robust to this general model of leaks. Besides potential applications in single molecule detection, the error-correction ideas developed here might enable a new class of robust-by-design chemical algorithms. Our analysis is based on a non-standard hybrid argument, combining ideas from discrete analysis of population protocols with classic Markov chain techniques.},
author = {Alistarh, Dan-Adrian and Dudek, Bartłomiej and Kosowski, Adrian and Soloveichik, David and Uznański, Przemysław},
pages = {155 -- 171},
publisher = {Springer},
title = {{Robust detection in leak-prone population protocols}},
doi = {10.1007/978-3-319-66799-7_11},
volume = {10467 LNCS},
year = {2017},
}
@inproceedings{791,
abstract = {Consider the following random process: we are given n queues, into which elements of increasing labels are inserted uniformly at random. To remove an element, we pick two queues at random, and remove the element of lower label (higher priority) among the two. The cost of a removal is the rank of the label removed, among labels still present in any of the queues, that is, the distance from the optimal choice at each step. Variants of this strategy are prevalent in state-of-the-art concurrent priority queue implementations. Nonetheless, it is not known whether such implementations provide any rank guarantees, even in a sequential model. We answer this question, showing that this strategy provides surprisingly strong guarantees: Although the single-choice process, where we always insert and remove from a single randomly chosen queue, has degrading cost, going to infinity as we increase the number of steps, in the two choice process, the expected rank of a removed element is O(n) while the expected worst-case cost is O(n log n). These bounds are tight, and hold irrespective of the number of steps for which we run the process. The argument is based on a new technical connection between "heavily loaded" balls-into-bins processes and priority scheduling. Our analytic results inspire a new concurrent priority queue implementation, which improves upon the state of the art in terms of practical performance.},
author = {Alistarh, Dan-Adrian and Kopinsky, Justin and Li, Jerry and Nadiradze, Giorgi},
booktitle = {Proceedings of the ACM Symposium on Principles of Distributed Computing},
isbn = {978-145034992-5},
location = {Washington, WA, USA},
pages = {283 -- 292},
publisher = {ACM},
title = {{The power of choice in priority scheduling}},
doi = {10.1145/3087801.3087810},
volume = {Part F129314},
year = {2017},
}
@article{792,
abstract = {The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics.},
author = {Budanur, Nazmi B and Short, Kimberly and Farazmand, Mohammad and Willis, Ashley and Cvitanović, Predrag},
issn = {00221120},
journal = {Journal of Fluid Mechanics},
pages = {274 -- 301},
publisher = {Cambridge University Press},
title = {{Relative periodic orbits form the backbone of turbulent pipe flow}},
doi = {10.1017/jfm.2017.699},
volume = {833},
year = {2017},
}
@article{793,
abstract = {Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c > 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). },
author = {Fulek, Radoslav and Mojarrad, Hossein and Naszódi, Márton and Solymosi, József and Stich, Sebastian and Szedlák, May},
issn = {09257721},
journal = {Computational Geometry: Theory and Applications},
pages = {28 -- 31},
publisher = {Elsevier},
title = {{On the existence of ordinary triangles}},
doi = {10.1016/j.comgeo.2017.07.002},
volume = {66},
year = {2017},
}
@article{794,
abstract = {We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle.},
author = {Fulek, Radoslav},
journal = {Computational Geometry: Theory and Applications},
pages = {1 -- 13},
publisher = {Elsevier},
title = {{C-planarity of embedded cyclic c-graphs}},
doi = {10.1016/j.comgeo.2017.06.016},
volume = {66},
year = {2017},
}
@article{795,
abstract = {We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof.},
author = {Fulek, Radoslav and Kynčl, Jan and Pálvölgyi, Dömötör},
issn = {10778926},
journal = {Electronic Journal of Combinatorics},
number = {3},
publisher = {International Press},
title = {{Unified Hanani Tutte theorem}},
volume = {24},
year = {2017},
}
@article{463,
abstract = {We investigate transient behaviors induced by magnetic fields on the dynamics of the flow of a ferrofluid in the gap between two concentric, independently rotating cylinders. Without applying any magnetic fields, we uncover emergence of flow states constituted by a combination of a localized spiral state (SPIl) in the top and bottom of the annulus and different multi-cell flow states (SPI2v, SPI3v) with toroidally closed vortices in the interior of the bulk (SPIl+2v = SPIl + SPI2v and SPIl+3v = SPIl + SPI3v). However, when a magnetic field is presented, we observe the transient behaviors between multi-cell states passing through two critical thresholds in a strength of an axial (transverse) magnetic field. Before the first critical threshold of a magnetic field strength, multi-stable states with different number of cells could be observed. After the first critical threshold, we find the transient behavior between the three- and two-cell flow states. For more strength of magnetic field or after the second critical threshold, we discover that multi-cell states are disappeared and a localized spiral state remains to be stimulated. The studied transient behavior could be understood by the investigation of various quantities including a modal kinetic energy, a mode amplitude of the radial velocity, wavenumber, angular momentum, and torque. In addition, the emergence of new flow states and the transient behavior between their states in ferrofluidic flows indicate that richer and potentially controllable dynamics through magnetic fields could be possible in ferrofluic flow.},
author = {Altmeyer, Sebastian and Do, Younghae and Ryu, Soorok},
issn = {10541500},
journal = {Chaos},
number = {11},
publisher = {AIP},
title = {{Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow}},
doi = {10.1063/1.5002771},
volume = {27},
year = {2017},
}
@article{464,
abstract = {The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years.},
author = {Chatterjee, Krishnendu and Henzinger, Monika and Loitzenbauer, Veronika},
issn = {18605974},
journal = {Logical Methods in Computer Science},
number = {3},
publisher = {International Federation of Computational Logic},
title = {{Improved algorithms for parity and Streett objectives}},
doi = {10.23638/LMCS-13(3:26)2017},
volume = {13},
year = {2017},
}
@article{465,
abstract = {The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. },
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Ibsen-Jensen, Rasmus and Otop, Jan},
issn = {18605974},
journal = {Logical Methods in Computer Science},
number = {3},
publisher = {International Federation of Computational Logic},
title = {{Edit distance for pushdown automata}},
doi = {10.23638/LMCS-13(3:23)2017},
volume = {13},
year = {2017},
}
@article{466,
abstract = {We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. },
author = {Chatterjee, Krishnendu and Křetínská, Zuzana and Kretinsky, Jan},
issn = {18605974},
journal = {Logical Methods in Computer Science},
number = {2},
publisher = {International Federation of Computational Logic},
title = {{Unifying two views on multiple mean-payoff objectives in Markov decision processes}},
doi = {10.23638/LMCS-13(2:15)2017},
volume = {13},
year = {2017},
}
@article{467,
abstract = {Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
issn = {15293785},
journal = {ACM Transactions on Computational Logic (TOCL)},
number = {4},
publisher = {ACM},
title = {{Nested weighted automata}},
doi = {10.1145/3152769},
volume = {18},
year = {2017},
}
@article{470,
abstract = {This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios.},
author = {Jeschke, Stefan and Wojtan, Christopher J},
issn = {07300301},
journal = {ACM Transactions on Graphics},
number = {4},
publisher = {ACM},
title = {{Water wave packets}},
doi = {10.1145/3072959.3073678},
volume = {36},
year = {2017},
}
@article{471,
abstract = {We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. },
author = {Daca, Przemyslaw and Henzinger, Thomas A and Kretinsky, Jan and Petrov, Tatjana},
issn = {15293785},
journal = {ACM Transactions on Computational Logic (TOCL)},
number = {2},
publisher = {ACM},
title = {{Faster statistical model checking for unbounded temporal properties}},
doi = {10.1145/3060139},
volume = {18},
year = {2017},
}
@article{481,
abstract = {We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.},
author = {Biedl, Therese and Huber, Stefan and Palfrader, Peter},
journal = {International Journal of Computational Geometry and Applications},
number = {3-4},
pages = {211 -- 229},
publisher = {World Scientific Publishing},
title = {{Planar matchings for weighted straight skeletons}},
doi = {10.1142/S0218195916600050},
volume = {26},
year = {2017},
}
@article{483,
abstract = {We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices.},
author = {Bourgade, Paul and Erdös, László and Yau, Horng and Yin, Jun},
issn = {10950761},
journal = {Advances in Theoretical and Mathematical Physics},
number = {3},
pages = {739 -- 800},
publisher = {International Press},
title = {{Universality for a class of random band matrices}},
doi = {10.4310/ATMP.2017.v21.n3.a5},
volume = {21},
year = {2017},
}