@article{1120,
abstract = {The existence of a self-localization transition in the polaron problem has been under an active debate ever since Landau suggested it 83 years ago. Here we reveal the self-localization transition for the rotational analogue of the polaron -- the angulon quasiparticle. We show that, unlike for the polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of the symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. The predicted effects can potentially be addressed in experiments on cold molecules trapped in superfluid helium droplets and ultracold quantum gases, as well as on electronic excitations in solids and Bose-Einstein condensates. },
author = {Li, Xiang and Seiringer, Robert and Lemeshko, Mikhail},
issn = {24699926},
journal = {Physical Review A},
number = {3},
publisher = {American Physical Society},
title = {{Angular self-localization of impurities rotating in a bosonic bath}},
doi = {10.1103/PhysRevA.95.033608},
volume = {95},
year = {2017},
}
@phdthesis{1127,
abstract = {Plant hormone auxin and its transport between cells belong to the most important
mechanisms controlling plant development. Auxin itself could change localization of PINs and
thereby control direction of its own flow. We performed an expression profiling experiment
in Arabidopsis roots to identify potential regulators of PIN polarity which are transcriptionally
regulated by auxin signalling. We identified several novel regulators and performed a detailed
characterization of the transcription factor WRKY23 (At2g47260) and its role in auxin
feedback on PIN polarity. Gain-of-function and dominant-negative mutants revealed that
WRKY23 plays a crucial role in mediating the auxin effect on PIN polarity. In concordance,
typical polar auxin transport processes such as gravitropism and leaf vascular pattern
formation were disturbed by interfering with WRKY23 function.
In order to identify direct targets of WRKY23, we performed consequential expression
profiling experiments using a WRKY23 inducible gain-of-function line and dominant-negative
WRKY23 line that is defunct in PIN re-arrangement. Among several genes mostly related to
the groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE
TRANSPORTER 1 (LHT1; At5g40780), a small amino acid permease gene from the amino
acid/auxin permease family (AAAP), we present its detailed characterisation in auxin feedback
on PIN repolarization, identified its transcriptional regulation, we propose a potential
mechanism of its action. Moreover, we identified also a member of receptor-like protein
kinase LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;
LRRK1; At1g05700), which also affects auxin-dependent PIN re-arrangement. We described
its transcriptional behaviour, subcellular localization. Based on global expression data, we
tried to identify ligand responsible for mechanism of signalling and suggest signalling partner
and interactors. Additionally, we described role of novel phytohormone group, strigolactone,
in auxin-dependent PIN re-arrangement, that could be a fundament for future studies in this
field.
Our results provide first insights into an auxin transcriptional network targeting PIN
localization and thus regulating plant development. We highlighted WRKY23 transcriptional
network and characterised its mediatory role in plant development. We identified direct
effectors of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement and
PIN-dependent auxin transport processes.},
author = {Prat, Tomas},
pages = {131},
publisher = {IST Austria},
title = {{Identification of novel regulators of PIN polarity and development of novel auxin sensor}},
year = {2017},
}
@article{1132,
abstract = {The hippocampus is thought to initiate systems-wide mnemonic processes through the reactivation of previously acquired spatial and episodic memory traces, which can recruit the entorhinal cortex as a first stage of memory redistribution to other brain areas. Hippocampal reactivation occurs during sharp wave-ripples, in which synchronous network firing encodes sequences of places.We investigated the coordination of this replay by recording assembly activity simultaneously in the CA1 region of the hippocampus and superficial layers of the medial entorhinal cortex. We found that entorhinal cell assemblies can replay trajectories independently of the hippocampus and sharp wave-ripples. This suggests that the hippocampus is not the sole initiator of spatial and episodic memory trace reactivation. Memory systems involved in these processes may include nonhierarchical, parallel components.},
author = {O'Neill, Joseph and Boccara, Charlotte and Stella, Federico and Schönenberger, Philipp and Csicsvari, Jozsef L},
issn = {00368075},
journal = {Science},
number = {6321},
pages = {184 -- 188},
publisher = {American Association for the Advancement of Science},
title = {{Superficial layers of the medial entorhinal cortex replay independently of the hippocampus}},
doi = {10.1126/science.aag2787},
volume = {355},
year = {2017},
}
@article{1133,
abstract = {It is a common knowledge that an effective interaction of a quantum impurity with an electromagnetic field can be screened by surrounding charge carriers, whether mobile or static. Here we demonstrate that very strong, "anomalous" screening can take place in the presence of a neutral, weakly polarizable environment, due to an exchange of orbital angular momentum between the impurity and the bath. Furthermore, we show that it is possible to generalize all phenomena related to isolated impurities in an external field to the case when a many-body environment is present, by casting the problem in terms of the angulon quasiparticle. As a result, the relevant observables such as the effective Rabi frequency, geometric phase, and impurity spatial alignment are straightforward to evaluate in terms of a single parameter: the angular-momentum-dependent screening factor.},
author = {Yakaboylu, Enderalp and Lemeshko, Mikhail},
issn = {00319007},
journal = {Physical Review Letters},
number = {8},
publisher = {American Physical Society},
title = {{Anomalous screening of quantum impurities by a neutral environment}},
doi = {10.1103/PhysRevLett.118.085302},
volume = {118},
year = {2017},
}
@article{1144,
abstract = {We show that matrix elements of functions of N × N Wigner matrices fluctuate on a scale of order N−1/2 and we identify the limiting fluctuation. Our result holds for any function f of the matrix that has bounded variation thus considerably relaxing the regularity requirement imposed in [7, 11].},
author = {Erdös, László and Schröder, Dominik J},
journal = {Electronic Communications in Probability},
publisher = {Institute of Mathematical Statistics},
title = {{Fluctuations of functions of Wigner matrices}},
doi = {10.1214/16-ECP38},
volume = {21},
year = {2017},
}
@article{1146,
abstract = {Aim: The present study was to compare the effects of nicotinic acid and nicotinamide on the plasma methyl donors, choline and betaine. Methods: Thirty adult subjects were randomly divided into three groups of equal size, and orally received purified water (C group), nicotinic acid (300 mg, NA group) or nicotinamide (300 mg, NM group). Plasma nicotinamide, N 1-methylnicotinamide, homocysteine, betaine and choline levels before and 1.5-h and 3-h post-dosing, plasma normetanephrine and metanephrine concentrations at 3-h post-dosing, and the urinary excretion of N 1-methyl-2-pyridone-5-carboxamide during the test period were examined. Results: The level of 3-h plasma nicotinamide, N 1-methylnicotinamide, homocysteine, the urinary excretion of N 1-methyl-2-pyridone-5-carboxamide and pulse pressure (PP) in the NM group was 221%, 3972%, 61%, 1728% and 21.2% higher than that of the control group (P < 0.01, except homocysteine and PP P < 0.05), while the 3-h plasma betaine, normetanephrine and metanephrine level in the NM group was 24.4%, 9.4% and 11.7% lower (P < 0.05, except betaine P < 0.01), without significant difference in choline levels. Similar but less pronounced changes were observed in the NA group, with a lower level of 3-h plasma N 1-methylnicotinamide (1.90 ± 0.20 μmol/l vs. 3.62 ± 0.27 μmol/l, P < 0.01) and homocysteine (12.85 ± 1.39 μmol/l vs. 18.08 ± 1.02 μmol/l, P < 0.05) but a higher level of betaine (27.44 ± 0.71 μmol/l vs. 23.52 ± 0.61 μmol/l, P < 0.05) than that of the NM group. Conclusion: The degradation of nicotinamide consumes more betaine than that of nicotinic acid at identical doses. This difference should be taken into consideration in niacin fortification. © 2016 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism.},
author = {Sun, Wuping and Zhai, Ming-Zhu and Li, Da and Zhou, Yiming and Chen, Nana and Guo, Ming and Zhou, Shisheng},
journal = {Clinical Nutrition},
number = {4},
pages = {1136--1142},
publisher = {Churchill Livingstone},
title = {{Comparison of the effects of nicotinic acid and nicotinamide degradation on plasma betaine and choline levels}},
doi = {10.1016/j.clnu.2016.07.016},
volume = {36},
year = {2017},
}
@article{1152,
abstract = {We propose a new memetic strategy that can solve the multi-physics, complex inverse problems, formulated as the multi-objective optimization ones, in which objectives are misfits between the measured and simulated states of various governing processes. The multi-deme structure of the strategy allows for both, intensive, relatively cheap exploration with a moderate accuracy and more accurate search many regions of Pareto set in parallel. The special type of selection operator prefers the coherent alternative solutions, eliminating artifacts appearing in the particular processes. The additional accuracy increment is obtained by the parallel convex searches applied to the local scalarizations of the misfit vector. The strategy is dedicated for solving ill-conditioned problems, for which inverting the single physical process can lead to the ambiguous results. The skill of the selection in artifact elimination is shown on the benchmark problem, while the whole strategy was applied for identification of oil deposits, where the misfits are related to various frequencies of the magnetic and electric waves of the magnetotelluric measurements. 2016 Elsevier B.V.},
author = {Gajda-Zagorska, Ewa P and Schaefer, Robert and Smołka, Maciej and Pardo, David and Alvarez Aramberri, Julen},
issn = {18777503},
journal = {Journal of Computational Science},
pages = {85 -- 94},
publisher = {Elsevier},
title = {{A multi objective memetic inverse solver reinforced by local optimization methods}},
doi = {10.1016/j.jocs.2016.06.007},
volume = {18},
year = {2017},
}
@phdthesis{1155,
abstract = {This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results.},
author = {Daca, Przemyslaw},
pages = {163},
publisher = {IST Austria},
title = {{Statistical and logical methods for property checking}},
doi = {10.15479/AT:ISTA:TH_730},
year = {2017},
}
@article{1160,
abstract = {We investigate fundamental nonlinear dynamics of ferrofluidic Taylor-Couette flow - flow confined be-tween two concentric independently rotating cylinders - consider small aspect ratio by solving the ferro-hydrodynamical equations, carrying out systematic bifurcation analysis. Without magnetic field, we find steady flow patterns, previously observed with a simple fluid, such as those containing normal one- or two vortex cells, as well as anomalous one-cell and twin-cell flow states. However, when a symmetry-breaking transverse magnetic field is present, all flow states exhibit stimulated, finite two-fold mode. Various bifurcations between steady and unsteady states can occur, corresponding to the transitions between the two-cell and one-cell states. While unsteady, axially oscillating flow states can arise, we also detect the emergence of new unsteady flow states. In particular, we uncover two new states: one contains only the azimuthally oscillating solution in the configuration of the twin-cell flow state, and an-other a rotating flow state. Topologically, these flow states are a limit cycle and a quasiperiodic solution on a two-torus, respectively. Emergence of new flow states in addition to observed ones with classical fluid, indicates that richer but potentially more controllable dynamics in ferrofluidic flows, as such flow states depend on the external magnetic field.},
author = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying},
issn = {20452322},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio}},
doi = {10.1038/srep40012},
volume = {7},
year = {2017},
}
@article{1161,
abstract = {Coordinated changes of cell shape are often the result of the excitable, wave-like dynamics of the actin cytoskeleton. New work shows that, in migrating cells, protrusion waves arise from mechanochemical crosstalk between adhesion sites, membrane tension and the actin protrusive machinery.},
author = {Müller, Jan and Sixt, Michael K},
issn = {09609822},
journal = {Current Biology},
number = {1},
pages = {R24 -- R25},
publisher = {Cell Press},
title = {{Cell migration: Making the waves}},
doi = {10.1016/j.cub.2016.11.035},
volume = {27},
year = {2017},
}
@article{1162,
abstract = {Selected universal experimental properties of high-temperature superconducting (HTS) cuprates have been singled out in the last decade. One of the pivotal challenges in this field is the designation of a consistent interpretation framework within which we can describe quantitatively the universal features of those systems. Here we analyze in a detailed manner the principal experimental data and compare them quantitatively with the approach based on a single-band model of strongly correlated electrons supplemented with strong antiferromagnetic (super)exchange interaction (the so-called t−J−U model). The model rationale is provided by estimating its microscopic parameters on the basis of the three-band approach for the Cu-O plane. We use our original full Gutzwiller wave-function solution by going beyond the renormalized mean-field theory (RMFT) in a systematic manner. Our approach reproduces very well the observed hole doping (δ) dependence of the kinetic-energy gain in the superconducting phase, one of the principal non-Bardeen-Cooper-Schrieffer features of the cuprates. The calculated Fermi velocity in the nodal direction is practically δ-independent and its universal value agrees very well with that determined experimentally. Also, a weak doping dependence of the Fermi wave vector leads to an almost constant value of the effective mass in a pure superconducting phase which is both observed in experiment and reproduced within our approach. An assessment of the currently used models (t−J, Hubbard) is carried out and the results of the canonical RMFT as a zeroth-order solution are provided for comparison to illustrate the necessity of the introduced higher-order contributions.},
author = {Spałek, Jozef and Zegrodnik, Michał and Kaczmarczyk, Jan},
issn = {24699950},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {2},
publisher = {American Physical Society},
title = {{Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment}},
doi = {10.1103/PhysRevB.95.024506},
volume = {95},
year = {2017},
}
@article{1163,
abstract = {We investigate the effect of the electron-hole (e-h) symmetry breaking on d-wave superconductivity induced by non-local effects of correlations in the generalized Hubbard model. The symmetry breaking is introduced in a two-fold manner: by the next-to-nearest neighbor hopping of electrons and by the charge-bond interaction - the off-diagonal term of the Coulomb potential. Both terms lead to a pronounced asymmetry of the superconducting order parameter. The next-to-nearest neighbor hopping enhances superconductivity for h-doping, while diminishes it for e-doping. The charge-bond interaction alone leads to the opposite effect and, additionally, to the kinetic-energy gain upon condensation in the underdoped regime. With both terms included, with similar amplitudes, the height of the superconducting dome and the critical doping remain in favor of h-doping. The influence of the charge-bond interaction on deviations from symmetry of the shape of the gap at the Fermi surface in the momentum space is briefly discussed.},
author = {Wysokiński, Marcin and Kaczmarczyk, Jan},
issn = {09538984},
journal = {Journal of Physics: Condensed Matter},
number = {8},
publisher = {IOP Publishing Ltd.},
title = {{Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms}},
doi = {10.1088/1361-648X/aa532f},
volume = {29},
year = {2017},
}
@article{1168,
abstract = {Optimum experimental design theory has recently been extended for parameter estimation in copula models. The use of these models allows one to gain in flexibility by considering the model parameter set split into marginal and dependence parameters. However, this separation also leads to the natural issue of estimating only a subset of all model parameters. In this work, we treat this problem with the application of the (Formula presented.)-optimality to copula models. First, we provide an extension of the corresponding equivalence theory. Then, we analyze a wide range of flexible copula models to highlight the usefulness of (Formula presented.)-optimality in many possible scenarios. Finally, we discuss how the usage of the introduced design criterion also relates to the more general issue of copula selection and optimal design for model discrimination.},
author = {Perrone, Elisa and Rappold, Andreas and Müller, Werner},
journal = {Statistical Methods and Applications},
number = {3},
pages = {403 -- 418},
publisher = {Springer},
title = {{D inf s optimality in copula models}},
doi = {10.1007/s10260-016-0375-6},
volume = {26},
year = {2017},
}
@article{1169,
abstract = {Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies.},
author = {Novak, Sebastian and Kollár, Richard},
issn = {00166731},
journal = {Genetics},
number = {1},
pages = {367 -- 374},
publisher = {Genetics Society of America},
title = {{Spatial gene frequency waves under genotype dependent dispersal}},
doi = {10.1534/genetics.116.193946},
volume = {205},
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},
}
@inproceedings{609,
abstract = {Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover.},
author = {Alwen, Joel F and Tackmann, Björn},
editor = {Kalai, Yael and Reyzin, Leonid},
isbn = {978-331970499-9},
location = {Baltimore, MD, United States},
pages = {493 -- 526},
publisher = {Springer},
title = {{Moderately hard functions: Definition, instantiations, and applications}},
doi = {10.1007/978-3-319-70500-2_17},
volume = {10677},
year = {2017},
}
@article{610,
abstract = {The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.},
author = {Goaoc, Xavier and Mabillard, Isaac and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
journal = {Israel Journal of Mathematics},
number = {2},
pages = {841 -- 866},
publisher = {Springer},
title = {{On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result}},
doi = {10.1007/s11856-017-1607-7},
volume = {222},
year = {2017},
}
@article{611,
abstract = {Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.},
author = {Bradley, Desmond and Xu, Ping and Mohorianu, Irina and Whibley, Annabel and Field, David and Tavares, Hugo and Couchman, Matthew and Copsey, Lucy and Carpenter, Rosemary and Li, Miaomiao and Li, Qun and Xue, Yongbiao and Dalmay, Tamas and Coen, Enrico},
issn = {00368075},
journal = {Science},
number = {6365},
pages = {925 -- 928},
publisher = {American Association for the Advancement of Science},
title = {{Evolution of flower color pattern through selection on regulatory small RNAs}},
doi = {10.1126/science.aao3526},
volume = {358},
year = {2017},
}
@article{6113,
author = {Oda, Shigekazu and Toyoshima, Yu and de Bono, Mario},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {23},
pages = {E4658--E4665},
publisher = {National Academy of Sciences},
title = {{Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans}},
doi = {10.1073/pnas.1614596114},
volume = {114},
year = {2017},
}
@article{6115,
abstract = {Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.},
author = {Fenk, Lorenz A. and de Bono, Mario},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {16},
pages = {4195--4200},
publisher = {National Academy of Sciences},
title = {{Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans}},
doi = {10.1073/pnas.1618934114},
volume = {114},
year = {2017},
}
@article{6117,
abstract = {Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates responses to pathogens or tissue damage, and drives autoimmune diseases. Little is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter their response properties and contribution to behaviour. Using unbiased genetic screens, we delineate an IL-17 signalling pathway and show that it acts in the RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to input from oxygen sensors, and renders sustained escape from 21% oxygen transient and contingent on additional stimuli. Over-activating IL-17 receptors abnormally heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in adults can rescue mutant defects within 6 h. These findings reveal a non-immunological role of IL-17 modulating circuit function and behaviour.},
author = {Chen, Changchun and Itakura, Eisuke and Nelson, Geoffrey M. and Sheng, Ming and Laurent, Patrick and Fenk, Lorenz A. and Butcher, Rebecca A. and Hegde, Ramanujan S. and de Bono, Mario},
issn = {0028-0836},
journal = {Nature},
number = {7639},
pages = {43--48},
publisher = {Springer Nature},
title = {{IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses}},
doi = {10.1038/nature20818},
volume = {542},
year = {2017},
}
@article{613,
abstract = {Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.},
author = {Chait, Remy P and Ruess, Jakob and Bergmiller, Tobias and Tkacik, Gasper and Guet, Calin C},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{Shaping bacterial population behavior through computer interfaced control of individual cells}},
doi = {10.1038/s41467-017-01683-1},
volume = {8},
year = {2017},
}
@article{614,
abstract = {Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.},
author = {Fraisse, Christelle and Picard, Marion A and Vicoso, Beatriz},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W}},
doi = {10.1038/s41467-017-01663-5},
volume = {8},
year = {2017},
}
@article{615,
abstract = {We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law.},
author = {Erdös, László and Schnelli, Kevin},
issn = {02460203},
journal = {Annales de l'institut Henri Poincare (B) Probability and Statistics},
number = {4},
pages = {1606 -- 1656},
publisher = {Institute of Mathematical Statistics},
title = {{Universality for random matrix flows with time dependent density}},
doi = {10.1214/16-AIHP765},
volume = {53},
year = {2017},
}
@article{618,
abstract = {Background: Increasing temperatures are predicted to strongly impact host-parasite interactions, but empirical tests are rare. Host species that are naturally exposed to a broad temperature spectrum offer the possibility to investigate the effects of elevated temperatures on hosts and parasites. Using three-spined sticklebacks, Gasterosteus aculeatus L., and tapeworms, Schistocephalus solidus (Müller, 1776), originating from a cold and a warm water site of a volcanic lake, we subjected sympatric and allopatric host-parasite combinations to cold and warm conditions in a fully crossed design. We predicted that warm temperatures would promote the development of the parasites, while the hosts might benefit from cooler temperatures. We further expected adaptations to the local temperature and mutual adaptations of local host-parasite pairs. Results: Overall, S. solidus parasites grew faster at warm temperatures and stickleback hosts at cold temperatures. On a finer scale, we observed that parasites were able to exploit their hosts more efficiently at the parasite’s temperature of origin. In contrast, host tolerance towards parasite infection was higher when sticklebacks were infected with parasites at the parasite’s ‘foreign’ temperature. Cold-origin sticklebacks tended to grow faster and parasite infection induced a stronger immune response. Conclusions: Our results suggest that increasing environmental temperatures promote the parasite rather than the host and that host tolerance is dependent on the interaction between parasite infection and temperature. Sticklebacks might use tolerance mechanisms towards parasite infection in combination with their high plasticity towards temperature changes to cope with increasing parasite infection pressures and rising temperatures.},
author = {Franke, Frederik and Armitage, Sophie and Kutzer, Megan and Kurtz, Joachim and Scharsack, Jörn},
issn = {17563305},
journal = {Parasites & Vectors},
number = {252},
publisher = {BioMed Central},
title = {{Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association }},
doi = {10.1186/s13071-017-2192-7},
volume = {10},
year = {2017},
}
@article{6196,
abstract = {PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem.},
author = {Gazi, Peter and Pietrzak, Krzysztof Z and Rybar, Michal},
issn = {2519-173X},
journal = {IACR Transactions on Symmetric Cryptology},
number = {2},
pages = {145--161},
publisher = {Ruhr University Bochum},
title = {{The exact security of PMAC}},
doi = {10.13154/TOSC.V2016.I2.145-161},
volume = {2016},
year = {2017},
}
@article{621,
abstract = {The mammalian cerebral cortex is responsible for higher cognitive functions such as perception, consciousness, and acquiring and processing information. The neocortex is organized into six distinct laminae, each composed of a rich diversity of cell types which assemble into highly complex cortical circuits. Radial glia progenitors (RGPs) are responsible for producing all neocortical neurons and certain glia lineages. Here, we discuss recent discoveries emerging from clonal lineage analysis at the single RGP cell level that provide us with an inaugural quantitative framework of RGP lineage progression. We further discuss the importance of the relative contribution of intrinsic gene functions and non-cell-autonomous or community effects in regulating RGP proliferation behavior and lineage progression.},
author = {Beattie, Robert J and Hippenmeyer, Simon},
issn = {00145793},
journal = {FEBS letters},
number = {24},
pages = {3993 -- 4008},
publisher = {Wiley-Blackwell},
title = {{Mechanisms of radial glia progenitor cell lineage progression}},
doi = {10.1002/1873-3468.12906},
volume = {591},
year = {2017},
}
@inbook{623,
abstract = {Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology.},
author = {Hill Yardin, Elisa and Mckeown, Sonja and Novarino, Gaia and Grabrucker, Andreas},
booktitle = {Translational Anatomy and Cell Biology of Autism Spectrum Disorder},
editor = {Schmeisser, Michael and Boekers, Tobias},
isbn = {978-3-319-52496-2},
issn = {03015556},
pages = {159 -- 187},
publisher = {Springer},
title = {{Extracerebral dysfunction in animal models of autism spectrum disorder}},
doi = {10.1007/978-3-319-52498-6_9},
volume = {224},
year = {2017},
}
@article{624,
abstract = {Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.},
author = {Nikolic, Nela and Didara, Zrinka and Moll, Isabella},
issn = {21678359},
journal = {PeerJ},
number = {9},
publisher = {PeerJ},
title = {{MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations}},
doi = {10.7717/peerj.3830},
volume = {2017},
year = {2017},
}
@article{626,
abstract = {Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.},
author = {Barton, Nicholas H and Etheridge, Alison and Véber, Amandine},
issn = {00405809},
journal = {Theoretical Population Biology},
pages = {50 -- 73},
publisher = {Academic Press},
title = {{The infinitesimal model: Definition derivation and implications}},
doi = {10.1016/j.tpb.2017.06.001},
volume = {118},
year = {2017},
}
@article{627,
abstract = {Beige adipocytes are a new type of recruitable brownish adipocytes, with highly mitochondrial membrane uncoupling protein 1 expression and thermogenesis. Beige adipocytes were found among white adipocytes, especially in subcutaneous white adipose tissue (sWAT). Therefore, beige adipocytes may be involved in the regulation of energy metabolism and fat deposition. Transient receptor potential melastatin 8 (TRPM8), a Ca2+-permeable non-selective cation channel, plays vital roles in the regulation of various cellular functions. It has been reported that TRPM8 activation enhanced the thermogenic function of brown adiposytes. However, the involvement of TRPM8 in the thermogenic function of WAT remains unexplored. Our data revealed that TRPM8 was expressed in mouse white adipocytes at mRNA, protein and functional levels. The mRNA expression of Trpm8 was significantly increased in the differentiated white adipocytes than pre-adipocytes. Moreover, activation of TRPM8 by menthol enhanced the expression of thermogenic genes in cultured white aidpocytes. And menthol-induced increases of the thermogenic genes in white adipocytes was inhibited by either KT5720 (a protein kinase A inhibitor) or BAPTA-AM. In addition, high fat diet (HFD)-induced obesity in mice was significantly recovered by co-treatment with menthol. Dietary menthol enhanced WAT "browning" and improved glucose metabolism in HFD-induced obesity mice as well. Therefore, we concluded that TRPM8 might be involved in WAT "browning" by increasing the expression levels of genes related to thermogenesis and energy metabolism. And dietary menthol could be a novel approach for combating human obesity and related metabolic diseases.},
author = {Jiang, Changyu and Zhai, Ming-Zhu and Yan, Dong and Li, Da and Li, Chen and Zhang, Yonghong and Xiao, Lizu and Xiong, Donglin and Deng, Qiwen and Sun, Wuping},
issn = {19492553},
journal = {Oncotarget},
number = {43},
pages = {75114 -- 75126},
publisher = {Impact Journals LLC},
title = {{Dietary menthol-induced TRPM8 activation enhances WAT “browning” and ameliorates diet-induced obesity}},
doi = {10.18632/oncotarget.20540},
volume = {8},
year = {2017},
}
@inproceedings{628,
abstract = {We consider the problem of developing automated techniques for solving recurrence relations to aid the expected-runtime analysis of programs. The motivation is that several classical textbook algorithms have quite efficient expected-runtime complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., Quick-Sort), or completely ineffective (e.g., Coupon-Collector). Since the main focus of expected-runtime analysis is to obtain efficient bounds, we consider bounds that are either logarithmic, linear or almost-linear (O(log n), O(n), O(n · log n), respectively, where n represents the input size). Our main contribution is an efficient (simple linear-time algorithm) sound approach for deriving such expected-runtime bounds for the analysis of recurrence relations induced by randomized algorithms. The experimental results show that our approach can efficiently derive asymptotically optimal expected-runtime bounds for recurrences of classical randomized algorithms, including Randomized-Search, Quick-Sort, Quick-Select, Coupon-Collector, where the worst-case bounds are either inefficient (such as linear as compared to logarithmic expected-runtime complexity, or quadratic as compared to linear or almost-linear expected-runtime complexity), or ineffective.},
author = {Chatterjee, Krishnendu and Fu, Hongfei and Murhekar, Aniket},
editor = {Majumdar, Rupak and Kunčak, Viktor},
isbn = {978-331963386-2},
location = {Heidelberg, Germany},
pages = {118 -- 139},
publisher = {Springer},
title = {{Automated recurrence analysis for almost linear expected runtime bounds}},
doi = {10.1007/978-3-319-63387-9_6},
volume = {10426},
year = {2017},
}
@phdthesis{6287,
abstract = {The main objects considered in the present work are simplicial and CW-complexes with vertices forming a random point cloud. In particular, we consider a Poisson point process in R^n and study Delaunay and Voronoi complexes of the first and higher orders and weighted Delaunay complexes obtained as sections of Delaunay complexes, as well as the Čech complex. Further, we examine theDelaunay complex of a Poisson point process on the sphere S^n, as well as of a uniform point cloud, which is equivalent to the convex hull, providing a connection to the theory of random polytopes. Each of the complexes in question can be endowed with a radius function, which maps its cells to the radii of appropriately chosen circumspheres, called the radius of the cell. Applying and developing discrete Morse theory for these functions, joining it together with probabilistic and sometimes analytic machinery, and developing several integral geometric tools, we aim at getting the distributions of circumradii of typical cells. For all considered complexes, we are able to generalize and obtain up to constants the distribution of radii of typical intervals of all types. In low dimensions the constants can be computed explicitly, thus providing the explicit expressions for the expected numbers of cells. In particular, it allows to find the expected density of simplices of every dimension for a Poisson point process in R^4, whereas the result for R^3 was known already in 1970's.},
author = {Nikitenko, Anton},
pages = {86},
publisher = {IST Austria},
title = {{Discrete Morse theory for random complexes }},
doi = {10.15479/AT:ISTA:th_873},
year = {2017},
}
@inbook{629,
abstract = {Even simple cells like bacteria have precisely regulated cellular anatomies, which allow them to grow, divide and to respond to internal or external cues with high fidelity. How spatial and temporal intracellular organization in prokaryotic cells is achieved and maintained on the basis of locally interacting proteins still remains largely a mystery. Bulk biochemical assays with purified components and in vivo experiments help us to approach key cellular processes from two opposite ends, in terms of minimal and maximal complexity. However, to understand how cellular phenomena emerge, that are more than the sum of their parts, we have to assemble cellular subsystems step by step from the bottom up. Here, we review recent in vitro reconstitution experiments with proteins of the bacterial cell division machinery and illustrate how they help to shed light on fundamental cellular mechanisms that constitute spatiotemporal order and regulate cell division.},
author = {Loose, Martin and Zieske, Katja and Schwille, Petra},
booktitle = {Prokaryotic Cytoskeletons},
pages = {419 -- 444},
publisher = {Springer},
title = {{Reconstitution of protein dynamics involved in bacterial cell division}},
doi = {10.1007/978-3-319-53047-5_15},
volume = {84},
year = {2017},
}
@phdthesis{6291,
abstract = {Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population.},
author = {Payne, Pavel},
pages = {83},
publisher = {IST Austria},
title = {{Bacterial herd and social immunity to phages}},
year = {2017},
}
@inproceedings{630,
abstract = {Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years.},
author = {Sauermann, Stefan and David, Veronika and Schlögl, Alois and Egelkraut, Reinhard and Frohner, Matthias and Pohn, Birgit and Urbauer, Philipp and Mense, Alexander},
isbn = {978-161499758-0},
location = {Vienna, Austria},
pages = {356 -- 362},
publisher = {IOS Press},
title = {{Biosignals standards and FHIR: The way to go}},
doi = {10.3233/978-1-61499-759-7-356},
volume = {236},
year = {2017},
}
@inproceedings{631,
abstract = {Template polyhedra generalize intervals and octagons to polyhedra whose facets are orthogonal to a given set of arbitrary directions. They have been employed in the abstract interpretation of programs and, with particular success, in the reachability analysis of hybrid automata. While previously, the choice of directions has been left to the user or a heuristic, we present a method for the automatic discovery of directions that generalize and eliminate spurious counterexamples. We show that for the class of convex hybrid automata, i.e., hybrid automata with (possibly nonlinear) convex constraints on derivatives, such directions always exist and can be found using convex optimization. We embed our method inside a CEGAR loop, thus enabling the time-unbounded reachability analysis of an important and richer class of hybrid automata than was previously possible. We evaluate our method on several benchmarks, demonstrating also its superior efficiency for the special case of linear hybrid automata.},
author = {Bogomolov, Sergiy and Frehse, Goran and Giacobbe, Mirco and Henzinger, Thomas A},
isbn = {978-366254576-8},
location = {Uppsala, Sweden},
pages = {589 -- 606},
publisher = {Springer},
title = {{Counterexample guided refinement of template polyhedra}},
doi = {10.1007/978-3-662-54577-5_34},
volume = {10205},
year = {2017},
}
@article{632,
abstract = {We consider a 2D quantum system of N bosons in a trapping potential |x|s, interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all 0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of the many-body system is described in the large N limit by the corresponding cubic nonlinear Schrödinger energy functional. Our result covers the focusing case (w < 0) where even the stability of the many-body system is not obvious. This answers an open question mentioned by X. Chen and J. Holmer for harmonic traps (s = 2). Together with the BBGKY hierarchy approach used by these authors, our result implies the convergence of the many-body quantum dynamics to the focusing NLS equation with harmonic trap for all 0 < β < 3/4. },
author = {Lewin, Mathieu and Nam, Phan and Rougerie, Nicolas},
journal = {Proceedings of the American Mathematical Society},
number = {6},
pages = {2441 -- 2454},
publisher = {American Mathematical Society},
title = {{A note on 2D focusing many boson systems}},
doi = {10.1090/proc/13468},
volume = {145},
year = {2017},
}
@inproceedings{633,
abstract = {A Rapidly-exploring Random Tree (RRT) is an algorithm which can search a non-convex region of space by incrementally building a space-filling tree. The tree is constructed from random points drawn from system’s state space and is biased to grow towards large unexplored areas in the system. RRT can provide better coverage of a system’s possible behaviors compared with random simulations, but is more lightweight than full reachability analysis. In this paper, we explore some of the design decisions encountered while implementing a hybrid extension of the RRT algorithm, which have not been elaborated on before. In particular, we focus on handling non-determinism, which arises due to discrete transitions. We introduce the notion of important points to account for this phenomena. We showcase our ideas using heater and navigation benchmarks.},
author = {Bak, Stanley and Bogomolov, Sergiy and Henzinger, Thomas A and Kumar, Aviral},
editor = {Abate, Alessandro and Bodo, Sylvie},
isbn = {978-331963500-2},
location = {Heidelberg, Germany},
pages = {83 -- 89},
publisher = {Springer},
title = {{Challenges and tool implementation of hybrid rapidly exploring random trees}},
doi = {10.1007/978-3-319-63501-9_6},
volume = {10381},
year = {2017},
}
@inbook{634,
abstract = {As autism spectrum disorder (ASD) is largely regarded as a neurodevelopmental condition, long-time consensus was that its hallmark features are irreversible. However, several studies from recent years using defined mouse models of ASD have provided clear evidence that in mice neurobiological and behavioural alterations can be ameliorated or even reversed by genetic restoration or pharmacological treatment either before or after symptom onset. Here, we review findings on genetic and pharmacological reversibility of phenotypes in mouse models of ASD. Our review should give a comprehensive overview on both aspects and encourage future studies to better understand the underlying molecular mechanisms that might be translatable from animals to humans.},
author = {Schroeder, Jan and Deliu, Elena and Novarino, Gaia and Schmeisser, Michael},
booktitle = {Translational Anatomy and Cell Biology of Autism Spectrum Disorder},
editor = {Schmeisser, Michael and Boekers, Tobias},
pages = {189 -- 211},
publisher = {Springer},
title = {{Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder}},
doi = {10.1007/978-3-319-52498-6_10},
volume = {224},
year = {2017},
}
@inproceedings{635,
abstract = {Memory-hard functions (MHFs) are hash algorithms whose evaluation cost is dominated by memory cost. As memory, unlike computation, costs about the same across different platforms, MHFs cannot be evaluated at significantly lower cost on dedicated hardware like ASICs. MHFs have found widespread applications including password hashing, key derivation, and proofs-of-work. This paper focuses on scrypt, a simple candidate MHF designed by Percival, and described in RFC 7914. It has been used within a number of cryptocurrencies (e.g., Litecoin and Dogecoin) and has been an inspiration for Argon2d, one of the winners of the recent password-hashing competition. Despite its popularity, no rigorous lower bounds on its memory complexity are known. We prove that scrypt is optimally memory-hard, i.e., its cumulative memory complexity (cmc) in the parallel random oracle model is Ω(n2w), where w and n are the output length and number of invocations of the underlying hash function, respectively. High cmc is a strong security target for MHFs introduced by Alwen and Serbinenko (STOC’15) which implies high memory cost even for adversaries who can amortize the cost over many evaluations and evaluate the underlying hash functions many times in parallel. Our proof is the first showing optimal memory-hardness for any MHF. Our result improves both quantitatively and qualitatively upon the recent work by Alwen et al. (EUROCRYPT’16) who proved a weaker lower bound of Ω(n2w/ log2 n) for a restricted class of adversaries.},
author = {Alwen, Joel F and Chen, Binchi and Pietrzak, Krzysztof Z and Reyzin, Leonid and Tessaro, Stefano},
editor = {Coron, Jean-Sébastien and Buus Nielsen, Jesper},
isbn = {978-331956616-0},
location = {Paris, France},
pages = {33 -- 62},
publisher = {Springer},
title = {{Scrypt is maximally memory hard}},
doi = {10.1007/978-3-319-56617-7_2},
volume = {10212},
year = {2017},
}
@inproceedings{636,
abstract = {Signal regular expressions can specify sequential properties of real-valued signals based on threshold conditions, regular operations, and duration constraints. In this paper we endow them with a quantitative semantics which indicates how robustly a signal matches or does not match a given expression. First, we show that this semantics is a safe approximation of a distance between the signal and the language defined by the expression. Then, we consider the robust matching problem, that is, computing the quantitative semantics of every segment of a given signal relative to an expression. We present an algorithm that solves this problem for piecewise-constant and piecewise-linear signals and show that for such signals the robustness map is a piecewise-linear function. The availability of an indicator describing how robustly a signal segment matches some regular pattern provides a general framework for quantitative monitoring of cyber-physical systems.},
author = {Bakhirkin, Alexey and Ferrere, Thomas and Maler, Oded and Ulus, Dogan},
editor = {Abate, Alessandro and Geeraerts, Gilles},
isbn = {978-331965764-6},
location = {Berlin, Germany},
pages = {189 -- 206},
publisher = {Springer},
title = {{On the quantitative semantics of regular expressions over real-valued signals}},
doi = {10.1007/978-3-319-65765-3_11},
volume = {10419},
year = {2017},
}
@inproceedings{637,
abstract = {For many cryptographic primitives, it is relatively easy to achieve selective security (where the adversary commits a-priori to some of the choices to be made later in the attack) but appears difficult to achieve the more natural notion of adaptive security (where the adversary can make all choices on the go as the attack progresses). A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption (Panjwani, TCC ’07 and Fuchsbauer et al., CRYPTO ’15), constrained PRFs (Fuchsbauer et al., ASIACRYPT ’14), and Yao garbled circuits (Jafargholi and Wichs, TCC ’16b). Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework that connects all of these works and allows us to present them in a unified and simplified fashion. Moreover, we use the framework to derive a new result for adaptively secure secret sharing over access structures defined via monotone circuits. We envision that further applications will follow in the future. Underlying our framework is the following simple idea. It is well known that selective security, where the adversary commits to n-bits of information about his future choices, automatically implies adaptive security at the cost of amplifying the adversary’s advantage by a factor of up to 2n. However, in some cases the proof of selective security proceeds via a sequence of hybrids, where each pair of adjacent hybrids locally only requires some smaller partial information consisting of m ≪ n bits. The partial information needed might be completely different between different pairs of hybrids, and if we look across all the hybrids we might rely on the entire n-bit commitment. Nevertheless, the above is sufficient to prove adaptive security, at the cost of amplifying the adversary’s advantage by a factor of only 2m ≪ 2n. In all of our examples using the above framework, the different hybrids are captured by some sort of a graph pebbling game and the amount of information that the adversary needs to commit to in each pair of hybrids is bounded by the maximum number of pebbles in play at any point in time. Therefore, coming up with better strategies for proving adaptive security translates to various pebbling strategies for different types of graphs.},
author = {Jafargholi, Zahra and Kamath Hosdurg, Chethan and Klein, Karen and Komargodski, Ilan and Pietrzak, Krzysztof Z and Wichs, Daniel},
editor = {Katz, Jonathan and Shacham, Hovav},
isbn = {978-331963687-0},
location = {Santa Barbara, CA, United States},
pages = {133 -- 163},
publisher = {Springer},
title = {{Be adaptive avoid overcommitting}},
doi = {10.1007/978-3-319-63688-7_5},
volume = {10401},
year = {2017},
}
@inproceedings{640,
abstract = {Data-independent Memory Hard Functions (iMHFS) are finding a growing number of applications in security; especially in the domain of password hashing. An important property of a concrete iMHF is specified by fixing a directed acyclic graph (DAG) Gn on n nodes. The quality of that iMHF is then captured by the following two pebbling complexities of Gn: – The parallel cumulative pebbling complexity Π∥cc(Gn) must be as high as possible (to ensure that the amortized cost of computing the function on dedicated hardware is dominated by the cost of memory). – The sequential space-time pebbling complexity Πst(Gn) should be as close as possible to Π∥cc(Gn) (to ensure that using many cores in parallel and amortizing over many instances does not give much of an advantage). In this paper we construct a family of DAGs with best possible parameters in an asymptotic sense, i.e., where Π∥cc(Gn) = Ω(n2/ log(n)) (which matches a known upper bound) and Πst(Gn) is within a constant factor of Π∥cc(Gn). Our analysis relies on a new connection between the pebbling complexity of a DAG and its depth-robustness (DR) – a well studied combinatorial property. We show that high DR is sufficient for high Π∥cc. Alwen and Blocki (CRYPTO’16) showed that high DR is necessary and so, together, these results fully characterize DAGs with high Π∥cc in terms of DR. Complementing these results, we provide new upper and lower bounds on the Π∥cc of several important candidate iMHFs from the literature. We give the first lower bounds on the memory hardness of the Catena and Balloon Hashing functions in a parallel model of computation and we give the first lower bounds of any kind for (a version) of Argon2i. Finally we describe a new class of pebbling attacks improving on those of Alwen and Blocki (CRYPTO’16). By instantiating these attacks we upperbound the Π∥cc of the Password Hashing Competition winner Argon2i and one of the Balloon Hashing functions by O (n1.71). We also show an upper bound of O(n1.625) for the Catena functions and the two remaining Balloon Hashing functions.},
author = {Alwen, Joel F and Blocki, Jeremiah and Pietrzak, Krzysztof Z},
editor = {Coron, Jean-Sébastien and Buus Nielsen, Jesper},
isbn = {978-331956616-0},
location = {Paris, France},
pages = {3 -- 32},
publisher = {Springer},
title = {{Depth-robust graphs and their cumulative memory complexity}},
doi = {10.1007/978-3-319-56617-7_1},
volume = {10212},
year = {2017},
}
@inproceedings{641,
abstract = {We introduce two novel methods for learning parameters of graphical models for image labelling. The following two tasks underline both methods: (i) perturb model parameters based on given features and ground truth labelings, so as to exactly reproduce these labelings as optima of the local polytope relaxation of the labelling problem; (ii) train a predictor for the perturbed model parameters so that improved model parameters can be applied to the labelling of novel data. Our first method implements task (i) by inverse linear programming and task (ii) using a regressor e.g. a Gaussian process. Our second approach simultaneously solves tasks (i) and (ii) in a joint manner, while being restricted to linearly parameterised predictors. Experiments demonstrate the merits of both approaches.},
author = {Trajkovska, Vera and Swoboda, Paul and Åström, Freddie and Petra, Stefanie},
editor = {Lauze, François and Dong, Yiqiu and Bjorholm Dahl, Anders},
isbn = {978-331958770-7},
location = {Kolding, Denmark},
pages = {323 -- 334},
publisher = {Springer},
title = {{Graphical model parameter learning by inverse linear programming}},
doi = {10.1007/978-3-319-58771-4_26},
volume = {10302},
year = {2017},
}
@article{642,
abstract = {Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable.},
author = {Gerencser, Mate and Gyöngy, István},
issn = {00255718},
journal = {Mathematics of Computation},
number = {307},
pages = {2373 -- 2397},
publisher = {American Mathematical Society},
title = {{Localization errors in solving stochastic partial differential equations in the whole space}},
doi = {10.1090/mcom/3201},
volume = {86},
year = {2017},
}
@misc{6426,
abstract = {Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent asynchronous computation threads. We show that specifications and correctness proofs for asynchronous programs can be structured by introducing the fiction, for proof purposes, that intermediate, non-quiescent states of asynchronous operations can be ignored. Then, the task of specification becomes relatively simple and the task of verification can be naturally decomposed into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure of an asynchronous program, the atomic effect of non-atomic operations and the synchronous effect of asynchronous operations. This structuring of specifications and proofs corresponds to the introduction of multiple layers of stepwise refinement for asynchronous programs. We present the first proof rule, called synchronization, to reduce asynchronous invocations on a lower layer to synchronous invocations on a higher layer. We implemented our proof method in CIVL and evaluated it on a collection of benchmark programs.},
author = {Henzinger, Thomas A and Kragl, Bernhard and Qadeer, Shaz},
issn = {2664-1690},
pages = {28},
publisher = {IST Austria},
title = {{Synchronizing the asynchronous}},
doi = {10.15479/AT:IST-2018-853-v2-2},
year = {2017},
}
@article{643,
abstract = {It has been reported that nicotinamide-overload induces oxidative stress associated with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT) were also carried out in adult Sprague-Dawley rats treated with or without cumulative doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration significantly increased the plasma H2O2 levels associated with high insulin levels. Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration of nicotinic acid, another form of Vitamin B3, also significantly increased plasma insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic acid or nicotinamide impaired glucose metabolism. This study suggested that excess Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance.},
author = {Sun, Wuping and Zhai, Ming-Zhu and Zhou, Qian and Qian, Chengrui and Jiang, Changyu},
issn = {03044920},
journal = {Chinese Journal of Physiology},
number = {4},
pages = {207 -- 214},
publisher = {Chinese Physiological Society},
title = {{Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats}},
doi = {10.4077/CJP.2017.BAF469},
volume = {60},
year = {2017},
}
@article{644,
abstract = {An instance of the valued constraint satisfaction problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P 6= NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in f0;1g corresponds to ordinary CSPs, where one deals only with the feasibility issue, and there is no optimization. This case is the subject of the algebraic CSP dichotomy conjecture predicting for which constraint languages CSPs are tractable (i.e., solvable in polynomial time) and for which they are NP-hard. The case when all allowed functions take only finite values corresponds to a finitevalued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Živný. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e., the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.},
author = {Kolmogorov, Vladimir and Krokhin, Andrei and Rolinek, Michal},
journal = {SIAM Journal on Computing},
number = {3},
pages = {1087 -- 1110},
publisher = {SIAM},
title = {{The complexity of general-valued CSPs}},
doi = {10.1137/16M1091836},
volume = {46},
year = {2017},
}
@inproceedings{645,
abstract = {Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks.},
author = {Ashok, Pranav and Chatterjee, Krishnendu and Daca, Przemyslaw and Kretinsky, Jan and Meggendorfer, Tobias},
editor = {Majumdar, Rupak and Kunčak, Viktor},
isbn = {978-331963386-2},
location = {Heidelberg, Germany},
pages = {201 -- 221},
publisher = {Springer},
title = {{Value iteration for long run average reward in markov decision processes}},
doi = {10.1007/978-3-319-63387-9_10},
volume = {10426},
year = {2017},
}
@inproceedings{646,
abstract = {We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations.},
author = {Kuske, Jan and Swoboda, Paul and Petra, Stefanie},
editor = {Lauze, François and Dong, Yiqiu and Bjorholm Dahl, Anders},
isbn = {978-331958770-7},
location = {Kolding, Denmark},
pages = {235 -- 246},
publisher = {Springer},
title = {{A novel convex relaxation for non binary discrete tomography}},
doi = {10.1007/978-3-319-58771-4_19},
volume = {10302},
year = {2017},
}
@inproceedings{647,
abstract = {Despite researchers’ efforts in the last couple of decades, reachability analysis is still a challenging problem even for linear hybrid systems. Among the existing approaches, the most practical ones are mainly based on bounded-time reachable set over-approximations. For the purpose of unbounded-time analysis, one important strategy is to abstract the original system and find an invariant for the abstraction. In this paper, we propose an approach to constructing a new kind of abstraction called conic abstraction for affine hybrid systems, and to computing reachable sets based on this abstraction. The essential feature of a conic abstraction is that it partitions the state space of a system into a set of convex polyhedral cones which is derived from a uniform conic partition of the derivative space. Such a set of polyhedral cones is able to cut all trajectories of the system into almost straight segments so that every segment of a reach pipe in a polyhedral cone tends to be straight as well, and hence can be over-approximated tightly by polyhedra using similar techniques as HyTech or PHAVer. In particular, for diagonalizable affine systems, our approach can guarantee to find an invariant for unbounded reachable sets, which is beyond the capability of bounded-time reachability analysis tools. We implemented the approach in a tool and experiments on benchmarks show that our approach is more powerful than SpaceEx and PHAVer in dealing with diagonalizable systems.},
author = {Bogomolov, Sergiy and Giacobbe, Mirco and Henzinger, Thomas A and Kong, Hui},
isbn = {978-331965764-6},
location = {Berlin, Germany},
pages = {116 -- 132},
publisher = {Springer},
title = {{Conic abstractions for hybrid systems}},
doi = {10.1007/978-3-319-65765-3_7},
volume = {10419 },
year = {2017},
}
@inproceedings{648,
abstract = {Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) diﬀers from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method.},
author = {Skórski, Maciej},
editor = {Jäger, Gerhard and Steila, Silvia},
isbn = {978-331955910-0},
location = {Bern, Switzerland},
pages = {600 -- 613},
publisher = {Springer},
title = {{On the complexity of breaking pseudoentropy}},
doi = {10.1007/978-3-319-55911-7_43},
volume = {10185},
year = {2017},
}
@inproceedings{650,
abstract = {In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy.},
author = {Skórski, Maciej},
editor = {Jäger, Gerhard and Steila, Silvia},
issn = {03029743},
location = {Bern, Switzerland},
pages = {586 -- 599},
publisher = {Springer},
title = {{A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds}},
doi = {10.1007/978-3-319-55911-7_42},
volume = {10185},
year = {2017},
}
@article{651,
abstract = {Superhydrophobic surfaces reduce the frictional drag between water and solid materials, but this effect is often temporary. The realization of sustained drag reduction has applications for water vehicles and pipeline flows.
},
author = {Hof, Björn},
issn = {00280836},
journal = {Nature},
number = {7636},
pages = {161 -- 162},
publisher = {Nature Publishing Group},
title = {{Fluid dynamics: Water flows out of touch}},
doi = {10.1038/541161a},
volume = {541},
year = {2017},
}
@inproceedings{6517,
abstract = {A (possibly degenerate) drawing of a graph G in the plane is approximable by an embedding if it can be turned into an embedding by an arbitrarily small perturbation. We show that testing, whether a drawing of a planar graph G in the plane is approximable by an embedding, can be carried out in polynomial time, if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation system (or equivalently the faces) of the embedding of G and the choice of outer face are fixed. In other words, we show that c-planarity with embedded pipes is tractable for graphs with fixed embeddings. To the best of our knowledge an analogous result was previously known essentially only when G is a cycle.},
author = {Fulek, Radoslav},
location = {Phuket, Thailand},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Embedding graphs into embedded graphs}},
doi = {10.4230/LIPICS.ISAAC.2017.34},
volume = {92},
year = {2017},
}
@inproceedings{652,
abstract = {We present an approach that enables robots to self-organize their sensorimotor behavior from scratch without providing specific information about neither the robot nor its environment. This is achieved by a simple neural control law that increases the consistency between external sensor dynamics and internal neural dynamics of the utterly simple controller. In this way, the embodiment and the agent-environment coupling are the only source of individual development. We show how an anthropomorphic tendon driven arm-shoulder system develops different behaviors depending on that coupling. For instance: Given a bottle half-filled with water, the arm starts to shake it, driven by the physical response of the water. When attaching a brush, the arm can be manipulated into wiping a table, and when connected to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said to discover the affordances of the world. When allowing two (simulated) humanoid robots to interact physically, they engage into a joint behavior development leading to, for instance, spontaneous cooperation. More social effects are observed if the robots can visually perceive each other. Although, as an observer, it is tempting to attribute an apparent intentionality, there is nothing of the kind put in. As a conclusion, we argue that emergent behavior may be much less rooted in explicit intentions, internal motivations, or specific reward systems than is commonly believed.},
author = {Der, Ralf and Martius, Georg S},
isbn = {978-150905069-7},
location = {Cergy-Pontoise, France},
publisher = {IEEE},
title = {{Dynamical self consistency leads to behavioral development and emergent social interactions in robots}},
doi = {10.1109/DEVLRN.2016.7846789},
year = {2017},
}
@inproceedings{6526,
abstract = {This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity.},
author = {Skórski, Maciej},
booktitle = {2017 IEEE International Symposium on Information Theory (ISIT)},
isbn = {9781509040964},
location = {Aachen, Germany},
publisher = {IEEE},
title = {{On the complexity of estimating Rènyi divergences}},
doi = {10.1109/isit.2017.8006529},
year = {2017},
}
@inproceedings{6527,
abstract = {A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.
Essentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called "depth-robustness") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.
In this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:
*Prove that their depth-robustness is asymptotically maximal.
*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.
*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks.
We find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.
Along the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).
},
author = {Alwen, Joel F and Blocki, Jeremiah and Harsha, Ben},
booktitle = {Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security},
isbn = {9781450349468},
location = {Dallas, TX, USA},
pages = {1001--1017},
publisher = {ACM Press},
title = {{Practical graphs for optimal side-channel resistant memory-hard functions}},
doi = {10.1145/3133956.3134031},
year = {2017},
}
@article{654,
abstract = {In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.},
author = {Kicheva, Anna and Rivron, Nicolas},
issn = {09501991},
journal = {Development},
number = {5},
pages = {733 -- 736},
publisher = {Company of Biologists},
title = {{Creating to understand – developmental biology meets engineering in Paris}},
doi = {10.1242/dev.144915},
volume = {144},
year = {2017},
}
@article{655,
abstract = {The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell.},
author = {Renault, Thibaud and Abraham, Anthony and Bergmiller, Tobias and Paradis, Guillaume and Rainville, Simon and Charpentier, Emmanuelle and Guet, Calin C and Tu, Yuhai and Namba, Keiichi and Keener, James and Minamino, Tohru and Erhardt, Marc},
issn = {2050084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Bacterial flagella grow through an injection diffusion mechanism}},
doi = {10.7554/eLife.23136},
volume = {6},
year = {2017},
}
@article{656,
abstract = {Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets.},
author = {Novarino, Gaia},
issn = {19466234},
journal = {Science Translational Medicine},
number = {381},
publisher = {American Association for the Advancement of Science},
title = {{Modeling Alzheimer's disease in mice with human neurons}},
doi = {10.1126/scitranslmed.aam9867},
volume = {9},
year = {2017},
}
@article{657,
abstract = {Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.},
author = {Möller, Barbara and Ten Hove, Colette and Xiang, Daoquan and Williams, Nerys and López, Lorena and Yoshida, Saiko and Smit, Margot and Datla, Raju and Weijers, Dolf},
issn = {00278424},
journal = {PNAS},
number = {12},
pages = {E2533 -- E2539},
publisher = {National Academy of Sciences},
title = {{Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo}},
doi = {10.1073/pnas.1616493114},
volume = {114},
year = {2017},
}
@article{658,
abstract = {With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors "waiting" to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics.},
author = {Der, Ralf and Martius, Georg S},
issn = {16625218},
journal = {Frontiers in Neurorobotics},
number = {MAR},
publisher = {Frontiers Research Foundation},
title = {{Self organized behavior generation for musculoskeletal robots}},
doi = {10.3389/fnbot.2017.00008},
volume = {11},
year = {2017},
}
@article{659,
abstract = {Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching.},
author = {Kage, Frieda and Winterhoff, Moritz and Dimchev, Vanessa and Müller, Jan and Thalheim, Tobias and Freise, Anika and Brühmann, Stefan and Kollasser, Jana and Block, Jennifer and Dimchev, Georgi A and Geyer, Matthias and Schnittler, Hams and Brakebusch, Cord and Stradal, Theresia and Carlier, Marie and Sixt, Michael K and Käs, Josef and Faix, Jan and Rottner, Klemens},
issn = {20411723},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{FMNL formins boost lamellipodial force generation}},
doi = {10.1038/ncomms14832},
volume = {8},
year = {2017},
}
@article{660,
abstract = {Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth.},
author = {Rickman, Jamie and Düllberg, Christian F and Cade, Nicholas and Griffin, Lewis and Surrey, Thomas},
issn = {00278424},
journal = {PNAS},
number = {13},
pages = {3427 -- 3432},
publisher = {National Academy of Sciences},
title = {{Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation}},
doi = {10.1073/pnas.1620274114},
volume = {114},
year = {2017},
}
@article{662,
abstract = {We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays.},
author = {Shi, Liang and Hof, Björn and Rampp, Markus and Avila, Marc},
issn = {10706631},
journal = {Physics of Fluids},
number = {4},
publisher = {American Institute of Physics},
title = {{Hydrodynamic turbulence in quasi Keplerian rotating flows}},
doi = {10.1063/1.4981525},
volume = {29},
year = {2017},
}
@inproceedings{663,
abstract = {In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. },
author = {Kong, Hui and Bogomolov, Sergiy and Schilling, Christian and Jiang, Yu and Henzinger, Thomas A},
booktitle = {Proceedings of the 20th International Conference on Hybrid Systems},
isbn = {978-145034590-3},
location = {Pittsburgh, PA, United States},
pages = {163 -- 172},
publisher = {ACM},
title = {{Safety verification of nonlinear hybrid systems based on invariant clusters}},
doi = {10.1145/3049797.3049814},
year = {2017},
}
@article{665,
abstract = {The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria.},
author = {Bergmiller, Tobias and Andersson, Anna M and Tomasek, Kathrin and Balleza, Enrique and Kiviet, Daniel and Hauschild, Robert and Tkacik, Gasper and Guet, Calin C},
issn = {00368075},
journal = {Science},
number = {6335},
pages = {311 -- 315},
publisher = {American Association for the Advancement of Science},
title = {{Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity}},
doi = {10.1126/science.aaf4762},
volume = {356},
year = {2017},
}
@article{666,
abstract = {Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors.},
author = {Mitosch, Karin and Rieckh, Georg and Bollenbach, Tobias},
issn = {24054712},
journal = {Cell Systems},
number = {4},
pages = {393 -- 403},
publisher = {Cell Press},
title = {{Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment}},
doi = {10.1016/j.cels.2017.03.001},
volume = {4},
year = {2017},
}
@article{667,
abstract = {Perinatal exposure to penicillin may result in longlasting gut and behavioral changes.},
author = {Novarino, Gaia},
issn = {19466234},
journal = {Science Translational Medicine},
number = {387},
publisher = {American Association for the Advancement of Science},
title = {{The antisocial side of antibiotics}},
doi = {10.1126/scitranslmed.aan2786},
volume = {9},
year = {2017},
}
@inproceedings{6679,
abstract = {Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption [1]. In this paper, we examine the paradigm of PSCL decoding from both theoretical and practical standpoints: (i) by changing the construction of the code, we are able to improve the performance at no additional computational, latency or memory cost, (ii) we present an optimal scheme to allocate cyclic redundancy checks (CRCs), and (iii) we provide an upper bound on the list size that allows MAP performance.},
author = {Hashemi, Seyyed Ali and Mondelli, Marco and Hassani, Hamed and Urbanke, Ruediger and Gross, Warren},
booktitle = {2017 IEEE Global Communications Conference},
location = {Singapore, Singapore},
pages = {1--7},
publisher = {IEEE},
title = {{Partitioned list decoding of polar codes: Analysis and improvement of finite length performance}},
doi = {10.1109/glocom.2017.8254940},
year = {2017},
}
@article{668,
abstract = {Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading.},
author = {Horsthemke, Markus and Bachg, Anne and Groll, Katharina and Moyzio, Sven and Müther, Barbara and Hemkemeyer, Sandra and Wedlich Söldner, Roland and Sixt, Michael K and Tacke, Sebastian and Bähler, Martin and Hanley, Peter},
issn = {00219258},
journal = {Journal of Biological Chemistry},
number = {17},
pages = {7258 -- 7273},
publisher = {American Society for Biochemistry and Molecular Biology},
title = {{Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion}},
doi = {10.1074/jbc.M116.766923},
volume = {292},
year = {2017},
}
@article{669,
abstract = {The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. },
author = {Synek, Lukáš and Vukašinović, Nemanja and Kulich, Ivan and Hála, Michal and Aldorfová, Klára and Fendrych, Matyas and Žárský, Viktor},
issn = {00320889},
journal = {Plant Physiology},
number = {1},
pages = {223 -- 240},
publisher = {American Society of Plant Biologists},
title = {{EXO70C2 is a key regulatory factor for optimal tip growth of pollen}},
doi = {10.1104/pp.16.01282},
volume = {174},
year = {2017},
}
@article{670,
abstract = {We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears.},
author = {Schreck, Camille and Rohmer, Damien and Hahmann, Stefanie},
issn = {01677055},
journal = {Computer Graphics Forum},
number = {2},
pages = {95 -- 106},
publisher = {Wiley},
title = {{Interactive paper tearing}},
doi = {10.1111/cgf.13110},
volume = {36},
year = {2017},
}
@article{671,
abstract = {Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation.},
author = {Hilbe, Christian and Martinez, Vaquero and Chatterjee, Krishnendu and Nowak, Martin},
issn = {00278424},
journal = {PNAS},
number = {18},
pages = {4715 -- 4720},
publisher = {National Academy of Sciences},
title = {{Memory-n strategies of direct reciprocity}},
doi = {10.1073/pnas.1621239114},
volume = {114},
year = {2017},
}
@article{672,
abstract = {Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration.},
author = {Vaahtomeri, Kari and Brown, Markus and Hauschild, Robert and De Vries, Ingrid and Leithner, Alexander F and Mehling, Matthias and Kaufmann, Walter and Sixt, Michael K},
issn = {22111247},
journal = {Cell Reports},
number = {5},
pages = {902 -- 909},
publisher = {Cell Press},
title = {{Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia}},
doi = {10.1016/j.celrep.2017.04.027},
volume = {19},
year = {2017},
}
@inproceedings{6729,
abstract = {Consider the problem of constructing a polar code of block length N for the transmission over a given channel W. Typically this requires to compute the reliability of all the N synthetic channels and then to include those that are sufficiently reliable. However, we know from [1], [2] that there is a partial order among the synthetic channels. Hence, it is natural to ask whether we can exploit it to reduce the computational burden of the construction problem. We show that, if we take advantage of the partial order [1], [2], we can construct a polar code by computing the reliability of roughly N/ log 3/2 N synthetic channels. Such a set of synthetic channels is universal, in the sense that it allows one to construct polar codes for any W, and it can be identified by solving a maximum matching problem on a bipartite graph. Our proof technique consists in reducing the construction problem to the problem of computing the maximum cardinality of an antichain for a suitable partially ordered set. As such, this method is general and it can be used to further improve the complexity of the construction problem in case a new partial order on the synthetic channels of polar codes is discovered.},
author = {Mondelli, Marco and Hassani, S. Hamed and Urbanke, Rudiger},
booktitle = {2017 IEEE International Symposium on Information Theory },
isbn = {9781509040964},
issn = {2157-8117},
location = {Aachen, Germany},
pages = {1853--1857},
publisher = {IEEE},
title = {{Construction of polar codes with sublinear complexity}},
doi = {10.1109/isit.2017.8006850},
year = {2017},
}
@article{673,
abstract = {We present a numerical study of wavy supercritical cylindrical Couette flow between counter-rotating cylinders in which the wavy pattern propagates either prograde with the inner cylinder or retrograde opposite the rotation of the inner cylinder. The wave propagation reversals from prograde to retrograde and vice versa occur at distinct values of the inner cylinder Reynolds number when the associated frequency of the wavy instability vanishes. The reversal occurs for both twofold and threefold symmetric wavy vortices. Moreover, the wave propagation reversal only occurs for sufficiently strong counter-rotation. The flow pattern reversal appears to be intrinsic in the system as either periodic boundary conditions or fixed end wall boundary conditions for different system sizes always result in the wave propagation reversal. We present a detailed bifurcation sequence and parameter space diagram with respect to retrograde behavior of wavy flows. The retrograde propagation of the instability occurs when the inner Reynolds number is about two times the outer Reynolds number. The mechanism for the retrograde propagation is associated with the inviscidly unstable region near the inner cylinder and the direction of the global average azimuthal velocity. Flow dynamics, spatio-temporal behavior, global mean angular velocity, and torque of the flow with the wavy pattern are explored.},
author = {Altmeyer, Sebastian and Lueptow, Richard},
issn = {24700045},
journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter Physics},
number = {5},
publisher = {American Physiological Society},
title = {{Wave propagation reversal for wavy vortices in wide gap counter rotating cylindrical Couette flow}},
doi = {10.1103/PhysRevE.95.053103},
volume = {95},
year = {2017},
}
@article{6730,
abstract = {We introduce a new approach to proving that a sequence of deterministic linear codes achieves capacity on an erasure channel under maximum a posteriori decoding. Rather than relying on the precise structure of the codes, our method exploits code symmetry. In particular, the technique applies to any sequence of linear codes where the blocklengths are strictly increasing, the code rates converge, and the permutation group of each code is doubly transitive. In other words, we show that symmetry alone implies near-optimal performance. An important consequence of this result is that a sequence of Reed-Muller codes with increasing block length and converging rate achieves capacity. This possibility has been suggested previously in the literature but it has only been proven for cases where the limiting code rate is 0 or 1. Moreover, these results extend naturally to all affine-invariant codes and, thus, to extended primitive narrow-sense BCH codes. This also resolves, in the affirmative, the existence question for capacity-achieving sequences of binary cyclic codes. The primary tools used in the proof are the sharp threshold property for symmetric monotone Boolean functions and the area theorem for extrinsic information transfer functions.},
author = {Kudekar, Shrinivas and Kumar, Santhosh and Mondelli, Marco and Pfister, Henry D. and Sasoglu, Eren and Urbanke, Ridiger L.},
issn = {1557-9654},
journal = {IEEE Transactions on Information Theory},
number = {7},
pages = {4298--4316},
publisher = {IEEE},
title = {{Reed–Muller codes achieve capacity on erasure channels}},
doi = {10.1109/tit.2017.2673829},
volume = {63},
year = {2017},
}
@inproceedings{6731,
abstract = {We present a rate-compatible polar coding scheme that achieves the capacity of any family of channels. Our solution generalizes the previous results [1], [2] that provide capacity-achieving rate-compatible polar codes for a degraded family of channels. The motivation for our extension comes from the fact that in many practical scenarios, e.g., MIMO systems and non-Gaussian interference, the channels cannot be ordered by degradation. The main technical contribution of this paper consists in removing the degradation condition. To do so, we exploit the ideas coming from the construction of universal polar codes. Our scheme possesses the usual attractive features of polar codes: low complexity code construction, encoding, and decoding; super-polynomial scaling of the error probability with the block length; and absence of error floors. On the negative side, the scaling of the gap to capacity with the block length is slower than in standard polar codes, and we prove an upper bound on the scaling exponent.},
author = {Mondelli, Marco and Hassani, Hamed and Maric, Ivana and Hui, Dennis and Hong, Song-Nam},
booktitle = {2017 IEEE Wireless Communications and Networking Conference Workshops },
isbn = {9781509059089},
location = {San Francisco, CA, USA},
publisher = {IEEE},
title = {{Capacity-achieving rate-compatible polar codes for general channels}},
doi = {10.1109/wcncw.2017.7919107},
year = {2017},
}
@article{674,
abstract = {Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo.},
author = {Schwarz, Jan and Bierbaum, Veronika and Vaahtomeri, Kari and Hauschild, Robert and Brown, Markus and De Vries, Ingrid and Leithner, Alexander F and Reversat, Anne and Merrin, Jack and Tarrant, Teresa and Bollenbach, Tobias and Sixt, Michael K},
issn = {09609822},
journal = {Current Biology},
number = {9},
pages = {1314 -- 1325},
publisher = {Cell Press},
title = {{Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6}},
doi = {10.1016/j.cub.2017.04.004},
volume = {27},
year = {2017},
}
@article{675,
abstract = {We report the enhancement of infrared absorption of chemisorbed carbon monoxide on platinum in the gap of plasmonic nanoantennas. Our method is based on the self-assembled formation of platinum nanoislands on nanoscopic dipole antenna arrays manufactured via electron beam lithography. We employ systematic variations of the plasmonic antenna resonance to precisely couple to the molecular stretch vibration of carbon monoxide adsorbed on the platinum nanoislands. Ultimately, we reach more than 1500-fold infrared absorption enhancements, allowing for an ultrasensitive detection of a monolayer of chemisorbed carbon monoxide. The developed procedure can be adapted to other metal adsorbents and molecular species and could be utilized for coverage sensing in surface catalytic reactions. },
author = {Haase, Johannes and Bagiante, Salvatore and Sigg, Hans and Van Bokhoven, Jeroen},
journal = {Optics Letters},
number = {10},
pages = {1931 -- 1934},
publisher = {OSA},
title = {{Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas}},
doi = {10.1364/OL.42.001931},
volume = {42},
year = {2017},
}
@article{677,
abstract = {The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR.},
author = {Lademann, Claudio and Renkawitz, Jörg and Pfander, Boris and Jentsch, Stefan},
issn = {22111247},
journal = {Cell Reports},
number = {7},
pages = {1294 -- 1303},
publisher = {Cell Press},
title = {{The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination}},
doi = {10.1016/j.celrep.2017.04.051},
volume = {19},
year = {2017},
}
@article{678,
abstract = {The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development.},
author = {Petridou, Nicoletta and Spiro, Zoltan P and Heisenberg, Carl-Philipp J},
issn = {14657392},
journal = {Nature Cell Biology},
number = {6},
pages = {581 -- 588},
publisher = {Nature Publishing Group},
title = {{Multiscale force sensing in development}},
doi = {10.1038/ncb3524},
volume = {19},
year = {2017},
}
@article{680,
abstract = {In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics.},
author = {Chalk, Matthew J and Masset, Paul and Gutkin, Boris and Denève, Sophie},
issn = {1553734X},
journal = {PLoS Computational Biology},
number = {6},
publisher = {Public Library of Science},
title = {{Sensory noise predicts divisive reshaping of receptive fields}},
doi = {10.1371/journal.pcbi.1005582},
volume = {13},
year = {2017},
}
@inproceedings{683,
abstract = {Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.},
author = {Lubiw, Anna and Masárová, Zuzana and Wagner, Uli},
location = {Brisbane, Australia},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{A proof of the orbit conjecture for flipping edge labelled triangulations}},
doi = {10.4230/LIPIcs.SoCG.2017.49},
volume = {77},
year = {2017},
}
@article{684,
abstract = {We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic.},
author = {Chatterjee, Krishnendu and Piterman, Nir},
issn = {1943-5886},
journal = {Journal of Symbolic Logic},
number = {2},
pages = {420 -- 452},
publisher = {Cambridge University Press},
title = {{Obligation blackwell games and p-automata}},
doi = {10.1017/jsl.2016.71},
volume = {82},
year = {2017},
}
@inproceedings{6841,
abstract = {In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified.},
author = {Martius, Georg S and Lampert, Christoph},
booktitle = {5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings},
location = {Toulon, France},
publisher = {International Conference on Learning Representations},
title = {{Extrapolation and learning equations}},
year = {2017},
}
@article{685,
abstract = {By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube.},
author = {Briscoe, James and Kicheva, Anna},
issn = {09254773},
journal = {Mechanisms of Development},
pages = {26 -- 31},
publisher = {Elsevier},
title = {{The physics of development 100 years after D'Arcy Thompson's “on growth and form”}},
doi = {10.1016/j.mod.2017.03.005},
volume = {145},
year = {2017},
}
@article{686,
abstract = {Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology.},
author = {Heisenberg, Carl-Philipp J},
issn = {09254773},
journal = {Mechanisms of Development},
pages = {32 -- 37},
publisher = {Elsevier},
title = {{D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization}},
doi = {10.1016/j.mod.2017.03.006},
volume = {145},
year = {2017},
}
@article{687,
abstract = {Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs.},
author = {Davison, Ben},
issn = {00335606},
journal = {Quarterly Journal of Mathematics},
number = {2},
pages = {635 -- 703},
publisher = {Oxford University Press},
title = {{The critical CoHA of a quiver with potential}},
doi = {10.1093/qmath/haw053},
volume = {68},
year = {2017},
}
@inproceedings{688,
abstract = {We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. },
author = {Edelsbrunner, Herbert and Wagner, Hubert},
issn = {18688969},
location = {Brisbane, Australia},
pages = {391--3916},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Topological data analysis with Bregman divergences}},
doi = {10.4230/LIPIcs.SoCG.2017.39},
volume = {77},
year = {2017},
}
@article{689,
abstract = {Rett syndrome modeling in monkey mirrors the human disorder.},
author = {Novarino, Gaia},
issn = {19466234},
journal = {Science Translational Medicine},
number = {393},
publisher = {American Association for the Advancement of Science},
title = {{Rett syndrome modeling goes simian}},
doi = {10.1126/scitranslmed.aan8196},
volume = {9},
year = {2017},
}
@article{693,
abstract = {Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. },
author = {Miki, Takafumi and Kaufmann, Walter and Malagon, Gerardo and Gomez, Laura and Tabuchi, Katsuhiko and Watanabe, Masahiko and Shigemoto, Ryuichi and Marty, Alain},
issn = {00278424},
journal = {PNAS},
number = {26},
pages = {E5246 -- E5255},
publisher = {National Academy of Sciences},
title = {{Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses}},
doi = {10.1073/pnas.1704470114},
volume = {114},
year = {2017},
}
@inproceedings{6932,
abstract = {LCLs or locally checkable labelling problems (e.g. maximal independent set, maximal matching, and vertex colouring) in the LOCAL model of computation are very well-understood in cycles (toroidal 1-dimensional grids): every problem has a complexity of O(1), Θ(log* n), or Θ(n), and the design of optimal algorithms can be fully automated. This work develops the complexity theory of LCL problems for toroidal 2-dimensional grids. The complexity classes are the same as in the 1-dimensional case: O(1), Θ(log* n), and Θ(n). However, given an LCL problem it is undecidable whether its complexity is Θ(log* n) or Θ(n) in 2-dimensional grids.
Nevertheless, if we correctly guess that the complexity of a problem is Θ(log* n), we can completely automate the design of optimal algorithms. For any problem we can find an algorithm that is of a normal form A' o Sk, where A' is a finite function, Sk is an algorithm for finding a maximal independent set in kth power of the grid, and k is a constant.
Finally, partially with the help of automated design tools, we classify the complexity of several concrete LCL problems related to colourings and orientations.},
author = {Brandt, Sebastian and Hirvonen, Juho and Korhonen, Janne H. and Lempiäinen, Tuomo and Östergård, Patric R.J. and Purcell, Christopher and Rybicki, Joel and Suomela, Jukka and Uznański, Przemysław},
isbn = {9781450349925},
location = {Washington, DC, United States},
pages = {101--110},
publisher = {ACM Press},
title = {{LCL problems on grids}},
doi = {10.1145/3087801.3087833},
year = {2017},
}
@article{694,
abstract = {A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells.},
author = {Veß, Astrid and Blache, Ulrich and Leitner, Laura and Kurz, Angela and Ehrenpfordt, Anja and Sixt, Michael K and Posern, Guido},
issn = {00219533},
journal = {Journal of Cell Science},
number = {13},
pages = {2172 -- 2184},
publisher = {Company of Biologists},
title = {{A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity}},
doi = {10.1242/jcs.200899},
volume = {130},
year = {2017},
}
@article{9065,
abstract = {Magnetic anisotropy in strontium iridate (Sr2IrO4) is found to be large because of the strong spin-orbit interactions. In our work, we studied the in-plane magnetic anisotropy of Sr2IrO4 and traced the anisotropic exchange interactions between the isospins in the crystal. The magnetic-field-dependent torque τ(H) showed a prominent transition from the canted antiferromagnetic state to the weak ferromagnetic (WFM) state. A comprehensive analysis was conducted to examine the isotropic and anisotropic regimes and probe the easy magnetization axis along the a b plane. The angle-dependent torque τ(θ) revealed a deviation from the sinusoidal behavior, and small differences in hysteresis were observed around 0° and 90° in the low-magnetic-field regime. This indicates that the orientation of the easy axis of the FM component is along the b axis, where the antiferromagnetic to WFM spin-flop transition occurs. We compared the coefficients of the magnetic susceptibility tensors and captured the anisotropy of the material. The in-plane τ(θ) revealed a tendency toward isotropic behavior for fields with values above the field value of the WFM transition.},
author = {Nauman, Muhammad and Hong, Yunjeong and Hussain, Tayyaba and Seo, M. S. and Park, S. Y. and Lee, N. and Choi, Y. J. and Kang, Woun and Jo, Younjung},
issn = {2469-9950},
journal = {Physical Review B},
number = {15},
publisher = {American Physical Society},
title = {{In-plane magnetic anisotropy in strontium iridate Sr2IrO4}},
doi = {10.1103/physrevb.96.155102},
volume = {96},
year = {2017},
}
@article{909,
abstract = {We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor ½ cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape.},
author = {Akopyan, Arseniy and Vysotsky, Vladislav},
issn = {00029890},
journal = {The American Mathematical Monthly},
number = {7},
pages = {588 -- 596},
publisher = {Mathematical Association of America},
title = {{On the lengths of curves passing through boundary points of a planar convex shape}},
doi = {10.4169/amer.math.monthly.124.7.588},
volume = {124},
year = {2017},
}