@article{1331, abstract = {Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response.}, author = {Zwack, Paul and De Clercq, Inge and Howton, Timothy and Hallmark, H Tucker and Hurny, Andrej and Keshishian, Erika and Parish, Alyssa and Benková, Eva and Mukhtar, M Shahid and Van Breusegem, Frank and Rashotte, Aaron}, issn = {1532-2548}, journal = {Plant Physiology}, number = {2}, pages = {1249 -- 1258}, publisher = {American Society of Plant Biologists}, title = {{Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress}}, doi = {10.1104/pp.16.00415}, volume = {172}, year = {2016}, } @article{1332, abstract = {Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance.}, author = {Chait, Remy P and Palmer, Adam and Yelin, Idan and Kishony, Roy}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments}}, doi = {10.1038/ncomms10333}, volume = {7}, year = {2016}, } @article{1333, abstract = {Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the "representatives" treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most.}, author = {Milinski, Manfred and Hilbe, Christian and Semmann, Dirk and Sommerfeld, Ralf and Marotzke, Jochem}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Humans choose representatives who enforce cooperation in social dilemmas through extortion}}, doi = {10.1038/ncomms10915}, volume = {7}, year = {2016}, } @article{1334, abstract = {Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping.}, author = {Schönenberger, Philipp and O'Neill, Joseph and Csicsvari, Jozsef L}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Activity dependent plasticity of hippocampal place maps}}, doi = {10.1038/ncomms11824}, volume = {7}, year = {2016}, } @inproceedings{1335, abstract = {In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan}, location = {Edinburgh, United Kingdom}, pages = {23 -- 38}, publisher = {Springer}, title = {{Quantitative monitor automata}}, doi = {10.1007/978-3-662-53413-7_2}, volume = {9837}, year = {2016}, } @inbook{19991, abstract = {When applying machine learning techniques to real-world problems, prior knowledge plays a crucial role in enriching the learning system. This prior knowledge is typically defined by domain experts and can be integrated into machine learning algorithms in a variety of ways: as a preference of certain prediction functions over others, as a Bayesian prior over parameters, or as additional information about the samples in the training set used for learning a prediction function. The latter setup is called learning using privileged information (LUPI) and was adopted by Vapnik and Vashist in (Neural Netw, 2009). Formally, LUPI refers to the setting when, in addition to the main data modality, the learning system has access to an extra source of information about the training examples. The additional source of information is only available during training and therefore is called privileged. The main goal of LUPI is to utilize privileged information and to learn a better model in the main data modality than one would learn without the privileged source. As an illustration, for protein classification based on amino-acid sequences, the protein tertiary structure can be considered additional information. Another example is recognizing objects in images; the textual information in the form of image tags contains additional object descriptions and can be used as privileged.}, author = {Sharmanska, Viktoriia and Quadrianto, Novi}, booktitle = {Encyclopedia of Machine Learning and Data Mining}, pages = {1--4}, publisher = {Springer Nature}, title = {{Learning Using Privileged Information}}, doi = {10.1007/978-1-4899-7502-7_892-1}, year = {2016}, } @article{1881, abstract = {We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal random matrix of size N with i.i.d.\ entries that are independent of W. We assume subexponential decay for the matrix entries of W and we choose λ∼1, so that the eigenvalues of W and λV are typically of the same order. Further, we assume that the density of the entries of V is supported on a single interval and is convex near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such that the largest eigenvalues of H are in the limit of large N determined by the order statistics of V for λ>λ+. In particular, the largest eigenvalue of H has a Weibull distribution in the limit N→∞ if λ>λ+. Moreover, for N sufficiently large, we show that the eigenvectors associated to the largest eigenvalues are partially localized for λ>λ+, while they are completely delocalized for λ<λ+. Similar results hold for the lowest eigenvalues. }, author = {Lee, Jioon and Schnelli, Kevin}, journal = {Probability Theory and Related Fields}, number = {1-2}, pages = {165 -- 241}, publisher = {Springer}, title = {{Extremal eigenvalues and eigenvectors of deformed Wigner matrices}}, doi = {10.1007/s00440-014-0610-8}, volume = {164}, year = {2016}, } @article{1475, abstract = {The actin cytoskeleton plays important roles in the formation and internalization of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes along actin cables, however, the molecular machinery regulating interaction between endocytic vesicles and actin cables is poorly understood. The Eps15-like protein Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several endocytic compartments. Early endosomes were highly localized in the actin concentrations and displayed movement along actin cables. The dephosphorylated form of Pan1p also caused stable associations between endocytic vesicles and actin cables, and between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of a novel mechanism that regulates endocytic compartment interactions with each other and with actin cables.}, author = {Toshima, Junko and Furuya, Eri and Nagano, Makoto and Kanno, Chisa and Sakamoto, Yuta and Ebihara, Masashi and Siekhaus, Daria E and Toshima, Jiro}, journal = {eLife}, number = {February 2016}, publisher = {eLife Sciences Publications}, title = {{Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton}}, doi = {10.7554/eLife.10276}, volume = {5}, year = {2016}, } @article{1476, abstract = {The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis}, author = {Toshima, Junko and Horikomi, Chika and Okada, Asuka and Hatori, Makiko and Nagano, Makoto and Masuda, Atsushi and Yamamoto, Wataru and Siekhaus, Daria E and Toshima, Jiro}, journal = {Journal of Cell Science}, number = {2}, pages = {367 -- 379}, publisher = {Company of Biologists}, title = {{Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis}}, doi = {10.1242/jcs.176651}, volume = {129}, year = {2016}, } @article{1477, abstract = {We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples.}, author = {Chatterjee, Krishnendu and Chmelik, Martin and Tracol, Mathieu}, journal = {Journal of Computer and System Sciences}, number = {5}, pages = {878 -- 911}, publisher = {Elsevier}, title = {{What is decidable about partially observable Markov decision processes with ω-regular objectives}}, doi = {10.1016/j.jcss.2016.02.009}, volume = {82}, year = {2016}, } @article{1478, abstract = {We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature.}, author = {Seiringer, Robert and Warzel, Simone}, journal = {New Journal of Physics}, number = {3}, publisher = {IOP Publishing}, title = {{Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas}}, doi = {10.1088/1367-2630/18/3/035002}, volume = {18}, year = {2016}, } @article{1479, abstract = {Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero. Our counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable. Finally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object.}, author = {Krenn, Stephan and Pietrzak, Krzysztof Z and Wadia, Akshay and Wichs, Daniel}, journal = {Computational Complexity}, number = {3}, pages = {567 -- 605}, publisher = {Springer}, title = {{A counterexample to the chain rule for conditional HILL entropy}}, doi = {10.1007/s00037-015-0120-9}, volume = {25}, year = {2016}, } @article{1480, abstract = {Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. }, author = {Michałek, Mateusz and Sturmfels, Bernd and Uhler, Caroline and Zwiernik, Piotr}, journal = {Proceedings of the London Mathematical Society}, number = {1}, pages = {27 -- 56}, publisher = {Oxford University Press}, title = {{Exponential varieties}}, doi = {10.1112/plms/pdv066}, volume = {112}, year = {2016}, } @article{1482, abstract = {Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.}, author = {Adibi, Milad and Yoshida, Saiko and Weijers, Dolf and Fleck, Christian}, journal = {PLoS One}, number = {2}, publisher = {Public Library of Science}, title = {{Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization}}, doi = {10.1371/journal.pone.0147830}, volume = {11}, year = {2016}, } @article{1484, author = {Chen, Xu and Wu, Shuang and Liu, Zengyu and Friml, Jiřĺ}, journal = {Trends in Cell Biology}, number = {6}, pages = {409 -- 419}, publisher = {Cell Press}, title = {{Environmental and endogenous control of cortical microtubule orientation}}, doi = {10.1016/j.tcb.2016.02.003}, volume = {26}, year = {2016}, } @article{1485, abstract = {In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.}, author = {De Martino, Daniele}, journal = {Physical Biology}, number = {1}, publisher = {IOP Publishing}, title = {{Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis}}, doi = {10.1088/1478-3975/13/1/016003}, volume = {13}, year = {2016}, } @article{1486, abstract = {We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer (BCS) functional of superconductivity, which were obtained in a series of papers, partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej. Our discussion includes, in particular, an investigation of the critical temperature for a general class of interaction potentials, as well as a study of its dependence on external fields. We shall explain how the Ginzburg-Landau model can be derived from the BCS theory in a suitable parameter regime.}, author = {Hainzl, Christian and Seiringer, Robert}, journal = {Journal of Mathematical Physics}, number = {2}, publisher = {American Institute of Physics}, title = {{The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties}}, doi = {10.1063/1.4941723}, volume = {57}, year = {2016}, } @article{1487, abstract = {Rhythms with time scales of multiple cycles per second permeate the mammalian brain, yet neuroscientists are not certain of their functional roles. One leading idea is that coherent oscillation between two brain regions facilitates the exchange of information between them. In rats, the hippocampus and the vibrissal sensorimotor system both are characterized by rhythmic oscillation in the theta range, 5–12 Hz. Previous work has been divided as to whether the two rhythms are independent or coherent. To resolve this question, we acquired three measures from rats—whisker motion, hippocampal local field potential (LFP), and barrel cortex unit firing—during a whisker-mediated texture discrimination task and during control conditions (not engaged in a whisker-mediated memory task). Compared to control conditions, the theta band of hippocampal LFP showed a marked increase in power as the rats approached and then palpated the texture. Phase synchronization between whisking and hippocampal LFP increased by almost 50% during approach and texture palpation. In addition, a greater proportion of barrel cortex neurons showed firing that was phase-locked to hippocampal theta while rats were engaged in the discrimination task. Consistent with a behavioral consequence of phase synchronization, the rats identified the texture more rapidly and with lower error likelihood on trials in which there was an increase in theta-whisking coherence at the moment of texture palpation. These results suggest that coherence between the whisking rhythm, barrel cortex firing, and hippocampal LFP is augmented selectively during epochs in which the rat collects sensory information and that such coherence enhances the efficiency of integration of stimulus information into memory and decision-making centers.}, author = {Grion, Natalia and Akrami, Athena and Zuo, Yangfang and Stella, Federico and Diamond, Mathew}, journal = {PLoS Biology}, number = {2}, publisher = {Public Library of Science}, title = {{Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination}}, doi = {10.1371/journal.pbio.1002384}, volume = {14}, year = {2016}, } @article{1488, abstract = {Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.}, author = {Riccio, Paul and Cebrián, Cristina and Zong, Hui and Hippenmeyer, Simon and Costantini, Frank}, journal = {PLoS Biology}, number = {2}, publisher = {Public Library of Science}, title = {{Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis}}, doi = {10.1371/journal.pbio.1002382}, volume = {14}, year = {2016}, } @article{1489, abstract = {We prove optimal local law, bulk universality and non-trivial decay for the off-diagonal elements of the resolvent for a class of translation invariant Gaussian random matrix ensembles with correlated entries. }, author = {Ajanki, Oskari H and Erdös, László and Krüger, Torben H}, journal = {Journal of Statistical Physics}, number = {2}, pages = {280 -- 302}, publisher = {Springer}, title = {{Local spectral statistics of Gaussian matrices with correlated entries}}, doi = {10.1007/s10955-016-1479-y}, volume = {163}, year = {2016}, }