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Cong Hu, Zhi Li, Tian Zhou, Aijun Zhu, Chuanpei Xu
We propose a new meta-heuristic algorithm named Levy flights multi-verse optimizer (LFMVO), which incorporates Levy flights into multi-verse optimizer (MVO) algorithm to solve numerical and engineering optimization problems. The Original MVO easily falls into stagnation when wormholes stochastically re-span a number of universes (solutions) around the best universe achieved over the course of iterations. Since Levy flights are superior in exploring unknown, large-scale search space, they are integrated into the previous best universe to force MVO out of stagnation...
2016: PloS One
Ramakanth Neeli-Venkata, Sofia Startceva, Teppo Annila, Andre S Ribeiro
We studied whether nucleoid exclusion contributes to the segregation and retention of Tsr chemoreceptor clusters at the cell poles. Using live time-lapse, single-cell microscopy measurements, we show that the single-cell spatial distributions of Tsr clusters have heterogeneities and asymmetries that are consistent with nucleoid exclusion and cannot be explained by the diffusion-and-capture mechanism supported by Tol-Pal complexes at the poles. Also, in cells subjected to ampicillin, which enhances relative nucleoid lengths, Tsr clusters locate relatively closer to the cell extremities, whereas in anucleated cells (deletion mutants for mukB), the Tsr clusters are closer to midcell...
December 6, 2016: Biophysical Journal
Arianna Bottinelli, David T J Sumpter, Jesse L Silverberg
Collective motion of large human crowds often depends on their density. In extreme cases like heavy metal concerts and black Friday sales events, motion is dominated by physical interactions instead of conventional social norms. Here, we study an active matter model inspired by situations when large groups of people gather at a point of common interest. Our analysis takes an approach developed for jammed granular media and identifies Goldstone modes, soft spots, and stochastic resonance as structurally driven mechanisms for potentially dangerous emergent collective motion...
November 25, 2016: Physical Review Letters
Gabriel Kocher, Nana Ofori-Opoku, Nikolas Provatas
A tacit assumption underlying most phase field models of nonequilibrium phase transformations is that of scale separation. Stochastic order parameter field theories utilize noise to separate atomic-scale fluctuations from the slowly varying fields that describe microstructure patterns. The mesoscale distribution of such stochastic variables is generally assumed to follow Gaussian statistics, with their magnitude following fluctuation-dissipation relations. However, there is still much debate about how atomic-scale fluctuations map onto the mesoscale upon coarse graining of microscopic theories...
November 25, 2016: Physical Review Letters
Efrat M Cohen, Oren Kobiler
Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants...
December 6, 2016: PLoS Pathogens
Anna Klimovskaia, Stefan Ganscha, Manfred Claassen
Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The topology of these networks typically is only partially characterized due to experimental limitations. Current approaches for refining network topology are based on the explicit enumeration of alternative topologies and are therefore restricted to small problem instances with almost complete knowledge. We propose the reactionet lasso, a computational procedure that derives a stepwise sparse regression approach on the basis of the Chemical Master Equation, enabling large-scale structure learning for reaction networks by implicitly accounting for billions of topology variants...
December 2016: PLoS Computational Biology
Giorgia Zampardi, Christopher Batchelor-McAuley, Enno Kätelhön, Richard G Compton
A stochastic investigation of lithium deinsertion from individual 200-nm-sized particles of LiMn2 O4 reveals the rate-determining step at high overpotentials to be the transfer of the cation across the particle-electrolyte interface. Measurement of the (electro)chemical behavior of the spinel is undertaken without forming a conductive composite electrode. The kinetics of the interfacial ion transfer defines a theoretical upper limit for the discharge rates of batteries using LiMn2 O4 in an aqueous environment...
December 6, 2016: Angewandte Chemie
Weiwei Qin, Tianhuan Peng, Yanjing Gao, Fei Wang, Xiaocai Hu, Kun Wang, Jiye Shi, Di Li, Jicun Ren, Chunhai Fan
It is highly demanding to design active nanomotors that can move in response to specific signals with controllable rate and direction. A catalysis-driven nanomotor was constructed by designing catalytically and plasmonically active Janus gold nanoparticles (Au NPs), which generate an asymmetric temperature gradient of local solvent surrounding NPs in catalytic reactions. The self-thermophoresis behavior of the Janus nanomotor is monitored from its inherent plasmonic response. The diffusion coefficient of the self-thermophoresis motion is linearly dependent on chemical reaction rate, as described by a stochastic model...
December 6, 2016: Angewandte Chemie
Mathieu Miras, David Dubnau
The K-state in the model bacterium Bacillus subtilis is associated with transformability (competence) as well as with growth arrest and tolerance for antibiotics. Entry into the K-state is determined by the stochastic activation of the transcription factor ComK and occurs in about ∼15% of the population in domesticated strains. Although the upstream mechanisms that regulate the K-state have been intensively studied and are well understood, it has remained unexplained why undomesticated isolates of B. subtilis are poorly transformable compared to their domesticated counterparts...
2016: Frontiers in Microbiology
Pierre-Olivier Cheptou, Anna L Hargreaves, Dries Bonte, Hans Jacquemyn
Fragmentation-the process by which habitats are transformed into smaller patches isolated from each other-has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Pedro Olivares-Chauvet, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Noa Oded Elkayam, Yaniv Lubling, Gintaras Deikus, Robert P Sebra, Amos Tanay
Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species. Whether pairwise loops synergize to form higher-order structures is still unclear. Here we develop a conformation capture assay to study higher-order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains in human and mouse cells...
November 30, 2016: Nature
Kai Wang, Xiansen Ye, Huajun Zhang, Heping Chen, Demin Zhang, Lian Liu
Knowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions...
December 5, 2016: Scientific Reports
Qian Li, Qingxin Zhu, Shouming Zhong, Fuli Zhong
This paper is concerned with the problem of extended dissipativity-based state estimation for uncertain discrete-time Markov jump neural networks with finite piecewise homogeneous Markov chain and mixed time delays. The aim of this paper is to present a Markov switching estimator design method, which ensures that the resulting error system is extended stochastically dissipative. A triple-summable term is introduced in the constructed Lyapunov function and the reciprocally convex approach is utilized to bound the forward difference of the triple-summable term...
December 1, 2016: ISA Transactions
Monjur Morshed, Brian Ingalls, Silvana Ilie
Sensitivity analysis characterizes the dependence of a model's behaviour on system parameters. It is a critical tool in the formulation, characterization, and verification of models of biochemical reaction networks, for which confident estimates of parameter values are often lacking. In this paper, we propose a novel method for sensitivity analysis of discrete stochastic models of biochemical reaction systems whose dynamics occur over a range of timescales. This method combines finite-difference approximations and adaptive tau-leaping strategies to efficiently estimate parametric sensitivities for stiff stochastic biochemical kinetics models, with negligible loss in accuracy compared with previously published approaches...
November 30, 2016: Bio Systems
Ian M Goodyer, Shirley Reynolds, Barbara Barrett, Sarah Byford, Bernadka Dubicka, Jonathan Hill, Fiona Holland, Raphael Kelvin, Nick Midgley, Chris Roberts, Rob Senior, Mary Target, Barry Widmer, Paul Wilkinson, Peter Fonagy
BACKGROUND: Psychological treatments for adolescents with unipolar major depressive disorder are associated with diagnostic remission within 28 weeks in 65-70% of patients. We aimed to assess the medium-term effects and costs of psychological therapies on maintenance of reduced depression symptoms 12 months after treatment. METHODS: We did this multicentre, pragmatic, observer-blind, randomised controlled superiority trial (IMPACT) at 15 National Health Service child and adolescent mental health service (CAMHS) clinics in three regions in England...
November 30, 2016: Lancet Psychiatry
Tsair-Chuan Lin, Kainam Thomas Wong, Macario O Cordel, Joel Paz Ilao
A "triaxial velocity sensor" consists of three uniaxial velocity sensors, which are nominally identical, orthogonally oriented among themselves, and co-centered at one point in space. A triaxial velocity sensor measures the acoustic particle velocity vector, by its three Cartesian components, individually component-by-component, thereby offering azimuth-elevation two-dimensional spatial directivity, despite the physical compactness that comes with the collocation of its three components. This sensing system's azimuth-elevation beam-pattern has been much analyzed in the open literature, but only for an idealized case of the three uniaxial velocity sensors being exactly identical in gain...
September 2016: Journal of the Acoustical Society of America
Christian Mittermaier, Maximilian Schindler, Benjamin Loader, Thomas Waldhoer, Clemens Ambrozy, Richard Crevenna, Karin Pieber
Sensorimotor training with a wide variety of available devices represents an important component in rehabilitation and prevention of different sports injuries and chronic diseases. The purpose of this study was to evaluate the effects of a sensorimotor training with a newly developed device, which consists of an instable platform moving on an air cushion, providing dynamic balance training by tilting and unanticipated stochastic translations on postural control. Seventy-two healthy young subjects were included in this prospective, randomized, controlled, and observer-blinded study...
November 25, 2016: Gait & Posture
Seydou Traoré, David Allouche, Isabelle André, Thomas Schiex, Sophie Barbe
One main challenge in Computational Protein Design (CPD) lies in the exploration of the amino-acid sequence space, while considering, to some extent, side chain flexibility. The exorbitant size of the search space urges for the development of efficient exact deterministic search methods enabling identification of low-energy sequence-conformation models, corresponding either to the global minimum energy conformation (GMEC) or an ensemble of guaranteed near-optimal solutions. In contrast to stochastic local search methods that are not guaranteed to find the GMEC, exact deterministic approaches always identify the GMEC and prove its optimality in finite but exponential worst-case time...
2017: Methods in Molecular Biology
Marc D Ryser, Walter T Lee, Neal E Ready, Kevin Z Leder, Jasmine Foo
High rates of local recurrence in tobacco-related head and neck squamous cell carcinoma (HNSCC) are commonly attributed to unresected fields of precancerous tissue. Because they are not easily detectable at the time of surgery without additional biopsies, there is a need for noninvasive methods to predict the extent and dynamics of these fields. Here, we developed a spatial stochastic model of tobacco-related HNSCC at the tissue level and calibrated the model using a Bayesian framework and population-level incidence data from the Surveillance, Epidemiology, and End Results (SEER) registry...
October 20, 2016: Cancer Research
Ci Chen, Zhi Liu, Kan Xie, Yun Zhang, C L Philip Chen
Most existing control results for pure-feedback stochastic systems are limited to a condition that tracking errors are bounded in probability. Departing from such bounded results, this paper proposes an asymptotic fuzzy neural network control for pure-feedback stochastic systems. The control goal is realized by proposing a novel semi-Nussbaum function-based technique and employing it in adaptive backstepping controller design. The proposed Nussbaum function is integrated with adaptive control technique to guarantee that the tracking error is asymptotically stable in probability...
November 28, 2016: IEEE Transactions on Cybernetics
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