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Kerry Marie Goodman, Rotem Rubinstein, Chan Aye Thu, Seetha Mannepalli, Fabiana Bahna, Göran Ahlsén, Chelsea Rittenhouse, Tom Maniatis, Barry Honig, Lawrence Shapiro
Stochastic cell-surface expression of α-, β-, and γ-clustered protocadherins (Pcdhs) provides vertebrate neurons with single-cell identities that underlie neuronal self-recognition. Here we report crystal structures of ectodomain fragments comprising cell-cell recognition regions of mouse γ-Pcdhs γA1, γA8, γB2, and γB7 revealing trans-homodimers, and of C-terminal ectodomain fragments from γ-Pcdhs γA4 and γB2, which depict cis-interacting regions in monomeric form. Together these structures span the entire Pcdhγ ectodomain...
October 26, 2016: ELife
Ved Prakash Kumar, Anupam Shrivastwa, Parag Nigam, Dhyanendra Kumar, Surendra Prakash Goyal
Swamp deer (Rucervus duvaucelii) is an endemic, Scheduled I species under the Wildlife (Protection) Act 1972, India. According to variations in antler size, it has been classified into three subspecies, namely Western (R. duvaucelii duvaucelii), Central (R. duvaucelii branderi), and Eastern (R. duvaucelii ranjitsinhii). For planning effective ex situ and in situ conservation of a wide-ranging species in different bioclimatic regions and in wildlife forensic, the use of genetic characterization in defining morpho/ecotypes has been suggested because of the geographic clines and reproductive isolation...
October 26, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Luigi Cannavacciuolo, Jürg Hulliger
Stochastic formation of a bi-polar state in three dimensional arrays of polar molecules with full Coulomb interactions is reproduced by Monte Carlo simulation. The size of the system is comparable to that of a real crystal seed. The spatial decay of the average order parameter is significantly slowed down by the long range interactions and the exact representation of correlation effects in terms of a single characteristic length becomes impossible. Finite size effects and possible scale invariance symmetry of the order parameter are extensively discussed...
September 28, 2016: Journal of Chemical Physics
S Orioli, P Faccioli
Renormalization Group (RG) theory provides the theoretical framework to define rigorous effective theories, i.e., systematic low-resolution approximations of arbitrary microscopic models. Markov state models are shown to be rigorous effective theories for Molecular Dynamics (MD). Based on this fact, we use real space RG to vary the resolution of the stochastic model and define an algorithm for clustering microstates into macrostates. The result is a lower dimensional stochastic model which, by construction, provides the optimal coarse-grained Markovian representation of the system's relaxation kinetics...
September 28, 2016: Journal of Chemical Physics
Mingge Deng, Zhen Li, Oleg Borodin, George Em Karniadakis
We develop a "charged" dissipative particle dynamics (cDPD) model for simulating mesoscopic electrokinetic phenomena governed by the stochastic Poisson-Nernst-Planck and the Navier-Stokes equations. Specifically, the transport equations of ionic species are incorporated into the DPD framework by introducing extra degrees of freedom and corresponding evolution equations associated with each DPD particle. Diffusion of ionic species driven by the ionic concentration gradient, electrostatic potential gradient, and thermal fluctuations is captured accurately via pairwise fluxes between DPD particles...
October 14, 2016: Journal of Chemical Physics
Cole M Johnson, Alexander E Doran, Jinmei Zhang, Edward F Valeev, So Hirata
A stochastic algorithm is proposed and implemented that computes a basis-set-incompleteness (F12) correction to an ab initio second-order many-body perturbation energy as a short sum of 6- to 15-dimensional integrals of Gaussian-type orbitals, an explicit function of the electron-electron distance (geminal), and its associated excitation amplitudes held fixed at the values suggested by Ten-no. The integrals are directly evaluated (without a resolution-of-the-identity approximation or an auxiliary basis set) by the Metropolis Monte Carlo method...
October 21, 2016: Journal of Chemical Physics
Roger F Loring
Optically detected single-turnover measurements of biological and inorganic catalysts provide a detailed picture of structural and dynamical influences on catalytic activity. Measurement at the single-molecule level of catalysis of a fluorogenic reaction (or its reverse) yields a stochastic fluorescence trajectory reflecting the statistics of individual reaction and product dissociation events. Analysis of time correlations displayed by this trajectory reveals reaction details inaccessible in a bulk measurement of averaged dynamics...
October 7, 2016: Journal of Chemical Physics
Chen Ruyin, Pan Wanli, Zhang Jianqiang, Nie Linru
In this paper, we investigate transport of an inertial particle in a spatially symmetric potential and subjected to two harmonic signals with different frequencies in both deterministic and stochastic cases. Numerical results indicate that: (i) In the deterministic case, the two harmonic signals can induce many (up to six) segments of negative slopes in the curve of mean velocity vs. external constant force, i.e., a multiple absolute negative mobilities (ANMs) effect. But the occurrence of the effect depends on their frequencies and amplitudes...
September 2016: Chaos
Jeffrey Emenheiser, Airlie Chapman, Márton Pósfai, James P Crutchfield, Mehran Mesbahi, Raissa M D'Souza
Following the long-lived qualitative-dynamics tradition of explaining behavior in complex systems via the architecture of their attractors and basins, we investigate the patterns of switching between distinct trajectories in a network of synchronized oscillators. Our system, consisting of nonlinear amplitude-phase oscillators arranged in a ring topology with reactive nearest-neighbor coupling, is simple and connects directly to experimental realizations. We seek to understand how the multiple stable synchronized states connect to each other in state space by applying Gaussian white noise to each of the oscillators' phases...
September 2016: Chaos
Otti D'Huys, Johannes Lohmann, Nicholas D Haynes, Daniel J Gauthier
Autonomous Boolean networks are commonly used to model the dynamics of gene regulatory networks and allow for the prediction of stable dynamical attractors. However, most models do not account for time delays along the network links and noise, which are crucial features of real biological systems. Concentrating on two paradigmatic motifs, the toggle switch and the repressilator, we develop an experimental testbed that explicitly includes both inter-node time delays and noise using digital logic elements on field-programmable gate arrays...
September 2016: Chaos
Fabio A Labra, Jose M Bogdanovich, Francisco Bozinovic
Complex physiological dynamics have been argued to be a signature of healthy physiological function. Here we test whether the complexity of metabolic rate fluctuations in small endotherms decreases with lower environmental temperatures. To do so, we examine the multifractal temporal scaling properties of the rate of change in oxygen consumption r(VO2), in the laboratory mouse Mus musculus, assessing their long range correlation properties across seven different environmental temperatures, ranging from 0 °C to 30 °C...
2016: PeerJ
Shichao Liu, Peter Xiaoping Liu, Xiaoyu Wang
This survey is to summarize and compare existing and recently emerging approaches for the analysis and compensation of the effects of network-induced delays on the stability and performance of communication-based power control systems. Several important communication-based power control systems are briefly introduced. The deterministic and stochastic methodologies of analyzing the impacts of network-induced delays on the stability of the communication-based power control systems are summarized and compared...
October 22, 2016: ISA Transactions
Gregory Peter Horne, Thomas Ashley Donoclift, Howard Sims, Robin Orr, Simon M Pimblott
A multi-scale modelling approach has been developed for the extended timescale long-term radiolysis of aqueous systems. The approach uses a combination of stochastic track structure and track chemistry as well as deterministic homogeneous chemistry techniques and involves four key stages; radiation track structure simulation, the subsequent physicochemical processes, nonhomogeneous diffusion-reaction kinetic evolution, and homogeneous bulk chemistry modelling. The first three components model the physical and chemical evolution of an isolated radiation chemical track and provide radiolysis yields, within the extremely low dose isolated track paradigm, as the input parameters for a bulk deterministic chemistry model...
October 25, 2016: Journal of Physical Chemistry. B
Felicity M Davis, Bethan Lloyd-Lewis, Olivia B Harris, Sarah Kozar, Douglas J Winton, Leila Muresan, Christine J Watson
The mammary gland undergoes cycles of growth and regeneration throughout reproductive life, a process that requires mammary stem cells (MaSCs). Whilst recent genetic fate-mapping studies using lineage-specific promoters have provided valuable insights into the mammary epithelial hierarchy, the true differentiation potential of adult MaSCs remains unclear. To address this, herein we utilize a stochastic genetic-labelling strategy to indelibly mark a single cell and its progeny in situ, combined with tissue clearing and 3D imaging...
October 25, 2016: Nature Communications
P Kovalenko, A T DiCioccio, J D Davis, M Li, M Ardeleanu, Nmh Graham, R Soltys
An exploratory population pharmacokinetic model for functional dupilumab was developed. Data from healthy volunteers and patients with atopic dermatitis (AD) receiving intravenous or subcutaneous doses were integrated. The data included 197 participants (2,518 measurements of dupilumab in serum) from six phase I and II studies. The data were analyzed using stochastic approximation expectation-maximization and importance sampling methods. The best structural model was a two-compartment model with parallel linear and Michaelis-Menten elimination from the central compartment...
October 25, 2016: CPT: Pharmacometrics & Systems Pharmacology
Antonio Di Crescenzo, Serena Spina
We propose a new deterministic growth model which captures certain features of both the Gompertz and Korf laws. We investigate its main properties, with special attention to the correction factor, the relative growth rate, the inflection point, the maximum specific growth rate, the lag time and the threshold crossing problem. Some data analytic examples and their performance are also considered. Furthermore, we study a stochastic counterpart of the proposed model, that is a linear time-inhomogeneous birth-death process whose mean behaves as the deterministic one...
October 21, 2016: Mathematical Biosciences
Takaharu Kato, Sergio Alonso, Yuta Muto, Hiroshi Noda, Yasuyuki Miyakura, Koichi Suzuki, Shingo Tsujinaka, Masaaki Saito, Manuel Perucho, Toshiki Rikiyama
BACKGROUND: Incidence and clinical characteristics of synchronous colorectal cancer (sCRC) patients significantly vary among studies, likely due to differences in surveillance methodology. If remain undetected, sCRC can progress to more advanced stages seriously aggravating patient prognosis. We studied the incidence and clinicopathological characteristics of Japanese patients with sCRCs who underwent surgery for primary CRC and received exhaustive perioperative surveillance. METHODS: We recruited 1005 patients with surgically resected CRCs between January 2007 and December 2011...
October 24, 2016: World Journal of Surgical Oncology
Dean R Freestone, Kelvin J Layton, Levin Kuhlmann, Mark J Cook
Data-driven model-based analysis of electrophysiological data is an emerging technique for understanding the mechanisms of seizures. Model-based analysis enables tracking of hidden brain states that are represented by the dynamics of neural mass models. Neural mass models describe the mean firing rates and mean membrane potentials of populations of neurons. Various neural mass models exist with different levels of complexity and realism. An ideal data-driven model-based analysis framework will incorporate the most realistic model possible, enabling accurate imaging of the physiological variables...
June 9, 2016: International Journal of Neural Systems
Roman Dvorkin, Noam E Ziv
The idea that synaptic properties are defined by specific pre- and postsynaptic activity histories is one of the oldest and most influential tenets of contemporary neuroscience. Recent studies also indicate, however, that synaptic properties often change spontaneously, even in the absence of specific activity patterns or any activity whatsoever. What, then, are the relative contributions of activity history-dependent and activity history-independent processes to changes synapses undergo? To compare the relative contributions of these processes, we imaged, in spontaneously active networks of cortical neurons, glutamatergic synapses formed between the same axons and neurons or dendrites under the assumption that their similar activity histories should result in similar size changes over timescales of days...
October 2016: PLoS Biology
Andreas Widder, Christian Kuehn
In this paper, we focus on the influence of heterogeneity and stochasticity of the population on the dynamical structure of a basic susceptible-infected-susceptible (SIS) model. First we prove that, upon a suitable mathematical reformulation of the basic reproduction number, the homogeneous system and the heterogeneous system exhibit a completely analogous global behaviour. Then we consider noise terms to incorporate the fluctuation effects and the random import of the disease into the population and analyse the influence of heterogeneity on warning signs for critical transitions (or tipping points)...
October 1, 2016: Mathematical Biosciences and Engineering: MBE
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