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Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip Paliwal, Yuedong Yang, Yaoqi Zhou
It has been long established that cis conformations of amino acid residues play many biologically important roles despite their rare occurrence in protein structure. Due to this rarity, few methods have been developed for predicting cis-isomers from protein sequences, most of which are based on outdated datasets and lack the means for independent testing. In this work, using a database of >10000 high-resolution protein structures, we update the statistics of cis-isomers and develop a sequence-based prediction technique using an ensemble of residual convolutional and Long Short-Term Memory bidirectional recurrent neural networks which allow learning from the whole protein sequence...
August 17, 2018: Journal of Chemical Information and Modeling
Eefei Chen, Raymond M Esquerra, Philipp A Meléndez, Sita S Chandrasekaran, David S Kliger
A protein's folding or function depends on its mobility through the viscous environment that is defined by the presence of macromolecules throughout the cell. The relevant parameter for this mobility is microviscosity - the viscosity on a time and distance scale that is important for protein folding/function movements. A quasi-null, ultrasensitive time-resolved linear dichroism (TRLD) spectroscopy is proving to be a useful tool for measurements of viscosity on this scale, with previous in vitro studies reporting on the microviscosities of crowded environments mimicked by high concentrations of different macromolecules...
August 17, 2018: Journal of Physical Chemistry. B
Efstratios K Kosmidis, Yiannis F Contoyiannis, Costas Papatheodoropoulos, Fotios K Diakonos
Evidence that neural circuits are operating near criticality has been provided at various levels of brain organization with a presumed role in maximizing information processing and multiscale activity association. Criticality has been linked to excitation at both the single cell and network levels, as action potential generation marks an obvious phase transition from a resting to an excitable state. Using in vitro intracellular recordings, we examine irregular, small amplitude membrane potential fluctuations from CA1 pyramidal neurons of Wistar male rats...
August 17, 2018: European Journal of Neuroscience
J Aguilar, D Monaenkova, V Linevich, W Savoie, B Dutta, H-S Kuan, M D Betterton, M A D Goodisman, D I Goldman
Groups of interacting active particles, insects, or humans can form clusters that hinder the goals of the collective; therefore, development of robust strategies for control of such clogs is essential, particularly in confined environments. Our biological and robophysical excavation experiments, supported by computational and theoretical models, reveal that digging performance can be robustly optimized within the constraints of narrow tunnels by individual idleness and retreating. Tools from the study of dense particulate ensembles elucidate how idleness reduces the frequency of flow-stopping clogs and how selective retreating reduces cluster dissolution time for the rare clusters that still occur...
August 17, 2018: Science
Leslie R Whitaker, Bruce T Hope
Given that addiction has been characterized as a disorder of maladaptive learning and memory, one critical question is whether there are unique physical adaptations within neuronal ensembles that support addiction-related learned behavior. The search for the physical mechanisms of encoding these and other memories in the brain, often called the engram as a whole, continues despite decades of research. As we develop new technologies and tools that allow us to study cue- and behavior-activated Fos-expressing neuronal ensembles, the possibility of identifying the engrams of learning and memory is moving into the realm of reality rather than speculation...
September 2018: Learning & Memory
M Eckstein, R S Lacruz
Enamel mineralization relies on Ca2+ availability provided by Ca2+ release activated Ca2+ (CRAC) channels. CRAC channels are modulated by the endoplasmic reticulum Ca2+ sensor STIM1 which gates the pore subunit of the channel known as ORAI1, found the in plasma membrane, to enable sustained Ca2+ influx. Mutations in the STIM1 and ORAI1 genes result in CRAC channelopathy, an ensemble of diseases including immunodeficiency, muscular hypotonia, ectodermal dysplasia with defects in sweat gland function and abnormal enamel mineralization similar to amelogenesis imperfecta (AI)...
August 9, 2018: Cell Calcium
Bing Xie, John Dylan Clark, David D L Minh
Molecular docking can account for receptor flexibility by combining the docking score over multiple rigid receptor conformations, such as snapshots from a molecular dynamics simulation. Here, we evaluate a number of common snapshot selection strategies using a quality metric from stratified sampling, the efficiency of stratification, which compares the variance of a selection strategy to simple random sampling. We also extend the metric to estimators of exponential averages (which involve an exponential transformation, averaging, and inverse transformation) and minima...
August 16, 2018: Journal of Chemical Information and Modeling
Jing-Wei Fan, Jingping Xu, Mu-Tian Cheng, Yaping Yang
For the cavity-based electromagnetically induced transparent (EIT), as the coherent driving field is enhanced by the optical cavity, the weak probe field can propagate through the atomic ensemble without absorption even if the driving field is weak. The extreme case of vacuum in the cavity is called "vacuum-induced transparency" (VIT) to distinguish it from the cavity EIT. Here we construct a new kind of cavity made of Metamaterials, i.e. ε-negative (EN) and μ-negative (MN) slabs, and study the VIT phenomena of the atomic ensemble doped within it...
July 23, 2018: Optics Express
Yusef Maleki, Aleksei M Zheltikov
A hybrid quantum device consisting of three ensembles of nitrogen-vacancy centers (NVEs) whose spins are collectively coupled to a superconducting coplanar waveguide resonator is shown to enable the generation of controllable tripartite macroscopic entangled states. The density matrix of such NVEs can be encoded to recast a three-qubit system state, which can be characterized in terms of the entanglement witnesses in relation to the Greenberger-Horne-Zeilinger (GHZ) states. We identify the parameter space within which the generated entangled states can have an arbitrarily large overlap with GHZ states, indicating an enhanced entanglement in the system...
July 9, 2018: Optics Express
Debarghya China, Alfredo Illanes, Prabal Poudel, Michael Friebe, Pabitra Mitra, Debdoot Sheet
Ultrasound (US) is a widely used as a low-cost alternative to computed tomography (CT) or magnetic resonance (MRI) and primarily for preliminary imaging. Since speckle intensity in US images is inherently stochastic, readers are often challenged in their ability to identify the pathological regions in a volume of a large number of images. This paper introduces a generalized approach for volumetric segmentation of structures in US images and volumes. We employ an iterative random walks (IRW) solver, random forest (RF) learning model, and a gradient vector flow (GVF) based inter-frame belief propagation technique for achieving cross-frame volumetric segmentation...
August 15, 2018: IEEE Journal of Biomedical and Health Informatics
Whitney E Muhlestein, Dallin S Akagi, Jason M Davies, Lola B Chambless
BACKGROUND: Current outcomes prediction tools are largely based on and limited by regression methods. Utilization of machine learning (ML) methods that can handle multiple diverse inputs could strengthen predictive abilities and improve patient outcomes. Inpatient length of stay (LOS) is one such outcome that serves as a surrogate for patient disease severity and resource utilization. OBJECTIVE: To develop a novel method to systematically rank, select, and combine ML algorithms to build a model that predicts LOS following craniotomy for brain tumor...
August 3, 2018: Neurosurgery
L G Popova, D V Belyaev, A V Shuvalov, A A Yurchenko, D A Matalin, D E Khramov, Y V Orlova, Y V Balnokin
De novo assembled transcriptomes of the marine microalga Dunaliella tertiolecta (Chlorophyta) were analyzed. Transcriptome assemblies were performed using short-read RNA-seq data deposited in the SRA database (DNA and RNA Sequence Read Archive, NCBI). A merged transcriptome was assembled using a pooled RNA-seq data set. The goal of the study was in silico identification of nucleotide sequences encoding P-type ATPases in D. tertiolecta transcriptomes. P-type ATPases play a considerable role in the adaptation of an organism to a variable environment, and this problem is particularly significant for microalgae inhabiting an environment with an unstable ionic composition...
July 2018: Molekuliarnaia Biologiia
Laura Bernardi, Costanza Giampietro, Vita Marina, Martina Genta, Edoardo Mazza, Aldo Ferrari
Mature epithelial monolayers share the ability to coherently respond to external mechanical stimuli. Tissue remodeling requires cell shape changes and coordinated movements. Human endothelia provide an exquisite example of such emerging collective activities. As part of their function in maintaining body homeostasis under variable hemodynamic loadings, endothelial ensembles must dynamically adapt to wall shear stress and cyclic deformation. While the alignment of several types of cells, including fibroblasts, osteoblasts and epithelial tissues, in response to various flow conditions or wall shear stress levels has been described in detail, less is known about collective endothelial remodeling under pure wall deformation...
August 16, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Yukai Li, Huling Li, Hua Yao
The focus of this study is the use of machine learning methods that combine feature selection and imbalanced process (SMOTE algorithm) to classify and predict diabetes follow-up control satisfaction data. After the feature selection and unbalanced process, diabetes follow-up data of the New Urban Area of Urumqi, Xinjiang, was used as input variables of support vector machine (SVM), decision tree, and integrated learning model (Adaboost and Bagging) for modeling and prediction. The experimental results show that Adaboost algorithm produces better classification results...
2018: Computational and Mathematical Methods in Medicine
James S Borrell, Nian Wang, Richard A Nichols, Richard J A Buggs
Dwarf birch (Betula nana) has a widespread boreal distribution but has declined significantly in Britain where populations are now highly fragmented. We analyzed the genetic diversity of these fragmented populations using markers that differ in mutation rate: conventional microsatellites markers (PCR-SSRs), RADseq generated transition and transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq reads (RAD-SSRs). We estimated the current population sizes by census and indirectly, from the linkage-disequilibrium found in the genetic surveys...
August 15, 2018: Heredity
Samuel Cajahuaringa, Alex Antonelli
A methodology to sample the isothermal-isobaric ensemble using Langevin dynamics is proposed, which combines novel features of geometric integrators for the equations of motion. By employing the Trotter expansion, the methodology generates a robust, symmetric, and accurate numerical algorithm. In order to show that the proposed method correctly samples the phase-space, simulations in the isotropic NPT ensemble were carried out for two analytical examples. Also this method lets us study a solid-solid phase transition by conducting a fully flexible-cell molecular dynamics simulation...
August 14, 2018: Journal of Chemical Physics
Evgeniy Khain
The granular Leidenfrost state consists of a dense granular cluster levitating above a hot granular gas. The density of particles inside the cluster can be very high and even close to the density of crystalline packing. To describe this state theoretically, one needs to know the density dependence of constitutive relations (pressure, heat losses, thermal conductivity) at these very high densities. However, the accurate expression for the coefficient of thermal conductivity is lacking. In this work, the constitutive relations were measured at high densities in molecular dynamics simulations in three different settings: a uniform freely cooling dense granulate (to measure heat losses), a uniform ensemble of elastically colliding particles (to measure pressure), and a dense granular medium between two thermal walls under gravity (to measure thermal conductivity)...
July 2018: Physical Review. E
Luca Biferale, Massimo Cencini, Massimo De Pietro, Giovanni Gallavotti, Valerio Lucarini
Understanding under what conditions it is possible to construct equivalent ensembles is key to advancing our ability to connect microscopic and macroscopic properties of nonequilibrium statistical mechanics. In the case of fluid dynamical systems, one issue is to test whether different models for viscosity lead to the same macroscopic properties of the fluid systems in different regimes. Such models include, besides the standard choice of constant viscosity, cases where the time symmetry of the evolution equations is exactly preserved, as it must be in the corresponding microscopic systems, when available...
July 2018: Physical Review. E
Eric G Arrais, Diego A Wisniacki, Lucas C Céleri, Norton G de Almeida, Augusto J Roncaglia, Fabricio Toscano
In the context of nonequilibrium quantum thermodynamics, variables like work behave stochastically. A particular definition of the work probability density function (pdf) for coherent quantum processes allows the verification of the quantum version of the celebrated fluctuation theorems, due to Jarzynski and Crooks, that apply when the system is driven away from an initial equilibrium thermal state. Such a particular pdf depends basically on the details of the initial and final Hamiltonians, on the temperature of the initial thermal state, and on how some external parameter is changed during the coherent process...
July 2018: Physical Review. E
Marco Baldovin
In systems with long-range interactions, since energy is a nonadditive quantity, ensemble inequivalence can arise: it is possible that different statistical ensembles lead to different equilibrium descriptions, even in the thermodynamic limit. The microcanonical ensemble should be considered the physically correct equilibrium distribution as long as the system is isolated. The canonical ensemble, on the other hand, can always be defined mathematically, but it is quite natural to wonder to which physical situations it does correspond...
July 2018: Physical Review. E
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