bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data Mining using the Theory Cooperative Games in C-core to form clusters
Authors: Egorova Anastasia A. 
Published: December 2019

AbstractFor data analysis, objects can be clustered in a variety of ways and methods. The tree of possible options appears. To make decisions, we use the methods of game theory. The game-theoretic model can be considered as a coalition game. The characteristic function is considered as a function that depends on the degree of similarity of objects. Thus, we will form clusters. The game is considered as a differential control game. To make a decision, we will form a highly dynamically stable solution in the C-core.
Hyperbolic decomposition for hydrostatic approximation of free surface flow problems
Authors: Goloviznin V M , Mayorov P A , Mayorov P A 
Published: December 2019

Abstract
The article is devoted to the description of a new method of numerical solution for hydrostatic approximation of incompressible hydrodynamic problems with free surfaces and variable density. This technique develops a model of multilayer shallow water, taking into account the mass and momentum exchange between the layers.
Mathematical modelling of hydrogen safety problems with CABARET scheme
Authors: Kanaev A.A. , Glotov V.Yu. , Goloviznin V.M. , Kondakov V.G. , Kiselev A.E. 
Published: December 2019

Abstract
Experiments on overall fluid transfer and mixing in the large scale experimental facility (PANDA), where the initial helium-rich layer is eroded by a flow resulting from the interaction of a jet/plume with horizontal flow obstruction, were simulated with the CABARET scheme. Computational simulation results are provided for two mesh resolutions and are compared with the experimental data. Good agreement between calculated and measured gas temperature and the breakup of the helium layer dynamics was achieved by refining the mesh in the jet area and by adding the model of radiation heat transfer.
Algorithms for numerical solution of integral equations of three-dimensional scalar diffraction problem
Authors: Kashirin A A , Smagin S I 
Published: December 2019

Abstract
The three-dimensional diffraction problem of stationary acoustic waves on a homogeneous inclusion is considered. It is reduced to the weakly singular boundary Fredholm integral equations of the first kind with one unknown function, each of which is conditionally equivalent to the original problem. By using the original method of averaging the integral operators kernels, these equations are approximated by systems of linear algebraic equations. The resulting systems are solved numerically by the generalized minimal residual method (GMRES). Then the solution of the initial problem is calculated. To find the solution on the spectrum of integral operators, where the condition of equivalence of integral equations to the original problem is violated, the interpolation solution method is proposed. It does not require knowledge of the spectrum and allows us to find the approximated solutions with high accuracy. The proposed algorithms have been implemented in the computing cluster of Computing Center FEB RAS. The results of the calculations that allow us to assess the possibilities of this approach are presented.
Numerical simulation of a spatial – temporal model of epidemic distribution
Authors: Timofeeva T.S. , Farago I. , Kim E.L. 
Published: December 2019

Abstract
The problem of epidemiological situation forecasting is considered. The system of differential equations that describes the development of the epidemic process with regard to spatial dependence, proposed in works I.Farago and based on the Kermak-MacKendrick model. The paper presents the results of numerical calculations for different mathematical models of the spread of infectious diseases with different levels of detail.
3-D electronic density maps for enzyme reaction intermediates: big data and high performance computing services in a virtualized environment
Authors: Brekhov Anton , Mironov Vladimir , Moskovsky Alexander , Podgainiy Dmitry , Streltsova Oksana , Delyakov Dmitry 
Published: December 2019

Abstract
Enzymatic reactions play key role in metabolism of all living organisms. Recent advances in computational methods allow detailed study of enzyme-catalyzed processes, providing data on all intermediate states along reaction path. Furthermore, experimental data on the structure of the reaction intermediates become more available due to advancing of ultrafast X-Ray spectroscopy. These data describes electronic density of intermediates, sometimes even in time series. Currently, prominent Protein Data Bank (PDB) keeps records on the raw crystallographic data on electron density, but usually describes only enzymes or enzymes-inhibitor complexes. A database service where the both experimental and simulated data can be stored and analyzed simultaneously will be a valuable scientific tool for bringing theory and experiment together.
There are hundreds of enzymes known and one should expect large volumes of data on three-dimensional property like electronic density. At the same time, quantum chemistry simulations of large biomolecules require extensive computing resources. Thus, we turned into service model using Nautilus environment of Cognitive Hardware And Software Ecosystem Community Infrastructure (CHASE-CI) project as a blueprint. In that environment, each participating organization can donate their hardware resources, like storage or compute elements, while retaining flexible access control to running services and datasets. We have installed and tested a small-scale environment prototype using resources of LCC laboratory at Chemistry Department Lomonosov Moscow State University, Joint Institute of Nuclear Research (Dubna) and RSC Group company (Moscow). As it was efficiently implemented in Sloan Digital Sky Survey (SDSS) project, we identified basic search queries and structured database accordingly.
Supercomputer technologies for solving problems of computational physics
Authors: Glinskiy Boris , Zagorulko Yury , Kulikov Igor , Sapetina Anna 
Published: December 2019

Abstract
The issues of using supercomputer technologies developed by the authors to solve compute-intensive problems of mathematical physics are discussed. The technology of developing algorithms and software for supercomputers contains the three related stages: co-design, by which we understand the adaptation of the problem statement, the mathematical method and the computational algorithm to the parallel architecture of the supercomputer at all stages of the problem solution; studying the scalability of computational algorithms for the most promising supercomputers based on simulation modeling; evaluation of the energy efficiency of algorithms for various implementations on a given supercomputer architecture. It is proposed to further develop this approach with the use of the intelligence support for solving compute-intensive problems using the ontology of computational methods and algorithms for solving the problems of computational physics, the ontology of computational heterogeneous architectures and decision rules.
Propagating large open quantum systems towards their asymptotic states: cluster implementation of the time-evolving block decimation scheme
Authors: Volokitin Valentin , Vakulchyk Ihor , Kozinov Evgeny , Liniov Alexey , Meyerov Iosif , Ivanchenko Michail , Laptyeva Tatyana , Denisov Sergey 
Published: December 2019

Abstract
Many-body quantum systems are subjected to the Curse of Dimensionality: The dimension of the Hilbert space H, where these systems live in, grows exponentially with number of their components. However, with some systems, it is possible to escape the curse by using a low-rank tensor approximation known as “matrix-product state/operator (MPS/O) representation” in the quantum community and “tensor-train decomposition” among applied mathematicians. Motivated by recent advances in computational quantum physics, we consider chains of N spins coupled by nearest-neighbor interactions. The spins are subjected to an action coming from the environment. Spatially disordered interaction and environment-induced decoherence drive systems into non-trivial asymptotic states. The dissipative evolution is modeled with a Markovian master equation in the Lindblad form. By implementing the MPO technique and propagating system states with the time-evolving block decimation scheme, which allows keeping the length of the state descriptions fixed, it is in principle possible to reach the asymptotic states. We propose and realize a cluster implementation of this idea. The implementation on four nodes allowed us to resolve the asymptotic states of the model systems with N = 128 spins (total dimension of the Hilbert space dimH = 2128 ≈ 1039).
Numerical homogenization of elastoplastic deformations of composite material with small proportion of inclusions
Authors: Sivtsev Petr V. , Kolesov Aleksandr E. , Zakharov Petr E. , Yang Ying 
Published: December 2019

Abstract
Numerical simulation of the stress-strain state of a composite material may be difficult due to large computational complexity associated with a grid resolution of a large number of inclusions. To overcome the problem one may use the homogenization method. But for material with plastic properties, proper modeling of yield stress and hardening may be overcomplicated. In this work we use some simplification associated with a small proportion of inclusions and restriction of stress values by matrix material strength. As model problem, we use deformation of concrete deep beam reinforced with steel or basalt fiber inclusions. For the numerical solution, the finite element method was applied using the FEniCS computing platform.
Comparison of discrete fiber and asymptotic homogenization methods for modeling deformations of fiber-reinforced materials
Authors: Zakharov Petr E. , Sivtsev Petr V. 
Published: December 2019

Abstract
The main issue in a numerical simulation of fiber-reinforced materials deformation is high computational complexity. Exact resolution of fibers thickness leads to a huge number of degrees of freedom. In this work, we compare discrete fiber and asymptotic homogenization methods for modeling deformations. The discrete fiber method considers fibers as one-dimensional lines and the asymptotic homogenization method averages elasticity coefficients. We investigate the accuracy of these methods for a large range of models and approximation parameters.
Identification of the spacewise dependent right-hand side in one-dimensional parabolic equation
Authors: De Su Ling , Vasil’ev V. I. 
Published: December 2019

Abstract
In this paper we consider numerical solution of the inverse problem of determining a spacewise dependent right-hand side function, which is also called source function, in parabolic equation from measured data of the solution at the final time point. Such inverse problem occurs in mathematical modeling of various physics or engineering areas. Special iterative method is constructed for the approximate solution of the inverse problem, based on the source function at the new iterative step can be identified by the time derivative and space derivative at final time moment. The capabilities of the proposed computational algorithm is confirmed by the results of several numerical experiments.
Microstructure changes responsible for the degradation of the 10CrMo9-10 and 13CrMo4-5 steels during long-term operation
Authors: Gwoździk Monika , Motylenko Mykhaylo , Rafaja David 
Published: December 2019

Abstract
The paper presents results of microstructure and mechanical testing examinations performed using optical and transmission electron microscopy, tensile tests and Charpy tests on 10CrMo9-10 and 13CrMo4-5 steels, before and after they were long-term operated at elevated temperatures in a steam heater. In the 10CrMo9-10 steel, the optical microscopy detected a degradation of original bainite that was accompanied by the formation of ferrite, precipitates and micropores. The transmission electron microscopy revealed that the precipitates are M23C6 and M7C3 type carbides, which are located mainly at the boundaries of former austenite grains, and M3C type carbides, which appear inside the grains. The 13CrMo4-5 steel contained a relatively high amount of ferrite in the ferritic-bainitic/perlitic microstructure already in the originally state. The degradation of the microstructure was less serious than for the 10CrMo9-10 steel. The thermal treatment of the 13CrMo4-5 steel led mainly to the precipitation of carbides. The M23C6 and M7C3 type carbides form in perlitic-bainitic areas, while M3C and M6C type carbides precipitate in ferrite. The higher density of the grain boundary precipitates in the long-term operated 10CrMo9-10 steel facilitated the formation of creep-induced micropores and contributed to the hardness reduction.
Structural and electronic properties of Stanene-BeO heterobilayer
Authors: Chakraborty Bipradip , Borgohain Madhurjya M , Adhikary Nirab C 
Published: December 2019

Abstract
Properties of Sn/BeO heterostructure formed with beryllium oxide (BeO) monolayer and 2D stanene (Sn) is studied in this work. The first-principle study is employed here to systematically investigate the structural stability and electrical properties of the Sn/BeO heterostructure. The results from simulations reveal that the introduction of BeO not only leads to a significant bandgap opening of 98 meV, but it also retains the various intrinsic electrical properties of stanene to a large extent. The effect of spin-orbit coupling (SOC) is studied both in pristine stanene as well as in Sn/BeO heterostructure. The Sn/BeO heterostructure shows the Rashba-type of spin-splitting under SOC, which is very promising for application in spintronic devices. Moreover, it is also observed that the bandgap can be tuned by applying external strain and electric field, while the characteristic Dirac cone is maintained throughout. The application of an external electric field is found to be more effective in bandgap modulation. It leads to a linear change in the bandgap, with a bandgap value of 402 meV for 4 V nm−1. The results obtained from our study indicate that Sn/BeO heterostructure can be a suitable material for the development of spintronic devices.
Microstructure and creep strength evolution in G115 steel during creep at 650 °C
Authors: Liu Zhen , Liu Zhengdong , Chen Zhengzong , Wang Xitao , Bao Hansheng , Dong Chen 
Published: December 2019

Abstract
Microstructure and creep strength evolution in the ruptured 2.6 wt% W G115 specimens after creep tests were investigated under stresses of 120∼200 MPa at 650 °C. The growth of the lath during the creep tests was accompanied with the coarsening of second phase particles and the reduction of dislocation density. The tempered martensitic lath structure (TMLS) transformed into polygonal sub-grain structure when the pinning force due to the precipitates was lower than about 0.68 MPa. The Laves phase particles were irregular during the short-term creep and grew to be equiaxed shape after long-term creep.
Optical properties of Cr doped ZnAl2O4 nanoparticles with Spinel structure synthesized by hydrothermal method
Authors: Shang-Pan Huang , Zhi-Qiang Wei , Xiao-Juan Wu , Ji-Wen Shi 
Published: December 2019

Abstract
Zn1−xCrxAl2O4 (x = 0, 0.01, 0.03, 0.05 and 0.07) nanoparticles were synthesized by hydrothermal method and heat treatment technology, and the effects of Chromium doping ratios on the microstructure, morphology, element distribution, binding energy and optical property of the samples were characterized by x-ray diffraction (XRD), scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), x-ray energy dispersive spectroscopy (XEDS), x-ray photoemission spectroscopy (XPS), ultraviolet-visible (UV–vis) spectroscopy, photoluminescence spectra (PL) and fourier transform infrared spectroscopy (FT-IR). The experimental results show that Zn1−xCrxAl2O4 nanoparticles possess cubic spinel structure without other impurity phases. The average crystallite size decrease and the lattice parameter increase with the increase of Cr doping concentration. The morphology of the samples exhibits irregular spherical or ellipsoid particles with uniform particle size. XEDS spectra display Cr3+ successfully used as doping agent replaced Zn2+ and entered ZnAl2O4 matrix. XPS spectra demonstrate that the doped Cr ions mainly occupy the tetrahedral sites in Zn0.95Cr0.05Al2O4 sample. UV–vis spectra indicate the band gap of the doped sample decrease and exhibit red shift with the increase of Cr ion concentration. The intensity of FT-IR spectra for Zn1−xCrxAl2O4 samples decreases slowly and occurs red shift. PL spectra show the intensity decrease and occur luminescence quenching phenomenon for Cr doped sample.
Achieving high volumetric EDLC carbons via hydrothermal carbonization and cyclic activation
Authors: Gao Qiang , Titirici Maria-Magdalena 
Published: December 2019

Abstract
A novel activation method involving hydrothermal carbonization (HTC) and a pressure-induced low temperature oxidation has been demonstrated for cellulose derived HTC char by using hydrogen peroxide as an active di-oxygen source. The optimized porosity versus gravimetric capacitance results from cellulose derived HTC char synthesized at 220 °C. Almost homogeneous and small particle size micro-ellipse/sphere, relatively high surface area and narrow pore size distributions lead to a high bulk density, i.e. 0.73 g cm−3, of coating-type electrodes, which is much denser than those manufactured from steam-activated carbons for supercapacitor industry, i.e. 0.52 g cm−3. The resulting carbon prepared herein achieves a relatively high volumetric capacitance in an organic electrolyte-based supercapacitor, reaching a competitive value of an industrial system with the features being environment-friendly, cost-effective as well as high yield, and less energy consumption.
ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files
Authors: Ward Christopher M , To Thu-Hien , Pederson Stephen M 
Published: December 2019

Abstract

Motivation
High throughput next generation sequencing (NGS) has become exceedingly cheap, facilitating studies to be undertaken containing large sample numbers. Quality control (QC) is an essential stage during analytic pipelines and the outputs of popular bioinformatics tools such as FastQC and Picard can provide information on individual samples. Although these tools provide considerable power when carrying out QC, large sample numbers can make inspection of all samples and identification of systemic bias a challenge.

Results
We present ngsReports, an R package designed for the management and visualization of NGS reports from within an R environment. The available methods allow direct import into R of FastQC reports along with outputs from other tools. Visualization can be carried out across many samples using default, highly customizable plots with options to perform hierarchical clustering to quickly identify outlier libraries. Moreover, these can be displayed in an interactive shiny app or HTML report for ease of analysis.

Availability and implementation
The ngsReports package is available on Bioconductor and the GUI shiny app is available at https://github.com/UofABioinformaticsHub/shinyNgsreports.

Supplementary information
Supplementary data are available at Bioinformatics online.
Piperacillin-Tazobactam Added to Vancomycin Increases Risk for Acute Kidney Injury: Fact or Fiction?
Authors: Avedissian Sean N , Pais Gwendolyn M , Liu Jiajun , Rhodes Nathaniel J , Scheetz Marc H 
Published: December 2019

Abstract
Vancomycin and piperacillin-tazobactam are 2 of the most commonly prescribed antibiotics in hospitals. Recent data from multiple meta-analyses suggest that the combination increases the risk for vancomycin-induced kidney injury when compared to alternative viable options. However, these studies are unable to prove biologic plausibility and causality as randomized controlled trials have not been performed. Furthermore, these studies define acute kidney injury according to thresholds of serum creatinine rise. Serum creatinine is not a direct indicator of renal injury, rather a surrogate of glomerular function. More reliable, specific, and sensitive biomarkers are needed to truly define if there is a causal relationship with increased toxicity when piperacillin-tazobactam is added to vancomycin. This viewpoint will explore the available evidence for and against increased acute kidney injury in the setting of vancomycin and piperacillin-tazobactam coadministration.
RyR2 regulates Cx43 hemichannel intracellular Ca2+-dependent activation in cardiomyocytes
Authors: Lissoni Alessio , Hulpiau Paco , Martins-Marques Tânia , Wang Nan , Bultynck Geert , Schulz Rainer , Witschas Katja , Girao Henrique , De Smet Maarten , Leybaert Luc 
Published: December 2019

Abstract

Aims
Connexin-based gap junctions are crucial for electrical communication in the heart; they are each composed of two docked hemichannels (HCs), supplied as unpaired channels via the sarcolemma. When open, an unpaired HC forms a large pore, high-conductance and Ca2+-permeable membrane shunt pathway that may disturb cardiomyocyte function. HCs composed of connexin 43 (Cx43), a major cardiac connexin, can be opened by electrical stimulation but only by very positive membrane potentials. Here, we investigated the activation of Cx43 HCs in murine ventricular cardiomyocytes voltage-clamped at −70 mV.

Methods and results
Using whole-cell patch-clamp, co-immunoprecipitation, western blot analysis, immunocytochemistry, proximity ligation assays, and protein docking studies, we found that stimulation of ryanodine receptors (RyRs) triggered unitary currents with a single-channel conductance of ∼220 pS, which were strongly reduced by Cx43 knockdown. Recordings under Ca2+-clamp conditions showed that both RyR activation and intracellular Ca2+ elevation were necessary for HC opening. Proximity ligation studies indicated close Cx43-RyR2 apposition (&lt;40 nm), and both proteins co-immunoprecipitated indicating physical interaction. Molecular modelling suggested a strongly conserved RyR-mimicking peptide sequence (RyRHCIp), which inhibited RyR/Ca2+ HC activation but not voltage-triggered activation. The peptide also slowed down action potential repolarization. Interestingly, alterations in the concerned RyR sequence are known to be associated with primary familial hypertrophic cardiomyopathy.

Conclusion
Our results demonstrate that Cx43 HCs are intimately linked to RyRs, allowing them to open at negative diastolic membrane potential in response to RyR activation.