bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reweighting in Monte-Carlo calculation Renormalized Coupling Constant for the Three-Dimensional Ising Model
Authors: Brazhnik V , Kostashchuk A , Vakilov A 
Published: January 2021

Abstract
We investigated the thermodynamic behaviour of the three-dimensional Ising model near the critical temperature region using Monte Carlo calculations. The magnetic susceptibility, the correlation-length and renormalized coupling constant were calculated using the reweighting method.
Monte Carlo simulation of the critical behavior near the percolation threshold with invaded cluster algorithm
Authors: Shlyakhtich Maria , Prudnikov Pavel 
Published: January 2021

Abstract
We investigated the critical behavior of the disordered three-dimensional Ising model with an impurity concentration close to the threshold of impurity percolation p = pc
= 0.688 313 500 on high-performance computing systems. The system was updated using Metropolis algorithm and invaded cluster algorithm from initial configurations. The values of dynamic critical exponent z and static critical exponents β and v were obtained in this paper.
On boundaries in social dynamics models with large number of agents
Authors: Ignatovskaya Valeriya , Manita Larisa , Manita Anatoly 
Published: January 2021

Abstract
It is known that community boundaries in social systems evolve in a rather complicated manner. We investigate several well-known models of interpersonal interaction as well as their modifications in order to establish some asymptotic results of the long time behaviour of the edge in large (or infinite) configurations of agents. We also show that the introduction of randomness in such models can lead to promising applications of some powerful probabilistic tools.
Predictive models for metrological data of engineering systems
Authors: Alexander Lukankin , Sergey Slastnikov 
Published: January 2021

Abstract
Paper is devoted to the predictive models for metrological indicators on the real estate engineering infrastructure. The solution is in demand among many enterprises both in terms of security and economic considerations. The key task is to build a mathematical model performing predictions on the real data samples. We study both classical predictive models (ARIMA, SARIMA) and modern machine learning based approaches (RBF, LSTM), and compare them.
Application of multigrid methods for solving systems of linear algebraic equations of large dimension in the context of model differential equations
Authors: Vikulin Sergey Dmitrievich , Pershin Anton Yurevich , Sokolov Alexander Pavlovich 
Published: January 2021

Abstract
The geometric multigrid method has been implemented using the V-cycle for solving the high-dimensional linear algebraic equation systems that appear when applying the finite element and finite difference methods for the problems of mathematical physics. The results of the convergence comparison between the classical iterative methods (Jacobi, Gauss-Seidel or the conjugate gradient method) and the implemented geometric multigrid method have been obtained.
Extending the Problem Data Size for GPU Simulation Beyond the GPU Memory Storage with LRnLA Algorithms
Authors: Perepelkina Anastasia , Levchenko Vadim , Zakirov Andrey 
Published: January 2021

Abstract
To use the CPU RAM to store the data of a GPU simulation, the data exchange between CPU and GPU is required. With LRnLA algorithms, the computation without data exchange is made longer, and the data exchange may be concealed. In this work, the concept is demonstrated with the Lattice Boltzmann method simulation with ConeTorre LRnLA algorithm on GPU. A new method of data storage is proposed. The data on the synchronization planes are stored in tiles, and on the wavefront slopes a new data structure is used, which is optimized for cell data exchange between LRnLA sub-tasks. The performance tests show less than 5% overhead for CPU-GPU communication, and the GPU performance persists for simulations where the main storage site is the CPU RAM.
Efficient implementation of space-time adaptive ADER-DG finite element method with LST-DG predictor and a posteriori sub-cell WENO finite-volume limiting for simulation of non-stationary compressible multicomponent reactive flows
Authors: Popov Ivan S 
Published: January 2021

Abstract
The present work is devoted to the study of efficient implementation of spacetime adaptive ADER finite element discontinuous Galerkin method with a posteriori correction technique of solutions on subcells by the finite-volume ADER-WENO limiter scheme for simulation of non-stationary compressible multicomponent reactive flows. The multicomponent and reaction properties of the flow are considered in the form of convection-reaction equations. Therefore an effective scheme of splitting the original nonlinear system of algebraic equations of LST-DG predictor was developed to obtain an efficient iterative solution method. This approach is based on the use of the linearity property of the system of equations for the discrete spacetime solution for the system of convection equations, which makes it possible to pre-compute the inverse matrices, and allows the vectorized calculation of the transfer of individual components. The change in the concentrations of the components in the convection-reaction equations and the energy yield in the gas-dynamic equations due to the reactions are calculated using the global iterations. The iterative scheme for the original essentially nonlinear system of equations is split into a sequence of smaller systems. The approach is well applicable for the problems, especially in the case of a large number of components and reactions in the flow.
The system of predictive analysis of Bank investments using technologies of supercomputer simulation
Authors: Belov A V , Kurmanova K A 
Published: January 2021

Abstract
The article discusses an approach to building a system for generating a bank investment prediction with the technology of parallel computing. We develop a predictive model of the price of securities for the banking business on the stock market. For predictive analysis of investments, the choice of a mathematical model was justified using the Monte Carlo method. Computer simulation was carried out to form a forecast of securities prices based on historical data on securities of Goldman Sachs. Estimates of the execution time of the forecasting algorithm by the parallel programming method are obtained. The conclusion is made about the applicability of the proposed model when using the method of algorithmic trading in the stock market. The technical requirements for the development of a predictive analytics system for the Bank's investment portfolio are formulated.
Solitary waves in a two-dimensional graphene-based superlattice
Authors: Glazov Sergey , Syrodoev Gennadii 
Published: January 2021

Abstract
The article is about the features of the propagation of solitary electromagnetic waves in the two-dimensional graphene superlattice both in the collisionless mode and in the collision mode. The quasiclassical approach has been used, in which the law of the dispersion of charge carriers is determined by the approximation of the quantum mechanical calculations. The magnitude of the electric current has been calculated by using the classic kinetic Boltzman equation with the model collision integral in the constant relaxation frequency approximation. The effect of the high-frequency electric field and the nonadditivity of the energy spectrum on the propagation of a solitary electromagnetic pulse in the arbitrary directions inside a sample has been determined. The numerical simulation of the evolution of solitary electromagnetic pulses is performed by using the method of difference schemes.
Ensemble approach to weather forecasting
Authors: Astakhova Elena , Alferov Dmitry , Alferov Yuri , Bundel Anastasia 
Published: January 2021

Abstract
Numerical simulations of the Earth System evolution are the basis of weather forecasts. Due to chaotic nature of the atmosphere, an inevitable inaccuracy of initial state information, and models imperfection their results are always uncertain. To be correctly interpreted by a user, each weather forecast should be supplemented by an estimate of its uncertainty. An ensemble approach is the only practically affordable method to solve the problem. With this approach, it is possible not only to get an a priori estimate of forecast uncertainty, but also to improve a mean forecast skill and to present alternative scenarios of future weather evolution. Ensemble prediction systems are highly time-consuming and can be implemented only on powerful supercomputers. A global ensemble medium-range prediction system has been running operationally at the Hydrometcenter of Russia since 2015. A short-range limited-area convection-permitting ensemble prediction system was developed for meteorological support of the Sochi Olympic Games 2014 and is now applied for research. Characteristics of the systems, peculiarities of their computer implementation and verification results are discussed.
Effectiveness and impact of a structured research approach for health-system pharmacy administration and leadership residents
Authors: Vest Tyler A , Amerine Lindsey B , Savage Scott W , Rao Kamakshi V , Eckel Stephen F 
Published: January 2021

Abstract

Purpose
Required competency areas, goals, and objectives for both postgraduate year 1 (PGY1) pharmacy residencies and postgraduate year 2 (PGY2) health-system pharmacy administration and leadership (HSPAL) residencies indicate the importance of research in the residency program by specifying it as a required part of the training process. Research is critical in the field of health-system pharmacy administration, which is built upon the principles of evaluation and assessment, ensuring that all activities implemented in an organization are evaluated through data collection and assessment to determine their impact. Additionally, the research structure provides residents the opportunity to share research broadly, and it also provides the platform for other institutions to implement successful ideas of interest to them.

Summary
This article describes the impact of having a structured, publication-focused research program in an HSPAL residency. The research process has provided follow-up projects (n = 7) and grant participation (n = 6). Additionally, the process has yielded a 66% publication rate, with 21 of 32 thesis substitutes published in various journals. The department of pharmacy at the residency site has noticed that the continued refinement, scoping, and robust methodologies of projects have been essential to their impact in the literature and in dissemination of the accumulated body of knowledge.

Conclusion
A structured residency research program has provided direction to HSPAL residents and ensured successful scoping and completion of their research. Intentionality in this aspect has provided HSPAL residents with opportunities for publications, grants, and strong research experiences. Overall, the department of pharmacy has been positively impacted through implementation of services that were evaluated through a structured HSPAL pharmacy residency research program.
Molecular mechanism of negative cooperativity of ferredoxin-NADP+ reductase by ferredoxin and NADP(H): involvement of a salt bridge between Asp60 of ferredoxin and Lys33 of FNR
Authors: Chikuma Yutaro , Miyata Masayuki , Lee Young-Ho , Hase Toshiharu , Kimata-Ariga Yoko 
Published: January 2021

ABSTRACT
Ferredoxin-NADP+ reductase (FNR) in plants receives electrons from ferredoxin (Fd) and converts NADP+ to NADPH at the end of the photosynthetic electron transfer chain. We previously showed that the interaction between FNR and Fd was weakened by the allosteric binding of NADP(H) on FNR, which was considered as a part of negative cooperativity. In this study, we investigated the molecular mechanism of this phenomenon using maize FNR and Fd, as the three-dimensional structure of this Fd:FNR complex is available. NMR chemical shift perturbation analysis identified a site (Asp60) on Fd molecule which was selectively affected by NADP(H) binding on FNR. Asp60 of Fd forms a salt bridge with Lys33 of FNR in the complex. Site-specific mutants of FdD60 and FNRK33 suppressed the negative cooperativity (downregulation of the interaction between FNR and Fd by NADPH), indicating that a salt bridge between FdD60 and FNRK33 is involved in this negative cooperativity.
Bridging the gap from research to practice for enhanced health-related quality of life in people with chronic kidney disease
Authors: Segura-Orti Eva , Koufaki Pelagia , Kouidi Evangelia 
Published: January 2021

Abstract
Improving the health status of people with chronic kidney disease (CKD) through physical activity (PA) or exercise interventions is challenging. One of the gaps in the process of translating the general public PA activity guidelines as well as the CKD-specific guidelines into routine clinical practice is the lack of systematic recording and monitoring of PA and physical function attributes, which can also be used to develop individualized and measurable plans of action to promote PA for health. We aim to present an overview of key considerations for PA, physical function and health-related quality of life (HRQoL) evaluation in people with CKD, with the aim of encouraging health professionals to integrate assessment of these outcomes in routine practices. Physical inactivity and impaired physical function, sometimes to the extent of physical and social disability levels, and subsequently lower perceived HRQoL, are highly prevalent in this population. Enhanced PA is associated with better physical function that also translates into multiple health benefits. Breaking the vicious circle of inactivity and physical dysfunction as early as possible in the disease trajectory may confer huge benefits and enhanced life satisfaction in the longer term. With this in mind, the importance of PA/exercise interventions in CKD to improve HRQoL is also summarized.
Genome analysis of Salmonella enterica serovar Typhimurium bacteriophage L, indicator for StySA (StyLT2III) restriction-modification system action
Authors: Zaworski Julie , McClung Colleen , Ruse Cristian , Weigele Peter R , Hendrix Roger W , Ko Ching-Chung , Edgar Robert , Hatfull Graham F , Casjens Sherwood R , Raleigh Elisabeth A 
Published: January 2021

Abstract
Bacteriophage L, a P22-like phage of Salmonella enterica sv Typhimurium LT2, was important for definition of mosaic organization of the lambdoid phage family and for characterization of restriction-modification systems of Salmonella. We report the complete genome sequences of bacteriophage L cI–40 13–am43 and L cII–101; the deduced sequence of wildtype L is 40,633 bp long with a 47.5% GC content. We compare this sequence with those of P22 and ST64T, and predict 72 Coding Sequences, 2 tRNA genes and 14 intergenic rho-independent transcription terminators. The overall genome organization of L agrees with earlier genetic and physical evidence; for example, no secondary immunity region (immI: ant, arc) or known genes for superinfection exclusion (sieA and sieB) are present. Proteomic analysis confirmed identification of virion proteins, along with low levels of assembly intermediates and host cell envelope proteins. The genome of L is 99.9% identical at the nucleotide level to that reported for phage ST64T, despite isolation on different continents ∼35 years apart. DNA modification by the epigenetic regulator Dam is generally incomplete. Dam modification is also selectively missing in one location, corresponding to the P22 phase-variation-sensitive promoter region of the serotype-converting gtrABC operon. The number of sites for SenLTIII (StySA) action may account for stronger restriction of L (13 sites) than of P22 (3 sites).
Chasing breeding footprints through structural variations inCucumis meloand wild relatives
Authors: Demirci Sevgin , Fuentes Roven Rommel , Dooijeweert Willem van , Aflitos Saulo , Schijlen Elio , Hesselink Thamara , de Ridder Dick , Dijk Aalt D J van , Peters Sander 
Published: January 2021

AbstractCucumis melo (melon or muskmelon) is an important crop in the family of the Cucurbitaceae. Melon is cross pollinated and domesticated at several locations throughout the breeding history, resulting in highly diverse genetic structure in the germplasm. Yet, the relations among the groups and cultivars are still incomplete. We shed light on the melonbreeding history, analyzing structural variations ranging from 50 bp up to 100 kb, identified from whole genome sequences of 100 selected melon accessions and wild relatives. Phylogenetic trees based on SV types completely resolve cultivars and wild accessions into two monophyletic groups and clustering of cultivars largely correlates with their geographic origin. Taking into account morphology, we found six mis-categorized cultivars. Unique inversions are more often shared between cultivars, carrying advantageous genes and do not directly originate from wild species. Approximately 60% of the inversion breaks carry a long poly A/T motif, and following observations in other plant species, suggest that inversions in melon likely resulted from meiotic recombination events. We show that resistance genes in the linkage V region are expanded in the cultivar genomes compared to wild relatives. Furthermore, particular agronomic traits such as fruit ripening, fragrance, and stress response are specifically selected for in the melon subspecies. These results represent distinctive footprints of selective breeding that shaped today’s melon. The sequences and genomic relations between land races, wild relatives, and cultivars will serve the community to identify genetic diversity, optimize experimental designs, and enhance crop development.
Local adaptation contributes to gene expression divergence in maize
Authors: Blanc Jennifer , Kremling Karl A G , Buckler Edward , Josephs Emily B 
Published: January 2021

AbstractGene expression links genotypes to phenotypes, so identifying genes whose expression is shaped by selection will be important for understanding the traits and processes underlying local adaptation. However, detecting local adaptation for gene expression will require distinguishing between divergence due to selection and divergence due to genetic drift. Here, we adapt a QST−FST framework to detect local adaptation for transcriptome-wide gene expression levels in a population of diverse maize genotypes. We compare the number and types of selected genes across a wide range of maize populations and tissues, as well as selection on cold-response genes, drought-response genes, and coexpression clusters. We identify a number of genes whose expression levels are consistent with local adaptation and show that genes involved in stress response show enrichment for selection. Due to its history of intense selective breeding and domestication, maize evolution has long been of interest to researchers, and our study provides insight into the genes and processes important for in local adaptation of maize.
Reference genome assembly for AustralianAscochyta lentisisolate Al4
Authors: Lee Robert C , Farfan-Caceres Lina , Debler Johannes W , Williams Angela H , Syme Robert A , Henares Bernadette M 
Published: January 2021

AbstractAscochyta lentis causes ascochyta blight in lentil (Lens culinaris Medik.) and yield loss can be as high as 50%. With careful agronomic management practices, fungicide use, and advances in breeding resistant lentil varieties, disease severity and impact to farmers have been largely controlled. However, evidence from major lentil producing countries, Canada and Australia, suggests that A. lentis isolates can change their virulence profile and level of aggressiveness over time and under different selection pressures. In this paper, we describe the first genome assembly for A. lentis for the Australian isolate Al4, through the integration of data from Illumina and PacBio SMRT sequencing. The Al4 reference genome assembly is almost 42 Mb in size and encodes 11,638 predicted genes. The Al4 genome comprises 21 full-length and gapless chromosomal contigs and two partial chromosome contigs each with one telomere. We predicted 31 secondary metabolite clusters, and 38 putative protein effectors, many of which were classified as having an unknown function. Comparison of A. lentis genome features with the recently published reference assembly for closely related A. rabiei show that genome synteny between these species is highly conserved. However, there are several translocations and inversions of genome sequence. The location of secondary metabolite clusters near transposable element and repeat-rich genomic regions was common for A. lentis as has been reported for other fungal plant pathogens.
Neighbor QTL: an interval mapping method for quantitative trait loci underlying plant neighborhood effects
Authors: Sato Yasuhiro , Takeda Kazuya , Nagano Atsushi J 
Published: January 2021

AbstractPhenotypes of sessile organisms, such as plants, rely not only on their own genotypes but also on those of neighboring individuals. Previously, we incorporated such neighbor effects into a single-marker regression using the Ising model of ferromagnetism. However, little is known regarding how neighbor effects should be incorporated in quantitative trait locus (QTL) mapping. In this study, we propose a new method for interval QTL mapping of neighbor effects, designated “neighbor QTL,” the algorithm of which includes: (1) obtaining conditional self-genotype probabilities with recombination fraction between flanking markers; (2) calculating conditional neighbor genotypic identity using the self-genotype probabilities; and (3) estimating additive and dominance deviations for neighbor effects. Our simulation using F2 and backcross lines showed that the power to detect neighbor effects increased as the effective range decreased. The neighbor QTL was applied to insect herbivory on Col × Kas recombinant inbred lines of Arabidopsis thaliana. Consistent with previous results, the pilot experiment detected a self-QTL effect on the herbivory at the GLABRA1 locus. Regarding neighbor QTL effects on herbivory, we observed a weak QTL on the top of chromosome 4, at which a weak self-bolting QTL was also identified. The neighbor QTL method is available as an R package (https://cran.r-project.org/package=rNeighborQTL), providing a novel tool to investigate neighbor effects in QTL studies.
What to do when the parathyroid gland is not found during a transcervical exploration?
Authors:  Planas Georgina , Trujillo-Reyes Juan Carlos , Guarino Mauro , Martínez-Téllez Elisabeth , Cladellas Esther , Pérez Jose Ignacio , Moral Antonio , Belda José 
Published: January 2021

Abstract
The most frequent cause of suboptimal results in a parathyroid adenoma resection is an ectopic location, mainly in the anterior mediastinum. These cases may not always be resected through a traditional cervical access. We present 2 cases of primary hyperparathyroidism who underwent an unsuccessful bilateral cervical exploration due to parathyroid tissue located inside the thymic gland. A video-assisted thoracoscopic surgery thymectomy with intraoperative determination of blood parathormone levels was performed. A 50% reduction of intraoperatory parathyroid hormone blood from the highest basal level at 5 and 10 min after resection was obtained. Final pathological results showed an intra-thymic parathyroid adenoma in the first patient and an intra-thymic focus of parathyroid hyperplasia in the second patient. In conclusion, video-assisted thoracoscopic surgery thymectomy could be the optimal approach to resect ectopic parathyroid adenomas located in the anterior mediastinum.