bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of constant high-voltage electric field on wheat seed germination
Authors: Krivov S A , Lazukin A V , Serdyukov Y A , Gundareva S V , Romanov G A 
Published: July 2020

Abstract
In this work an effect of the 10-min pre-sowing treatment by the constant electric field with the 3 kV cm−1 electric field strength on the soft spring wheat seed germination is studied at various positions of the seeds in a plane-parallel electrode system. The effects of the electric field direction and contact conditions of the seeds with a plane aluminum electrode (no contact, when the seeds lie on the isolating plate; contact with the positive or negative high-voltage or grounded electrode) are compared. The treatment response is estimated by the morphological characteristics of 3-day seedlings—germination, the shoot length and the length of individual roots. At all modes, the treatment does not change seed germination. At each considered variant of seed location, the electric field effect did not reduce the average length of the root system and the shoot length below the ones at the control variant. The significant increase of morphological characteristics is achieved at the seed contact with the high voltage electrode.
Development of a novel CdTe/ZnS/ZnTe heterojunction thin-film solar cells: a numerical approach
Authors: Ahmed Sheikh Rashel Al , Ferdous Jannatul , Mian Md Suruz 
Published: July 2020

Abstract
A novel heterojunction structure of cadmium telluride (CdTe)/zinc sulfide (ZnS)/zinc telluride (ZnTe) for thin-film solar cell (TFSC) applications was investigated numerically by Solar Cell Capacitance Simulator in One Dimension (SCAPS-1D). We made a comparative study on the performance of single-layer of Si/CdTe and multi-layers of Si/CdTe/ZnS/ZnTe structures. The optimum values for the thicknesses of CdTe absorber, ZnS, and ZnTe layers in the cell were found to be 2500, 40, and 80 nm, respectively. In the present work, the conversion efficiency (η) of 21.38% was obtained with open-circuit voltage, V
oc = 1.01 V, short-circuit current density, J
sc = 29.32 mA cm−2, and fill-factor, FF = 72.06% in case of multi-layer structure with antireflection coatings (ARCs). The simulation results suggest that the ARC layers presented in this study would be effective to fabricate the high-efficiency solar cells.
Literature and Other White-Man Tricks: Borges and Jarmusch Imagine the Frontier
Authors: Montero Gonzalo 
Published: July 2020

AbstractIn this article, I analyze the representation of the Frontier in the short story ‘El Sur’ by the Argentine Jorge Luis Borges and the movie Dead Man by American director Jim Jarmusch. Going beyond explicit plot similarities, I argue that Jarmusch’s movie carries out an implicit form of adaptation of Borges’s literary text. Both works not only narrate the violent encounter of urban subjects with an unknown and threatening space, but also underscore how the ‘civilized’ subjectivity experiences a crisis that challenges foundational cultural assumptions. Due to its relevance in the process of nation formation, the Frontier served as a source for symbolic discourses, literary representations, and cultural imaginaries. In the case of Argentina and the United States, specific artistic genres fictionalized the life on the Frontier. Stylistically, both Borges and Jarmusch use tropes and narrative devices from these seemingly outdated genres—gauchesca literature and Western movies—but the use of these devices is highly experimental and installs a much more complex depiction of the symbolic space of the Frontier, thus challenging hegemonic accounts of processes of territorial expansion and racial superiority.
Integrated omics analysis reveals the alteration of gut microbe–metabolites in obese adults
Authors: Li Rong , Huang Xue , Liang Xiao , Su Min , Lai Keng Po , Chen Jian 
Published: July 2020

Abstract
Obesity, a risk to health, is a global problem in modern society. The prevalence of obesity was approximately 13% among world’s adult population. Recently, several reports suggested that the interference of gut microbiota composition and function is associated with metabolic disorders, including obesity. Gut microbiota produce a board range of metabolites involved in energy and glucose homeostasis, leading to the alteration in host metabolism. However, systematic evaluation of the relationship between gut microbiota, gut metabolite and host metabolite profiles in obese adults is still lacking. In this study, we used comparative metagenomics and metabolomics analysis to determine the gut microbiota and gut–host metabolite profiles in six normal and obese adults of Chinese origin, respectively. Following the functional and pathway analysis, we aimed to understand the possible impact of gut microbiota on the host metabolites via the change in gut metabolites. The result showed that the change in gut microbiota may result in the modulation of gut metabolites contributing to glycolysis, tricarboxylic acid cycle and homolactic fermentation. Furthermore, integrated metabolomic analysis demonstrated a possible positive correlation of dysregulated metabolites in the gut and host, including l-phenylalanine, l-tyrosine, uric acid, kynurenic acid, cholesterol sulfate and glucosamine, which were reported to contribute to metabolic disorders such as obesity and diabetes. The findings of this study provide the possible association between gut microbiota–metabolites and host metabolism in obese adults. The identified metabolite changes could serve as biomarkers for the evaluation of obesity and metabolic disorders.
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
Authors: Piro Vitor C , Dadi Temesgen H , Seiler Enrico , Reinert Knut , Renard Bernhard Y 
Published: July 2020

Abstract

Motivation
The exponential growth of assembled genome sequences greatly benefits metagenomics studies. However, currently available methods struggle to manage the increasing amount of sequences and their frequent updates. Indexing the current RefSeq can take days and hundreds of GB of memory on large servers. Few methods address these issues thus far, and even though many can theoretically handle large amounts of references, time/memory requirements are prohibitive in practice. As a result, many studies that require sequence classification use often outdated and almost never truly up-to-date indices.

Results
Motivated by those limitations, we created ganon, a k-mer-based read classification tool that uses Interleaved Bloom Filters in conjunction with a taxonomic clustering and a k-mer counting/filtering scheme. Ganon provides an efficient method for indexing references, keeping them updated. It requires &lt;55 min to index the complete RefSeq of bacteria, archaea, fungi and viruses. The tool can further keep these indices up-to-date in a fraction of the time necessary to create them. Ganon makes it possible to query against very large reference sets and therefore it classifies significantly more reads and identifies more species than similar methods. When classifying a high-complexity CAMI challenge dataset against complete genomes from RefSeq, ganon shows strongly increased precision with equal or better sensitivity compared with state-of-the-art tools. With the same dataset against the complete RefSeq, ganon improved the F1-score by 65% at the genus level. It supports taxonomy- and assembly-level classification, multiple indices and hierarchical classification.

Availability and implementation
The software is open-source and available at: https://gitlab.com/rki_bioinformatics/ganon.

Supplementary information
Supplementary data are available at Bioinformatics online.
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens
Authors: Hasegawa Takanori , Hayashi Shuto , Shimizu Eigo , Mizuno Shinichi , Niida Atsushi , Yamaguchi Rui , Miyano Satoru , Nakagawa Hidewaki , Imoto Seiya 
Published: July 2020

Abstract

Summary
It is known that some mutant peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T cells on the surface of a tumor cell. These peptides are termed neoantigen, and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package termed Neoantimon that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions and structural variants. Beyond the existing applications, Neoantimon is capable of attaching and reflecting several additional information, e.g. wild-type binding capability, allele specific RNA expression levels, single nucleotide polymorphism information and combinations of mutations to filter out infeasible peptides as neoantigen.

Availability and implementation
The R package is available at http://github/hase62/Neoantimon.
Right Posterior Insula and Putamen Volume Mediate the Effect of Oxytocin Receptor Polygenic Risk for Autism Spectrum Disorders on Reward Dependence in Healthy Adults
Authors: Wang Junping , Zhang Peng , Li Wei , Wen Qin , Liu Feng , Xu Jiayuan , Xu Qiang , Zhu Dan , Ye Zhaoxiang , Yu Chunshui 
Published: July 2020

Abstract
Much evidence indicates the influence of the oxytocin receptor (OXTR) gene on autism spectrum disorders (ASDs), a set of disorders characterized by a range of deficits in prosocial behaviors, which are closely related to the personality trait of reward dependence (RD). However, we do not know the effect of the OXTR polygenic risk score for ASDs (OXTR-PRSASDs) on RD and its underlying neuroanatomical substrate. Here, we aimed to investigate associations among the OXTR-PRSASDs, gray matter volume (GMV), and RD in two independent datasets of healthy young adults (n = 450 and 540). We found that the individuals with higher OXTR-PRSASDs had lower RD and significantly smaller GMV in the right posterior insula and putamen. The GMV of this region showed a positive correlation with RD and a mediation effect on the association between OXTR-PRSASDs and RD. Moreover, the correlation map between OXTR-PRSASDs and GMV showed spatial correlation with OXTR gene expression. All results were highly consistent between the two datasets. These findings highlight a possible neural pathway by which the common variants in the OXTR gene associated with ASDs may jointly impact the GMV of the right posterior insula and putamen and further affect the personality trait of RD.
Spatiotemporal Characteristics of the COVID-19 Epidemic in the United States
Authors: Wang Yun , Liu Ying , Struthers James , Lian Min 
Published: July 2020

Abstract

Background
A range of near-real-time online/mobile mapping dashboards and applications have been used to track the coronavirus disease 2019 (COVID-19) pandemic worldwide; however, small area-based spatiotemporal patterns of COVID-19 in the United States remain unknown.

Methods
We obtained county-based counts of COVID-19 cases confirmed in the United States from 22 January to 13 May 2020 (N = 1 386 050). We characterized the dynamics of the COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis.

Results
Along with the national plateau reached in early April, COVID-19 incidence significantly decreased in the Northeast (estimated weekly percentage change [EWPC]: −16.6%) but continued increasing in the Midwest, South, and West (EWPCs: 13.2%, 5.6%, and 5.7%, respectively). Higher risks of clustering and incidence of COVID-19 were consistently observed in metropolitan versus rural counties, counties closest to core airports, the most populous counties, and counties with the highest proportion of racial/ethnic minorities. However, geographic differences in incidence have shrunk since early April, driven by a significant decrease in the incidence in these counties (EWPC range: −2.0%, −4.2%) and a consistent increase in other areas (EWPC range: 1.5–20.3%).

Conclusions
To substantially decrease the nationwide incidence of COVID-19, strict social-distancing measures should be continuously implemented, especially in geographic areas with increasing risks, including rural areas. Spatiotemporal characteristics and trends of COVID-19 should be considered in decision making on the timeline of re-opening for states and localities.
The Role of Remdesivir in South Africa: Preventing COVID-19 Deaths Through Increasing Intensive Care Unit Capacity
Authors: Nichols Brooke E , Jamieson Lise , Zhang Sabrina R C , Rao Gabriella A , Silal Sheetal , Pulliam Juliet R C , Sanne Ian , Meyer-Rath Gesine 
Published: July 2020

Abstract
Countries such as South Africa have limited intensive care unit (ICU) capacity to handle the expected number of patients with COVID-19 requiring ICU care. Remdesivir can prevent deaths in countries such as South Africa by decreasing the number of days people spend in ICU, therefore freeing up ICU bed capacity.
On providing systematized access to consolidated principles, guidelines and patterns for usable security research and development†
Authors: Gorski Peter L , von Zezschwitz Emanuel , Lo Iacono Luigi , Smith Matthew 
Published: July 2020

Abstract
We present a systematization of usable security principles, guidelines and patterns to facilitate the transfer of existing knowledge to researchers and practitioners. Based on a literature review, we extracted 23 principles, 11 guidelines and 47 patterns for usable security and identified their interconnection. The results indicate that current research tends to focus on only a subset of important principles. The fact that some principles are not yet addressed by any design patterns suggests that further work on refining these patterns is needed. We developed an online repository, which stores the harmonized principles, guidelines and patterns. The tool enables users to search for relevant guidance and explore it in an interactive and programmatic manner. We argue that both the insights presented in this article and the web-based repository will be highly valuable for students to get a good overview, practitioners to implement usable security and researchers to identify areas of future research.
Evidence against a geographic gradient of Alzheimer's disease and the hygiene hypothesis
Authors: Lathe J Constance , Lathe Richard 
Published: July 2020

Abstract
A significant positive correlation was previously reported (Fox et al.Evol Med Public Health 2013; 2013:173–86) between hygiene and the global prevalence of Alzheimer's disease (AD) based on World Health Organization (2004) data. These data have now been updated by the Global Burden of Disease (GBD; 2016) dataset that takes into account under-registration and other potential confounds. We therefore addressed whether the association between hygiene and AD is maintained in light of these more recent data. We report a significant positive correlation between GBD AD prevalence rates and parasite burden, and a negative association with hygiene. These newer data argue that hygiene is not a risk factor for AD, and instead suggest that parasite burden may increase AD risk.
Lay summary: It was previously hypothesized that hygeine might be a risk factor for the development of Alzheimer disease (AD), based on a global gradient of dementia. Newer data that correct global AD rates for under-reporting now demonstrate that parasite burden is positively correlated with AD.
Viewing Cortical Collecting Duct Function Through Phenotype-guided Single-Tubule Proteomics
Authors: Himmerkus Nina , Svendsen Samuel L , Quintanova Catarina , Bleich Markus , Von Schwerdtner Otto , Benzing Thomas , Welling Paul A , Leipziger Jens , Rinschen Markus M 
Published: July 2020

AbstractThe revolution of the omics technologies has enabled profiling of the molecules of any sample. However, the heterogeneity of the kidney with highly specialized nephron segments like the cortical collecting duct (CCD) poses a challenge regarding integration of omics data and functional analysis. We examined function and proteome from the same single CCDs of C57Bl6 mice by investigating them in a double-barreled perfusion system before targeted mass spectrometry. Transepithelial voltage (Vte), transepithelial resistance, as well as amiloride-sensitive voltage (ΔVteamil) were recorded. CCDs were of 400–600 µm of length, showed lumen negative Vte between −8.5 and −32.5 mV and an equivalent short circuit current I’sc between 54 and 192 µA/cm2. On a single-tubule proteome level, intercalated cell (IC) markers strongly correlated with other intercalated cell markers and negatively with principal cell markers. Integration of proteome data with phenotype data revealed that tubular length correlated with actin and Na+-K+-ATPase expression. ΔVte(amil) reflected the expression level of the β-subunit of the epithelial sodium channel. Intriguingly, ΔVte(amil) correlated inversely with the water channel AQP2 and the negative regulator protein NEDD4L (NEDD4-2). In pendrin knockout (KO) mice, the CCD proteome was accompanied by strong downregulation of other IC markers like CLCNKB, BSND (Barttin), and VAA (vH+-ATPase), a configuration that may contribute to the salt-losing phenotype of Pendred syndrome. Proteins normally coexpressed with pendrin were decreased in pendrin KO CCDs. In conclusion, we show that functional proteomics on a single nephron segment scale allows function–proteome correlations, and may potentially help predicting function from omics data.
The Relationship Between Intermuscular Fat and Physical Performance Is Moderated by Muscle Area in Older Adults
Authors: Farsijani Samaneh , Santanasto Adam J , Miljkovic Iva , Boudreau Robert M , Goodpaster Bret H , Kritchevsky Stephen B , Newman Anne B 
Published: July 2020

Abstract

Background
Age-related deposition of fat in skeletal muscle is associated with functional limitations. Skeletal muscle fat may be present in people with preserved muscle mass or accompanied by muscle wasting. However, it is not clear if the association between muscle fat deposition and physical performance is moderated by muscle mass.

Objective
To determine whether the association between midthigh intermuscular fat and physical performance is moderated by muscle area.

Methods
We performed a cross-sectional analysis of the Health, Aging, and, Body Composition (ABC) study data collected in 2002–2003 (n = 1897, women: 52.2%). Midthigh muscle cross-sectional area (by computed tomography) and physical performance measures were compared across quartiles of intermuscular fat absolute area. Moderation analysis was performed to determine the conditional effect of intermuscular fat on physical performance as a function of muscle area. Conditional effects were evaluated at three levels of muscle area (mean and ± 1 standard deviation [SD]; 213.2 ± 53.2 cm2).

Results
Simple slope analysis showed that the negative association between intermuscular fat area (cm2) and leg strength (N·m) was of greater magnitude (beta coefficient [b], 95% confidence interval [CI] = −0.288 [−0.427, −0.148]) in participants with greater muscle area (ie, 1 SD above the mean) compared to those with lower muscle area (ie, at mean [b = −0.12 {−0.248, 0.008}] or 1 SD below the mean [b = 0.048 {−0.122, 0.217}]). Similarly, the negative association of intermuscular fat with 400-m walk speed (m/s) and chair stand (seconds) was greater in those with higher muscle areas (p &lt; .001) compared to those with lower muscle areas.

Conclusions
The association between higher intermuscular fat area and impaired physical function in aging is moderated by muscle area.
A rock-physics model to determine the pore microstructure of cracked porous rocks
Authors: Zhang Lin , Ba Jing , Carcione José M 
Published: July 2020

SUMMARY
Determining rock microstructure remains challenging, since a proper rock-physics model is needed to establish the relation between pore microstructure and elastic and transport properties. We present a model to estimate pore microstructure based on porosity, ultrasonic velocities and permeability, assuming that the microstructure consists on randomly oriented stiff equant pores and penny-shaped cracks. The stiff pore and crack porosity varying with differential pressure is estimated from the measured total porosity on the basis of a dual porosity model. The aspect ratio of pores and cracks and the crack density as a function of differential pressure are obtained from dry-rock P- and S-wave velocities, by using a differential effective medium model. These results are used to invert the pore radius from the matrix permeability by using a circular pore model. Above a crack density of 0.13, the crack radius can be estimated from permeability, and below that threshold, the radius is estimated from P-wave velocities, taking into account the wave dispersion induced by local fluid flow between pores and cracks. The approach is applied to experimental data for dry and saturated Fontainebleau sandstone and Chelmsford Granite.
Distribution and diversity of glycocin biosynthesis gene clusters beyond Firmicutes
Authors: Singh Vaidhvi , Rao Alka 
Published: July 2020

Abstract
Glycocins are the ribosomally synthesized glycosylated bacteriocins discovered and characterized in Firmicutes, only. These peptides have antimicrobial activity against several pathogenic bacteria, including Streptococcus pyogenes , methicillin-resistant Staphylococcus aureus and food-spoilage bacteria Listeria monocytogenes. Glycocins exhibit immunostimulatory properties and make a promising source of new antibiotics and food preservatives akin to Nisin. Biochemical studies of Sublancin, Glycocin F, Pallidocin and ASM1 prove that the nested disulfide-bonds are essential for their bioactivities. Using in silico approach of genome mining coupled with manual curation, here we identify 220 new putative glycocin biosynthesis gene clusters (PGBCs) spread across 153 bacterial species belonging to seven different bacterial phyla. Based on gene composition, we have grouped these PGBCs into five distinct conserved cluster Types I–V. All experimentally identified glycocins belong to Type I PGBCs. From protein sequence based phylograms, tanglegrams, global similarity heat-maps and cumulative mutual information analysis, it appears that glycocins may have originated from closely related bacteriocins, whereas recruitment of cognate glycosyltransferases (GTs) might be an independent event. Analysis further suggests that GTs may have coevolved with glycocins in cluster-specific manner to define distinctive donor specificities of GTs or to contribute to glycocin diversity across these clusters. We further identify 162 hitherto unreported PGBCs wherein the corresponding product glycocins have three or less than three cysteines. Secondary structure predictions suggest that these putative glycocins may not form di-nested disulfide-bonds. Therefore, production of such glycocins in heterologous host Escherichia coli is feasible and may provide novel antimicrobial spectrum and or mechanism of action for varied applications.