bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab initio electronic structure and prospects for the formation of ultracold calcium–alkali-metal-atom molecular ions
Authors: Zrafi Wissem , Ladjimi Hela , Said Halima , Berriche Hamid , Tomza Michał 
Published: May 2020

Abstract
Experiments with cold ion–atom mixtures have recently opened the way for the production and application of ultracold molecular ions. Here, in a comparative study, we theoretically investigate ground and several excited electronic states and prospects for the formation of molecular ions composed of a calcium ion and an alkali-metal atom: CaAlk+ (Alk = Li, Na, K, Rb, Cs). We use a quantum chemistry approach based on non-empirical pseudopotentials, operatorial core-valence correlation, large Gaussian basis sets, and full configuration interaction method for valence electrons. Adiabatic potential energy curves, spectroscopic constants, and transition and permanent electric dipole moments are determined and analyzed for the ground and excited electronic states. We examine the prospects for ion-neutral reactive processes and the production of molecular ions via spontaneous radiative association and laser-induced photoassociation. After that, spontaneous and stimulated blackbody radiation transition rates are calculated and used to obtain radiative lifetimes of vibrational states of the ground and first-excited electronic states. The present results pave the way for the formation and spectroscopy of calcium–alkali-metal-atom molecular ions in modern experiments with cold ion–atom mixtures.
Microwave-assisted synthesis of ZnO nanoflakes: structural, optical and dielectric characterization
Authors: Yalcin Mesut 
Published: May 2020

Abstract
In this study, we produced ZnO nanoflakes (ZnO-Nfs) by using microwave-assisted techniques. The structural properties of ZnO-Nfs were analyzed by x-ray diffraction (XRD) technique, Raman scattering spectroscopy and field-emission scanning microscopy (FESEM). The Crystallite size (D) and lattice constants of ZnO-Nfs were calculated. The optical properties of ZnO-Nfs were investigated by using UV-visible diffuse reflectance spectrum and photoluminescence (PL) spectra. Also, dielectric constants of ZnO-Nfs were calculated as related to the refractive index (n) an extinction coefficient (k).
Solid Tumor Metastases to the Pancreas Diagnosed Using Fine-Needle Aspiration
Authors: Hou Tieying , Stewart John M , Lee Jeffrey H , Gan Qiong 
Published: May 2020

AbstractObjectivesSolid tumor metastases to the pancreas are rare, and only limited literature on the topic is available. In this retrospective study, we reviewed 107 cases of solid tumor metastases to the pancreas diagnosed by fine-needle aspiration (FNA) from 2005 to 2019.MethodsInformation including the patients’ clinical histories, radiologic and pathologic findings, treatments, and follow-up were collected.ResultsThe mean age of the patients was 62.4 years. The mean tumor size was 2.64 cm with even distribution throughout the pancreas (head, neck and body, and tail). The most common primary site was the kidney, followed by the lung, skin, and breast and the gynecologic, gastrointestinal, and genitourinary tracts. The most common tumor type was carcinoma, followed by melanoma and sarcoma. In comparison to patients with nonkidney primary cancers, those with primary renal cell carcinoma had a longer median interval between primary diagnosis and metastasis (8.5 vs 4.0 years; P &lt; .01), less often had metastasis outside the pancreas (38% vs 74%; P &lt; .01), and had a significantly longer 5-year survival rate (65.7% vs 24.8%; P &lt; .01).ConclusionsFNA plays a crucial role in diagnosing metastases to the pancreas. Metastases originating from kidney and nonkidney primary tumors have distinct clinicopathologic features and prognoses.
Racial/Ethnic Disparities in the Relationship of Alcohol-Related Injury and Perceived Driving Under the Influence from Hours of Exposure to High Blood Alcohol Concentration: Data From Four US National Alcohol Surveys (2000–2015)
Authors: Cherpitel Cheryl J , Williams Edwina , Ye Yu , Kerr William C 
Published: May 2020

Abstract

Aims
To analyze racial/ethnic disparities in risk of two alcohol-related events, alcohol-related injury and self-reported perceived driving under the influence (DUI) from hours of exposure to an elevated blood alcohol concentration (BAC).

Methods
Risk curves for the predicted probability of these two outcomes from the number of hours of exposure to a BAC ≥ 0.08 mg% in the past year were analyzed separately for whites, blacks and Hispanics in a merged sample of respondents from four US National Alcohol Surveys (2000–2015).

Results
Hours of exposure to a BAC ≥ 0.08 showed a stronger association with perceived DUI than with alcohol-related injury for all racial/ethnic groups. Greater risk was found for whites than blacks or Hispanics for outcomes at nearly all BAC exposure levels, and most marked at the highest level of exposure. Risk of both outcomes was significant for whites at all exposure levels, but small for alcohol-related injury. Little association was found for alcohol-related injury for blacks or Hispanics. For perceived DUI, risk for blacks was significantly elevated at lower levels of exposure, while risk for Hispanics was significantly elevated beginning at 30 h of exposure.

Conclusions
Findings showed racial/ethnic differences in risk of alcohol-related injury and perceived DUI from hours of exposure to elevated BAC. Risk increased at relatively low levels of exposure to a BAC ≥ 0.08, especially for whites, highlighting the importance of preventive efforts to reduce harmful outcomes for moderate drinkers.
Genetic variation in early fitness traits across European populations of silver birch (Betula pendula)
Authors: Solé-Medina Aida , Heer Katrin , Opgenoorth Lars , Kaldewey Phillip , Danusevicius Darius , Notivol Eduardo , Robledo-Arnuncio Juan J , Ramírez-Valiente José A 
Published: May 2020

AbstractGiven that the ecological niche of tree species is typically narrower for earlier life stages, intraspecific genetic variation at early fitness traits may greatly influence the adaptive response of tree populations to changing environmental conditions. In this study, we evaluated genetic variation in early fitness traits among 12 populations of Betula pendula from a wide latitudinal range in Europe (41–55°N). We first conducted a chamber experiment to test for population differences in germination and the effect of pre-chilling treatment on seed dormancy release. We then established three common gardens spread across the species latitudinal range in order to evaluate levels of quantitative genetic variation and genotype-by-environment interaction at different early life traits. Our results showed significant variation in chamber germination rates among populations (0–60 %), with southern populations exhibiting lower germination. Pre-chilling treatments did not generally improve germination success. Population seedling emergence rates in the field were correlated with chamber germination rates, though being an order of magnitude lower, with an average ranging from 0 to 1.3 % across gardens. Highly significant variation was found in field emergence rates among populations, and between seed-crop years within populations, but not among families within populations. Populations differed in seedling height, diameter, slenderness and budburst date, with significant among-family variation. Population latitude was positively associated with chamber germination rate and with seedling emergence rate in one of the central field sites. Overall, genetic, environmental and demographic factors seem to influence the observed high levels of variation in early fitness traits among B. pendula populations. Our results suggest limited regeneration capacity for the study species under drier conditions, but further field trials with sufficient replication over environments and seed crops will improve our understanding of its vulnerability to climate change.
Spathial: an R package for the evolutionary analysis of biological data
Authors: Gardini Erika , Giorgi Federico M , Decherchi Sergio , Cavalli Andrea 
Published: May 2020

Abstract

Summary
A primary problem in high-throughput genomics experiments is finding the most important genes involved in biological processes (e.g. tumor progression). In this applications note, we introduce spathial, an R package for navigating high-dimensional data spaces. spathial implements the Principal Path algorithm, which is a topological method for locally navigating on the data manifold. The package, together with the core algorithm, provides several high-level functions for interpreting the results. One of the analyses we propose is the extraction of the genes that are mainly involved in the progress from one state to another. We show a possible application in the context of tumor progression using RNA-Seq and single-cell datasets, and we compare our results with two commonly used algorithms, edgeR and monocle3, respectively.

Availability and implementation
The R package spathial is available on the Comprehensive R Archive Network (https://cran.r-project.org/web/packages/spathial/index.html) and on GitHub (https://github.com/erikagardini/spathial). It is distributed under the GNU General Public License (version 3).

Supplementary information
Supplementary data are available at Bioinformatics online.
SVJedi: genotyping structural variations with long reads
Authors: Lecompte Lolita , Peterlongo Pierre , Lavenier Dominique , Lemaitre Claire 
Published: May 2020

Abstract

Motivation
Studies on structural variants (SVs) are expanding rapidly. As a result, and thanks to third generation sequencing technologies, the number of discovered SVs is increasing, especially in the human genome. At the same time, for several applications such as clinical diagnoses, it is important to genotype newly sequenced individuals on well-defined and characterized SVs. Whereas several SV genotypers have been developed for short read data, there is a lack of such dedicated tool to assess whether known SVs are present or not in a new long read sequenced sample, such as the one produced by Pacific Biosciences or Oxford Nanopore Technologies.

Results
We present a novel method to genotype known SVs from long read sequencing data. The method is based on the generation of a set of representative allele sequences that represent the two alleles of each structural variant. Long reads are aligned to these allele sequences. Alignments are then analyzed and filtered out to keep only informative ones, to quantify and estimate the presence of each SV allele and the allele frequencies. We provide an implementation of the method, SVJedi, to genotype SVs with long reads. The tool has been applied to both simulated and real human datasets and achieves high genotyping accuracy. We show that SVJedi obtains better performances than other existing long read genotyping tools and we also demonstrate that SV genotyping is considerably improved with SVJedi compared to other approaches, namely SV discovery and short read SV genotyping approaches.

Availability and implementation
https://github.com/llecompte/SVJedi.git

Supplementary information
Supplementary data are available at Bioinformatics online.
ProteinFishing: a protein complex generator within the ModelX toolsuite
Authors: Cianferoni Damiano , Radusky Leandro G , Head Sarah A , Serrano Luis , Delgado Javier 
Published: May 2020

Abstract

Summary
Accurate 3D modelling of protein–protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes known and/or putative alternative 3D PPI for a given protein complex. The algorithm exploits backbone compatibility of protein fragments to generate mutually exclusive protein interfaces that are quickly evaluated with a knowledge-based statistical force field. Using interleukin-10-R2 co-crystalized with interferon-lambda-3, and a database of X-ray structures containing interleukin-10, this algorithm was able to generate interleukin-10-R2/interleukin-10 structural models in agreement with experimental data.

Availability and implementation
ProteinFishing is a portable command-line tool included in the ModelX toolsuite, written in C++, that makes use of an SQL (tested for MySQL and MariaDB) relational database delivered with a template SQL dump called FishXDB. FishXDB contains the empty tables of ModelX fragments and the data used by the embedded statistical force field. ProteinFishing is compiled for Linux-64bit, MacOS-64bit and Windows-32bit operating systems. This software is a proprietary license and is distributed as an executable with its correspondent database dumps. It can be downloaded publicly at http://modelx.crg.es/. Licenses are freely available for academic users after registration on the website and are available under commercial license for for-profit organizations or companies.

Contact
javier.delgado@crg.eu or luis.serrano@crg.eu

Supplementary information
Supplementary data are available at Bioinformatics online.
Higher Solar Irradiance Is Associated With a Lower Incidence of Coronavirus Disease 2019
Authors: Guasp Mar , Laredo Carlos , Urra Xabier 
Published: May 2020

Abstract
We studied the relationship between the incidence of coronavirus disease 2019 (COVID-19), demographical, and climatological measurements in different regions across the world. Lower solar irradiance and higher population density were independent predictors of greater COVID-19 outbreaks. Further studies on the potential protective effect of sunlight over COVID-19 are warranted.
Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster
Authors: McBroome Jakob , Liang David , Corbett-Detig Russell 
Published: May 2020

AbstractChromosomal inversions are among the primary drivers of genome structure evolution in a wide range of natural populations. Although there is an impressive array of theory and empirical analyses that have identified conditions under which inversions can be positively selected, comparatively little data are available on the fitness impacts of these genome structural rearrangements themselves. Because inversion breakpoints can disrupt functional elements and alter chromatin domains, the precise positioning of an inversion’s breakpoints can strongly affect its fitness. Here, we compared the fine-scale distribution of low-frequency inversion breakpoints with those of high-frequency inversions and inversions that have gone to fixation between Drosophila species. We identified a number of differences among frequency classes that may influence inversion fitness. In particular, breakpoints that are proximal to insulator elements, generate large tandem duplications, and minimize impacts on gene coding spans which are more prevalent in high-frequency and fixed inversions than in rare inversions. The data suggest that natural selection acts to preserve both genes and larger cis-regulatory networks in the occurrence and spread of rearrangements. These factors may act to limit the availability of high-fitness arrangements when suppressed recombination is favorable.
Analytical spontaneous imbibition model for confined nanofractures
Authors: Zeng Fanhui , Zhang Qiang , Guo Jianchun , Zhang Yu , Ren Wenxi , Jiang Qifeng , Xiang Jianhua 
Published: May 2020

Abstract
The capillary spontaneous imbibition length of slick water in confined rectangular cross-sectional nanofractures is investigated in this paper. In the established model, the effective slip length, effective viscosity, wettability and nanofracture size are incorporated into the modified Hagen–Poiseuille equation. The calculated spontaneous imbibition length as a function of time, viscosity, wettability and pore size is qualitatively validated by experimental and previous theoretical Hagen–Poiseuille flow results. Our model calculation results agree well with the published experimental data. The ratio of the effective and bulk water viscosities is higher than one, and increases with an increase in the ratio of the nanofracture width to height and decreasing contact angle. The spontaneous imbibition capacity of confined water is enhanced ∼0.67–1.28 times, as determined by the Hagen–Poiseuille equation without the slip effect for various contact angles and nanofracture dimensions.
The effect of gas accretion on the radial gas metallicity profile of simulated galaxies
Authors: Collacchioni Florencia , Lagos Claudia D P , Mitchell Peter D , Schaye Joop , Wisnioski Emily , Cora Sofía A , Correa Camila A 
Published: May 2020

ABSTRACT
We study the effect of the gas accretion rate ($\dot{M}_{\rm accr}$) on the radial gas metallicity profile (RMP) of galaxies using the eagle cosmological hydrodynamic simulations, focusing on central galaxies of stellar mass M⋆ ≳ 109 M⊙ at z ≤ 1. We find clear relations between $\dot{M}_{\rm accr}$ and the slope of the RMP (measured within an effective radius), where higher $\dot{M}_{\rm accr}$ are associated with more negative slopes. The slope of the RMPs depends more strongly on $\dot{M}_{\rm accr}$ than on stellar mass, star formation rate (SFR), or gas fraction, suggesting $\dot{M}_{\rm accr}$ to be a more fundamental driver of the RMP slope of galaxies. We find that eliminating the dependence on stellar mass is essential for pinning down the properties that shape the slope of the RMP. Although $\dot{M}_{\rm accr}$ is the main property modulating the slope of the RMP, we find that it causes other correlations that are more easily testable observationally: At fixed stellar mass, galaxies with more negative RMP slopes tend to have higher gas fractions and SFRs, while galaxies with lower gas fractions and SFRs tend to have flatter metallicity profiles within an effective radius.
webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules
Authors: Felline Angelo , Seeber Michele , Fanelli Francesca 
Published: May 2020

AbstractA mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode Analysis (ENM-NMA)-based strategy (i.e. PSN-ENM) was developed to investigate structural communication in bio-macromolecules. Protein Structure Graphs (PSGs) are computed on a single structure, whereas information on system dynamics is supplied by ENM-NMA. The approach was implemented in a webserver (webPSN), which was significantly updated herein. The webserver now handles both proteins and nucleic acids and relies on an internal upgradable database of network parameters for ions and small molecules in all PDB structures. Apart from the radical restyle of the server and some changes in the calculation setup, other major novelties concern the possibility to: a) compute the differences in nodes, links, and communication pathways between two structures (i.e. network difference) and b) infer links, hubs, communities, and metapaths from consensus networks computed on a number of structures. These new features are useful to identify commonalties and differences between two different functional states of the same system or structural-communication signatures in homologous or analogous systems. The output analysis relies on 3D-representations, interactive tables and graphs, also available for download. Speed and accuracy make this server suitable to comparatively investigate structural communication in large sets of bio-macromolecular systems. URL: http://webpsn.hpc.unimore.it.
Regulatory sharing between estrogen receptor α bound enhancers
Authors: Carleton Julia B , Ginley-Hidinger Matthew , Berrett Kristofer C , Layer Ryan M , Quinlan Aaron R , Gertz Jason 
Published: May 2020

AbstractThe human genome encodes an order of magnitude more gene expression enhancers than promoters, suggesting that most genes are regulated by the combined action of multiple enhancers. We have previously shown that neighboring estrogen-responsive enhancers exhibit complex synergistic contributions to the production of an estrogenic transcriptional response. Here we sought to determine the molecular underpinnings of this enhancer cooperativity. We generated genetic deletions of four estrogen receptor α (ER) bound enhancers that regulate two genes and found that enhancers containing full estrogen response element (ERE) motifs control ER binding at neighboring sites, while enhancers with pre-existing histone acetylation/accessibility confer a permissible chromatin environment to the neighboring enhancers. Genome engineering revealed that two enhancers with half EREs could not compensate for the lack of a full ERE site within the cluster. In contrast, two enhancers with full EREs produced a transcriptional response greater than the wild-type locus. By swapping genomic sequences, we found that the genomic location of a full ERE strongly influences enhancer activity. Our results lead to a model in which a full ERE is required for ER recruitment, but the presence of a pre-existing permissible chromatin environment can also be needed for estrogen-driven gene regulation to occur.
Additional Assessment of Developed Occipital Sinus Using Intraoperative Indocyanine Green Videoangiography for a Safe Foramen Magnum Decompression—Technical Case Report
Authors: Omoto Koji , Takeshima Yasuhiro , Nishimura Fumihiko , Nakagawa Ichiro , Motoyama Yasushi , Park Young-Su , Nakase Hiroyuki 
Published: May 2020

Abstract

BACKGROUND AND IMPORTANCE
Although foramen magnum decompression (FMD) with expansive duraplasty is a popular procedure for treating chiari malformation (CM), the common Y-shaped dural incision can lead to a life-threatening cerebral venous circulation disturbance in patients with a developed occipital sinus. Here, we describe the effectiveness of intraoperative indocyanine green video angiography (ICG-VA) for a CM type 1 (CM1) patient with a highly developed unilateral occipital sinus.

CLINICAL PRESENTATION
A 40-yr-old woman presented with sensory disturbance on the left side of the body. Magnetic resonance imaging (MRI) revealed cerebellar tonsil herniation into the foramen magnum with cervical syringomyelia, and computed tomography additionally revealed skull anomalies: fontanel closure insufficiencies, cranial dysraphism, thin cranial bone, and dentition abnormalities. We diagnosed as symptomatic CM1 with syringomyelia associated with cleidocranial dysplasia, which is a dominantly inherited autosomal bone disease. Cerebral angiography revealed a developed right occipital sinus and hypoplasia of the bilateral transverse sinus. We performed FMD, paying special attention to the developed occipital sinus using ICG-VA to ensure a safe duraplasty. The angiography clearly highlighted a right-sided occipital sinus with a high contrast ratio, and no left-sided occipital sinus was visible. After a dural incision in a unilateral curvilinear fashion was safely completed, expansive duraplasty was performed. The sensory disorders experienced by the patient disappeared postoperatively. Postoperative MRI revealed elevation of the cerebellar tonsil and decreasing of the syringomyelia.

CONCLUSION
Additional assessment using intraoperative ICG-VA provides useful information for a safe FMD, particularly in patients with complicated cerebral venous circulation anomalies.