bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scoping review of health information technology usability methods leveraged in Africa
Authors: Dougherty Kylie , Hobensack Mollie , Bakken Suzanne 
Published: December 2022

AbstractObjectiveThe aim of this study was to explore the state of health information technology (HIT) usability evaluation in Africa.Materials and MethodsWe searched three electronic databases: PubMed, Embase, and Association for Computing Machinery. We categorized the stage of evaluations, the type of interactions assessed, and methods applied using Stead’s System Development Life Cycle (SDLC) and Bennett and Shackel’s usability models.ResultsAnalysis of 73 of 1002 articles that met inclusion criteria reveals that HIT usability evaluations in Africa have increased in recent years and mainly focused on later SDLC stage (stages 4 and 5) evaluations in sub-Saharan Africa. Forty percent of the articles examined system-user-task-environment (type 4) interactions. Most articles used mixed methods to measure usability. Interviews and surveys were often used at each development stage, while other methods, such as quality-adjusted life year analysis, were only found at stage 5. Sixty percent of articles did not include a theoretical model or framework.DiscussionThe use of multistage evaluation and mixed methods approaches to obtain a comprehensive understanding HIT usability is critical to ensure that HIT meets user needs.ConclusionsDeveloping and enhancing usable HIT is critical to promoting equitable health service delivery and high-quality care in Africa. Early-stage evaluations (stages 1 and 2) and interactions (types 0 and 1) should receive special attention to ensure HIT usability prior to implementing HIT in the field.
Thoracic chordoma in a 36-year-old female
Authors: Kassels Austin C , Melamed Joshua , Rogers Austin , Johnstone David 
Published: December 2022

Abstract
Chordomas are rare tumors that occur in the bones of the skull base and spine, affecting 1 in 1 000 000 people per year. Thoracic chordomas comprise just 1% of chordomas. A 36-year-old female underwent a right video-assisted thoracoscopic surgical resection for a cystic mass at the level of T2-3 which was well-circumscribed. Despite efforts to achieve an intact resection, there was tumor spillage due to friability, and it was taken off the bony vertebral body with no margin. The final pathologic diagnosis was chordoma. Thoracic chordomas are rare, slow-growing, recurring neoplasms that require proper preoperative diagnostic imaging and ideally preoperative trocar computed tomography-guided biopsy from a posterior approach if anatomic access is possible. They are prone to dissemination and sarcomatous differentiation. The surgical approaches for reported thoracic chordoma tumors vary due to their rarity and the variation in tumor location and presentation.
Proton exudation mediated by GmVP2 has widespread effects on plant growth, remobilization of soil phosphorus, and the structure of the rhizosphere microbial community
Authors: Xie Baoxing , Chen Qianqian , Lu Xing , Chen Kang , Yang Yuesheng , Tian Jiang , Liang Cuiyue 
Published: December 2022

AbstractIncreased root secretion of H+ is a known strategy in plant adaption to low phosphorus (P) stress as it enhances mobilization of sparingly soluble P sources in the soil. However, our knowledge of the full effects induced by this enhanced acidification of the rhizosphere remains incomplete. In this study we found that P deficiency increased the net H+ flux rate from soybean (Glycine max) roots. Among the eight H+-pyrophosphatase (GmVP) genes in the soybean genome, GmVP2 showed the highest expression level under low P conditions. Transient expression of a GmVP2-GFP construct in tobacco (Nicotiana tabacum) leaves, together with functional characterization of GmVP2 in transgenic soybean hairy roots demonstrated that it encodes a plasma-membrane transporter that mediates H+ exudation. Overexpression of GmVP2 in Arabidopsis resulted in enhanced root H+ exudation, promoted root growth, and improved the utilization of sparingly soluble Ca-P. The improved root growth caused by GmVP2-overexpression might be due to the differential expression of genes related to hormone and flavonoid metabolism, and to root development. Overexpression of GmVP2 also changed the structure of the rhizospheric microbial community, as reflected by a preferential accumulation of Acidobacteria. Overall, our results suggest that GmVP2 mediates H+ exudation in the root response to Pi starvation, and that this influences plant growth, the mobilization sparingly soluble P-sources, and the structure of the microbial community in a coordinated manner.
On the detection of the electromagnetic counterparts from lensed gravitational wave events by binary neutron star mergers
Authors: Ma Hao , Lu Youjun , Guo Xiao , Zhang Siqi , Chu Qingbo 
Published: December 2022

ABSTRACT
Future ground-based gravitational wave (GW) detectors, i.e. Einstein telescope (ET) and Cosmic Explorer (CE), are expected to detect a significant number of lensed binary neutron star (BNS) mergers, which may provide a unique tool to probe cosmology. In this paper, we investigate the detectability of the optical/infrared electromagnetic (EM) counterparts (kilonovae/afterglows) from these lensed BNS mergers by future GW detectors and EM telescopes using simple kilonova, afterglow, and lens models. ET and CE are expected to detect ${\sim}5.32^{+26.1}_{-5.10}$ and $67.3^{+332}_{-64.7}$ lensed BNS mergers per year. We find that the EM counterparts associated with all these mergers will be detectable by an all sky-survey in the H band with the limiting magnitude mlim ≳ 27, while the detectable fraction is ${\lesssim}0.4{{\ \rm per\ cent}}$ in the g/z band if with mlim ≲ 24. Generally, it is more efficient to search the lensed EM counterparts by adopting the infrared bands than the optical/UV bands with the same mlim. Future telescopes like Vera C. Rubin Observatory, China Space Station Telescope, and Euclid can hardly detect the EM counterparts of even one lensed BNS merger. Roman Space Telescope (RST) and James Webb Space Telescope (JWST) have the capability to detect about a few or more such events per year. Moreover, the time delays and separations between the lensed image pairs are typically in the ranges from minutes to months and from 0.1 to 1 arcsec, suggesting that both the GW and EM images of most lensed BNS mergers can be well resolved by not only CE/ET in the time domain but also RST/JWST spatially.
The evolution of circumstellar discs in the galactic centre: an application to the G-clouds
Authors: Owen James E , Lin Douglas N C 
Published: December 2022

ABSTRACT
The Galactic Centre is known to have undergone a recent star formation episode a few Myr ago, which likely produced many T Tauri stars hosting circumstellar discs. It has been suggested that these discs may be the compact and dusty ionized sources identified as ‘G-clouds’. Given the Galactic Centre’s hostile environment, we study the possible evolutionary pathways these discs experience. We compute new external photoevaporation models applicable to discs in the Galactic Centre that account for the subsonic launching of the wind and absorption of UV photons by dust. Using evolutionary disc calculations, we find that photoevaporation’s rapid truncation of the disc causes them to accrete onto the central star rapidly. Ultimately, an accreting circumstellar disc has a lifetime ≲ 1 Myr, which would fail to live long enough to explain the G-clouds. However, we identify a new evolutionary pathway for circumstellar discs in the Galactic Centre. Removal of disc material by photoevaporation prevents the young star from spinning down due to magnetic braking, ultimately causing the rapidly spinning young star to torque the disc into a ‘decretion disc’ state which prevents accretion. At the same time, any planetary companion in the disc will trap dust outside its orbit, shutting down photoevaporation. The disc can survive for up to ∼10 Myr in this state. Encounters with other stars are likely to remove the planet on Myr time-scales, causing photoevaporation to restart, giving rise to a G-cloud signature. A giant planet fraction of $\sim 10{{\ \rm per\ cent}}$ can explain the number of observed G-clouds.
Direct emission of strong radio pulses during magnetar flares
Authors: Thompson Christopher 
Published: December 2022

ABSTRACT
The emission of intense radio pulses by flaring magnetars is investigated. Small-scale current gradients can be imprinted into a strongly magnetized outflow by the same processes that source fireball radiation in the closed magnetosphere. This structure arises from a combination of crustal yielding, internal tearing, and turbulent cascade. We consider the quasi-linear development of weak, small-scale currents as (i) they are stretched out and frozen by relativistic expansion, and then (ii) pass through a shock. In particular, we derive the amplitudes of the ordinary and fast waves that emerge downstream of a relativistically magnetized shock in response to a mode that is frozen into the upstream flow (a frozen Alfvén wave or entropy wave). An upstream mode with comoving wavelength exceeding the skin depth can linearly convert to a secondary mode propagating above the plasma frequency. A simple and accurate treatment of shocks with extreme magnetization is developed, and the formation of internal shocks in the outflow from a bursting, rotating magnetar is outlined. The emission process described here does not require a strong shock or cool e± pairs (in contrast with the electromagnetic maser shock instability). In some cases, a high-frequency wave is reflected back to the observer, but with a minuscule amplitude that makes it subdominant to other emission channels. The dominant secondary electromagnetic mode is superluminal at emission, is subject to weak induced scattering within the outflow, and can reach the observer in the radio band.
Framing School Integration: A Computational Analysis of Newspaper Discourse, 1990–2020
Authors: Diehl David K 
Published: December 2022

ABSTRACT
Research on public opinion finds that most Americans support the racial integration of schools in theory. At the same time, however, they tend to oppose specific policies for achieving it. How is it that the American public comes to conceive of school integration as both an abstract idea and a set of concrete policies? Research has shown that one major source of the public’s understanding of complex social issues like school integration are news media organizations and the choices they make in how they cover them—that is, how they frame social issues. This article examines how school integration was framed in the news between 1990 and 2020. It does so with a dataset of over 13,000 articles from 25 newspapers. The article also examines determinants of those frames, asking what contextual factors shape the production of the news. The results reveal three overarching trends in how school integration was covered in the media over time: depoliticization, historicization, and neoliberalization. These trends varied by the political slant of the newspaper, by location (whether it is in a former Jim Crow state), and by whether the newspaper has a national readership. The author discusses implications for research and policy.
Cellular and molecular responses to ethyl-parathion in undifferentiated SH-SY5Y cells provide neurotoxicity pathway indicators for organophosphorus impacts
Authors: Amar Saroj K , Donohue Keri B , Gust Kurt A 
Published: December 2022

AbstractHigh-fidelity nonanimal screening methods are needed that can rapidly and accurately characterize organophosphorus compound (OP)-induced neurotoxicity. Herein, the efficacy of human neuroblastoma cell line (SH-SY5Y) to provide molecular and cellular responses characteristic of the OP neurotoxicity pathway was investigated in response to the OP-model compound, ethyl-parathion. Undifferentiated SH-SY5Y cells were exposed to ethyl-parathion for 30 min at 0 (control), 0.5, 2.5, 5, 10, and 25 µg/ml. Dose-responsive reductions in cell viability were observed with significant reductions at ≥10 µg/ml. From these results, ethyl-parathion exposures of 0 (control), 5, and 10 µg/ml were selected to examine bioindicators underlying the OP neurotoxicity pathway including: reactive oxygen species (ROS), cell membrane peroxidation, mitochondrial membrane potential (MMP), and apoptosis. Ethyl-parathion elicited highly significant increases in ROS relative to controls (p &lt; .01) at both exposure concentrations, confirmed using N-acetyl cysteine (NAC) as a ROS quencher which alleviated ROS increases. A response characteristic of increased ROS exposure, cell membrane-lipid peroxidation, significantly increased (p &lt; .05) at the highest ethyl-parathion exposure (10 µg/ml). As a likely consequence of membrane-lipid peroxidation, ethyl-parathion-induced reductions in MMP were observed with significant effects at 10 µg/ml, reducing MMP by 58.2%. As a culmination of these cellular-damage indicators, apoptosis progression was investigated by phosphatidylserine translocation where ethyl-parathion-induced dose-responsive, highly significant (p &lt; .01) increases at both 5 and 10 µg/ml. Overall, the mechanistic responses observed in undifferentiated SH-SY5Y cells corresponded with in vivo mammalian results demonstrating potential for this nonanimal model to provide accurate OP neurotoxicology screening.
The evolution of the HIV-1 protease folding stability
Authors: Ferreiro David , Khalil Ruqaiya , Gallego María J , Osorio Nuno S , Arenas Miguel 
Published: December 2022

Abstract
The evolution of structural proteins is generally constrained by the folding stability. However, little is known about the particular capacity of viral proteins to accommodate mutations that can potentially affect the protein stability and, in general, the evolution of the protein stability over time. As an illustrative model case, here, we investigated the evolution of the stability of the human immunodeficiency virus (HIV-1) protease (PR), which is a common HIV-1 drug target, under diverse evolutionary scenarios that include (1) intra-host virus evolution in a cohort of seventy-five patients sampled over time, (2) intra-host virus evolution sampled before and after specific PR-based treatments, and (3) inter-host evolution considering extant and ancestral (reconstructed) PR sequences from diverse HIV-1 subtypes. We also investigated the specific influence of currently known HIV-1 PR resistance mutations on the PR folding stability. We found that the HIV-1 PR stability fluctuated over time within a constant and wide range in any studied evolutionary scenario, accommodating multiple mutations that partially affected the stability while maintaining activity. We did not identify relationships between change of PR stability and diverse clinical parameters such as viral load, CD4+ T-cell counts, and a surrogate of time from infection. Counterintuitively, we predicted that nearly half of the studied HIV-1 PR resistance mutations do not significantly decrease stability, which, together with compensatory mutations, would allow the protein to adapt without requiring dramatic stability changes. We conclude that the HIV-1 PR presents a wide structural plasticity to acquire molecular adaptations without affecting the overall evolution of stability.
Improved Genome Assembly Resource of the Plant Pathogen Fusarium avenaceum
Authors: Gottschalk Christopher , Evans Breyn , Collum Tamara D. 
Published: December 2022

Fusarium avenaceum is a generalist plant pathogen of concern due to its potential to produce mycotoxins on plant products. Previous research efforts have sequenced and assembled genomes of F. avenaceum. However, those works relied on limited next-generation sequencing technologies that resulted in fragmented and incomplete genome assemblies. To address this, we utilized high-depth third-generation long-read sequencing and several different genome assembly software to generate a new, highly contiguous genome of F. avenaceum. Moreover, we conducted a thorough annotation of the genome using a mix of long-read cDNA and short-read RNAseq data. Our genome was more contiguous than the current reference genome Fustri1, matched the estimated genome size and chromosome number, and contained a similar number of annotated genes to other F. avenaceum genome assemblies. Lastly, we conducted a secondary metabolite (SM) cluster analysis that identified 60 gene clusters associated with SM biosynthesis, five more than the reference F. avenaceum genome. In conclusion, our genome and associated annotation information will help advance research on plant-fungal interactions, food safety, and Fusarium spp. diversity. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Draft Genomes of Five Fusarium oxysporum f. sp. niveum Strains Isolated from Infected Watermelon from Texas with Temporal and Spatial Differences
Authors: Thomas Vanessa E. , Isakeit Thomas , Antony-Babu Sanjay 
Published: December 2022

Fusarium oxysporum f. sp. niveum (FON) is a soilborne fungal pathogen of watermelon that has significantly impacted production worldwide. In the United States, watermelon growers can experience 30 to 100% yield loss from this soil pathogen. In this study, we present five draft genome sequences of FON-race 2 isolates collected from four different counties within Texas, spanning more than 23 years. The estimated genome sizes of the de novo assembled genomes were W2 = 49 Mb, COM = 48 Mb, HAR = 49 Mb, STORM = 49 Mb, and PRU = 48 Mb. These sizes were on par with the previously sequenced FON races 0 and 2 from Texas, which ranged from 49 to 54 Mb. Gene prediction program AUGUSTUS predicted 13,554 genes in W2, 13,658 genes in COM, 13,678 genes in HAR, 13,821 genes in STORM, and 13,347 genes in PRU. The information from our five genome drafts contributes to the southeast genomic dataset of FON for comparative genomic analysis. Furthermore, the sequences are beneficial in the understanding of changes within the FON genome over time. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing
Authors: Kakuk Balázs , Dörmő Ákos , Csabai Zsolt , Kemenesi Gábor , Holoubek Jiří , Růžek Daniel , Prazsák István , Dani Virág Éva , Dénes Béla , Torma Gábor , Jakab Ferenc , Tóth Gábor E. , Földes Fanni V. , Zana Brigitta , Lanszki Zsófia , Harangozó Ákos , Fülöp Ádám , Gulyás Gábor , Mizik Máté , Kiss András Attila , Tombácz Dóra , Boldogkői Zsolt 
Published: December 2022

AbstractThe recent Monkeypox outbreak showed the importance of studying the basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. Our direct cDNA and native RNA sequencing data enable the in-depth characterization of the transcriptomic architecture and dynamics of the gene expressions of monkeypox virus; and also the deeper understanding of the changes it causes in the host cells on a transcriptome level.
Hypotrochoidal scaffolds for cartilage regeneration
Authors: van Kampen Kenny A. , Olaret Elena , Stancu Izabela-Cristina , Duarte Campos Daniela F. , Fischer Horst , Mota Carlos , Moroni Lorenzo 
Published: December 2022

AbstractThe main function of articular cartilage is to provide a low friction surface and protect the underlying subchondral bone. The extracellular matrix composition of articular cartilage mainly consists of glycosaminoglycans and collagen type II. Specifically the collagen type II organization has a characteristic organization in three distinct zones; (1) the superficial zone which has collagen fibers oriented parallel to the surface, (2) the intermediate zone where there is no predominant orientation, and (3) the deep zone which shows a high orientation with fibers perpendicular to the underlying bone. Collagen type II fibers in these 3 zones take an arch-like organization that can be mimicked with segments of a hypotrochoidal curve. In this study, a script was developed that allowed the fabrication of scaffolds with a hypotrochoidal design. This design was investigated and compared to a regular 0-90 woodpile design. The results showed that the hypotrochoidal design was successfully fabricated. Micro-CT analyses divided the areas of the scaffold in their distinct zones. In addition, the mechanical analyses revealed that the hypotrochoidal design had a lower component Young’s modulus while the toughness and strain at yield were higher compared to the woodpile design. Fatigue tests showed that the hypotrochoidal design lost more energy per cycle due to the damping effect of the unique microarchitecture. Finite element analyses revealed that the hypotrochoidal design had an improved stress distribution compared to the 0-90 woodpile design due to the lower component stiffness. In addition, data from cell culture under dynamic stimulation demonstrated that the collagen type II deposition was improved in the hypotrochoidal design. Finally, Alcian blue staining revealed that the areas where the stress was higher during the stimulation produced more glycosaminoglycans. Our results highlight a new and simple scaffold design based on hypotrochoidal curves that could be used for cartilage tissue engineering.
Histone H1.0 Couples Cellular Mechanical Behaviors to Chromatin Structure
Authors: Hu Shuaishuai , Chapski Douglas J. , Gehred Natalie , Kimball Todd H. , Gromova Tatiana , Flores Angelina , Rowat Amy C. , Chen Junjie , Packard René R. Sevag , Olszewski Emily , Davis Jennifer , Rau Christoph D. , McKinsey Timothy A. , Garrido Manuel Rosa , Vondriska Thomas M. 
Published: December 2022

SummaryTuning of genome structure and function is accomplished by chromatin binding proteins, which determine the transcriptome and phenotype of the cell. We sought to investigate how communication between extracellular stress and chromatin structure may regulate cellular mechanical behaviors. We demonstrate that the linker histone H1.0, which compacts nucleosomes into higher order chromatin fibers, controls genome organization and cellular stress response. Histone H1.0 has privileged expression in fibroblasts across tissue types in mice and humans, and modulation of its expression is necessary and sufficient to mount a myofibroblast phenotype in these cells. Depletion of histone H1.0 prevents transforming growth factor beta (TGF-β)-induced fibroblast contraction, proliferation and migration in a histone H1 isoform-specific manner via inhibition of a transcriptome comprised of extracellular matrix, cytoskeletal and contractile genes. Histone H1.0 is associated with local regulation of gene expression via mechanisms involving chromatin fiber compaction and reprogramming of histone acetylation, rendering the cell stiffer in response to cytokine stimulation. Knockdown of histone H1.0 prevented locus-specific histone H3 lysine 27 acetylation by TGF-βand decreased levels of both HDAC1 and the chromatin reader BRD4, thereby preventing transcription of a fibrotic gene program. Transient depletion of histone H1.0in vivodecompacts chromatin and prevents fibrosis in cardiac muscle, thereby linking chromatin structure with fibroblast phenotype in response to extracellular stress. Our work identifies an unexpected role of linker histones to orchestrate cellular mechanical behaviors, directly coupling cellular force generation, nuclear organization and gene transcription.Graphical Abstract