bluuebunny/crossref_metadata_2025_split huggingface dataset:
FlexTaxD: flexible modification of taxonomy databases for improved sequence classification
Authors: Sundell David , Öhrman Caroline , Svensson Daniel , Karlsson Edvin , Brindefalk Björn , Myrtennäs Kerstin , Ahlinder Jon , Antwerpen Markus H , Walter Mathias C , Forsman Mats , Stenberg Per , Sjödin Andreas 
Published: September 2021

Abstract

Summary
The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.

Availability and implementation
Source code is freely available at https://github.com/FOI-Bioinformatics/flextaxd and installable through Bioconda.
Single-cell RNA sequencing analysis of mouse follicular somatic cells
Authors: Li Sen , Chen Lei-Ning , Zhu Hai-Jing , Feng Xie , Xie Feng-Yun , Luo Shi-Ming , Ou Xiang-Hong , Ma Jun-Yu 
Published: September 2021

Abstract
Within the development of ovarian follicle, in addition to cell proliferation and differentiation, sophisticated cell–cell cross talks are established among follicular somatic cells such as granulosa cells (GCs) and theca cells. To systematically reveal the cell differentiation and signal transductions in follicular somatic cells, we collected the mouse follicular somatic cells from secondary to ovulatory stage, and analyzed the single cell transcriptomes. Having data filtered and screened, we found 6883 high variable genes in 4888 single cells. Then follicular somatic cells were clustered into 26 cell clusters, including 18 GC clusters, 4 theca endocrine cell (TEC) clusters, and 4 other somatic cell clusters, which include immune cells and Acta2 positive theca externa cells. From our data, we found there was metabolic reprogramming happened during GC differentiation. We also found both Cyp19a1 and Cyp11a1 could be expressed in TECs. We analyzed the expression patterns of genes associated with cell–cell interactions such as steroid hormone receptor genes, insulin signaling genes, and cytokine/transformation growth factor beta associated genes in all cell clusters. Lastly, we clustered the highly variable genes into 300 gene clusters, which could be used to search new genes involved in follicle development. These transcriptomes of follicular somatic cells provide us potential clues to reveal how mammals regulating follicle development and could help us find targets to improve oocyte quality for women with low fertility.
Changes in histology, protein expression, and autophagy in dairy goat testes during nonbreeding season
Authors: Xi Huaming , Ren Fa , Li Yu , Du Yeqing , Wang Liqiang , Hu Jianhong 
Published: September 2021

Abstract
Seasonal reproduction contributes to increased chances of offspring survival in some animals. Dairy goats are seasonal breeding mammals. In this study, adult male Guanzhong dairy goats (10–12 months old) were used. Testis size, semen quality, hormone level, apoptosis of germ cells, and autophagy of Sertoli cells were analyzed in dairy goats during the breeding (October) and nonbreeding (April) seasons. We found that, during the nonbreeding season for dairy goats, semen quality, follicle-stimulating hormone (FSH) levels, and testosterone levels were reduced, and the number of apoptotic germ cells increased. The proliferation with decrease activity of germ cells in dairy goat during the nonbreeding season was significantly affected. However, the testis size did not change seasonally. Interestingly, Sertoli cell autophagy was more active during the nonbreeding season. The expression levels of FSH receptor, wilms tumor 1, androgen binding protein, glial cell derived neurotrophic factor, and stem cell factor decreased in dairy goats during the nonbreeding season. In summary, our results indicate that spermatogenesis in dairy goats during the nonbreeding season was not completely arrested. In addition, germ cell apoptosis and the morphology of Sertoli cells considerably changed in dairy goats during the nonbreeding season. Sertoli cell autophagy is involved in the seasonal regulation of spermatogenesis in dairy goats. These findings provide key insights into the fertility and spermatogenesis of seasonal breeding animals.
Bioelectrical signal associated with sweet taste transduction in humans is a hyperpolarizing potential on the lingual epithelium
Authors: Fukuda Satoshi , Murabe Naoyuki , Mizuta Haruno , Yamamoto Takashi , Nagai Takatoshi 
Published: September 2021

Abstract
The lingual surface potential (LSP), which hyperpolarizes in response to salt and bitter stimuli, is thought to be a bioelectrical signal associated with taste transduction in humans. In contrast, a recent study reported sweet and sour stimuli to evoke a depolarization of the LSP. We questioned the origin of such a depolarization because liquid junction potentials (JPs), which arise at the interfaces of recording electrode and taste solutions, are neglected in the report. We recorded the LSPs to sucrose and NaCl solutions on the human tongue using an Ag/AgCl electrode. To estimate JPs generated by each taste solution, we made an agar model to simulate the human tongue. The lingual surface was rinsed with a 10 mM NaCl solution that mimics the sodium content of the lingual fluid. In the human tongue, sucrose dissolved in distilled water evoked a depolarizing LSP that could be attributed to JPs, resulting from the change in electrolyte concentration of the taste solution. Sucrose dissolved in 10 mM NaCl solution evoked a hyperpolarizing LSP which became more negative in a concentration-dependent manner (300–1500 mM). Lactisole (3.75 mM), an inhibitor of sweet taste, significantly reduced the LSPs and decreased perceived intensity of sweetness by human subjects. The negative JPs generated by 100 mM NaCl in the agar model were not different from the LSPs to 100 mM NaCl. When the electrolyte environment on the lingual surface is controlled for JPs, the bioelectrical signal associated with sweet taste transduction is a hyperpolarizing potential.
Palliative Care in Inflammatory Bowel Disease: A New Partnership
Authors: Rivet Emily B , Bohl Jaime L , Al Yassin Sarmed , Bickston Stephen J 
Published: September 2021

Abstract

Background
Palliative care (PC) is being increasingly recognized for benefitting patients with a wide spectrum of chronic serious medical conditions.

Methods
Care models and principles of PC for patient with inflammatory bowel disease were explored.

Results
The use of a structured and systematic approach for emotionally laden conversations and the “Total Pain” paradigm are examples of PC expertise that can be applied through either primary or consultative PC models.

Conclusions
PC should be considered in clinical practice and as a topic for further scholarly investigation to further define its role and benefits.
Coevolution between Himalayan cuckoos and 2 sympatric Pycnonotidae hosts
Authors: Yang Canchao , Li Qihong , Su Tongping , Møller Anders Pape , Liang Wei 
Published: September 2021

Abstract
Selection due to cuckoo parasitism is responsible for the evolution of anti-parasitism defenses in hosts. Different host species breeding sympatrically with a single parasitic cuckoo may evolve different strategies to reduce the risk of counter cuckoo parasitism, resulting in different interactions between cuckoos and hosts in areas of sympatry. Here, we studied the coevolutionary interactions between Himalayan cuckoos Cuculus saturatus and 2 sympatric and closely related potential hosts belonging to the family Pycnonotidae, the brown-breasted bulbul Pycnonotus xanthorrhous and the collared finchbill Spizixos semitorques. We investigated parasitism rates and nest-site selection (nest height, nest cover, human disturbance, perch height, forest distance, and degree of concealment) related to parasitism risk, nest defense against a cuckoo dummy, and egg rejection against cuckoo model eggs. Bulbuls used specific nest sites that were further away from forests than those of finchbills, and they behaved more aggressively toward cuckoos than finchbills. In contrast, bulbuls possessed moderate egg rejection ability, whereas the finchbill rejected 100% of cuckoo model eggs. We suggest that selection of a nest site away from forests by the bulbul explains the absence of parasitism by Himalayan cuckoos. We suggest that these interspecific differences in nest-site selection and nest defense indicate alternative responses to selection due to cuckoos.
An RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans reveals the involvement of unexpected processes
Authors: Maheshwari Richa , Rahman Mohammad M , Joseph-Strauss Daphna , Cohen-Fix Orna 
Published: September 2021

Abstract
Aberration in nuclear morphology is one of the hallmarks of cellular transformation. However, the processes that, when mis-regulated, result aberrant nuclear morphology are poorly understood. In this study, we carried out a systematic, high-throughput RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans embryos. The screen employed over 1700 RNAi constructs against genes required for embryonic viability. Nuclei of early embryos are typically spherical, and their NPCs are evenly distributed. The screen was performed on early embryos expressing a fluorescently tagged component of the nuclear pore complex (NPC), allowing visualization of nuclear shape as well as the distribution of NPCs around the nuclear envelope. Our screen uncovered 182 genes whose downregulation resulted in one or more abnormal nuclear phenotypes, including multiple nuclei, micronuclei, abnormal nuclear shape, anaphase bridges, and abnormal NPC distribution. Many of these genes fall into common functional groups, including some that were not previously known to affect nuclear morphology, such as genes involved in mitochondrial function, the vacuolar ATPase, and the CCT chaperonin complex. The results of this screen add to our growing knowledge of processes that affect nuclear morphology and that may be altered in cancer cells that exhibit abnormal nuclear shape.
‘How come they don’t talk about it in school?’ Identifying adolescent barriers to PrEP use
Authors: Gailloud Leslie , Gonzalez-Argoti Tatiana , Philip Sophia , Josephs Lena S , Mantell Joanne E , Bauman Laurie J 
Published: September 2021

Abstract
Although 21% of new human immunodeficiency virus (HIV) diagnoses in the United States are in youth aged 13–24 years, adolescent awareness and uptake of the HIV prevention medication pre-exposure prophylaxis (PrEP) are low. This study explores the attitudes and challenges that adolescents face while taking PrEP. Thirty interviews were conducted with Black and Latine (we use the gender-inclusive term Latine rather than Latinx for more appropriate Spanish pronunciation) students aged 15–17 who received care at school-based health centers (SBHCs) in the Bronx, NY. Transcripts were coded inductively and deductively using thematic analysis. Most participants were unaware of PrEP, but nearly all were enthusiastic when informed about it; a majority denied that they would feel any stigma when taking PrEP. Despite this high receptivity, multiple barriers were identified, particularly confidentiality from parents, low perceived need of PrEP and concerns about daily adherence and side effects. Adolescents overall were enthusiastic about the availability of PrEP and felt it empowered them to have control over their health. SBHCs were considered trusted sources of confidential, accessible care, and we believe that they can be uniquely positioned to mitigate barriers to PrEP distribution in the future.
Effects of iron, vitamin A, and the interaction between the two nutrients on intestinal development and cell differentiation in piglets
Authors: Zhou Jing , Qin Yan , Xiong Xia , Wang Zhaobin , Wang Min , Wang Yancan , Wang Qiye Y , Yang Huansheng S , Yin Yulong 
Published: September 2021

Abstract
This study aimed to investigate the effects of iron, vitamin A (VA) and their interaction on intestinal development and differentiation of cells in suckling piglets. Therefore, 32 Duroc × Landrace × Yorkshire 0-d-old newborn boars with similar body weights were randomly divided into four groups, with eight replicates in each group and one pig in each replicate. All the piglets were breastfed. In addition, the piglets were given normal saline (CON group) or ferrous sulfate (OAFe group) or VA (VA group) or ferrous sulfate and VA (OAFe + VA group) on the 2nd, 7th, 12th, and 17th day, respectively. The piglets were then slaughtered on the 21st day, and intestinal samples were collected. The results showed that: 1) iron (P &lt; 0.001) significantly increased the length, weight, relative weight, and the length to weight ratio of the small intestine. On the other hand, VA had a significant effect on the weight to length ratio (P = 0.015) and relative weight (P &lt; 0.001) of the small intestine; 2) with regard to intestinal morphology, supplementation with iron (P &lt;0.05) had obvious effects on the villus height (VH), crypt depth (CD), villus width (VW), and surface area. Additionally, both VA and interaction of VA and iron increased the VH (P &lt; 0.05) and surface area (P = 0.001). The results also showed that iron (P &lt; 0.01) increased the number of crypt goblet cells, Ki67-positive cells, and endocrine cells. Moreover, both VA and the interaction between VA and iron increased the number of endocrine cells in the villi (P = 0.05); 3) With regard to the mRNA expression levels of stem cell differentiation marker genes, iron (P &lt; 0.05) decreased the expression of trophinin 2 (Trop2), leucine-rich repeat containing G protein-coupled receptor 5 positive (Lgr5+), male-specific lethal 1(Msl1), BMI 1 proto-oncogene, polycomb ring finger (Bmi1), and achaete-scute family bHLH transcription factor 2 (Ascl2). On the other hand, VA increased the expression of Ascl2 (P = 0.001) although the interaction of VA and iron (P &lt; 0.05) had an effect on the expression of secreted phosphoprotein 1 (Spp1) and Bmi1. In addition, VA decreased the gene or mRNA expression of aconitase 1 (Aco1; P &lt; 0.001), transferrin receptor (TFRC; P = 0.001), and solute carrier family 11 member 2 (DMT1; P = 0.003) in the Iron Reactive Element/Iron Regulatory Protein (IRE/IRP) signaling pathway although iron and the interaction of VA and iron had no effect on the genes’ expression. The results therefore showed that VA, iron, and their interaction can promote intestinal development and epithelial cell differentiation in piglets.
Factors Associated With Corticosteroid Treatment for Pediatric Acute Respiratory Tract Infections
Authors: Shapiro Daniel J , Palmer Nathan P , Bourgeois Florence T 
Published: September 2021

Abstract
Systemic corticosteroids are not recommended to treat children with acute respiratory tract infections (ARTIs). Using data from a national commercial health care company, we found that corticosteroid treatment occurred in 3.2% of ARTI encounters. The adjusted odds of corticosteroid treatment were highest for bronchitis/bronchiolitis, in emergency departments, and in the South.
A Case Report of Air Force Reserve Nurses Deployed to New York City for COVID-19 Support
Authors: Hernandez Stephen 
Published: September 2021

ABSTRACTInitial DoD support of Federal Emergency Management Agency (FEMA) operations for New York City (NYC) coronavirus disease 2019 (COVID-19) relief included the deployment of military medics to the Javits New York Medical Station and USNS Comfort. When Air Force (AF) Reservists arrived in NYC, 64th Air Expeditionary Group leaders worked with FEMA, Task Force New York/New Jersey, and NYC chains of command to send Airmen to NYC hospitals, including Lincoln Medical Center (LMC). Within 72 hours of arrival, 60 AF Reservists, including 30 registered nurses and 3 medical technicians, integrated into LMC to provide support during April and May 2020. This assistance began during the peak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Air Force nurses provided over 6,000 hours of care to over 800 patients in the emergency department and ad hoc intensive care and medical-surgical units. As infections declined, AF nurses shifted to providing care in established units. In these units, AF nurses provided patient care and worked directly with LMC nurses to provide directed teaching experiences to improve their comfort and competency with caring for acutely ill COVID-19 patients. The deployment of AF Reservists into civilian facilities was a success and bolstered the capability of three facilities struggling to care for SARS-CoV-2 patients. This effort was recognized by military and civilian healthcare leaders and resulted in over 600 military medical personnel being sent to support 11 NYC public hospitals.
Reducing Setup and Turnover Times in the OR With an Innovative Sterilization Container: Implications for the COVID-19 Era Military Medicine
Authors: Bradley David F , Romito Kenneth , Dockery James , Taylor Lance , ONeel Nicholas , Rodriguez Jose , Talbot Laura A 
Published: September 2021

ABSTRACT

Introduction
The global 2019 coronavirus pandemic (COVID-19) is setting unprecedented demands on the nation and the military and surgical services. Surgical demands include a large backlog of surgical cases, strain on available resources, and the need for additional measures to prevent exposure. The purpose of this project was to evaluate the feasibility, duration, adverse events, and potential gains associated with using a Turbett Sterilization Pod (TSP) for total joint replacements.

Materials and Methods
A multidisciplinary team used the Plan–Do–Study–Act model to guide this project. A time–motion study was completed in the operating room (OR) to measure the average time required to set up surgical instrumentation for total joint replacement cases that required 12 or more instrument trays. We compared the amount of time it took to complete the setting up of instrumentation using the traditional method versus the TSP method. The traditional method consisted of unwrapping each surgical tray, checking for holes in the blue wrapper, and placing the tray on the back table. In the case of the TSP, the door of the pod was opened, and the instrument trays were transferred directly to the back table. We measured the time the staff took to perform the task using each of these methods.

Results
When compared to the traditional method, the use of the TSP resulted in improved turnover time, decreased room setup time, reduced environmental waste, and eliminated both the effect of damage to wrappers and the time previously spent wrapping surgical trays.

Conclusion
The TSP minimizes the time needed by the staff to set up an OR suite for a total joint replacement, therefore permitting them to focus more on direct patient care. This time improvement suggests that all surgical specialties, including those requiring greater than 12 traditional instrument sets, may experience reduced turnover time between cases. The use of the TSP is one means to help rectify the OR backlog brought on by COVID-19.
Neonatal Aeromedical Evacuation During COVID-19: An Interview With Captain Danielle James
Authors: James Danielle , Talbot Laura A 
Published: September 2021

ABSTRACT
During the coronavirus-19 pandemic, limited information existed about the risks and consequences of severe acute respiratory syndrome coronavirus 2 infection associated with maternal transmission to neonates. With rapidly evolving evidence, Air Force Neonatal Intensive Care Unit nurses at U.S. Naval Hospital Okinawa, Japan, adapted their standard operating procedures to safeguard their at-risk neonatal patients. This interview describes an Air Force NICU nurse’s view of neonatal transport and nursing care during the coronavirus-19 pandemic.
A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees
Authors: McBroome Jakob , Thornlow Bryan , Hinrichs Angie S , Kramer Alexander , De Maio Nicola , Goldman Nick , Haussler David , Corbett-Detig Russell , Turakhia Yatish 
Published: September 2021

Abstract
The vast scale of SARS-CoV-2 sequencing data has made it increasingly challenging to comprehensively analyze all available data using existing tools and file formats. To address this, we present a database of SARS-CoV-2 phylogenetic trees inferred with unrestricted public sequences, which we update daily to incorporate new sequences. Our database uses the recently proposed mutation-annotated tree (MAT) format to efficiently encode the tree with branches labeled with parsimony-inferred mutations, as well as Nextstrain clade and Pango lineage labels at clade roots. As of June 9, 2021, our SARS-CoV-2 MAT consists of 834,521 sequences and provides a comprehensive view of the virus’ evolutionary history using public data. We also present matUtils—a command-line utility for rapidly querying, interpreting, and manipulating the MATs. Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/ and https://github.com/yatisht/usher, respectively.
Mechanisms of irreversible aquaporin-10 inhibition by organogold compounds studied by combined biophysical methods and atomistic simulations
Authors: Pimpão Catarina , Wragg Darren , Bonsignore Riccardo , Aikman Brech , Pedersen Per Amstrup , Leoni Stefano , Soveral Graça , Casini Angela 
Published: September 2021

AbstractThe inhibition of glycerol permeation via human aquaporin-10 (hAQP10) by organometallic gold complexes has been studied by stopped-flow fluorescence spectroscopy, and its mechanism has been described using molecular modelling and atomistic simulations. The most effective hAQP10 inhibitors are cyclometalated Au(III) C^N compounds known to efficiently react with cysteine residues leading to the formation of irreversible C–S bonds. Functional assays also demonstrate the irreversibility of the binding to hAQP10 by the organometallic complexes. The obtained computational results by metadynamics show that the local arylation of Cys209 in hAQP10 by one of the gold inhibitors is mapped into a global change of the overall free energy of glycerol translocation across the channel. Our study further pinpoints the need to understand the mechanism of glycerol and small molecule permeation as a combination of local structural motifs and global pore conformational changes, which are taking place on the scale of the translocation process and whose study, therefore, require sophisticated molecular dynamics strategies.