bluuebunny/crossref_metadata_2025_split huggingface dataset:
NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning
Authors: Hasan Md Mehedi , Alam Md Ashad , Shoombuatong Watshara , Deng Hong-Wen , Manavalan Balachandran , Kurata Hiroyuki 
Published: April 2021

AbstractNeuropeptides (NPs) are the most versatile neurotransmitters in the immune systems that regulate various central anxious hormones. An efficient and effective bioinformatics tool for rapid and accurate large-scale identification of NPs is critical in immunoinformatics, which is indispensable for basic research and drug development. Although a few NP prediction tools have been developed, it is mandatory to improve their NPs’ prediction performances. In this study, we have developed a machine learning-based meta-predictor called NeuroPred-FRL by employing the feature representation learning approach. First, we generated 66 optimal baseline models by employing 11 different encodings, six different classifiers and a two-step feature selection approach. The predicted probability scores of NPs based on the 66 baseline models were combined to be deemed as the input feature vector. Second, in order to enhance the feature representation ability, we applied the two-step feature selection approach to optimize the 66-D probability feature vector and then inputted the optimal one into a random forest classifier for the final meta-model (NeuroPred-FRL) construction. Benchmarking experiments based on both cross-validation and independent tests indicate that the NeuroPred-FRL achieves a superior prediction performance of NPs compared with the other state-of-the-art predictors. We believe that the proposed NeuroPred-FRL can serve as a powerful tool for large-scale identification of NPs, facilitating the characterization of their functional mechanisms and expediting their applications in clinical therapy. Moreover, we interpreted some model mechanisms of NeuroPred-FRL by leveraging the robust SHapley Additive exPlanation algorithm.
Coronavirus Disease 2019 (COVID-19) Outbreaks at 2 Construction Sites—New York City, October–November 2020
Authors: Bushman Dena , Sekaran Jency , Jeffery Nancy , Rath Caroline , Ackelsberg Joel , Weiss Don , Wu Winfred , Van Oss Katherine , Johnston Kolthida , Huang Jamie , Khatun Umaima , Sheikh Tara , Sutcliff Jennie , Tsoi Benjamin 
Published: April 2021

Abstract
During 23 October–16 November 2020, the New York City Department of Health and Mental Hygiene investigated coronavirus disease 2019 (COVID-19) outbreaks at 2 construction sites. Challenges in adhering to the New York State Department of Health “Interim COVID-19 Guidance for Construction” were reported. To minimize outbreaks, jurisdictions should increase tailored outreach to the construction industry, emphasizing infection prevention.
Knowledge co-construction in professional reading group discussions
Authors: Lee Kent K , Abbott Marilyn L 
Published: April 2021

AbstractAs part of our longitudinal study of TESOL instructors’ engagement with peer-reviewed journal articles in professional reading groups, we examined the processes involved in knowledge co-construction in three group discussions. Audio-recordings of the discussions were analysed using process coding to identify the quality and quantity of the group members’ (n = 18) contributions and the processes of knowledge co-construction. Findings revealed that the group members’ contributions were characterized by 16 different language functions. The most commonly used functions, agreeing, elaborating and sharing experiences, strengthened group rapport and promoted a positive learning environment. All 16 language functions contributed to the processes of introducing, developing, crystallizing, combining, and creating knowledge that stimulated innovative evidence-informed practices. An awareness of the processes of knowledge-co-construction and their potential to address professional learning and development needs may encourage teachers to engage in autonomous reading groups and support them in the creation of innovative next practices.
Sterol uptake analysis in Saccharomyces and non-Saccharomyces wine yeast species
Authors: Tesnière Catherine , Pradal Martine , Legras Jean-Luc 
Published: April 2021

ABSTRACT
Sterols are essential components of the yeast membrane and their synthesis requires oxygen. Yet, Saccharomyces cerevisiae has developed the ability to take up sterols from the medium under anaerobiosis. Here we investigated sterol uptake efficiency and the expression of genes related to sterol import in Saccharomyces and non-Saccharomyces wine yeast species fermenting under anaerobic conditions. The sterol uptake efficiency of 39 strains was evaluated by flow cytometry (with 25-NBD Cholesterol, a fluorescent cholesterol probe introduced in the medium) and we found an important discrepancy between Saccharomyces and non-Saccharomyces wine yeast species that we correlated to a lower final cell population and a lower fermentation rate. A high uptake of sterol was observed in the various Saccharomyces strains. Spot tests performed on 13 of these strains confirmed the differences between Saccharomyces and non-Saccharomyces strains, suggesting that the presence of the sterol uptake transporters AUS1 and PDR11 could cause these discrepancies. Indeed, we could not find any homologue to these genes in the genome of Hanseniaspora uvarum, H. guillermondii, Lachancea thermotolerans, Torulaspora delbreueckii, Metschnikowia pulcherrima, or Starmarella bacillaris species. The specialization of sterol import function for post genome-duplication species may have favored growth under anaerobiosis.
Active and inactive transplacement of the M26 recombination hotspot in Schizosaccharomyces pombe.
Authors: Virgin J B , Metzger J , Smith G R 
Published: April 2021

Abstract
The ade6-M26 mutation of the fission yeast Schizosaccharomyces pombe creates a meiotic recombination hotspot that elevates ade6 intragenic recombination approximately 10-15-fold. A heptanucleotide sequence including the M26 point mutation is required but not sufficient for hotspot activity. We studied the effects of plasmid and chromosomal context on M26 hotspot activity. The M26 hotspot was inactive on a multicopy plasmid containing M26 embedded within 3.0 or 5.9 kb of ade6 DNA. Random S. pombe genomic fragments totaling approximately 7 Mb did not activate the M26 hotspot on a plasmid. M26 hotspot activity was maintained when 3.0-, 4.4-, and 5.9-kb ade6-M26 DNA fragments, with various amounts of non-S. pombe plasmid DNA, were integrated at the ura4 chromosomal locus, but only in certain configurations relative to the ura4 gene and the cointegrated plasmid DNA. Several integrations created new M26-independent recombination hotspots. In all cases the non-ade6 DNA was located &gt; 1 kb from the M26 site, and in some cases &gt; 2 kb. Because the chromosomal context effect was transmitted over large distances, and did not appear to be mediated by a single discrete DNA sequence element, we infer that the local chromatin structure has a pronounced effect on M26 hotspot activity.
Genetic Analysis Demonstrates a Direct Link Between Rho Signaling and Nonmuscle Myosin Function During Drosophila Morphogenesis
Authors: Halsell Susan R , Chu Benjamin I , Kiehart Daniel P 
Published: April 2021

Abstract
A dynamic actomyosin cytoskeleton drives many morphogenetic events. Conventional nonmuscle myosin-II (myosin) is a key chemomechanical motor that drives contraction of the actin cytoskeleton. We have explored the regulation of myosin activity by performing genetic screens to identify gene products that collaborate with myosin during Drosophila morphogenesis. Specifically, we screened for second-site noncomplementors of a mutation in the zipper gene that encodes the nonmuscle myosin-II heavy chain. We determined that a single missense mutation in the zipperEbr allele gives rise to its sensitivity to second-site noncomplementation. We then identify the Rho signal transduction pathway as necessary for proper myosin function. First we show that a lethal P-element insertion interacts genetically with zipper. Subsequently we show that this second-site noncomplementing mutation disrupts the RhoGEF2 locus. Next, we show that two EMS-induced mutations, previously shown to interact genetically with zipperEbr, disrupt the RhoA locus. Further, we have identified their molecular lesions and determined that disruption of the carboxyl-terminal CaaX box gives rise to their mutant phenotype. Finally, we show that RhoA mutations themselves can be utilized in genetic screens. Biochemical and cell culture analyses suggest that Rho signal transduction regulates the activity of myosin. Our studies provide direct genetic proof of the biological relevance of regulation of myosin by Rho signal transduction in an intact metazoan.
Maternal-Zygotic Gene Conflict Over Sex Determination: Effects of Inbreeding
Authors: Werren John H , Hatcher Melanie J 
Published: April 2021

Abstract
There is growing evidence that sex determination in a wide range of organisms is determined by interactions between maternal-effect genes and zygotically expressing genes. Maternal-effect genes typically produce products (e.g., mRNA or proteins) that are placed into the egg during oogenesis and therefore depend upon maternal genotype. Here it is shown that maternal-effect and zygotic genes are subject to conflicting selective pressures over sex determination in species with partial inbreeding or subdivided populations. The optimal sex ratios for maternal-effect genes and zygotically expressing genes are derived for two models: partial inbreeding (sibmating) and subdivided populations with local mating in temporary demes (local mate competition). In both cases, maternal-effect genes are selected to bias sex determination more toward females than are zygotically expressed genes. By investigating the invasion criteria for zygotic genes in a population producing the maternal optimum (and vice versa), it is shown that genetic conflict occurs between these genes. Even relatively low levels of inbreeding or subdivision can result in maternalzygotic gene conflict over sex determination. The generality of maternal-zygotic gene conflict to sex determination evolution is discussed; such conflict should be considered in genetic studies of sex-determining mechanisms.
The fitness costs and benefits of trisomy of each Candida albicans chromosome
Authors: Yang Feng , Todd Robert T , Selmecki Anna , Jiang Yuan-ying , Cao Yong-bing , Berman Judith 
Published: April 2021

Abstract
Candida albicans is a prevalent human fungal pathogen. Rapid genomic change, due to aneuploidy, is a common mechanism that facilitates survival from multiple types of stresses including the few classes of available antifungal drugs. The stress survival of aneuploids occurs despite the fitness costs attributed to most aneuploids growing under idealized lab conditions. Systematic study of the aneuploid state in C. albicans has been hindered by the lack of a comprehensive collection of aneuploid strains. Here, we describe a collection of diploid C. albicans aneuploid strains, each carrying one extra copy of each chromosome, all from the same genetic background. We tested the fitness of this collection under several physiological conditions including shifts in pH, low glucose, oxidative stress, temperature, high osmolarity, membrane stress, and cell wall stress. We found that most aneuploids, under most conditions, were less fit than their euploid parent, yet there were specific conditions under which specific aneuploid isolates provided a fitness benefit relative to the euploid parent strain. Importantly, this fitness benefit was attributable to the change in the copy number of specific chromosomes. Thus, C. albicans can tolerate aneuploidy of each chromosome and some aneuploids confer improved growth under conditions that the yeast encounters in its host niches.
Prediction of patient disposition: comparison of computer and human approaches and a proposed synthesis
Authors: Barak-Corren Yuval , Agarwal Isha , Michelson Kenneth A , Lyons Todd W , Neuman Mark I , Lipsett Susan C , Kimia Amir A , Eisenberg Matthew A , Capraro Andrew J , Levy Jason A , Hudgins Joel D , Reis Ben Y , Fine Andrew M 
Published: April 2021

AbstractObjectiveTo compare the accuracy of computer versus physician predictions of hospitalization and to explore the potential synergies of hybrid physician–computer models.Materials and MethodsA single-center prospective observational study in a tertiary pediatric hospital in Boston, Massachusetts, United States. Nine emergency department (ED) attending physicians participated in the study. Physicians predicted the likelihood of admission for patients in the ED whose hospitalization disposition had not yet been decided. In parallel, a random-forest computer model was developed to predict hospitalizations from the ED, based on data available within the first hour of the ED encounter. The model was tested on the same cohort of patients evaluated by the participating physicians.Results198 pediatric patients were considered for inclusion. Six patients were excluded due to incomplete or erroneous physician forms. Of the 192 included patients, 54 (28%) were admitted and 138 (72%) were discharged. The positive predictive value for the prediction of admission was 66% for the clinicians, 73% for the computer model, and 86% for a hybrid model combining the two. To predict admission, physicians relied more heavily on the clinical appearance of the patient, while the computer model relied more heavily on technical data-driven features, such as the rate of prior admissions or distance traveled to hospital.DiscussionComputer-generated predictions of patient disposition were more accurate than clinician-generated predictions. A hybrid prediction model improved accuracy over both individual predictions, highlighting the complementary and synergistic effects of both approaches.ConclusionThe integration of computer and clinician predictions can yield improved predictive performance.
Application of QuantiFERON ELISA for Detection of Interferon-Gamma Autoantibodies in Adult-Onset Immunodeficiency Syndrome
Authors: Khositnithikul Rommanee , Laisuan Wannada , Setthaudom Chavachol , Sriwanichrak Kanchana , Kunakorn Mongkol , Srikhirin Toemsak , Lumjiaktase Putthapoom , Vongsakulyanon Apirom 
Published: April 2021

Abstract

Objective
Patients who develop interferon-gamma autoantibodies (IFN-ɤ autoAbs) in adult-onset immunodeficiency (AOID) syndrome are more likely to develop opportunistic and recurrent intracellular infections. The assay to detect IFN-ɤ autoAbs is essential for the diagnosis and therapeutic monitoring of AOID syndrome. Therefore, this study applied the QuantiFERON assay for the detection of IFN-ɤ autoAbs.

Methods
Serum from patients with AOID syndrome (n = 19) and serum from healthy patients (n = 20) was collected and applied using 2 neutralizing platforms of enzyme-linked immunosorbent assay (ELISA) kits (the BD ELISA and the QuantiFERON ELISA) for IFN-ɤ autoAbs detection.

Results
The pooled serum from patients with AOID syndrome showed &gt;50% inhibition at 1:5000 dilution (positive), whereas the pooled serum from healthy patients showed &lt;50% inhibition at 1:5000 dilution (negative) according to the neutralizing QuantiFERON ELISA. Each specimen showed the same result according to both the neutralizing BD ELISA and the neutralizing QuantiFERON ELISA. Moreover, the patient serum showed a variation in titer ranging from 1:5000 to &gt;1:5,000,000 according to the neutralizing QuantiFERON ELISA.

Conclusion
The QuantiFERON ELISA kit could be applied for the detection of IFN-ɤ autoAbs for the diagnosis and therapeutic monitoring of AOID syndrome.
An adaptive mesh, GPU-accelerated, and error minimized special relativistic hydrodynamics code
Authors: Tseng Po-Hsun , Schive Hsi-Yu , Chiueh Tzihong 
Published: April 2021

ABSTRACT
We present a new special relativistic hydrodynamics (SRHD) code capable of handling coexisting ultra-relativistically hot and non-relativistically cold gases. We achieve this by designing a new algorithm for conversion between primitive and conserved variables in the SRHD solver, which incorporates a realistic ideal-gas equation of state covering both the relativistic and non-relativistic regimes. The code can handle problems involving a Lorentz factor as high as 106 and optimally avoid the catastrophic cancellation. In addition, we have integrated this new SRHD solver into the code gamer (https://github.com/gamer-project/gamer) to support adaptive mesh refinement and hybrid OpenMP/MPI/GPU parallelization. It achieves a peak performance of 7 × 107 cell updates per second on a single Tesla P100 GPU and scales well to 2048 GPUs. We apply this code to two interesting astrophysical applications: (a) an asymmetric explosion source on the relativistic blast wave and (b) the flow acceleration and limb brightening of relativistic jets.
EFFECTIVE DOSE AND EFFECT OF DOSE MODULATION FOR LOCALIZER RADIOGRAPHS USING APPLIED AND ALTERNATIVE SETTINGS ON TOSHIBA/CANON CT SYSTEMS
Authors: Svahn Tony M , Ast Jennifer C 
Published: April 2021

AbstractThe purpose was to estimate the effective dose of Toshiba/Canon thorax localizer radiographs for available parameter settings, and to test their dose modulation ability. Localizer radiographs were acquired of anthropomorphic chest phantoms (body mass indices 29 and 23) using various settings (120–80 kV, 100–10 mA). The milliamperes values were compared from resulting helical scan data. Effective dose was computed for two computed tomography (CT) scanners (Aquilion Prime and One Genesis) using a Monte Carlo-based software. For the smaller phantom, all curves were superimposed. For the larger phantom, most curves were also superimposed, except for the one generated from the lowest parameters. The Aquilion Prime system yielded an effective dose of 0.40/0.56 mSv (male/female) using the default parameters. The localizer radiograph dose could be reduced by &gt;90% without affecting the dose modulation. The dose was further reduced by 30–50% in the One Genesis CT system due to improved beam filtration.
Author’s Response: Targeting Treatments to Health Disparities
Authors: Hunter Sharon K , Hoffman M Camille , McCarthy Lizbeth , D’Alessandro Angelo , Wyrwa Anna , Noonan Kathleen , Christians Uwe , Nakimuli-Mpungu Etheldreda , Zeisel Steven H , Law Amanda J , Freedman Robert 
Published: April 2021

Abstract
These initial data suggest that with prenatal vitamins and choline supplements, we might decrease one risk factor associated with poorer health outcomes disproportionally affecting Black families, ie, preterm birth. Dissemination of this research fulfills the principle of Justice in the Belmont Report, to ensure that participants from different racial, ethnic and socioeconomic groups receive benefits from research directed to their specific problems.
CVA-Flow novel telestroke system preliminary trial: reliability in determining NIHSS for acute ischemic stroke
Authors: Mor Saban , Anner Moskovitz , Sona Ohanian , Anna Reznik , Marc Ribo , Rotem Sivan-Hoffmann 
Published: April 2021

AbstractBackgroundThe National Institutes of Health Stroke Scale (NIHSS) is the most recommended tool for objectively quantifying the impairment caused by a suspected stroke. Nevertheless, it is used almost solely by trained neurologists in the emergency departments (ED) setting. CVA-Flow (CVAid medical Ltd., Tel-Aviv, Israel) is a smartphone-based Telestroke system that captures the full NIHSS by video and enables a distant stroke physician to assess the patient’s neurological status, bringing forward the NIHSS to the pre-hospital setting.ObjectiveWe aimed to compare the reliability of an NIHSS score determined by a neurologist from afar, using the CVA-Flow platform, with a standard NIHSS assessment performed in the ED).MethodsIn this multi-center prospective trial, Patients admitted to the ED in Rambam hospital in Haifa, Israel, and Vall d’Hebron hospital (VdH) in Barcelona, Spain, had a neurological exam based on the NIHSS while being recorded by the system. A neurologist blinded to the results rated the NIHSS according to the videos offline.ResultsA total of 95 patients with a suspected stroke were included. Overall ICC was 0.936 (0.99 in VdH and 0.84 in Rambam), indicating excellent and good reliability, respectively.ConclusionRemote stroke assessment based on the NIHSS, using videos collected by the CVA-Flow platform, installed on a standard smartphone, is a reliable measurement as compared with bedside evaluation.
Companionship for women using English maternity services during COVID-19: National and organisational perspectives
Authors: Thomson Gill , Balaam Marie-Clare , Nowland Rebecca , Crossland Nicola , Moncrieff Gill , Heys Stephanie , Sarian Arni , Cull Joanne , Downe Soo ,   ASPIRE-COVID19 Collaborative Group
Published: April 2021

ABSTRACTObjectivesTo explore the impact of COVID-19 on companionship for women using maternity services in England, as part of the Achieving Safe and Personalised maternity care In Response to Epidemics (ASPIRE COVID-19 UK) study.SettingMaternity care provision in England.ParticipantsInterviews were held with 26 national governmental, professional, and service-user organisation leads including representatives from the Royal College of Midwives, NHS England, Birthrights and AIMS (July-Dec). Other data included public-facing outputs logged from 25 maternity Trusts (Sept/Oct) and data extracted from 78 documents from 8 key governmental, professional and service-user organisations that informed national maternity care guidance and policy (Feb-Dec).ResultsSix themes emerged: ‘Postcode lottery of care’ highlights variations in companionship practices, ‘Confusion and stress around ‘rules’’ relates to a lack of and variable information concerning companionship, ‘Unintended consequences’ concerns the negative impacts of restricted companionship on service-users and staff, ‘Need for flexibility’ highlights concerns about applying companionship policies irrespective of need, ‘‘Acceptable’ time for support’ highlights variations in when and if companionship was ‘allowed’ antenatally and intrapartum; and ‘Loss of human rights for gain in infection control’ emphasizes how a predominant focus on infection control was at a cost to psychological safety and women’s human rights.ConclusionsPolicies concerning companionship have been inconsistently applied within English maternity services during the COVID-19 pandemic. In some cases, policies were not justified by the level of risk, and were applied indiscriminately regardless of need. This was associated with psychological harms for some women and staff. There is an urgent need to determine how to balance risks and benefits sensitively and flexibly and to optimise outcomes during the current and future crisis situations.Strengths and limitations of this studyThis is the first paper to consider links between policy and practice in companionship in maternity care during the COVID-19 pandemic;Data triangulation across stakeholders, policy and practice provides nuanced and context related perspectives on why and how companionship was impacted;Stakeholders included representatives from all key agencies involved in maternity care;Practice related issues were collected from the maternity Trust website and social media-based public facing information, which may or may not reflect actual care practices;The study does not include information directly reported by parents and healthcare professionals.