bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innovating Evaluation and Treatment of Intrapartum Fevers: Where Do We Go from Here?
Authors: Wilkie Gianna L. , James Kaitlyn , Ona Samsiya , Easter Sarah Rae , Chou Joseph , Roberts Drucilla , Sahin Zehra Ordulu , Tuomala Ruth , Diouf Khady , Riley Laura , Prabhu Malavika 
Published: April 2021

As intrapartum fevers are not always infectious in origin, determining whether antibiotics are indicated is challenging. We previously sought to create a point-of-care calculator using clinical data available at the time of an intrapartum fever to identify the subset of women who require antibiotic treatment to avoid maternal and neonatal morbidity. Despite the use of a comprehensive dataset from our institutions, we were unable to propose a valid and highly predictive model. In this commentary, we discuss why our model failed, as well as future research directions to identify and treat true intraamniotic infection. Developing a risk-stratification model is paramount to minimizing maternal and neonatal exposure to unnecessary antibiotics while allowing for early identification of women and babies at risk for infectious morbidity.
Key Points
β-arrestin–dependent PI(4,5)P2synthesis boosts GPCR endocytosis
Authors: Jung Seung-Ryoung , Jiang Yifei , Seo Jong Bae , Chiu Daniel T. , Hille Bertil , Koh Duk-Su 
Published: April 2021

SignificanceStimulation of protease-activated receptor 2 (PAR2) at the plasma membrane triggers a branching cascade of interrelated events in several cellular compartments. In one branch, the G protein Gqcouples to phospholipase C, and the membrane phosphoinositide lipids PI(4,5)P2and PI(4)P are depleted. In another branch, the receptor becomes desensitized by becoming phosphorylated, bound to β-arrestin, and internalized by clathrin-coated pits. This second branch needs PI(4,5)P2at several steps. We found that β-arrestin in complex with receptors stably binds to clathrin-coated pits and increases transient binding of the PI(4,5)P2synthetic enzyme PIP5K-Iγ. Then, this complex in clathrin-coated pits boosts the rate of PI(4,5)P2synthesis from Golgi and plasma membrane PI(4)P, so that PI(4,5)P2becomes elevated. The new PI(4,5)P2allows receptor internalization.
Transferrin receptor targeting by de novo sheet extension
Authors: Sahtoe Danny D. , Coscia Adrian , Mustafaoglu Nur , Miller Lauren M. , Olal Daniel , Vulovic Ivan , Yu Ta-Yi , Goreshnik Inna , Lin Yu-Ru , Clark Lars , Busch Florian , Stewart Lance , Wysocki Vicki H. , Ingber Donald E. , Abraham Jonathan , Baker David 
Published: April 2021

Significance
The de novo design of proteins that bind natural target proteins is useful for a variety of biomedical and biotechnological applications. We describe a design strategy to target proteins containing an exposed beta edge strand. We use the approach to design binders to the human transferrin receptor which shuttles back and forth across the blood–brain barrier. Such binders could be useful for the delivery of therapeutics into the brain.
DDX11 loss causes replication stress and pharmacologically exploitable DNA repair defects
Authors: Jegadesan Nanda Kumar , Branzei Dana 
Published: April 2021

Significance
Replication stress can affect development and is a hallmark of cancers. Warsaw breakage syndrome is a developmental disorder caused by mutations in the conserved DDX11 DNA helicase. Here, using human cellular models of DDX11 deficiency, we report that DDX11 helicase prevents replication stress and mediates homology-directed repair via homologous recombination. Mechanistically, DDX11 promotes resection, enabling RPA and RAD51 focus formation, and acts nonredundantly with the RAD51 mediators BRCA1 and BRCA2. As a result, targeting DDX11 confers improved chemotherapy responsiveness in both chemotherapy-sensitive and drug-resistant BRCA1/2-mutated cancers that regained homologous recombination proficiency by suppressor mutation or somatic reversion. The results pinpoint DDX11 as a critical replication stress mitigating factor whose targeting can improve chemotherapeutic response in a range of cancers.
Surface plasmon mediates the visible light–responsive lithium–oxygen battery with Au nanoparticles on defective carbon nitride
Authors: Zhu Zhuo , Ni Youxuan , Lv Qingliang , Geng Jiarun , Xie Wei , Li Fujun , Chen Jun 
Published: April 2021

Significance
Deployment of electric vehicles with long driving ranges demands new electrochemistry beyond the current Li-ion batteries. Aprotic lithium–oxygen batteries have gained considerable attention and promise to provide energy density of approximately three to five times that of state-of-the-art Li-ion batteries, but they are plagued by sluggish reaction kinetics at cathodes and induced large-voltage hysteresis. A photo-mediated strategy has been attempted to reduce the discharge/charge overvoltage, but it is obstructed by the limited ultraviolet light absorption and the inevitably high carrier recombination on semiconductor photocathodes. Here, a plasmonic heterojunction of gold nanoparticle-decorated carbon nitride with nitrogen vacancies is used as a bifunctional catalyst to accelerate the oxygen cathode reactions of the lithium–oxygen battery under visible light.
Paraphrase and parallel treebank for the comparison of French and Chinese syntax
Authors: Poiret Rafaël , Mille Simon , Liu Haitao 
Published: April 2021

AbstractThis paper proposes to study the contrastive syntax of French and Chinese through the lens of syntactic mismatches, and by making use of parallel treebanks. A syntactic mismatch is the non-similarity between the syntactic structures of one linguistic unit and its translation. Syntactic mismatches are formalized using the notion of paraphrase from the Meaning-Text Theory, which allows for capturing mismatches at different levels of the linguistic description (e.g. Semantic, Deep-Syntactic, and Surface-Syntactic). In this paper, we report in details on the types of paraphrases found in the seed corpus used, demonstrating that the Deep-Syntactic paraphrases constitute the best starting point for our study. Then, we show how, starting from the seed corpus, we semi-automatically constructed a multi-layer parallel treebank with the alignment and annotation of paraphrases.
Cost and responsibility sharing arrangements in the EU to prevent and control notifiable veterinary and phytosanitary risks.
Authors: Asseldonk M. A. P. M. van , Bergevoet R. H. M. 
Published: April 2021

Abstract
A cost and responsibility sharing scheme (CRSS) is gaining interest in Member States (MSs) to prevent and control notifiable veterinary and phytosanitary risks. A vital part of this is a public private partnership (PPP) in which farmers and national governments decide how costs and responsibilities are shared. A CRSS-PPP has the goal to raise more awareness, reduce risk exposure, provide incentives for rapid disclosure and increases support of control strategies if outbreaks occur. The main reason for farmers to participate in a CRSS is the responsibility sharing part. In many MSs, farmers lack influence on the decision-making process regarding prevention and control of outbreaks although they are most affected. However, implementing new CRSSs requires careful preparation, negotiations and trust building. An obligation for a gradual introduction of CRSSs by all MSs respecting certain harmonized criteria established at European Union level is not likely in the near future. A more dual approach is foreseen whereby individual MSs continue or establish CRSSs by means of PPPs while others will still opt for more hierarchical regulated disease policies.
Keeping it in the family: transgenerational memories of plant defence.
Authors: Prashant Singh Prashant Singh , Roberts M. R. 
Published: April 2021

Abstract
Plants possess a sophisticated array of systems with which to sense and respond to their internal and external environment. Biological changes triggered by such systems represent examples of phenotypic plasticity. One aspect of phenotypic plasticity that has recently emerged is transgenerational priming of plant defence responses - the persistence of induced resistance responses across generations. There has been a recent surge in interest in epigenetic mechanisms as a basis for phenotypic plasticity, including the ability for such epigenetic changes to be inherited across generations. In this review, we focus on the evidence that attack by pests and disease can stimulate plant defence responses that increase levels of resistance not only in attacked plants, but in their offspring, and discuss mechanisms by which environmental stress signals can be inherited. Finally, we consider the implications of transgenerational defence responses for plants in natural and agricultural systems.
A Randomized, Single-Blind, Crossover Study Evaluating the Impact of OnabotulinumtoxinA Treatment on Mood and Appearance During the COVID-19 Pandemic
Authors: Cristel Robert T , Gandhi Nimit D , Issa Tariq Z , Kola Eljona , Demesh Daniel , Dayan Steven H 
Published: April 2021

AbstractBackgroundThe emergence of COVID-19 led rapidly to one of the most severe disease outbreaks in modern history. This caused many aesthetic practices to close temporarily, providing a unique opportunity to evaluate the impact of neurotoxin use in the setting of an ongoing pandemic.ObjectivesThe aim of this study was to examine whether administration of onabotulinumtoxinA (BOTOX Cosmetic, Allergan plc, Dublin, Ireland) to regular users synergistically amplifies the elevation in mood/happiness, self-satisfaction with appearance, and overall satisfaction in the context of the ongoing pandemic.MethodsA randomized, single-blind, crossover study was designed to evaluate the impact of neurotoxin treatment in the upper third of the face on mood, self-satisfaction with appearance, and overall satisfaction. The placebo group crossed over to treatment after 1 month. Surveys evaluating patient happiness, self-satisfaction with appearance, and overall efficacy were completed by both groups, and again by the placebo group following crossover to treatment.ResultsForty-five subjects were enrolled: 30 in the treatment group and 15 in the control/crossover group. The placebo group demonstrated no change in happiness or self-satisfaction in appearance until crossover to the treatment group. Both groups, once receiving onabotulinumtoxinA, reported increased happiness, self-satisfaction with appearance, and overall treatment satisfaction.ConclusionsOnabotulinumtoxinA treatment to the upper face in the midst of the COVID-19 pandemic was found to increase patient happiness, self-satisfaction with appearance, and overall treatment satisfaction.Level of Evidence: 2
Quickomics: exploring omics data in an intuitive, interactive and informative manner
Authors: Gao Benbo , Zhu Jing , Negi Soumya , Zhang Xinmin , Gyoneva Stefka , Casey Fergal , Wei Ru , Zhang Baohong 
Published: April 2021

Abstract

Summary
We developed Quickomics, a feature-rich R Shiny-powered tool to enable biologists to fully explore complex omics statistical analysis results and perform advanced analysis in an easy-to-use interactive interface. It covers a broad range of secondary and tertiary analytical tasks after primary analysis of omics data is completed. Each functional module is equipped with customizable options and generates both interactive and publication-ready plots to uncover biological insights from data. The modular design makes the tool extensible with ease.

Availability and implementation
Researchers can experience the functionalities with their own data or demo RNA-Seq and proteomics datasets by using the app hosted at http://quickomics.bxgenomics.com and following the tutorial, https://bit.ly/3rXIyhL. The source code under GPLv3 license is provided at https://github.com/interactivereport/Quickomics for local installation.

Supplementary information
Supplementary data are available at Bioinformatics online.
Multimodality imaging of myocardial viability: an expert consensus document from the European Association of Cardiovascular Imaging (EACVI)
Authors: Almeida Ana G , Carpenter John-Paul , Cameli Matteo , Donal Erwan , Dweck Marc R , Flachskampf Frank A , Maceira Alicia M , Muraru Denisa , Neglia Danilo , Pasquet Agnès , Plein Sven , Gerber Bernhard L ,   Reviewers: This document was reviewed by members of the 2018–2020 EACVI Scientific Documents Committee:, Buechel Ronny , Buechel Ronny , Delgado Victoria , Sade Leyla Elif , Stankovic Ivan ,   chair of the 2018–2020 EACVI Scientific Documents Committee:, Cosyns Bernard ,   the 2018–2020 EACVI President:, Edvardsen Thor 
Published: April 2021

Abstract
In clinical decision making, myocardial viability is defined as myocardium in acute or chronic coronary artery disease and other conditions with contractile dysfunction but maintained metabolic and electrical function, having the potential to improve dysfunction upon revascularization or other therapy. Several pathophysiological conditions may coexist to explain this phenomenon. Cardiac imaging may allow identification of myocardial viability through different principles, with the purpose of prediction of therapeutic response and selection for treatment. This expert consensus document reviews current insight into the underlying pathophysiology and available methods for assessing viability. In particular the document reviews contemporary viability imaging techniques, including stress echocardiography, single photon emission computed tomography, positron emission tomography, cardiovascular magnetic resonance, and computed tomography and provides clinical recommendations for how to standardize these methods in terms of acquisition and interpretation. Finally, it presents clinical scenarios where viability assessment is clinically useful.
Echocardiographic phenogrouping by machine learning for risk stratification in the general population
Authors: Sabovčik František , Cauwenberghs Nicholas , Vens Celine , Kuznetsova Tatiana 
Published: April 2021

Abstract

Aims
There is a need for better phenotypic characterization of the asymptomatic stages of cardiac maladaptation. We tested the hypothesis that an unsupervised clustering analysis utilizing echocardiographic indexes reflecting left heart structure and function could identify phenotypically distinct groups of asymptomatic individuals in the general population.

Methods and results
We prospectively studied 1407 community-dwelling individuals (mean age, 51.2 years; 51.1% women), in whom we performed clinical and echocardiographic examination at baseline and collected cardiac events on average 8.8 years later. Cardiac phenotypes that were correlated at r &gt; 0.8 were filtered, leaving 21 echocardiographic features, and systolic blood pressure for phenogrouping. We employed hierarchical and Gaussian mixture model-based clustering. Cox regression was used to demonstrate the clinical validity of constructed phenogroups. Unsupervised clustering analyses classified study participants into three distinct phenogroups that differed markedly in echocardiographic indexes. Indeed, cluster 3 had the worst left ventricular (LV) diastolic function (i.e. lowest e’ velocity and left atrial (LA) reservoir strain, highest E/e’, and LA volume index) and LV remodelling. The phenogroups were also different in cardiovascular risk factor profiles. We observed increase in the risk for incidence of adverse events across phenogroups. In the third phenogroup, the multivariable adjusted risk was significantly higher than the average population risk for major cardiovascular events (51%, P = 0.0028).

Conclusion
Unsupervised learning algorithms integrating routinely measured cardiac imaging and haemodynamic data can provide a clinically meaningful classification of cardiac health in asymptomatic individuals. This approach might facilitate early detection of cardiac maladaptation and improve risk stratification.
Genetic diversity, population structure, and selection signature in Ethiopian sorghum [Sorghum bicolor L. (Moench)] germplasm
Authors: Wondimu Zeleke , Dong Hongxu , Paterson Andrew H , Worku Walelign , Bantte Kassahun 
Published: April 2021

Abstract
Ethiopia, the probable center of origin and diversity for sorghum [Sorghum bicolor L. (Moench)] and with unique ecogeographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing. We identified a total of 108,107 high-quality single-nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome-wide association studies. Although we found no evidence of genetic differentiation among administrative regions (FST = 0.02, P = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, P = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.
On the use of GBLUP and its extension for GWAS with additive and epistatic effects
Authors: Zhang Jie , Liu Fang , Reif Jochen C , Jiang Yong 
Published: April 2021

Abstract
Genomic best linear unbiased prediction (GBLUP) is the most widely used model for genome-wide predictions. Interestingly, it is also possible to perform genome-wide association studies (GWAS) based on GBLUP. Although the estimated marker effects in GBLUP are shrunken and the conventional test based on such effects has low power, it was observed that a modified test statistic can be produced and the result of test was identical to a standard GWAS model. Later, a mathematical proof was given for the special case that there is no fixed covariate in GBLUP. Since then, the new approach has been called “GWAS by GBLUP”. Nevertheless, covariates such as environmental and subpopulation effects are very common in GBLUP. Thus, it is necessary to confirm the equivalence in the general case. Recently, the concept was generalized to GWAS for epistatic effects and the new approach was termed rapid epistatic mixed-model association analysis (REMMA) because it greatly improved the computational efficiency. However, the relationship between REMMA and the standard GWAS model has not been investigated. In this study, we first provided a general mathematical proof of the equivalence between “GWAS by GBLUP” and the standard GWAS model for additive effects. Then, we compared REMMA with the standard GWAS model for epistatic effects by a theoretical investigation and by empirical data analyses. We hypothesized that the similarity of the two models is influenced by the relative contribution of additive and epistatic effects to the phenotypic variance, which was verified by empirical and simulation studies.
Septate junction proteins are required for egg elongation and border cell migration during oogenesis in Drosophila
Authors: Alhadyian Haifa , Shoaib Dania , Ward Robert E 
Published: April 2021

Abstract
Protein components of the invertebrate occluding junction—known as the septate junction (SJ)—are required for morphogenetic developmental events during embryogenesis in Drosophila melanogaster. In order to determine whether SJ proteins are similarly required for morphogenesis during other developmental stages, we investigated the localization and requirement of four representative SJ proteins during oogenesis: Contactin, Macroglobulin complement-related, Neurexin IV, and Coracle. A number of morphogenetic processes occur during oogenesis, including egg elongation, formation of dorsal appendages, and border cell (BC) migration. We found that all four SJ proteins are expressed in egg chambers throughout oogenesis, with the highest and the most sustained levels in the follicular epithelium (FE). In the FE, SJ proteins localize along the lateral membrane during early and mid-oogenesis, but become enriched in an apical-lateral domain (the presumptive SJ) by stage 11. SJ protein relocalization requires the expression of other SJ proteins, as well as Rab5 and Rab11 like SJ biogenesis in the embryo. Knocking down the expression of these SJ proteins in follicle cells throughout oogenesis results in egg elongation defects and abnormal dorsal appendages. Similarly, reducing the expression of SJ genes in the BC cluster results in BC migration defects. Together, these results demonstrate an essential requirement for SJ genes in morphogenesis during oogenesis, and suggest that SJ proteins may have conserved functions in epithelial morphogenesis across developmental stages.
Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii
Authors: de Melo Teixeira Marcus , Lang B Franz , Matute Daniel R , Stajich Jason E , Barker Bridget M 
Published: April 2021

Abstract
Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.