bluuebunny/crossref_metadata_2025_split huggingface dataset:
An open-source tool to assess the carbon footprint of research
Authors: Mariette Jérôme , Blanchard Odile , Berné Olivier , Aumont Olivier , Carrey Julian , Ligozat AnneLaure , Lellouch Emmanuel , Roche Philippe-Emmanuel , Guennebaud Gaël , Thanwerdas Joel , Bardou Philippe , Salin Gérald , Maigne Elise , Servan Sophie , Ben-Ari Tamara 
Published: July 2022

Abstract
The scrutiny over the carbon footprint of research and higher education has increased rapidly in the last few years. This has resulted in a series of publications providing various estimates of the carbon footprint of one or several research activities, principally at the scale of a university or a research center or, more recently, a field of research. The variety of tools or methodologies on which these estimates rely unfortunately prevents any aggregation or direct comparison. This is because carbon footprint assessments are very sensitive to key parameters (e.g., emission factors) or hypotheses (e.g., scopes). Hence, it is impossible to address fundamental questions such as: is the carbon footprint of research structurally different between disciplines? Are plane trips a major source of carbon emissions in academic research? Massive collection and curation of carbon footprint data, across a large array of research situations and disciplines, is hence an important, timely and necessary challenge to answer these questions. This paper presents a framework to collect and analyse large amounts of homogeneous research carbon emission data in a network of research entities at the national scale. It relies on an open-source web application, GES 1point5, designed to estimate the carbon footprint of a department, research lab or team in any country of the world. Importantly, GES 1point5 is also designed to aggregate all input data and corresponding GHG emissions estimates into a comprehensive database. GES 1point5 therefore enables (i) the identification of robust local or national determinants of the carbon footprint of research and (ii) the estimation of the carbon footprint of the entire research sector at national scale. A preliminary analysis of the carbon footprint of more than one hundred laboratories in France is presented to illustrate the potential of the framework. It shows that the average emissions are 479 t CO2e for a research lab and 3.6 t CO2e for an average lab member (respectively 404 and 3.1 t CO2e without accounting for the indirect radiative effects of aviation), with the current scope of GES 1point5. Availability and implementation: GES 1point5 is available online at http://labos1point5.org/ges-
1point5 and its source code can be downloaded from the GitLab platform at https://framagit.org/
labos1point5/l1p5-vuejs.
ColocQuiaL: a QTL-GWAS colocalization pipeline
Authors: Chen Brian Y , Bone William P , Lorenz Kim , Levin Michael , Ritchie Marylyn D , Voight Benjamin F 
Published: July 2022

AbstractSummaryIdentifying genomic features responsible for genome-wide association study (GWAS) signals has proven to be a difficult challenge; many researchers have turned to colocalization analysis of GWAS signals with expression quantitative trait loci (eQTL) and splicing quantitative trait loci (sQTL) to connect GWAS signals to candidate causal genes. The ColocQuiaL pipeline provides a framework to perform these colocalization analyses at scale across the genome and returns summary files and locus visualization plots to allow for detailed review of the results. As an example, we used ColocQuiaL to perform colocalization between a recent type 2 diabetes GWAS and Genotype-Tissue Expression (GTEx) v8 single-tissue eQTL and sQTL data.Availability and implementationColocQuiaL is primarily written in R and is freely available on GitHub: https://github.com/bvoightlab/ColocQuiaL.
Best templates outperform homology models in predicting the impact of mutations on protein stability
Authors: Pak Marina A , Ivankov Dmitry N 
Published: July 2022

AbstractMotivationPrediction of protein stability change upon mutation (ΔΔG) is crucial for facilitating protein engineering and understanding of protein folding principles. Robust prediction of protein folding free energy change requires the knowledge of protein three-dimensional (3D) structure. In case, protein 3D structure is not available, one can predict the structure from protein sequence; however, the perspectives of ΔΔG predictions for predicted protein structures are unknown. The accuracy of using 3D structures of the best templates for the ΔΔG prediction is also unclear.ResultsTo investigate these questions, we used a representative set of seven diverse and accurate publicly available tools (FoldX, Eris, Rosetta, DDGun, ACDC-NN, ThermoNet and DynaMut) for stability change prediction combined with AlphaFold or I-Tasser for protein 3D structure prediction. We found that best templates perform consistently better than (or similar to) homology models for all ΔΔG predictors. Our findings imply using the best template structure for the prediction of protein stability change upon mutation if the protein 3D structure is not available.Availability and implementationThe data are available at https://github.com/ivankovlab/template-vs-model.Supplementary informationSupplementary data are available at Bioinformatics online.
Combining CRISPR–Cas12a with terminal deoxynucleotidyl transferase dependent reporter elongation for pathogen detection using lateral flow test strips
Authors: Berghuis Nicole F , Mars-Groenendijk Roos , Busker Ruud W , Paauw Armand , van Leeuwen Hans C 
Published: July 2022

Abstract
CRISPR–Cas (CC)-based detection technologies have some exceptional features, which hold the promise of developing into the next-generation diagnostic platforms. One of these features is the ability to trigger non-specific single-stranded DNA/RNA cleavage activity after specific target recognition and Cas enzyme activation. This cleavage activity can be visualized either by single-stranded DNA/RNA fluorescence resonance energy transfer quenching reporters or via lateral flow strips, which separate and detect the cleaved reporters. In a previous study, we reported coupling CC-cleavage activity with the enzyme terminal deoxynucleotidyl transferase (TdT) that elongates cleaved ssDNA reporter fragments with dTTP nucleotides. These elongated poly(thymine) tails then act as scaffolds for the formation of copper nanoparticles which generate a bright fluorescent signal upon UV excitation. In the current study, we visualize the poly(thymine) tails on lateral flow strips, using different combinations of biotinylated or fluorescein-labeled nucleotides, various reporters, and capture oligos. One particular approach, using a fluorescein reporter, reached a target sensitivity of &lt;1 pM and was named Cas activity assay on a strip and was tested using Bacillus anthracis genomic DNA.
Using the Theory of Family Boundary Ambiguity and Ambiguous Loss to Understand the Experiences of Foster Carers’ Own Children
Authors: Tatton Allison 
Published: July 2022

Abstract
In England, nearly three-quarters of looked after children are cared for in foster families. Despite this, relatively little is known about the experiences of foster carers’ children in families who foster. This study used narrative interviews to explore the experiences of twelve adults now aged eighteen to fifty-four years who had been brought up in such families. Their families had fostered for much or all of their childhood and growing up in a fostering family had had a considerable impact on them. Most participants viewed some of the fostered children as siblings and continued to do so into adulthood. The analysis used the theory of family boundary ambiguity and ambiguous loss to gain a deeper understanding of the participants’ experiences. The findings suggest that there is a need for much greater awareness of the issues that foster carers’ own children face. They also suggest that a change in how foster placements are supported needs to include a greater focus on the children of foster carers.
Ultra-Short-Course Antibiotics for Suspected Pneumonia With Preserved Oxygenation
Authors: Klompas Michael , McKenna Caroline , Ochoa Aileen , Ji Wenjing , Chen Tom , Young Jessica , Rhee Chanu ,   for the Prevention Epicenters Program, Centers for Disease Control and Prevention
Published: July 2022

Abstract

Background
Suspected pneumonia is the most common indication for antibiotics in hospitalized patients but is frequently overdiagnosed. We explored whether normal oxygenation could be used as an indicator to support early discontinuation of antibiotics.

Methods
We retrospectively identified all patients started on antibiotics for pneumonia in 4 hospitals with oxygen saturations ≥95% on ambient air, May 2017–February 2021. We propensity-matched patients treated 1–2 days vs 5–8 days and compared hospital mortality and time to discharge using subdistribution hazard ratios (SHRs). Secondary outcomes included readmissions, 30-day mortality, Clostridioides difficile infections, hospital-free days, and antibiotic-free days.

Results
Among 39 752 patients treated for possible pneumonia, 10 012 had median oxygen saturations ≥95% without supplemental oxygen. Of these, 2871 were treated 1–2 days and 2891 for 5–8 days; 4478 patients were propensity-matched. Patients treated 1–2 vs 5–8 days had similar hospital mortality (2.1% vs 2.8%; SHR, 0.75 [95% confidence interval {CI}, .51–1.09]) but less time to discharge (6.1 vs 6.6 days; SHR, 1.13 [95% CI, 1.07–1.19]) and more 30-day hospital-free days (23.1 vs 22.7; mean difference, 0.44 [95% CI, .09–.78]). There were no significant differences in 30-day readmissions (16.0% vs 15.8%; odds ratio [OR], 1.01 [95% CI, .86–1.19]), 30-day mortality (4.6% vs 5.1%; OR, 0.91 [95% CI, .69–1.19]), or 90-day C. difficile infections (1.3% vs 0.8%; OR, 1.67 [95% CI, .94–2.99]).

Conclusions
One-quarter of hospitalized patients treated for pneumonia had oxygenation saturations ≥95% on ambient air. Outcomes were similar with 1–2 vs 5–8 days of antibiotics. Normal oxygenation levels may help identify candidates for early antibiotic discontinuation. Prospective trials are warranted.
Exercise-related major adverse cardiovascular events in asymptomatic recreational master athletes: a case series
Authors: Fruytier Lonneke A , van de Sande Danny AJP , Kemps Hareld MC 
Published: July 2022

Abstract

Background
In master athletes, atherosclerotic coronary artery disease (CAD) is the primary condition leading to major adverse cardiovascular events during sports. We report two cases of asymptomatic recreational athletes who suffered from an exercise-induced cardiovascular event.

Case summary
The first athlete is a 70-year-old male speed skater without known history of cardiovascular disease. He has no typical risk factors for CAD and denied preceding symptoms. During training at the speed skating rink, he suddenly experienced severe chest pain. Electrocardiogram (ECG) showed ST-segment elevation in the precordial leads. In the ambulance, an episode of ventricular fibrillation was converted to atrial fibrillation. Coronary angiography showed a thrombus in the left anterior descending (LAD) coronary artery, treated with a glycoprotein IIb/IIIa inhibitor intravenously.
The second athlete is a 59-year-old male endurance athlete who presented with chest pain during cycling. He had a history of cavotricuspid isthmus ablation and pulmonary vein isolation for paroxysmal atrial fibrillation and flutter but experienced no symptoms in the weeks prior to the event. He also had no risk factors for CAD. ECG showed ST-segment elevation in the inferior leads and reciprocal depression in V2–V4. Successful primary percutaneous intervention of the circumflex artery was performed.

Discussion
Limited data are available to guide recommendations for cardiovascular screening in master athletes. Since master athletes with CAD are often asymptomatic, more knowledge on the optimal pre-participation screening algorithm for identifying individuals at risk of adverse cardiac events is required.
Epigenetic mechanism of L-type calcium channel β-subunit downregulation in short QT human induced pluripotent stem cell-derived cardiomyocytes with CACNB2 mutation
Authors: Zhong Rujia , Zhang Feng , Yang Zhen , Li Yingrui , Xu Qiang , Lan Huan , Cyganek Lukas , El-Battrawy Ibrahim , Zhou Xiaobo , Akin Ibrahim , Borggrefe Martin 
Published: July 2022

Abstract

Aims
A loss-of-function mutation in L-type calcium (Ca2+) channel subunit gene CACNB2 has been reported to cause short QT syndrome subtype 5 (SQT5). However, the mechanism underlying the loss-of-function of the Ca2+ channel has not been clarified. In the present study, we aim to explore the DNA methylation mechanism of L-type Ca2+ channel downregulation in human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) of SQT5.

Methods and results
The hiPSC-CMs were generated from a healthy donor and a SQT5 patient carrying the CACNB2 variant c.1439C &gt; T/p.S480L. The variant was genetically corrected using ribonucleoprotein-based CRISPR/Cas9 technique to obtain an isogenic control cell line. The action potential (AP) and Ca2+ current were measured by patch clamp. Protein expression levels were determined by western blotting. Dot blotting and bisulfite sequence were performed for epigenetic study. Our results showed that AP durations at 10% repolarization (APD10) and 50% repolarization (APD50) were significantly shortened in SQT5 cells and both the expression level of the β-subunit and channel current of L-type Ca2+ channel were reduced. Besides, an increased level of whole-genome DNA methylation and DNA methylation of CpG island in the promoter region of CACNB2 gene was detected. Overexpression of demethylation enzyme could rescue the decreased expression of CACNB2 and the L-type Ca2+ current.

Conclusion
In SQT5 hiPSC-CMs carrying the CACNB2-S480L variant, the decreased L-type Ca2+ current resulting from decreased CACNB2 protein expression was caused by enhanced methylation in the promoter region of the CACNB2 gene and upregulation of DNA methyltransferases might be one of the mechanisms.
Comprehensive comparison of stroke risk score performance: a systematic review and meta-analysis among 6 267 728 patients with atrial fibrillation
Authors: van der Endt Vera H W , Milders Jet , Penning de Vries Bas B L , Trines Serge A , Groenwold Rolf H H , Dekkers Olaf M , Trevisan Marco , Carrero Juan J , van Diepen Merel , Dekker Friedo W , de Jong Ype 
Published: July 2022

Abstract

Aims
Multiple risk scores to predict ischaemic stroke (IS) in patients with atrial fibrillation (AF) have been developed. This study aims to systematically review these scores, their validations and updates, assess their methodological quality, and calculate pooled estimates of the predictive performance.

Methods and results
We searched PubMed and Web of Science for studies developing, validating, or updating risk scores for IS in AF patients. Methodological quality was assessed using the Prediction model Risk Of Bias ASsessment Tool (PROBAST). To assess discrimination, pooled c-statistics were calculated using random-effects meta-analysis. We identified 19 scores, which were validated and updated once or more in 70 and 40 studies, respectively, including 329 validations and 76 updates—nearly all on the CHA2DS2-VASc and CHADS2. Pooled c-statistics were calculated among 6 267 728 patients and 359 373 events of IS. For the CHA2DS2-VASc and CHADS2, pooled c-statistics were 0.644 [95% confidence interval (CI) 0.635–0.653] and 0.658 (0.644–0.672), respectively. Better discriminatory abilities were found in the newer risk scores, with the modified-CHADS2 demonstrating the best discrimination [c-statistic 0.715 (0.674–0.754)]. Updates were found for the CHA2DS2-VASc and CHADS2 only, showing improved discrimination. Calibration was reasonable but available for only 17 studies. The PROBAST indicated a risk of methodological bias in all studies.

Conclusion
Nineteen risk scores and 76 updates are available to predict IS in patients with AF. The guideline-endorsed CHA2DS2-VASc shows inferior discriminative abilities compared with newer scores. Additional external validations and data on calibration are required before considering the newer scores in clinical practice.

Clinical trial registration
ID CRD4202161247 (PROSPERO).
Bacterial diversity and community structure shapes pederin polymorphism but lacks association with host genotype specificity in the rove beetle, Paederus fuscipes
Authors: Teoh Miao-Ching , Veera Singham G 
Published: July 2022

Abstract
Paederus beetles are notorious for their irritant haemolymph toxin pederin, which is synthesised by an unculturable bacterial symbiont, causing dermatitis when in contact with human skin. Pederin polymorphism is observed when (+) females carrying the toxin pederin and (−) females lacking this co-occur in natural populations. Despite reports detecting pederin polymorphism in several Paederina beetles, symbiont infection frequencies in their natural populations and the bacterial diversity differences underlying the polymorphism between these female types are understudied. Herein we report a high prevalence (&gt;80%) of female Paederus fuscipes carrying bacterial ped genes in all six study populations. This finding suggests that selection pressure favouring pederin-producing females is crucial for survival in the natural environment. 16S rRNA metabarcoding analysis revealed significant dominance of the unculturable pederin-producing Pseudomonas-like bacterium (Gammaproteobacteria) in (+) females, consistent with previous studies. The microbial diversity of the (−) females revealed a significant abundance of Apibacter (Bacteroidia), previously undocumented, suggesting its importance in the functionality of (−) females. Predicted functions related to metabolisms are enriched in (−) females, suggesting fitness advantage possibilities in sustaining the population in the absence of predation. Further investigations on the possible genetic basis of the host genotype revealed no association of host mtDNA and pederin polymorphism in Pa. fuscipes.
Nitrite stress increases staphylococcal enterotoxin C transcription and triggers the SigB regulon
Authors: Etter Danai , Büchel Ramona , Patt Tabea , Biggel Michael , Tasara Taurai , Cernela Nicole , Stevens Marc J A , Johler Sophia 
Published: July 2022

Abstract
Staphylococcal food poisoning is a common food intoxication caused by staphylococcal enterotoxins. While growth of Staphylococcus aureus is not inhibited by the meat-curing agent nitrite, we hypothesize that nitrite has an influence on enterotoxin C (SEC) expression. We investigated the influence of 150 mg/l nitrite on SEC expression at mRNA and protein level in seven strains expressing different SEC variants. Additionally, regulatory knockout mutants (Δagr, ΔsarA, and ΔsigB) of high SEC producing strain SAI48 were investigated at mRNA level. Our findings suggest that nitrite effectively increases sec mRNA transcription, but the effects on SEC protein expression are less pronounced. While Δagr mutants exhibited lower sec mRNA transcription levels than wildtype strains, this response was not stress specific. ΔsigB mutants displayed a nitrite stress-specific response. Whole genome sequencing of the strains revealed a defective agr element in one strain (SAI3). In this strain, sec transcription and SEC protein synthesis was not affected by the mutation. Consequently, additional regulatory networks must be at play in SEC expression. Comparison of our findings about SEC with previous experiments on SEB and SED suggest that each SE can respond differently, and that the same stressor can trigger opposing responses in strains that express multiple toxins.
Systematic analysis of the roles of c-di-GMP signaling in Xanthomonas oryzae pv. oryzae virulence
Authors: Lin Yunuan , Mi Duo , Hou Yunyu , Lin Maojuan , Xie Qingbiao , Niu Xiaolei , Chen Yinhua , He Chaozu , Tao Jun , Li Chunxia 
Published: July 2022

Abstract
Cyclic di-guanosine monophosphate (c-di-GMP) is a ubiquitous second messenger, i.e. essential to bacterial adaptation to environments. Cellular c-di-GMP level is regulated by the diguanylate cyclases and the phosphodiesterases, and the signal transduction depends on its receptors. In Xanthomonas oryzae pv. oryzae strain PXO99A, 37 genes were predicted to encode GGDEF, EAL, GGDEF/EAL, HD-GYP, FleQ, MshE, PilZ, CuxR, Clp, and YajQ proteins that may be involved in c-di-GMP turnover or function as c-di-GMP receptors. Although the functions of some of these genes have been studied, but the rest have not been extensively studied. Here, we deleted these 37 genes from PXO99A and analyzed the virulence, motility, biofilm, and EPS production of these mutants. Our results show that most of these genes are required for PXO99A virulence, motility, biofilm formation, or exopolysaccharide production. Although some of them have been reported in previous studies, we found four novel genes (gedpX8, gdpX11, pliZX4, and yajQ) are implicated in X. oryzae pv. oryzae virulence. Our data demonstrate that c-di-GMP signaling is vital for X. oryzae pv. oryzae virulence and some virulence-related factors production, but there is no positive correlation between them in most cases. Taken together, our systematic research provides a new light to understand the c-di-GMP signaling network in X. oryzae pv. oryzae.
A chromosome-level reference genome of a Convolvulaceae species Ipomoea cairica
Authors: Jiang Fan , Wang Sen , Wang Hengchao , Wang Anqi , Xu Dong , Liu Hangwei , Yang Boyuan , Yuan Lihua , Lei Lihong , Chen Rong , Li Weihua , Fan Wei 
Published: July 2022

Abstract
Ipomoea cairica is a perennial creeper that has been widely introduced as a garden ornamental across tropical, subtropical, and temperate regions. Because it grows extremely fast and spreads easily, it has been listed as an invasive species in many countries. Here, we constructed the chromosome-level reference genome of Ipomoea cairica by Pacific Biosciences HiFi and Hi-C sequencing, with the assembly size of 733.0 Mb, the contig N50 of 43.8 Mb, the scaffold N50 of 45.7 Mb, and the Benchmarking Universal Single-Copy Orthologs complete rate of 98.0%. Hi-C scaffolding assigned 97.9% of the contigs to 15 pseudo-chromosomes. Telomeric repeat analysis reveals that 7 of the 15 pseudo-chromosomes are gapless and telomere to telomere. The transposable element content of Ipomoea cairica is 73.4%, obviously higher than that of other Ipomoea species. A total of 38,115 protein-coding genes were predicted, with the Benchmarking Universal Single-Copy Orthologs complete rate of 98.5%, comparable to that of the genome assembly, and 92.6% of genes were functional annotated. In addition, we identified 3,039 tRNA genes and 2,403 rRNA genes in the assembled genome. Phylogenetic analysis showed that Ipomoea cairica formed a clade with Ipomoea aquatica, and they diverged from each other 8.1 million years ago. Through comparative genome analysis, we reconfirmed that a whole genome triplication event occurred specific to Convolvulaceae family and in the ancestor of the genus Ipomoea and Cuscuta. This high-quality reference genome of Ipomoea cairica will greatly facilitate the studies on the molecular mechanisms of its rapid growth and invasiveness.