bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of enterotoxigenic Escherichia coli prophage in spreading antibiotic resistance in a porcine‐derived environment
Authors: Wang Mianzhi , Zeng Zhenling , Jiang Fengwei , Zheng Ying , Shen Huigang , Macedo Nubia , Sun Yongxue , Sahin Orhan , Li Ganwu 
Published: May 2020

SummaryEnterotoxigenic Escherichia coli (ETEC) cause acute secretory diarrhoea in pigs, posing a great economic loss to the swine industry. This study analysed the prevalence and genetic characteristics of prophages from 132 ETEC isolates from symptomatic pigs to determine their potential for spreading antibiotic resistance. A total of 1105 potential prophages were identified, and the distribution of the genome size showed three ‘overlapping’ trends. Similarity matrix comparison showed that prophages correlated with the ETEC lineage distribution, and further identification of these prophages corroborated the lineage specificity. In total, 1206 antibiotic resistance genes (ARGs) of 52 different categories were identified in 132 ETEC strains; among these, 2.65% (32/1206) of ARGs were found to be carried by prophages. Analysis of flanking sequences showed that almost all the ARGs could be grouped into two types: ‘blaTEM‐1B’ and ‘classic class 1 integron (IntI1)’. They co‐occurred with a strictly conserved recombinase and transposon Tn3 family but with a difference: the ‘blaTEM‐1B type’ prophages exhibited a classic Tn2 transposon structure with 100% sequence identity, whereas the ‘IntI1 type’ co‐occurred with the TnAs2 transposon with only 84% sequence identity. These results imply that ARGs might be pervasive in natural bacterial populations through transmission by transposable bacteriophages.
Who is steering the jurisprudence of the European Court of Justice? The influence of Member State submissions on copyright law
Authors: Favale Marcella , Kretschmer Martin , Torremans Paul L. C. 
Published: May 2020

AbstractThe juridification of the European policy process is increasingly fragile, and little understood. This study develops a novel methodology to investigate the influence of Member States on the rulings of the Court of Justice of the European Union (CJEU). The focus is on the domain of copyright law which has seen a dramatic escalation of preliminary references to the Court, indicating a normative void. Examining 170 documents relating to 42 cases registered between 1998 and 2015, we measure empirically the impact of submissions by Member States and the European Commission on the interpretation of copyright concepts. We show that France is the most influential country by some distance, both in terms of the number of interventions (an ‘investment’ in policy) and in terms of persuasive power (arguments adopted by the Court). The evidence also suggests that the departure of the UK from EU litigation will disturb the delicate balance of CJEU jurisprudence.
A core outcome set for pre‐eclampsia research: an international consensus development study
Authors: Duffy JMN , Cairns AE , Richards‐Doran D , van 't Hooft J , Gale C , Brown M , Chappell LC , Grobman WA , Fitzpatrick R , Karumanchi SA , Khalil A , Lucas DN , Magee LA , Mol BW , Stark M , Thangaratinam S , Wilson MJ , von Dadelszen P , Williamson PR , Ziebland S , McManus RJ ,   the International Collaboration to Harmonise Outcomes for Pre‐eclampsia (iHOPE)
Published: May 2020

ObjectiveTo develop a core outcome set for pre‐eclampsia.DesignConsensus development study.SettingInternational.PopulationTwo hundred and eight‐one healthcare professionals, 41 researchers and 110 patients, representing 56 countries, participated.MethodsModified Delphi method and Modified Nominal Group Technique.ResultsA long‐list of 116 potential core outcomes was developed by combining the outcomes reported in 79 pre‐eclampsia trials with those derived from thematic analysis of 30 in‐depth interviews of women with lived experience of pre‐eclampsia. Forty‐seven consensus outcomes were identified from the Delphi process following which 14 maternal and eight offspring core outcomes were agreed at the consensus development meeting. Maternal core outcomes: death, eclampsia, stroke, cortical blindness, retinal detachment, pulmonary oedema, acute kidney injury, liver haematoma or rupture, abruption, postpartum haemorrhage, raised liver enzymes, low platelets, admission to intensive care required, and intubation and ventilation. Offspring core outcomes: stillbirth, gestational age at delivery, birthweight, small‐for‐gestational‐age, neonatal mortality, seizures, admission to neonatal unit required and respiratory support.ConclusionsThe core outcome set for pre‐eclampsia should underpin future randomised trials and systematic reviews. Such implementation should ensure that future research holds the necessary reach and relevance to inform clinical practice, enhance women's care and improve the outcomes of pregnant women and their babies.Tweetable abstract281 healthcare professionals, 41 researchers and 110 women have developed #preeclampsia core outcomes @HOPEoutcomes @jamesmnduffy. [Correction added on 29 June 2020, after first online publication: the order has been corrected.]
Chromosome‐level assembly of the melon thrips genome yields insights into evolution of a sap‐sucking lifestyle and pesticide resistance
Authors: Guo Shao‐Kun , Cao Li‐Jun , Song Wei , Shi Pan , Gao Yong‐Fu , Gong Ya‐Jun , Chen Jin‐Cui , Hoffmann Ary Anthony , Wei Shu‐Jun 
Published: May 2020

AbstractThrips are tiny insects from the order Thysanoptera (Hexapoda: Condylognatha), including many sap‐sucking pests that are causing increasing damage to crops worldwide. In contrast to their closest relatives of Hemiptera (Hexapoda: Condylognatha), including numerous sap‐sucking species, there are few genomic resources available for thrips. In this study, we assembled the first thrips genome at the chromosomal level from the melon thrips, Thrips palmi, a notorious pest in agriculture, using PacBio long‐read and Illumina short‐read sequences. The assembled genome was 237.85 Mb in size, with 1,324 contigs and a contig N50 of 567 kb. All contigs were assembled into 16 linkage groups assisted by the Hi‐C technique. In total, 16,333 protein‐coding genes were predicted, of which 88.13% were functionally annotated. Among sap‐sucking insects, polyphagous species (e.g., T. palmi and Bemisia tabaci) usually possess more detoxification genes than oligophagous species (e.g., Diaphorina citri). The polyphagous thrips genomes characterized so far have relatively more detoxification genes in the GST and CCE families than polyphagous aphids, but they have fewer UGTs. HSP genes, especially from the Hsp70s group, have expanded in thrips compared to other hemipterans. These differences point to different genetic mechanisms associated with detoxification and stress responses in these two groups of sap‐sucking insects. The expansion of these gene families may contribute to the rapid development of pesticide resistance in thrips, as supported by a transcriptome comparison of resistant and sensitive populations of T. palmi. The high‐quality genome developed here provides an invaluable resource for understanding the ecology, genetics, and evolution of thrips as well as their relatives more generally.
Defining High‐risk Emergency Chief Complaints: Data‐driven Triage for Low‐ and Middle‐income Countries
Authors: Rice Brian , Leanza Joseph , Mowafi Hani , Thadeus Kamara Nicholas , Mugema Mulogo Edgar , Bisanzo Mark , Nikam Kian , Kizza Hilary , Newberry Jennifer A. , Strehlow Matthew ,   Global Emergency Care Investigator Group, Kohn Michael 
Published: May 2020

AbstractObjectivesEmergency medicine in low‐ and middle‐income countries (LMICs) is hindered by lack of research into patient outcomes. Chief complaints (CCs) are fundamental to emergency care but have only recently been uniquely codified for an LMIC setting in Uganda. It is not known whether CCs independently predict emergency unit patient outcomes.MethodsPatient data collected in a Ugandan emergency unit between 2009 and 2018 were randomized into validation and derivation data sets. A recursive partitioning algorithm stratified CCs by 3‐day mortality risk in each group. The process was repeated in 10,000 bootstrap samples to create an averaged risk ranking. Based on this ranking, CCs were categorized as “high‐risk” (>2× baseline mortality), “medium‐risk” (between 2 and 0.5× baseline mortality), and “low‐risk” (<0.5× baseline mortality). Risk categories were then included in a logistic regression model to determine if CCs independently predicted 3‐day mortality.ResultsOverall, the derivation data set included 21,953 individuals with 7,313 in the validation data set. In total, 43 complaints were categorized, and 12 CCs were identified as high‐risk. When controlled for triage data including age, sex, HIV status, vital signs, level of consciousness, and number of complaints, high‐risk CCs significantly increased 3‐day mortality odds ratio (OR = 2.39, 95% confidence interval [CI] = 1.95 to 2.93, p < 0.001) while low‐risk CCs significantly decreased 3‐day mortality odds (OR = 0.16, 95% CI = 0.09 to 0.29, p < 0.001).ConclusionsHigh‐risk CCs were identified and found to predict increased 3‐day mortality independent of vital signs and other data available at triage. This list can be used to expand local triage systems and inform emergency training programs. The methodology can be reproduced in other LMIC settings to reflect their local disease patterns.
Impact of Long‐Term Alcohol Consumption and Relapse on Genome‐Wide DNA Methylation Changes in Alcohol‐Dependent Subjects: A Longitudinal Study
Authors: Friedel Eva , Walter Henrik , Veer Ilya M. , Zimmermann Ulrich S. , Heinz Andreas , Frieling Helge , Zindler Tristan 
Published: May 2020

BackgroundGenetic factors play an important role in the development and maintenance of alcohol use disorder (AUD). Significant and widespread differences in methylation levels of multiple regions within the genome have been reported between AUD patients and healthy controls in large epigenome‐wide association studies (EWASs). Also, within patient populations, methylation changes over time (both during and after withdrawal) have been identified as sensitive indicators for disease activity. The detection of changes in methylation levels is a powerful tool to further explore and understand the biological correlates and underpinnings of AUD. Although there is strong and convincing evidence for differences in methylation of various sites between AUD patients and controls, only few studies assessed changes within patients over longer periods of time while taking into account alcohol consumption, relapse, and abstinence. So far, the longest period assessed as a within‐subject design using EWASs was 4 weeks.MethodsHere, we investigated changes in whole‐genome methylation levels within a sample of 69 detoxified AUD patients over a period as long as 12 months for the first time, comparing patients that relapsed within the follow‐up period to those that remained abstinent.ResultsWhole‐genome methylation patterns of individual CpG sites over time did not differ between abstinent and relapsing patients. However, there was a negative association between global mean methylation at the 12‐month follow‐up and alcohol consumption within our sample.ConclusionAlthough the present study represents the largest study of methylation levels in a sample of AUD patients with a follow‐up period of 1 year and accounting for alcohol consumption and relapse to date, the sample size might still not be large enough to detect genome‐wide significant effects. Therefore, large‐scale, long‐term studies with AUD subjects are needed to determine the utility of DNA methylation for the assessment and monitoring of persons with alcohol use disorders.
Survival, movements and habitat use of captive‐bred and reintroduced dusky gopher frogs
Authors: Roznik E. A. , Reichling S. B. 
Published: May 2020

AbstractDespite the growing roles of assisted reproduction and captive breeding in reintroductions, we have a limited understanding of the viability of these animals once released. We radiotracked endangered dusky gopher frogs Lithobates sevosus for up to 24 days after they were released into the wild to (1) assess the viability of juvenile frogs produced using artificial fertilization and raised in captivity until four weeks post‐metamorphosis, (2) investigate survival rates, movement patterns, and habitat use and (3) examine whether it is more beneficial to release frogs at the pond edge or into burrows in the uplands. Released frogs had a relatively high survival rate (76% overall, with mortality ceasing after 14 days) and behaved as expected, moving fairly long distances (up to 153 m daily and 426 m total) and locating suitable shelters, including burrows and stump holes. Frogs that sheltered underground had a 22% higher survival rate than frogs that did not, highlighting the importance of these habitat features. Compared to frogs released into burrows, frogs released at the pond had a 33% lower survival rate, spent less time underground and moved farther and more often, likely while searching for shelter. Frogs selected habitat characteristics that are associated with effects of fire, including an open canopy and abundant ground vegetation. Our study demonstrates that juvenile dusky gopher frogs successfully transitioned to their natural habitat, and that any effects of artificial fertilization or captivity on juvenile viability appear to be minimal. Releasing frogs into areas with abundant underground refuges and using frequent prescribed fire to maintain the habitat should benefit dusky gopher frog populations and improve the success of reintroductions.
‘It's just basically a box full of disease’—navigating sterile syringe scarcity in a rural New England state
Authors: Pollini Robin A. , Paquette Catherine E. , Slocum Susannah , LeMire Dean 
Published: May 2020

AbstractBackground and AimsInjection drug use has increased in non‐urban communities in the United States where sterile syringe access is limited. This study aimed to characterize how people who inject drugs in a predominantly rural state navigate syringe scarcity.DesignQualitative study.SettingNew Hampshire (NH), USA. At the time of our study, syringe services programs were illegal in NH but pharmacies could sell ≤ 10 syringes without prescription.Participants/CasesTwenty people aged ≥ 18 years who injected at least once in the past 30 days were recruited through provider referral, street‐based recruitment and snowball sampling.MeasurementsSemi‐structured interview guide. Verbatim transcripts were coded based on interview guide constructs and emergent themes. Analysis focused on pharmacy syringe access, unofficial syringe sources and related impacts on syringe sharing and reuseFindingsParticipants could identify no local pharmacies that sold syringes without prescription. Pharmacy purchase in neighboring counties, or across state lines, required private transportation and this, along with purchaser identification requirements, presented substantial access barriers. Interstate travel also exposed participants to vigilant policing of interstate highways and potential criminal justice involvement. Many participants thus resorted to informal syringe sources closer to home including purchasing syringes on the street, using discarded syringes, breaking into biohazard containers and constructing improvised syringes out of salvaged syringe parts, metals and plastics. Repeated re‐use of syringes until they were no longer operational was common. Overall, syringe scarcity gave participants few options but to engage in syringe sharing and re‐use, putting them at risk of serious injection‐related infections.ConclusionsLimited sterile syringe access contributes to an environment in which people who inject drugs report that they are less able to refrain from risky injection practices.
United in adversity: Aridity and cold influence aggregation behaviour in a social lizard, Egernia stokesii
Authors: Johnston Gregory R. , Lanham Elvira J. , Bull C. Michael 
Published: May 2020

AbstractSociality has evolved independently many times in a diverse array of animal taxa. While sociality in some invertebrates, birds and mammals is relatively well understood, complex social behaviour in Squamate reptiles is a comparatively recent discovery. The extent to which social behaviour is phylogenetically constrained, or free to respond to environmental conditions is a key question in understanding sociality. We sampled 74 aggregations involving 137 individuals of a social lizard (Egernia stokesii) from 13 sites across a 96 250 km2 area showing a wide range of environmental conditions. Over all locations, 70% of the lizards were found in aggregations, supporting the previous suggestion that aggregation in this species is phylogenetically constrained. However, the size of aggregations was negatively related to spatial variation in aridity and daily variation in maximum temperature, suggesting that social behaviour also varied in response to harsh environmental conditions. Lizards aggregated more in arid areas and on cold days. Our results show that it is overly simplistic to regard social behaviour in E. stokesii as either phylogenetically constrained or environmentally determined. A more nuanced appreciation of the extent to which social behaviour is free to vary in response to environmental conditions improves our understanding of social behaviour in Squamate reptiles.
Assessment of the FAM174A 11G allele as a risk allele for equine metabolic syndrome
Authors: Roy M. M. , Norton E. M. , Rendahl A. K. , Schultz N. E. , McFarlane D. , Geor R. J. , Mickelson J. R. , McCue M. E. 
Published: May 2020

SummaryAn 11G nucleotide repeat in the 3′ UTR of FAM174A was recently postulated as a risk allele with a dominant mode of inheritance for equine metabolic syndrome (EMS) and laminitis status in Arabian horses. The objective of this project was to evaluate this hypothesis in a large and diverse across‐breed population. A total of 301 ponies, 292 Morgans, 64 Arabians, 49 Tennessee Walking Horses and 59 Quarter Horses were genotyped for six observed G repeat alleles in the FAM174A 3′ UTR. Phenotype data included laminitis status, baseline insulin, glucose, non‐esterified fatty acids, triglycerides, adiponectin, leptin, ACTH, insulin and glucose post oral sugar test, and two proxies for insulin resistance. The 11G allele frequencies were 18.8, 6.9, 1.8, 0.2 and 0.0% in the Arabians, Tennessee Walkers, ponies, Morgans and Quarter Horses respectively. Association analyses between FAM174A genotype and EMS phenotypes, and between allele count and EMS phenotypes, identified no statistically significant associations. When a dominant effect for the 11G allele was evaluated, a statistically significant association with adiponectin levels was identified in the ponies, and pairwise comparisons revealed that the estimated marginal means were higher in ponies with the 11G allele vs. alternative alleles (i.e. the allele had a protective effect). In conclusion, our data do not support the FAM174A 11G allele as a risk allele for EMS in our studied breeds.
A CLOSE‐UP guide to capturing clinical images
Authors: Abbott Lisa M. , Soyer H. Peter 
Published: May 2020

AbstractTelemedicine is rapidly becoming ubiquitous as the medical profession adjusts its practice to provide optimal care to patients in the context of the COVID19 pandemic. The ability to provide accurate dermatological advice via telemedicine is dependent on the receipt of high‐quality clinical images and accurate clinical context, on which clinicians receive little education during medical school and subsequent training. Clinicians can improve their capture, delivery and storage of images using the CLOSE‐UP acronym, which encapsulates important considerations in the clinical photography process.
Woody vegetation damage by the African elephant during severe drought at Pongola Game Reserve, South Africa
Authors: Thornley Reece , Spencer Matthew , Zitzer Heike R. , Parr Catherine L. 
Published: May 2020

AbstractElephants (Loxodonta africana) significantly alter ecosystem structure and composition through browsing (e.g. pollarding, debarking and toppling). Such browsing is predicted to intensify during severe drought which may become more common with climate change. Here, we make use of an elephant impact survey from 2012 to 2015 and during the El Nino drought of 2015–2016 at Pongola Game Reserve (107 km2), KwaZulu‐Natal, to investigate how severe drought influenced damage severity of different tree heights and species by elephants in this small reserve. Contrary to expectations, damage to common species did not change with severe drought. Crown damage had the highest predicted probability across heights (29%–90%) and species (46%–75%) regardless of drought. However, we found severe drought increased the predicted probabilities of crown damage to smaller trees <4 m, mortality >6 m and severe damage at 4–6 m. Consequently, elephant damage during severe drought may alter vegetation structure by severely damaging or killing large trees (>4 m) and extensively damaging the crowns of trees <4 m. Long‐term monitoring of elephant effects on woody vegetation is essential to enable science‐based management in response to future drought and elephant damage (e.g. range expansion, beehive deterrents) to protect elephants and conserve woody vegetation.
A retrospective observational study of neuromuscular monitoring practice in 30,430 cases from six Danish hospitals
Authors: Thomsen J. L. D. , Staehr‐Rye A. K. , Mathiesen O. , Hägi‐Pedersen D. , Gätke M. R. 
Published: May 2020

SummaryTimely application of objective neuromuscular monitoring can avoid residual neuromuscular blockade. We assessed the frequency of objective neuromuscular monitoring with acceleromyography and the last recorded train‐of‐four ratio in a cohort of Danish patients. We extracted data from all patients receiving general anaesthesia from November 2014 to November 2016 at six hospitals in the Zealand Region of Denmark. Acceleromyography was available in all operating rooms and data were recorded automatically. The primary outcome measure was acceleromyography use in patients receiving neuromuscular blocking agents, divided into non‐depolarising agents and succinylcholine only. The dataset included 76,743 cases, of which 30,430 received a neuromuscular blocking drug. Non‐depolarising drugs were used in 16,525 (54%) and succinylcholine as the sole drug in 13,905 (46%) cases. Acceleromyography was used in 14,463 (88%) patients who received a non‐depolarising neuromuscular blocking drug and in 4224 (30%) receiving succinylcholine alone. Acceleromyography use varied between the departments from 58% to 99% for non‐depolarising drugs and from 3% to 79% for succinylcholine alone. The median (IQR [range]) of the last recorded train‐of‐four ratio before tracheal extubation was 0.97 (0.90–1.06 [0.01–2.20]) when non‐depolarising drugs were used, and was less than 0.9 in 22% of cases. The OR for oxygen desaturation was higher with the use of succinylcholine [2.51 (95%CI 2.33–2.70) p < 0.001] and non‐depolarising drugs [2.57 (95%CI 2.32–2.84) p < 0.001] as compared with cases where no neuromuscular blockade drug was used. In conclusion, acceleromyography was almost always used in cases where non‐depolarising neuromuscular blocking drugs were used, but a train‐of‐four ratio of 0.9 was not always achieved. Monitoring was used in less than 30% of cases where succinylcholine was the sole drug used.