bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genom‐wide analysis identifies single nucleotide polymorphism variations and altered pathways associated with poor semen quality in breeding bulls
Authors: Ebenezer Samuel King John Peter , Kumaresan Arumugam , Talluri Thirumala Rao , Sinha Manish Kumar , Raval Kathan , Nag Pradeep , Karuthadurai Thirumalaisamy , Aranganathan Veeramani 
Published: June 2022

AbstractThe reason for poor semen quality among the breeding bulls is not well understood. In the present study, we performed high‐throughput RNAseq analysis of spermatozoa to identify the SNPs present in good and poor‐quality semen‐producing Holstein Friesian breeding bulls. A total of 21,360 and 44,650 SNPs were identified in good and poor‐quality semen with a minimum read depth of 20, among which 4780 and 8710 novel variants were observed in good and poor‐quality semen, respectively. Greater SNPs and indels variations were observed in poor compared to good‐quality semen. In poor‐quality semen, SNP variations were observed in ZNF280B, SLC26A2, DMXL1, OR52A1, MACROD2 and REV1 genes, which are associated with regulation of spermatogenesis, post‐testicular maturation, Cl− channel activity, V‐ATPase‐mediated intracellular vesicle acidification, a mono‐ADP‐ribosyl hydrolase and ATR‐Chk1 checkpoint activation. GO analysis of filtered genes with significant variations between good and poor‐quality semen showed enrichment in important pathways related to semen quality such as MAPK signalling pathway, Akt signalling pathway, focal adhesion, cAMP signalling pathway, and Rap1 signalling pathway. Network analysis of filtered genes in poor‐quality semen showed variations in pathways of purine metabolism, pyrimidine metabolism, prolactin signalling pathway and RNA cap‐binding complex. It is inferred that SNP in genes involved in maintaining sperm functions could be the reason for poor‐quality semen production in bulls, and the identified SNPs hold potential to be used as biomarkers for semen quality in bulls.
Megaviruses contain various genes encoding for eukaryotic vesicle trafficking factors
Authors: Khalifeh Dany , Neveu Emilie , Fasshauer Dirk 
Published: June 2022

AbstractMany intracellular pathogens, such as bacteria and large viruses, enter eukaryotic cells via phagocytosis, then replicate and proliferate inside the host. To avoid degradation in the phagosomes, they have developed strategies to modify vesicle trafficking. Although several strategies of bacteria have been characterized, it is not clear whether viruses also interfere with the vesicle trafficking of the host. Recently, we came across SNARE proteins encoded in the genomes of several bacteria of the order Legionellales. These pathogenic bacteria may use SNAREs to interfere with vesicle trafficking, since SNARE proteins are the core machinery for vesicle fusion during transport. They assemble into membrane‐bridging SNARE complexes that bring membranes together. We now have also discovered SNARE proteins in the genomes of diverse giant viruses. Our biochemical experiments showed that these proteins are able to form SNARE complexes. We also found other key trafficking factors that work together with SNAREs such as NSF, SM, and Rab proteins encoded in the genomes of giant viruses, suggesting that viruses can make use of a large genetic repertoire of trafficking factors. Most giant viruses possess different collections, suggesting that these factors entered the viral genome multiple times. In the future, the molecular role of these factors during viral infection need to be studied.
Supply spillovers during the pandemic: Evidence from high‐frequency shipping data
Authors: Cerdeiro Diego A. , Komaromi Andras 
Published: June 2022

AbstractWorld trade contracted dramatically during the global economic crisis induced by the COVID‐19 pandemic. Disruptions in international supply chains were widely reported as governments imposed containment measures (lockdowns) to halt the spread of the disease. At the same time, demand declined as households and firms scaled back spending. This paper attempts to disentangle the supply and demand channels in trade by quantifying the causal effect of supply spillovers from lockdowns. We utilise a novel dataset of daily bilateral seaborne trade and design a shift‐share identification strategy that leverages geography‐induced cargo delivery lags to track the transmission of supply disruptions across space. We find strong but short‐lived supply spillovers of lockdowns through international trade. Moreover, the evidence is suggestive of the downstream propagation of countries' lockdowns through global supply chains. The short‐lived nature of the disruptions despite the unprecedented scale of the shock caution against any blunt use of trade and tax policies to create costly redundancies in global supply chains.
The epicentre model and American influence on Bahamian Englishes
Authors: Hackert Stephanie 
Published: June 2022

AbstractAmericanization has been described as one of the major sociocultural processes of language change currently affecting varieties of English worldwide; it is generally linked to the post‐World War II rise of the United States to global superpower status in political, military, economic, and cultural terms. Owing to their immediate geographical proximity, the Bahamas always had closer demographic, cultural, and institutional links with the North American mainland than other British colonies. The present paper applies the notion of epicentral influence, in the sense of a regionally dominant model influencing developments in neighboring areas, to Bahamian‐American linguistic relations and attempts to disentangle global from epicentral American influence. It considers not just standard Bahamian English but also Bahamian Creole, all levels of language, diachronic and synchronic data, and corpus findings as well as attitudinal studies and discusses the theoretical and methodological implications of the Bahamian data for the epicentre idea.
Early-onset sepsis in very preterm neonates in Australia and New Zealand, 2007–2018
Authors: Duggan Husharn L , Chow Sharon S W , Austin Nicola C , Shah Prakeshkumar S , Lui Kei , Tan Kenneth 
Published: June 2022

ObjectiveTo evaluate the epidemiology and population trends of early-onset sepsis in very preterm neonates admitted to neonatal intensive care units (NICU) in Australia and New Zealand.DesignRetrospective observational cohort study using a dual-nation registry database.Setting29 NICUs that have contributed to the Australian and New Zealand Neonatal Network.ParticipantsNeonates born at <32 weeks’ gestation born between 2007 and 2018 and then admitted to a NICU.Main outcome measuresMicroorganism profiles, incidence, mortality and morbidity.ResultsOver the 12-year period, 614 early-onset sepsis cases from 43 178 very preterm admissions (14.2/1000 admissions) were identified. The trends of early-onset sepsis incidence remained stable, varying between 9.8 and 19.4/1000 admissions (linear trend, p=0.56). The leading causative organisms wereEscherichia coli(E. coli) (33.7%) followed by group BStreptococcus(GBS) (16.1%). The incidence ofE. coliincreased between 2007 (3.2/1000 admissions) and 2018 (8.3/1000 admissions; p=0.02). Neonates withE. colihad higher odds of mortality compared with those withGBS(OR=2.8, 95% CI 1.2 to 6.1). Mortality due toGBSdecreased over the same period (2007: 0.6/1000 admissions, 2018: 0.0/1000 admissions; p=0.01). Early-onset sepsis tripled the odds of mortality (OR=3.0, 95% CI 2.4 to 3.7) and halved the odds of survival without morbidity (OR=0.5, 95% CI 0.4 to 0.6).ConclusionEarly-onset sepsis remains an important condition among very preterm populations. Furthermore,E. coliis a dominant microorganism of very preterm early-onset sepsis in Australia and New Zealand. Rates ofE. colihave been increasing in recent years, whileGBS-associated mortality has decreased.
Acceleration during neonatal transport and its impact on mechanical ventilation
Authors: Lantos Lajos , Széll András , Chong David , Somogyvári Zsolt , Belteki Gusztav 
Published: June 2022

ObjectiveDuring interhospital transfer, critically ill neonates frequently require mechanical ventilation and are exposed to physical forces related to movement of the ambulance. In an observational study, we investigated acceleration during emergency transfers and if they result from changes in ambulance speed and direction or from vibration due to road conditions. We also studied how these forces impact on performance of the fabian+nCPAP evolution neonatal ventilator and on patient-ventilator interactions.MethodsWe downloaded ventilator parameters at 125 Hz and acceleration data at 100 Hz sampling rates, respectively, during the emergency transfer of 109 infants. Study subjects included term, preterm and extremely preterm infants. We computationally analysed the magnitude, direction and frequency of ambulance acceleration. We also analysed maintenance and variability of ventilator parameters and the shape of pressure-volume loops.ResultsWhile acceleration was <1 m/s2most of the time, most babies were occasionally exposed to accelerations>5 m/s2. Vibration was responsible for most of the acceleration, rather than speed change or vehicle turning. There was no significant difference between periods of high or low vibration in ventilation parameters, their variability and how well targeted parameters were kept close to their target. Speed change or vehicle turning did not affect ventilator parameters or performance. However, during periods of intense vibration, pressure-volume ventilator loops became significantly more irregular.ConclusionsInfants are exposed to significant acceleration and vibration during emergency transport. While these forces do not interfere with overall maintenance of ventilator parameters, they make the pressure-volume loops more irregular.
Prevalence of SARS-CoV-2 positivity in infants with bronchiolitis: a multicentre international study
Authors: Cozzi Giorgio , Cortellazzo Wiel Luisa , Amaddeo Alessandro , Gatto Antonio , Giangreco Manuela , Klein-Kremer Adi , Bosis Samantha , Silvagni Davide , Debbia Carla , Nanni Laura , Chiappa Sara , Minute Marta , Corsini Ilaria , Morabito Giuliana , Gortan Anna Jolanda , Colombo Marco , Marchetti Federico , Garelli Davide , Piffer Arianna , Cardinale Fabio , Levy Nitai , Curatola Antonietta , Gojsina Bojana , Basu Suvradeep , Barbi Egidio , Sovtic Aleksandar 
Published: June 2022

BackgroundBronchiolitis is the leading acute respiratory tract infection in infants during the winter season. Since the beginning of the SARS-CoV-2 pandemic, a reduction in the number of bronchiolitis diagnoses has been registered.ObjectiveThe present study aimed to describe the incidence and clinical features of bronchiolitis during the 2020–2021 winter season in a large cohort of children in Europe and Israel, and to clarify the role of SARS-CoV-2.Setting, patients, interventionsWe conducted a multicentre observational cross-sectional study in 23 paediatric emergency departments in Europe and Israel. Clinical and demographic data about all the cases of infants diagnosed with bronchiolitis from 1 October 2020 to 30 April 2021 were collected. For each enrolled patient, diagnostic tests, treatments and outcomes were reported.Main outcome measuresThe main outcome was the prevalence of SARS-CoV-2-positive bronchiolitis.ResultsThree hundred and fourteen infants received a diagnosis of bronchiolitis during the study period. Among 535 infants who tested positive for SARS-CoV-2, 16 (3%) had bronchiolitis. Median age, male sex predominance, weight, history of prematurity and presence of comorbidities did not differ between the SARS-CoV-2-positive and SARS-CoV-2-negative groups. Rhinovirus was the most common involved pathogen, while respiratory syncytial virus (RSV) was detected in one case. SARS-CoV-2 bronchiolitis had a mild clinical course, with one patient receiving oxygen supplementation and none requiring paediatric or neonatal intensive care unit admission.ConclusionsDuring the SARS-CoV-2 pandemic, a marked decrease in the number of bronchiolitis diagnoses and the disappearance of the RSV winter epidemic were observed. SARS-CoV-2-related bronchiolitis was rare and mostly displayed a mild clinical course.
Designing and evaluating a patient decision aid for patients with locally advanced or locally recurrent rectal cancer: a national multicentre mixed methods study protocol
Authors: Williams Anwen , Hutchings Hayley Anne , Harris Dean Anthony , Evans Martyn , Harji Deena 
Published: June 2022

IntroductionApproximately 5%–10% of new rectal cancers are locally advanced (locally advanced rectal cancer (LARC)) at presentation with 4%–8% recurring (locally recurrent rectal cancer (LRRC)) after initial treatment. Patients with potentially curable disease have to consider many trade-offs when considering major exenterative surgery. There are no decision tools for these patients and current resources have found to not meet minimum international standards. The overall aim of this study is to produce a validated patient decision aid (PtDA) to assist patients considering radical pelvic exenteration for LARC and LRRC created in line with international minimum standards.Methods and analysisThis study is a national, multicentre mixed methods project and has been designed in keeping with guidance from the International Patient Decision Aids Standard.This study is in four stages. In stage 1, we will develop the PtDA and its content using agile developmental methodology. In stage 2, we will assess the content and face validity of the PtDA using mixed-methods with key stakeholders. In stage 3, we will assess the feasibility and efficacy of the PtDA. In stage 4, we will establish the barriers and facilitators to the use of a PtDA in the outpatient setting. Questionnaires including the QQ-10, EORTC PATSAT-C33, Preparation for Decision-Making Scale and the NoMAD survey will be analysed during the study. Interviews will be analysed using thematic analysis.Ethics and disseminationResearch ethics approval from North of Scotland Research Ethics Service 19/NS/0056 (IRAS 257890) has been granted. Results will be published in open access peer-reviewed journals, presented in conferences and distributed through bowel research UK charity. External endorsement will be sought from the International Patient Decision Standards Collaboration inventory of PtDAs.PROSPERO registration numberCRD42019122933.
Incidence of acute lower respiratory tract disease hospitalisations, including pneumonia, among adults in Bristol, UK, 2019, estimated using both a prospective and retrospective methodology
Authors: Hyams Catherine , Begier Elizabeth , Garcia Gonzalez Maria , Southern Jo , Campling James , Gray Sharon , Oliver Jennifer , Gessner Bradford D , Finn Adam 
Published: June 2022

ObjectivesTo determine the disease burden of acute lower respiratory tract disease (aLRTD) and its subsets (pneumonia, lower respiratory tract infection (LRTI) and heart failure) in hospitalised adults in Bristol, UK.SettingSingle-centre, secondary care hospital, Bristol, UK.DesignWe estimated aLRTD hospitalisations incidence in adults (≥18 years) in Bristol, UK, using two approaches. First, retrospective International Classification of Diseases 10th revision (ICD-10) code analysis (first five positions/hospitalisation) identified aLRTD events over a 12-month period (March 2018 to February 2019). Second, during a 21-day prospective review (19 August 2019 to 9 September 2019), aLRTD admissions were identified, categorised by diagnosis and subsequently annualised. Hospital catchment denominators were calculated using linked general practice and hospitalisation data, with each practice’s denominator contribution calculated based on practice population and per cent of the practices’ hospitalisations admitted to the study hospital.ParticipantsProspective review: 1322 adults screened; 410 identified with aLRTD. Retrospective review: 7727 adult admissions.Primary and secondary outcome measuresThe incidence of aLRTD and its subsets in the adult population of Southmead Hospital, Bristol UK.ResultsBased on ICD-10 code analysis, annual incidences per 100 000 population were: aLRTD, 1901; pneumonia, 591; LRTI, 739; heart failure, 402. aLRTD incidence was highest among those ≥65 years: 65–74 (3684 per 100 000 adults), 75–84 (6962 per 100 000 adults) and ≥85 (11 430 per 100 000 adults). During the prospective review, 410/1322 (31%) hospitalised adults had aLRTD signs/symptoms and annualised incidences closely replicated retrospective analysis results.ConclusionsThe aLRTD disease burden was high, increasing sharply with age. The aLRTD incidence is probably higher than estimated previously due to criteria specifying respiratory-specific symptoms or radiological change, usage of only the first diagnosis code and mismatch between case count sources and population denominators. This may have significant consequences for healthcare planning, including usage of current and future vaccinations against respiratory infection.
Burden and factors associated with perceived stress amidst COVID-19: a population web-based study in Pakistan
Authors: Lakhdir Maryam Pyar Ali , Peerwani Ghazal , Azam Syed Iqbal , Ali Nathwani Apsara , Iqbal Romaina , Asad Nargis 
Published: June 2022

ObjectiveThis study aims to determine the burden and factors associated with perceived stress in the Pakistani population amidst the COVID-19 pandemic.SettingA web-based cross-sectional survey was conducted from April to August 2020.PopulationThis survey was broadcasted on the web using a Google form link and 1654 Pakistani residents had completed this survey. Individuals belonging to any province, city, village, or district of Pakistan irrespective of any age, having internet access and a link of Google form, with English/Urdu competency, consent to participate, and currently residing in Pakistan were eligible to participate.Outcome measurePerceived stress was measured using a validated tool of perceived stress scale-10. Multiple ordinal regression was used, and an adjusted OR along with a 95% CI are reported.ResultsThe mean score of perceived stress was 19.32 (SD ±6.67). Most of the participants screened positive for moderate (69%) and high levels (14%) of stress, respectively. The odds of high-perceived stress among severely anxious participants were 44.67 (95% CI: 21.33 to 93.53) times than participants with no/minimal generalised anxiety during the complete lockdown. However, the odds of high levels of perceived stress among moderately anxious respondents were 15.79 (95% CI: 10.19 to 24.28) times compared with participants with no/minimal anxiety during the smart lockdown.ConclusionThis study evidence that the pandemic was highly distressing for the Pakistani population causing the maximum level of perceived stress in more than half of the population. Adequate and timely interventions are needed before high-stress levels culminate into psychological disorders.
Systematic review of the effectiveness of non-pharmacological interventions used to treat adults with inducible laryngeal obstruction
Authors: Haines Jemma , Smith Jacklyn Ann , Wingfield-Digby James , King Jenny , Yorke Janelle , Fowler Stephen J 
Published: June 2022

IntroductionInducible laryngeal obstruction (ILO) describes transient laryngeal closure during respiration and can cause significant morbidity. Non-pharmacological behavioural therapy is the commonly cited treatment but efficacy is largely unknown.AimTo synthesise the current evidence base on the effectiveness of non-pharmacological interventions used to treat adults with ILO.MethodsElectronic databases (Medline/Embase/CINAHL/PsycINFO/AMED/CENTRAL) were systematically searched, informed by a population, intervention, comparison, outcome framework. Two reviewers independently screened a representative sample, with lead-author completion due to excellent inter-rater reliability. Data was extracted using a predefined piloted form. Methodological quality was appraised (blindly by two reviewers) using the Joanna Briggs Institute Critical Appraisal Tools. A narrative synthesis was performed due to heterogeneity of studies (PROSPERO registration number: CRD42020213187).ResultsInitial searching identified 3359 records. Full-text screening occurred in 92 records and 14 studies, comprising 527 participants, were deemed eligible. All studies were low-level evidence (observational by design, with four case reports), with a high risk of bias; none contained control arms for comparison. Intervention description was inconsistently and poorly described but direction of effect was positive in 76% of outcomes measured. The majority of studies showed a reduction in symptom scores and improved direct laryngeal imaging post intervention; there was an overall reduction, 59.5%, in healthcare utilisation.DiscussionThe literature is in an embryonic state and lacks robust data to truly inform on the effectiveness of non-pharmacological interventions used to treat adults with ILO. However, positive signals in the synthesis performed support non-pharmacological treatment approaches and further development is warranted.
Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in a murine model of PSC
Authors: Awoniyi Muyiwa , Wang Jeremy , Ngo Billy , Meadows Vik , Tam Jason , Viswanathan Amba , Lai Yunjia , Montgomery Stephanie , Farmer Morgan , Kummen Martin , Thingholm Louise , Schramm Christoph , Bang Corinna , Franke Andre , Lu Kun , Zhou Huiping , Bajaj Jasmohan S , Hylemon Phillip B , Ting Jenny , Popov Yury V , Hov Johannes Roksund , Francis Heather L , Sartor Ryan Balfour 
Published: June 2022

ObjectiveConflicting microbiota data exist for primary sclerosing cholangitis (PSC) and experimental models. Goal: define the function of complex resident microbes and their association relevant to PSC patients by studying germ-free (GF) and antibiotic-treated specific pathogen-free (SPF) multidrug-resistant 2 deficient (mdr2−/−) mice and microbial profiles in PSC patient cohorts.DesignWe measured weights, liver enzymes, RNA expression, histological, immunohistochemical and fibrotic biochemical parameters, faecal 16S rRNA gene profiling and metabolomic endpoints in gnotobiotic and antibiotic-treated SPFmdr2−/−mice and targeted metagenomic analysis in PSC patients.ResultsGFmdr2−/−mice had 100% mortality by 8 weeks with increasing hepatic bile acid (BA) accumulation and cholestasis. Early SPF autologous stool transplantation rescued liver-related mortality. Inhibition of ileal BA transport attenuated antibiotic-accelerated liver disease and decreased total serum and hepatic BAs. Depletion of vancomycin-sensitive microbiota exaggerated hepatobiliary disease. Vancomycin selectively decreased Lachnospiraceae and short-chain fatty acids (SCFAs) but expanded Enterococcus and Enterobacteriaceae. Antibiotics increasedEnterococcus faecalisandEscherichia coliliver translocation. Colonisation of GFmdr2−/−mice with translocatedE. faecalisandE. colistrains accelerated hepatobiliary inflammation and mortality. Lachnospiraceae colonisation of antibiotic pretreatedmdr2−/−mice reduced liver fibrosis, inflammation and translocation of pathobionts, and SCFA-producing Lachnospiraceae and purified SCFA decreased fibrosis. Faecal Lachnospiraceae negatively associated, andE. faecalis/ Enterobacteriaceaepositively associated, with PSC patients’ clinical severity by Mayo risk scores.ConclusionsWe identified novel functionally protective and detrimental resident bacterial species inmdr2−/−mice and PSC patients with associated clinical risk score. These insights may guide personalised targeted therapeutic interventions in PSC patients.