bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of diet, activities, environmental exposures and trimethylamine metabolism on alveolar breath compounds: protocol for a retrospective case-cohort observational study
Authors: Gabashvili Irene S. 
Published: January 2021

ABSTRACTBackgroundExhaled breath contains thousands of volatile organic compounds (VOCs) that reflect on biochemical and biophysical activities both outside and within the human body. Breath analysis could provide non-invasive, cost-effective, real time early disease diagnosis and monitoring of therapeutic responses.ObjectivesThe primary objective of this study was to assess the effectiveness of alveolar breath testing in diagnosing idiopathic systemic body and breath odors. Key secondary objectives were to assess if breath tests can reliably differentiate subtypes of idiopathic malodor in different environments and dietary regimens, and to map metabolites to biomedical functions and pathways.Study DesignThe basic design was to measure a cohort of idiopathic odor in order to identify potential molecular correlates with genotypic and phenotypic variables. Participants were subdivided in several different ways allowing for different cases and controls within the cohort, using prior and later test results and observations. Thus, this study was an observational retrospective case-cohort/nested case-control study.Setting/ParticipantsParticipants were recruited online via MEBO and TMAU support groups and on site, during the 3rd Annual MEBO Research conference held at Miami South Beach on June 23, 2012 and local meetups of support groups (Miami, Florida; New York, New York; Chicago, Illinois, US and Birmingham, England). Study population is individuals self-reporting systemic idiopathic malodor production. Inclusion criteria were good general health, desire and ability to travel to one of the participating sites and pay the lab fee. Exclusion Criteria were medical conditions that could prevent participation and age under 18.Study Interventions and MeasuresThe main study procedure was the application of a rapid point-of-care breath testing system to collect and concentrate alveolar breath VOCs on a sorbent trap, using breath collection apparatus (BCA) 5.0. Samples were sent to central laboratory and analyzed with gas chromatography and mass spectroscopy. In addition, the participants filled out food frequency questionnaires and were offered to use Aurametrix, online software tool based on a participant-initiated ecological momentary assessment approach, allowing to recall the events at any time later. The tool analyzed dietary intakes, activities and environmental exposures for both individual and aggregate level data.The primary endpoint was the composition of VOCs in breath samples, while diet and activity data, and results of alternative testing assessments were secondary endpoints. The main study outcome measure is the diagnostic accuracy of alveolar breath test in differentiating profiles of two main pre-defined sub-cohorts. Index of concordance with accuracy, sensitivity, specificity, positive predictive value and negative predictive value will be reported. A number of factors was assessed for confounding.
Contamination of air and surfaces in workplaces with SARS-CoV-2 virus: a systematic review
Authors: Cherrie JW , Cherrie MPC , Davis A , Holmes D , Semple S , Steinle S , MacDonald E , Moore G , Loh M 
Published: January 2021

ABSTRACTObjectivesThis systematic review aimed to evaluate the evidence for air and surface contamination of workplace environments with SARS-CoV-2 RNA and the quality of the methods used to identify actions necessary to improve the quality of the data.MethodsWe searched Web of Science and Google Scholar until 24th December 2020 for relevant articles and extracted data on methodology and results.ResultsThe vast majority of data come from healthcare settings, with typically around 6 % of samples having detectable concentrations of SARS-CoV-2 RNA and almost none of the samples collected had viable virus. There were a wide variety of methods used to measure airborne virus, although surface sampling was generally undertaken using nylon flocked swabs. Overall, the quality of the measurements was poor. Only a small number of studies reported the airborne concentration of SARS-CoV-2 virus RNA, mostly just reporting the detectable concentration values without reference to the detection limit. Imputing the geometric mean air concentration assuming the limit of detection was the lowest reported value, suggests typical concentrations in health care settings may be around 0.01 SARS-CoV-2 virus RNA copies/m3. Data on surface virus loading per unit area were mostly unavailable.ConclusionThe reliability of the reported data is uncertain. The methods used for measuring SARS-CoV-2 and other respiratory viruses in work environments should be standardised to facilitate more consistent interpretation of contamination and to help reliably estimate worker exposure.Key messagesWhat is already known about this subject?Low level contamination of air and surfaces in hospitals with SARS-CoV-2 RNA have been reported during the Covid-19 pandemic.Limited data have published from non-healthcare settings.What are the new findings?Typically, around 6% of air and surface samples in hospitals were positive for SARS-COV-2 RNA, although there is very limited data for non-healthcare settings.The quality of the available measurement studies is generally poor, with little consistency in the sampling and analytical methods used.Few studies report the concentration of SARS-CoV-2 in air or as surface loading of virus RNA, and very few studies have reported culture of the virus.The best estimate of typical air concentrations in health care settings is around 0.01 SARS-CoV-2 virus RNA copies/m3How might this impact on policy or clinical practice in the foreseeable future?There should be concerted efforts to standardise the methods used for measuring SARS-CoV-2 and other respiratory viruses in work environments.
A cross-sectional survey of the workplace factors contributing to symptoms of anxiety and depression among nurses and physicians during the first wave of COVID-19 pandemic in two US healthcare systems
Authors: Burstyn Igor , Holt Karyn 
Published: January 2021

AbstractBackgroundAnxiety and depression among physicians and nurses during COVID-19 pandemic in the USA is not well described and its modifiable causes poorly understood.MethodsWe conducted a cross-sectional survey of symptoms of anxiety and depression (Hospital Anxiety and Depression Scale) among physicians and nurses in two US healthcare systems June-Sept 2020. We ascertained features of work as well as its perceptions and associated concerns in relation to risk of anxiety and depression, while controlling for health history via regression and path analyses.ResultsAbout a third of 684 nurses and 185 physicians surveyed showed symptoms of anxiety or depression, the excess was particularly prominent in nurses. Belief in having been infected was a dominant cause of anxiety and depression, more related to history of symptoms of pneumonia, then the contact with infected patients. Having confidence in competent use and access to personal protective equipment, maintaining usual working hours and being surrounded by colleagues who were both sufficient in numbers and not stressed, was protective. Having support of immediate family and religious communities lessened anxiety and depression after accounting for other factors. Involvement in aerosol-generating procedures with infected patients was linked with lower depression in nurses but higher among physicians. Likewise, the setting of recent patient encounters affected risk differently for physicians and nurses.ConclusionsOur findings may help develop mitigation measures and underscore the need to help nurses and physicians bear the psychological burden of COVID-19 pandemic and similar events in the future.
Trends and clinical characteristics of COVID-19 vaccine recipients: a federated analysis of 57.9 million patients’ primary care records in situ using OpenSAFELY
Authors:   The OpenSAFELY Collaborative, Curtis Helen J , Inglesby Peter , Morton Caroline E , MacKenna Brian , Walker Alex J , Morley Jessica , Mehrkar Amir , Bacon Seb , Hickman George , Bates Chris , Croker Richard , Evans David , Ward Tom , Cockburn Jonathan , Davy Simon , Bhaskaran Krishnan , Schultze Anna , Rentsch Christopher T , Williamson Elizabeth , Hulme William , Green Amelia , Rowan Anna , Fisher Louis , McDonald Helen I , Tomlinson Laurie , Mathur Rohini , Drysdale Henry , Eggo Rosalind M , Wing Kevin , Wong Angel YS , Forbes Harriet , Parry John , Hester Frank , Harper Sam , O’Hanlon Shaun , Eavis Alex , Jarvis Richard , Avramov Dima , Griffiths Paul , Fowles Aaron , Parkes Nasreen , Douglas Ian J , Evans Stephen JW , Smeeth Liam , Goldacre Ben 
Published: January 2021

AbstractBackgroundOn December 8th 2020, NHS England administered the first COVID-19 vaccination as part of an ambitious vaccination programme during a global health emergency.AimsTo describe trends and variation in vaccine coverage by key clinical and demographic groups; to create a framework for near-real-time monitoring of vaccine coverage in key subgroups.MethodsWorking on behalf of NHS England we analysed 57.9 million patient records in situ and in near-real-time within the infrastructure of the Electronic Health Record (EHR) software vendors EMIS and TPP using OpenSAFELY. We describe vaccine coverage and time trends across a range of demographic and fine-grained clinical subgroups in eight Joint Committee on Vaccination and Immunisation (JCVI) priority cohorts.Results20,852,692 patients (36%) received a COVID-19 vaccine between December 8th 2020 and March 17th 2021. Of patients aged ≥80 not in a care home (JCVI group 2) 94.7% received a vaccine, but with substantial variation by ethnicity (White 96.2% vaccinated, Black 68.3%) and deprivation (least deprived 96.6%, most deprived 90.7%). Overall, patients with pre-existing medical conditions were equally or more likely to be vaccinated with two exceptions: severe mental illness (89.5% vaccinated) and learning disability (91.4%). 275,205 vaccine recipients were identified as care home residents (priority group 1; 91.2% coverage). 1,257,914 (6.0%) recipients have had a second dose. Detailed characteristics of recipients in all cohorts are reported.ConclusionsThe NHS in England has rapidly delivered mass vaccination. We were able to deploy a data monitoring framework using publicly auditable methods and a secure, in-situ processing model, using linked but pseudonymised patient-level NHS data on 57.9 million patients with very short delays from vaccine administration to completed analysis. Targeted activity may be needed to address lower vaccination coverage observed among certain key groups: ethnic minorities, those living in deprived areas, and people with severe mental illness or learning disabilities.
Individual-level and neighborhood-level factors associated with longitudinal changes in cardiometabolic measures in participants of a care coordination program
Authors: Patil Sonal J , Golzy Mojgan , Johnson Angela , Wang Yan , Parker Jerry C , Haire-Joshu Debra , Mehr David R , Foraker Randi E , Kruse Robin L 
Published: January 2021

AbstractIntroductionIdentifying individual and neighborhood-level factors associated with less improvement or worsening cardiometabolic measures in participants of clinic-based interventions may help identify candidates for supplementary community-based interventions.MethodsStudy design: Secondary data analysis of data from care coordination program cohort, Leveraging Information Technology to Guide High Tech, High Touch Care (LIGHT2). Participants: Medicare, Medicaid, or dual-eligible adults from the University of Missouri Health System enrolled in LIGHT2. Intervention: Nurse-led care coordination in ten primary care clinics. Outcomes: Hemoglobin A1C, low-density-lipoprotein (LDL) cholesterol, and blood pressure. Multivariable generalized linear regression models assessed changes in outcomes after adjusting for clinical and sociodemographic factors, neighborhood-level factors, and driving time to primary care clinics.Results6378 participants had pre-and post-intervention cardiometabolic measures reported (61% women, 86.3% White, non-Hispanic ethnicity, mean age 62.7 [SD, 18.5] years). In adjusted models, pre-intervention measures and female gender were associated with worsening of all cardiometabolic measures. Women’s LDL-cholesterol worsened compared to men irrespective of pre-intervention levels (β 7.87, 95% CI 5.24 to 10.5, p<.001). Women with hemoglobin A1C> 6.8% had worsening hemoglobin A1C compared to men (main effect β −1.28, 95% CI −1.95 to −0.61, p<.001; interaction effect β 0.19, 95% CI 0.09 to 0.28, p<.001). Women with systolic blood pressure >121 mm of Hg had worsening diastolic blood pressure compared to men (main effect β −5.42, 95% CI −9.8 to 0.098, p = 0.016; interaction effect β 0.04, 95% CI 0.01 to 0.078, p = 0.009). Adding neighborhood-level factors or driving time to primary care clinics did not improve the overall fit of the models.ConclusionsIn a solely clinic-based care coordination program, increasing baseline cardiometabolic measures and female gender were associated with worsening cardiometabolic outcomes. Further research to understand the causes of these associations may help tailor clinic-community-linked interventions.
Geographic Variation in Influenza Vaccination among US Nursing Home Residents: A National Study
Authors: Silva Joe B. B. , Bosco Elliott , Riester Melissa R. , McConeghy Kevin W. , Moyo Patience , van Aalst Robertus , Bardenheier Barbara H. , Gravenstein Stefan , Baier Rosa , Loiacono Matthew M. , Chit Ayman , Zullo Andrew R. 
Published: January 2021

ABSTRACTObjectiveEstimates of influenza vaccine use are not available at the county level for U.S. nursing home (NH) residents but are critically necessary to guide implementation of quality improvement programs aimed at increasing vaccination rates. Furthermore, estimates that account for differences in resident characteristics between counties are unavailable. We estimated risk-standardized vaccination rates among short- and long-stay NH residents by U.S. county and identified drivers of geographic variation.MethodsWe conducted a retrospective cohort study utilizing 100% of 2013-2015 fee-for-service Medicare claims, Minimum Data Set assessments, Certification and Survey Provider Enhanced Reports, and LTCFocUS. We separately evaluated short-stay (<100 days) and long-stay (≥100 days) residents aged ≥65 years old across the 2013-2014 and 2014-2015 influenza seasons. We estimated county-level risk-standardized vaccination rates (RSVRs) via hierarchical logistic regression adjusting for 32 resident-level covariates. We then used multivariable linear regression models to assess associations between county-level NHs predictors and RSVRs.ResultsThe overall study cohort consisted of 2,817,217 residents in 14,658 NHs across 2,798 counties. Short-stay residents had lower RSVRs than long-stay residents (2013-2014: median [IQR], 69.6% [62.8-74.5] vs 84.0% [80.8-86.4]). Counties with the highest vaccination rates were concentrated in the Midwestern, Southern, and Northeast US. Several modifiable facility-level characteristics were associated with increased RSVRs, including higher registered nurse to total nurse ratio and higher total staffing for licensed practical nurses, speech language pathologists, and social workers. Characteristics associated with lower RSVRs included higher percentage of residents restrained, with a pressure ulcer, and NH-level hospitalizations per resident-year.ConclusionsSubstantial county-level variation in influenza vaccine use exists among short- and long-stay NH residents. Quality improvement interventions to improve vaccination rates can leverage these results to target NHs located in counties with lower risk-standardized vaccine use.
Computational structural genomics unravels common folds and predicted functions in the secretome of fungal phytopathogenMagnaporthe oryzae
Authors: Seong Kyungyong , Krasileva Ksenia V 
Published: January 2021

AbstractMagnaporthe oryzaerelies on a diverse collection of secreted effector proteins to reprogram the host metabolic and immune responses for the pathogen’s benefit. Characterization of the effectors is thus critical for understanding the biology and host infection mechanisms of this phytopathogen. In rapid, divergent effector evolution, structural information has the potential to illuminate the unknown aspects of effectors that sequence analyses alone cannot reveal. It has recently become feasible to reliably predict the protein structures without depending on homologous templates. In this study, we tested structure modeling on 1854 secreted proteins fromM. oryzaeand evaluated success and obstacles involved in effector structure prediction. With sensitive homology search and structure-based clustering, we defined both distantly related homologous groups and structurally related analogous groups. With this dataset, we propose sequence-unrelated, structurally similar effectors are a common theme inM. oryzaeand possibly in other phytopathogens. We incorporated the predicted models for structure-based annotations, molecular docking and evolutionary analyses to demonstrate how the predicted structures can deepen our understanding of effector biology. We also provide new experimentally testable structure-derived hypotheses of effector functions. Collectively, we propose that computational structural genomic approaches can now be an integral part of studying effector biology and provide valuable resources that were inaccessible before the advent of reliable, machine learning-based structure prediction.
DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as Alk target in theDrosophilavisceral mesoderm
Authors: Mendoza-Garcia Patricia , Basu Swaraj , Sukumar Sanjay Kumar , Arefin Badrul , Wolfstetter Georg , Anthonydhason Vimala , Molander Linnea , Lindehell Henrik , Larsson Jan , Larsson Erik , Bemark Mats , Palmer Ruth H. 
Published: January 2021

AbstractDevelopment of the midgut visceral muscle ofDrosophilacrucially depends on Anaplastic Lymphoma Kinase (Alk) receptor tyrosine kinase (RTK) signalling, which is needed to specify founder cells (FCs) in the circular visceral mesoderm (VM). While activation of the Alk receptor by its ligand Jelly Belly (Jeb) is well characterized, only a small number of target molecules have been identified. Here, we assayed RNA polymerase II (Pol II) occupancy in VM cells by using the targeted DamID (TaDa) approach. To identify Alk targets we employed comparative analysis of embryos overexpressing Jebversusembryos with abrogated Alk activity, revealing differential expression of a number of genes, including the Snail/Scratch family transcription factorKahuli(Kah). Upon furtherin vivovalidation, we confirmed that Alk signalling regulatesKahmRNA expression in the VM. We show thatKahmutants display defects in the formation of midgut constrictions, similar to that ofpointed(pnt) mutants. Analysis of publicly available ChIP data defined a Kah target-binding site similar to that of Snail. In addition, we compared genes that were differentially expressed inKahmutants with publicly available Kah- and Pnt-ChIP datasets identifying a set of common target genes putatively regulated by Kah and Pnt in midgut constriction. Taken together, we (i) report a rich dataset of Alk responsive loci in the embryonic VM, (ii) provide the first functional characterization of the Kah transcription factor, identifying a role in embryonic midgut constriction, and (iii) suggest a model in which Kah and Pnt cooperate in embryonic midgut morphogenesis.
Comparison of endogenously expressed fluorescent protein fusions behaviour for protein quality control and cellular aging research
Authors: Schneider Kara L. , Wollman Adam , Nyström Thomas , Shashkova Sviatlana 
Published: January 2021

AbstractThe yeast Hsp104 protein disaggregase is often used as a reporter for misfolded or damaged protein aggregates and protein quality control and ageing research. Observing endogenously expressed Hsp104 fusions with fluorescent proteins is a popular approach to follow post stress protein aggregation, inclusion formation and disaggregation. Overall, such protein fusions used in molecular and microbiology research are often sparsely characterised. To address this issue, we performed a comparative assessment of Hsp104 fluorescent fusions function and behaviour. We provide experimental evidence that molecular behaviour may not only be altered by introducing a fluorescent protein tag but also varies depending on the fluorophore within the fusion. Although our findings are especially applicable to protein quality control and ageing research in yeast, similar effects and points may play a role in other eukaryotic systems.
Distance-based exclusion method for parentage analysis using microsatellites (SSR) markers
Authors: Francisco Gil-Muñoz , Sara Abrahamsson , Rosario García-Gil M 
Published: January 2021

AbstractGenotyping mistakes represent a challenge in parental assignment where even small errors can lead to significant amounts of unassigned siblings. Different parental assignment algorithms have been designed to approach this problem. The Exclusion method is the most applied for its reliability and biological meaning. However, the resolving power of this method is the lowest for data containing genotyping errors. We introduce a new distance-based approach which we coin as Distance-Based Exclusion (DBE). The DBE method calculates the distance between the offspring haplotype and haplotype of each of the potential fathers. The father with the lowest distance is then assigned as candidate father according to a distance ratio (α). We have tested the Exclusion and DBE methods using a real dataset of 1230 offsprings subdivided into families of 25 individuals. Each family had six potential fathers and one known mother. Compared with the Exclusion method, the DBE method is able to solve 4.7% more individuals (64.4% Exclusion vs 69.1% DBE) using the most restrictive α tested without errors. DBE method can also be used together with the Exclusion method for error calculation and to further solve unassigned individuals. Using a two-step approach, we were able to assign 98.1% of the offsprings with a total predicted error of 4.7%. Considering the results obtained, we propose the use of the DBE method in combination with the Exclusion method for parental assignment.