bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Identification of SARS-CoV-2 Emergence in the DoD via Retrospective Analysis of 2019-2020 Upper Respiratory Illness Samples
Authors: Chapleau Richard R. , Christian Monica , Connors Benjamin , Premo Christa , Chao Tim C. , Rodriguez Juan , Huntsberger Shana , Meyer Jennifer , Javorina Amanda , Reynolds Kenney , Riddle David , Lisanby Mark , Starr Clarise 
Published: February 2021

ABSTRACTThe first case of non-travel related SARS-COV-2 was detected late February 2020 in California, however the delay of diagnostic testing and initial stringent testing criteria made it difficult to identify those who could have acquired it through community spread. There was speculation by many that the virus may have been circulating at least a month earlier [1], and environmental sampling has suggested that versions of this virus were found many months before the first human samples were identified [2]. Here we performed a retrospective study from residual samples collected from a global DoD Respiratory Surveillance Program to establish a tentative timeline by which this virus was circulating in our DoD population. We performed RT-PCR for SARS-COV-2 and compared to the dates of these cases to the first cases identified in respective states and counties using the Johns Hopkins COVID tracker website. Twenty-four positive samples were identified out of approximately 7,000 tested. Although we found some early cases in certain regions, we did not see circulation before late February in samples collected both in the US and outside the USA.SUMMARYWhat is already known about this topic?We know that the first reported case of SARS-COV-2 was mid-January; however, there has been conjecture that the virus was found in the community before this date.What is added by this report?Here we took samples collection from a global respiratory surveillance program and evaluated for the presence of SARS-COV-2 RNA. The first case we found in the surveillance program was approximately 30-60 days before the first case was identified on military installations via diagnostic testing, however was not earlier than the mid-January reported case in California.What are the implications for public health practice?The implementation of new and emerging pathogen detection assays into already established surveillance programs could detect early community spread and possibly reduce spread of pathogen among vulnerable populations.
Visuospatial processing impairment following mild COVID-19
Authors: de Paula Jonas Jardim , Paiva Rachel Elisa Rodrigues Pereira , Costa Danielle de Souza , Souza e Silva Nathália Gualberto , Rosa Daniela Valadão , Januário José Nélio , Silva Luciana Costa , de Miranda Débora Marques , Romano-Silva Marco Aurélio 
Published: February 2021

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 infection causes coronavirus disease 2019. COVID-19 was an unknown infection that reached pandemic proportions in 2020 and has shown to bring long-term negative consequences. Here, we used a case-control design to investigate the performance of relatively young people recovered from COVID 19 in objective neuropsychological tests. We found significant differences between groups for all measures of the ROCFT with a large difference in the copy, a moderate difference in immediate recall, and a large difference in delayed recall. No significant differences were found for the measures from all the other five neuropsychological tests used.About one quarter of COVID 19 patients were below the 10th percentile according to normative data.
Low somatosensory cortex excitability in the acute stage of low back pain causes chronic pain
Authors: Jenkins Luke C , Chang Wei-Ju , Buscemi Valentina , Liston Matthew , Skippen Patrick , Cashin Aidan G , McAuley James H , Schabrun Siobhan M 
Published: February 2021

ABSTRACTBACKGROUNDDetermining the mechanistic causes of complex biopsychosocial health conditions such as low back pain (LBP) is challenging, and research is scarce. Cross-sectional studies demonstrate altered excitability and organisation of the primary somatosensory and primary motor cortex in people with acute and chronic LBP, however, no study has explored these mechanisms longitudinally or attempted to draw causal inferences.METHODSProspective, longitudinal, cohort study including 120 people with an acute episode of LBP. Sensory evoked potential area measurements were used to assess primary and secondary somatosensory cortex excitability. Transcranial magnetic stimulation derived map volume was used to assess corticomotor excitability. Directed acyclic graphs identified variables potentially confounding the exposure-outcome relationship. The effect of acute-stage sensorimotor cortex excitability on six-month LBP outcome was estimated using multivariable regression modelling, with adjusted and unadjusted estimates reported. Sensitivity analyses were performed to explore the effect of unmeasured confounding and missing data.RESULTSLower primary (OR = 2.08, 95% CI = 1.22 to 3.57) and secondary (OR = 2.56, 95% CI = 1.37 to 4.76) somatosensory cortex excitability in the acute stage of LBP increased the odds of developing chronic pain at six-month follow-up. This finding was robust to confounder adjustment and unmeasured confounding (E-Value = 2.24 & 2.58, respectively). Corticomotor excitability in the acute stage of LBP was associated with higher pain intensity at 6-month follow-up (B = −0.15, 95% CI: −0.28 to −0.02) but this association did not remain after confounder adjustment.CONCLUSIONThese data provide the first evidence that low somatosensory cortex excitability in the acute stage of LBP is a cause of chronic pain. Interventions designed to increase somatosensory cortex excitability in acute LBP may be relevant to the prevention of chronic pain.
Rapid increase of SARS-CoV-2 seroprevalence during the 2020 pandemic year in the population of the city of Tirana, Albania
Authors: Sulcebe Genc , Ylli Alban , Cenko Fabian , Kurti-Prifti Margarita 
Published: February 2021

AbstractIntroductionWhile the identification of anti SARS-CoV-2 antibodies has been used to measure the hidden circulation of the COVID-19 in communities, there are few publications on the dynamics of SARS-CoV-2 seroprevalence during both waves of 2020. This study provides original data about the change in proportion of individuals showing immune response to COVID-19 between beginning of July and end of December 2020.MethodsThe study was conducted in two rounds, 27 June −3 July, and 21-28 December 2020, using two independently selected samples of individuals 20-70 years old. Study participants were randomly selected from lists of the inhabitants of the catchment communities of four primary health care centers in Tirana City. Serological testing was performed by an ELISA method which determines IgG class antibodies anti S1 protein of SARS-CoV-2 virus. The validity of the method was tested in a sample of blood donor’s sera of 2018.ResultsThe proportion of individuals classified as seropositive during the first round, in early July was 7.5% (95% CI: 4.3% −10.7%). The proportion rose sharply in the second round, by late December 2020, reaching 48.2% (95% CI: 44.8% −51.7%). The same increasing pattern was observed in all studied categories. No statistical significance was found between men and women and between age categories. The prevalence of seropositive individuals was always significantly higher among those who reported symptoms and those who had done the molecular test.ConclusionThe ratio of total infected cases over confirmed cases was estimated to be higher than 10 to 1 in Albania. The rapid increase in SARS-CoV-2 seroprevalence observed in Tirana City may have been facilitated by a number of factors, including the very low infection exposure during the period March -May 2020, and the consecutive high susceptibility in population. Despite the observed high seroprevalence, one month after the study, COVID-19 incidence continued to increase in Tirana.
Gut microbiota link dietary fiber intake and short-chain fatty acid metabolism with eating behaviour
Authors: Medawar Evelyn , Haange Sven-Bastiaan , Rolle-Kampczyk Ulrike , Engelmann Beatrice , Dietrich Arne , Thieleking Ronja , Wiegank Charlotte , Fries Charlotte , Horstmann Annette , Villringer Arno , von Bergen Martin , Fenske Wiebke , Witte A. Veronica 
Published: February 2021

AbstractBackgroundThe gut microbiome modulates human brain function and eating behavior through multiple factors, including short-chain fatty acid (SCFA) signaling. We aimed to explore which bacterial genera relate to eating behavior, diet and SCFA metabolites in overweight adults. In addition, we tested whether eating-related microbiota relate to treatment success in patients after Roux-en-Y gastric bypass (RYGB).MethodsAnthropometrics, dietary fibre intake, eating behaviour, 16S-rRNA-derived microbiota and SCFA measured in feces and blood were correlated in young overweight adults (n=27 (9F), 21-36 years, BMI 25-31 kg/m2). Correlated genera were compared in RYGB (n=23 (16F), 41-70 years, BMI 25-62 kg/m2) and in control patients (n=17 (11F), 26-69 years, BMI 25-48 kg/m2).ResultsIn young adults, 7 bacteria genera, i.e. Alistipes, Blautia, Clostridiales cluster XVIII, Gemmiger, Roseburia, Ruminococcus and Streptococcus, correlated with healthier eating behavior, while 5 genera, i.e. Clostridiales cluster IV and XIVb, Collinsella, Fusicatenibacter and Parabacteroides, correlated with unhealthier eating (all |r| > 0.4, FDR-corrected p < 0.05). Some of these genera including Parabacteroides related to fiber intake and SCFA metabolites, and to weight status and treatment response in overweight/obese patients.ConclusionsSpecific bacterial genera, particularly Parabacteroides, were associated with weight status and eating behavior in two independent well-characterized cross-sectional samples. These exploratory findings indicate two groups of presumably beneficial and unfavourable genera that relate to eating behaviour and weight status, and indicate that dietary fiber and SCFA metabolism may modify these relationships.
The source of individual heterogeneity shapes infectious disease outbreaks
Authors: Elie Baptiste , Selinger Christian , Alizon Samuel 
Published: February 2021

AbstractThere is known heterogeneity between individuals in infectious disease transmission patterns. The source of this heterogeneity is thought to affect epidemiological dynamics but studies tend not to control for the overall heterogeneity in the number of secondary cases caused by an infection. To explore the role of individual variation in infection duration and transmission rate on parasite emergence and spread, while controlling for this potential bias, we simulate stochastic outbreaks with and without parasite evolution. As expected, heterogeneity in the number of secondary cases decreases the probability of outbreak emergence. Furthermore, for epidemics that do emerge, assuming more realistic infection duration distributions leads to faster outbreaks and higher epidemic peaks. When parasites require adaptive mutations to cause large epidemics, the impact of heterogeneity depends on the underlying evolutionary model. If emergence relies on within-host evolution, decreasing the infection duration variance decreases the probability of emergence. These results underline the importance of accounting for realistic distributions of infection rates to anticipate the effect of individual heterogeneity on epidemiological dynamics.
openEHR is FAIR-Enabling by Design
Authors: Frexia Francesca , Mascia Cecilia , Lianas Luca , Delussu Giovanni , Sulis Alessandro , Meloni Vittorio , Del Rio Mauro , Zanetti Gianluigi 
Published: February 2021

AbstractThe FAIR Principles are a set of recommendations that aim to underpin knowledge discovery and integration by making the research outcomes Findable, Accessible, Interoperable and Reusable. These guidelines encourage the accurate recording and exchange of structured data, coupled with contextual information about their creation, expressed in domain-specific standards and machine readable formats. This paper analyses the potential support to FAIRness of the openEHR e-health standard, by theoretically assessing the compliance with each of the 15 FAIR principles of a hypothetical Clinical Data Repository (CDR) developed according to the openEHR specifications. Our study highlights how the openEHR approach, thanks to its computable semantics-oriented design, is inherently FAIR-enabling and is a promising implementation strategy for creating FAIR-compliant CDRs.
Association between benzodiazepine receptor agonist use and increased mortality among patients hospitalized for COVID-19: results from an observational study
Authors: Hoertel N. , Sánchez-Rico M. , Gulbins E. , Kornhuber J. , Vernet R. , Beeker N. , Neuraz A. , Blanco C. , Olfson M. , Airagnes G. , Lemogne C. , Alvarado J. M. , Arnaout M. , Meneton P. , Limosin F. 
Published: February 2021

ABSTRACTObjectiveTo examine the association between benzodiazepine receptor agonist (BZRA) use and mortality in patients hospitalized for COVID-19.MethodsWe conducted an observational multicenter retrospective cohort study at AP-HP Greater Paris University hospitals. The sample involved 14,381 adult patients hospitalized for COVID-19. 686 (4.8%) inpatients received a BZRA within at the time of hospital admission at a mean daily diazepam-equivalent dose of 19.7 mg (SD=25.4). The study baseline was the date of hospital admission and the primary endpoint was death. We compared this endpoint between patients who received BZRAs and those who did not in time-to-event analyses adjusted for patient characteristics (such as age, sex, obesity and comorbidity) and other medications. The primary analysis was a Cox regression model with inverse probability weighting (IPW).ResultsOver a mean follow-up of 14.5 days (SD=18.1), the primary endpoint occurred in 186 patients (27.1%) who received a BZRA and in 1,134 patients (8.3%) who did not. There was a significant association between BZRA use and increased mortality both in the crude analysis (HR=3.20; 95% CI=2.74-3.74; p<0.01) and in the primary IPW analysis (HR=1.61; 95% CI=1.31-1.98, p<0.01), with a significant dose-dependent relationship (HR=1.55; 95% CI=1.08-2.22; p=0.02). This association remained significant in multiple sensitivity analyses.ConclusionsBZRA use was associated with increased mortality among patients hospitalized for COVID-19 with a dose-dependent relationship, suggesting a potential benefit of decreasing dose or tapering off these medications when possible in these patients.
A computationally efficient approach to segmentation of the aorta and coronary arteries using deep learning
Authors: Cheung Wing Keung , Bell Robert , Nair Arjun , Menezies Leon , Patel Riyaz , Wan Simon , Chou Kacy , Chen Jiahang , Torii Ryo , Davies Rhodri H. , Moon James C. , Alexander Daniel C. , Jacob Joseph 
Published: February 2021

AbstractA fully automatic two-dimensional Unet model is proposed to segment aorta and coronary arteries in computed tomography images. Two models are trained to segment two regions of interest, (1) the aorta and the coronary arteries or (2) the coronary arteries alone. Our method achieves 91.20% and 88.80% dice similarity coefficient accuracy on regions of interest 1 and 2 respectively. Compared with a semi-automatic segmentation method, our model performs better when segmenting the coronary arteries alone. The performance of the proposed method is comparable to existing published two-dimensional or three-dimensional deep learning models. Furthermore, the algorithmic and graphical processing unit memory efficiencies are maintained such that the model can be deployed within hospital computer networks where graphical processing units are typically not available.
Statewide Impact of COVID-19 on Social Determinants of Health - A First Look: Findings from the Survey of the Health of Wisconsin
Authors: Malecki Kristen M.C. , Schultz Amy A. , Nikodemova Maria , Walsh Matt C. , Bersch Andrew J. , Cronin Jacquie , Cadmus-Bertram Lisa , Engelman Corinne D. , Lubsen Julia R. , Peppard Paul E. , Sethi Ajay K. 
Published: February 2021

ABSTRACTThere is an urgent need to track the early and ongoing impact of the COVID-19 pandemic on population health from local to global scales. At the same time, there is an overall lack of U.S. state-specific surveillance data tracking social determinants of health (SDOH) and associations with population well-being, individual mitigation and coping strategies, family dynamics and other economic shocks of the pandemic in populations. Statewide data can offer important insights into how SDOH shape the long-term effects of COVID-19 in the population since implementation of many policies and programs varied widely early on in the pandemic. In May of 2020, the Survey of the Health of Wisconsin (SHOW) program launched a statewide online/phone survey of early and ongoing impacts of COVID-19 on health and well-being across diverse communities and families. The goal of this study is to provide descriptive data including perceived COVID-19 risks, access to and results of COVID-19 antigen testing, individual mitigation and coping strategies, family dynamics and other economic shocks of the pandemic on health and mental health in populations. Key findings include higher rates of testing and perceived past infection from COVID-19 among non-white respondents. Higher economic shifts and job changes in female vs male respondents. Families with children reported overall higher levels of stress, and stress from the pandemic. There were urban and rural differences in changes to access to care. Rural regions, which had a lower prevalence of infections early in the pandemic as compared to urban areas, also reported fewer delays or missed appointments due to COVID-19. Key findings show that SDOH are shaping impacts of health and well-being early on in the pandemic and future longitudinal follow-up will be important to shape policies and programs well into the future.
quincunx: an R package to query, download and wrangle PGS Catalog data
Authors: Magno Ramiro , Duarte Isabel , Maia Ana -Teresa 
Published: February 2021

AbstractMotivationThe Polygenic Score (PGS) Catalog is a recently established open database of published polygenic scores that, to date, has collected, curated, and made available 721 polygenic scores from over 133 publications. The PGS Catalog REST API is the only method allowing programmatic access to this resource.ResultsHere, we describequincunx, an R package that provides the first client interface to the PGS Catalog REST API.quincunxenables users to query and quickly retrieve, filter and integrate metadata associated with polygenic scores, as well as polygenic scoring files in tidy table format.Availabilityquincunxis freely available under an MIT License, and can be accessed fromhttps://github.com/maialab/quincunx.
High Light and High Temperature Reduce Photosynthesis via Different Mechanisms in the C4ModelSetaria viridis
Authors: Anderson Cheyenne M. , Mattoon Erin M. , Zhang Ningning , Becker Eric , McHargue William , Yang Jiani , Patel Dhruv , Dautermann Oliver , McAdam Scott A. M. , Tarin Tonantzin , Pathak Sunita , Avenson Tom J. , Berry Jeffrey , Braud Maxwell , Niyogi Krishna K. , Wilson Margaret , Nusinow Dmitri A. , Vargas Rodrigo , Czymmek Kirk J. , Eveland Andrea L. , Zhang Ru 
Published: February 2021

AbstractC4plants frequently experience damaging high light (HL) and high temperature (HT) conditions in native environments, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4model plantSetaria viridisresponded to a four-hour HL or HT treatment at the photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in HL- or HT-treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to HL and HT. We provide a systematic analysis of HL and HT responses inS. viridis, reveal different acclimation strategies to these two stresses in C4plants, discover unique light/temperature responses in C4plants in comparison to C3plants, and identify potential targets to improve abiotic stress tolerance in C4crops.
Cohesin-independent STAG proteins interact with RNA and localise to R-loops to promote complex loading
Authors: Porter Hayley , Li Yang , Neguembor Maria Victoria , Beltran Manuel , Varsally Wazeer , Martin Laura , Cornejo Manuel Tavares , Pezic Dubravka , Bhamra Amandeep , Surinova Silvia , Jenner Richard G. , Cosma Maria Pia , Hadjur Suzana 
Published: February 2021

ABSTRACTMost studies of cohesin function consider the Stromalin Antigen (STAG/SA) proteins as core complex members given their ubiquitous interaction with the cohesin ring. Here, we provide functional data to support the notion that the SA subunit is not a mere passenger in this structure, but instead plays a key role in the localization of cohesin to diverse biological processes and promotes loading of the complex at these sites. We show that in cells acutely depleted for RAD21, SA proteins remain bound to chromatin, cluster in 3D and interact with CTCF, as well as with a wide range of RNA binding proteins involved in multiple RNA processing mechanisms. Accordingly, SA proteins interact with RNA and are localised to R-loops where they contribute to R-loop regulation. Our results place SA1 within R-loop domains upstream of the cohesin complex and reveal a role for SA1 in cohesin loading which is independent of NIPBL, the canonical cohesin loader. We propose that SA1 takes advantage of structural R-loop platforms to link cohesin loading and chromatin structure with diverse functions. Since SA proteins are pan-cancer targets, and R-loops play an increasingly prevalent role in cancer biology, our results have important implications for the mechanistic understanding of SA proteins in cancer and disease.
Waves of sumoylation support transcription dynamics during adipocyte differentiation
Authors: Zhao Xu , Hendriks Ivo A. , Gras Stéphanie Le , Ye Tao , Nguéa P Aurélie , Ramos-Alonso Lucia , Lien Guro Flor , Klungland Arne , Jost Bernard , Enserink Jorrit M. , Nielsen Michael L. , Chymkowitch Pierre 
Published: February 2021

SummaryTight control of gene expression networks required for adipose tissue formation and plasticity is essential for adaptation to energy needs and environmental cues. However, little is known about the mechanisms that orchestrate the dramatic transcriptional changes leading to adipocyte differentiation. We investigated the regulation of nascent transcription by the sumoylation pathway during adipocyte differentiation using SLAMseq and ChIPseq. We discovered that the sumoylation pathway has a dual function in differentiation; it supports the initial downregulation of pre-adipocyte-specific genes, while it promotes the establishment of the mature adipocyte transcriptional program. By characterizing sumoylome dynamics in differentiating adipocytes by mass spectrometry, we found that sumoylation of specific transcription factors like Pparγ/RXR and their co-factors is associated with the transcription of adipogenic genes. Our data demonstrate that the sumoylation pathway coordinates the rewiring of transcriptional networks required for formation of functional adipocytes. This study also provides an in-depth resource of gene transcription dynamics, SUMO-regulated genes and sumoylation sites during adipogenesis.