bluuebunny/crossref_metadata_2025_split huggingface dataset:
C-Reactive protein and SOFA score as early predictors of critical care requirement in patients with COVID-19 pneumonia in Spain
Authors: Vaquero-Roncero Luis Mario , Sánchez-Barrado Elisa , Escobar-Macias Daniel , Arribas-Pérez Pilar , Gonzalez-Porras Jose Ramón , Bermejo-Martín Jesús F , Doncel Cristina , Bastida JM , Hernández-Valero Azucena , Montoto Carolina Jambrina-García , Sánchez-Crespo José , Alonso-Hernández Pablo , Bustos-García Domingo , Rodríguez-Calvo Antonio , Riesco-Galache Gerardo , Alzibeíro Raúl , Hernández-Sánchez Alberto , Eiros Rocío , Vargas M Carmen , Martín María Ángeles , López Teresa , Sastre José Alfonso , Garzón José Carlos , Fernández Mar , García Belén , Muñoz M Magdalena , Martínez María Isabel , García Gonzalo , Díaz Agustín , Marcano Edgar , Sagredo-Meneses Víctor , Sánchez-Hernandez Miguel Vicente 
Published: May 2020

AbstractBackgroundSome patients infected by SARS-CoV-2 in the recent pandemic have required critical care, becoming one of the main limitations of the health systems. Our objective has been to identify potential markers at admission predicting the need for critical care in patients with COVID-19 pneumonia.MethodsWe retrospectively collected and analyzed data from electronic medical records of patients with laboratory-confirmed SARS-CoV-19 infection by real-time RT-PCR. A comparison was made between patients staying in the hospitalization ward with those who required critical care. Univariable and multivariable logistic regression methods were used to identify risk factors predicting critical care need.FindingsBetween March 15 and April 15, 2020, 150 patients under the age of 75 were selected (all with laboratory confirmed SARS-CoV-19 infection), 75 patients requiring intensive care assistance and 75 remaining the regular hospitalization ward. Most patients requiring critical care were males, 76% compared with 60% in the non-critical care group (p<0.05). Multivariable regression showed increasing odds of in-hospital critical care associated with increased C-reactive protein (CRP) (odds ratio 1.052 (1.009-1.101); p=0.0043) and higher Sequential Organ Failure Assessment (SOFA) score (1.968 (1.389-2.590) p<0.0001) both at the time of hospital admission. The AUC-ROC for the combined model was 0.83 (0.76-0.90) (vs AUC-ROC SOFA p<0.05).InterpretationPatients COVID-19 positive presenting at admission with high SOFA score ≥2 combined with CRP ≥ 9,1 mg/mL could help clinicians to identify them as a group that will more likely require critical care so further actions might be implemented to improve their prognosis.
Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France
Authors: Sofonea Mircea T. , Reyné Bastien , Elie Baptiste , Djidjou-Demasse Ramsès , Selinger Christian , Michalakis Yannis , Alizon Samuel 
Published: May 2020

AbstractSARS-Cov-2 virus has spread over the world creating one of the fastest pandemics ever. The absence of immunity, asymptomatic transmission, and the relatively high level of virulence of the COVID-19 infection it causes led to a massive flow of patients in intensive care units (ICU). This unprecedented situation calls for rapid and accurate mathematical models to best inform public health policies. We develop an original parsimonious model that accounts for the effect of the age of infection on the natural history of the disease. Analysing the ongoing COVID-19 in France, we estimate the value of the key epidemiological parameters, such as the basic reproduction number , and the efficiency of the national control strategy. We then use our deterministic model to explore several scenarios posterior to lock-down lifting and compare the efficiency of non pharmaceutical interventions (NPI) described in the literature.
Eat, Pray, Work: A meta-analysis of COVID-19 Transmission Risk in Common Activities of Work and Leisure
Authors: Prakash Meher K. 
Published: May 2020

ABSTRACTBACKGROUNDWhen the lockdowns are relaxed, the responsibility of mitigating the COVID-19 spread shifts from the governments to the individuals. To know how to conduct one-self, it is important for everyone to know the risks of transmission during the quotidian activities - meetings, meals, etc, from individuals who are known to them and looking healthy.METHODSThe detailed case-studies corresponding to 425 infections upon point-exposures over a specified duration are curated. The data from the case studies is summarized and reorganized to reflect different situations from the daily life. A meta-analysis of the attack rates of transmission and the number of infections per infected person are performed.RESULTSThe attack rates are very high in family dinners (66.7% (48.8-80.8%)) compared to sit-down dinners with lesser mixing among people eating at different tables (15.7% (12.1-20.1%)), both lasting a couple of hours. In an open workspace office floor organized in a two-half structure with shared elevators and restrooms and the employees speaking continuously, the average attack rate over the course of a few days was much higher in one half (78.7% (70.3-85.3%)) than the one for the entire floor (43.5% (37.0-50.1%)). Inferred data suggests that the transmission in elevators and trains may be lower under the conditions of using masks. In most of the instances we studied, the infected individuals spreading (35/44) and even super-spreading (3/6) were mostly without symptoms of coughing, sneezing or a fever.CONCLUSIONSAlthough the basic reproduction number R0 is around 3.0, the number of infections caused, including the super-spreading events, seem to be limited by the number of personal interactions in a group and their proximity. By acknowledging the risks in daily life, from healthy-looking persons, one may be able to organize their interactions better to reduce the chances of spreading or super-spreading infections.
Ethnics and economics in COVID-19: Meta-regression of data from countries in the New York metropolitan area
Authors: Takagi Hisato , Kuno Toshiki , Yokoyama Yujiro , Ueyama Hiroki , Matsushiro Takuya , Hari Yosuke , Ando Tomo 
Published: May 2020

AbstractEthnics and economics may affect prevalence and case fatality of Coronavirus disease 2019 (COVID-19). To determine whether COVID-19 prevalence and fatality are modulated by ethnics and economics, meta-regression of data from the countries in the New York metropolitan area were herein conducted. We selected 31 countries in the New York metropolitan area. 1) Prevalence and case-fatality rates of confirmed COVID-19 cases on May 20, 2020 and 2) income and poverty estimates were obtained in each country. We performed random-effects meta-regression using OpenMetaAnalys. The covariates included 1) black (%), 2) Hispanic or Latino (%), 3) poverty rates (%), and 4) median household income ($). Statistically significant (P < .05) covariates in the univariable model were together entered into the multivariable model. A slope (coefficient) of the univariable meta-regression line for COVID-19 prevalence was not significant for household income (P = .639), whereas the coefficient was significantly positive for black (coefficient, 0.021; P = .015), Hispanic/Latino (0.033; P < .001), and poverty (0.039; P = .02), which indicated that COVID-19 prevalence increased significantly as black, Hispanic/Latino, and poverty increased. The multivariable model revealed that the slope was significantly positive for only Hispanic/Latino (P < .001). The coefficient in the univariable model for COVID-19 fatality, however, was not significant for all the covariate. In conclusion, black, Hispanic/Latino, and poverty (not household income), especially Hispanic/Latino independently, may be associated with COVID-19 prevalence. There may be no association of black, Hispanic/Latino, poverty, and household income with COVID-19 fatality.
Succumbing to the COVID-19 Pandemic – Healthcare Workers not Satisfied and Intend to Leave Their Jobs
Authors: Zhang Stephen X. , Chen Jiyao , Jahanshahi Asghar Afshar , Alvarez-Risco Aldo , Dai Huiyang , Li Jizhen , Patty-Tito Ross Mary 
Published: May 2020

AbstractBackgroundHealthcare workers are under such a tremendous amount of pressure during the COVID-19 pandemic that many have become concerned about their jobs and even intend to leave them. It is paramount for healthcare workers to feel satisfied with their jobs and lives during a pandemic.MethodsBetween 10 to 30 April, 2020, 240 healthcare workers in Bolivia completed a cross-sectional online survey, which assessed their job satisfaction, life satisfaction, and turnover intention in the ongoing COVID-19 pandemic.ResultsThe results revealed that their number of office days predicted job satisfaction, life satisfaction, and turnover intention, but the relationships varied by their age. For example, healthcare workers’ office days negatively predicted job satisfaction for the young (e.g. at 25 years old: b=-0.21; 95% CI: −0.36 to −0.60) but positively predicted job satisfaction for the old (e.g. at 65 years old: b=0.25; 95% CI: 0.06 to 0.44).ConclusionsThese findings provide evidence to enable healthcare organizations to identify staff concerned about job satisfaction, life satisfaction, and turnover intention to enable early actions so that these staff can remain motivated to fight the prolonged COVID-19 pandemic.
Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues
Authors: Cao Xiaolong , Zhang Yeting , Payer Lindsay M , Lords Hannah , Steranka Jared P , Burns Kathleen H , Xing Jinchuan 
Published: May 2020

AbstractBackgroundMobile elements are a major source of human structural variants and some mobile elements can regulate gene expression and alternative splicing. However, the impact of polymorphic mobile element insertions (pMEIs) on gene expression and splicing in diverse human tissues has not been thoroughly studied. The multi-tissue gene expression and whole genome sequencing data generated by the Genotype-Tissue Expression (GTEx) project provide a great opportunity to systematic determine pMEIs’ role in gene expression regulation in human tissues.ResultsUsing the GTEx whole genome sequencing data, we identified 20,545 high-quality pMEIs from 639 individuals. We then identified pMEI-associated expression quantitative trait loci (eQTLs) and splicing quantitative trait loci (sQTLs) in 48 tissues by joint analysis of variants including pMEIs, single-nucleotide polymorphisms, and insertions/deletions. pMEIs were predicted to be the potential causal variant for 3,522 of the 30,147 significant eQTLs, and 3,717 of the 21,529 significant sQTLs. The pMEIs associated eQTLs and sQTLs show high level of tissue-specificity, and the pMEIs were enriched in the proximity of affected genes and in regulatory elements. Using reporter assays, we confirmed that several pMEIs associated with eQTLs and sQTLs can alter gene expression levels and isoform proportions.ConclusionOverall, our study shows that pMEIs are associated with thousands of gene expression and splicing variations in different tissues, and pMEIs could have a significant role in regulating tissue-specific gene expression/splicing. Detailed mechanisms for pMEI’s role in gene regulation in different tissues will be an important direction for future human genomic studies.
Differences of clinical and imaging findings in multiple generations of secondary COVID-19 infection in Xi’an, China
Authors: Li Runqing , Jian Zhijie , Jin Chao , Wang Yan , Liang Ting , Liu Zhe , Zhao Huifang , Wang Zekun , Zhou Jie , Zeng Lingxia , Yang Jian 
Published: May 2020

AbstractPURPOSEIn the global presence of secondary infections with the coronavirus disease 2019 (COVID-19), little is known about the transmission characteristics of COVID-19 outside Wuhan, China. We evaluated differences in clinic and radiologic findings of multiple generations of COVID-19 infection in Xi’an (Shaanxi, China) to provide more clues for the correct estimate of the disease.METHODSAll COVID-19 infected patients reported in Xi’an up to 10 February 2020 were included for this analysis. Among these cases, clinical and chest CT data of 62 cases were obtained from three hospital in Xi’an. With this information, patients were grouped on basis of exposure history and transmission chains as first-generation, second-generation and third-generation patients. We described clinical characteristics and evaluated CT score/patterns in these COVID-19 cases.RESULTSThere was a clear age differences in multiple generations with COVID-19 infection. Above two thirds of the second-generation (75.0%) and third-generation patients (77.8%) were aged ≥45 years while 40.0% of first-generation cases at this age (p=0.001). More than half of second-generation patients (52.8%) and third-generation patients (55.6%) have comorbidities and is predominantly hypertensive (22.8% of second-generation vs. 27.8% of third-generation infections). The main exposure of second- and third-generation patients in Xi’an is family exposure (35.2%). For evaluation of CT findings of pulmonary involvement, the total CT score were 4.22±3.00 in first-generation group, 4.35±3.03 in second-generation group and 7.62±3.56 in third-generation group (p<0.001). In all of three generations, the predominant pattern of abnormality observed was organizing pneumonia (65.5% in first-generation group, 61.5% in second-generation group and 71.4% in third-generation group). The average courses of the disease in third-generation infections has obviously extension (22.93±7.22 days of first-generation, 21.53±8.31 days of second-generation vs. 31.00±8.12 days of third-generation group,p=0.004). There were no significant differences of the pulmonary sequelae among three generation patients.CONCLUSIONThere is more serious pulmonary infection of COVID-19 pneumonia in second- and third-generation patients, which might be attribute to the elder age and comorbidity of these patients.
Relationship ofDUX4and target gene expression in FSHD myocytes
Authors: Chau Jonathan , Kong Xiangduo , Nguyen Nam , Williams Katherine , Tawil Rabi , Kiyono Tohru , Mortazavi Ali , Yokomori Kyoko 
Published: May 2020

AbstractFacioscapulohumeral dystrophy (FSHD) is linked to misexpression of the transcription factor,DUX4. Although DUX4 target gene expression is often readily detectable, analysis ofDUX4expression has been limited due to its low expression in patient samples. Recently, single cell/nucleus RNA-sequencing was used to detect the native expression ofDUX4for the first time, but important spatial relationships with its target gene expression was missing. Furthermore, dynamics ofDUX4expression during myoblast differentiation has not been fully explored. In order to study the spatiotemporal relationship ofDUX4and key target genes, we performed RNA FISH on immortalized FSHD2 patient skeletal muscle cells. Using two probe sets,DUX4transcripts were detected in 1-4% of myotubes after 3-day differentiationin vitro. We found thatDUX4transcripts mainly localize as foci in one or two nuclei in a myotube compared to abundant accumulation of the target gene transcripts in the cytoplasm. Over a 13-day differentiation timecourse,DUX4expression without target gene expression significantly increased and peaked at day 7. Target gene expression correlates better withDUX4expression early in differentiation while the expression of target genes without detectableDUX4transcripts increases later. Consistently, shRNA depletion of DUX4-activated transcription factors, DUXA and LEUTX, specifically repressed a DUX4-target gene,KDM4E, later in differentiation, suggesting that following the initial activation by DUX4, target genes themselves contribute to the maintenance of downstream gene expression. Together,in situdetection of theDUX4and target gene transcripts provided new insight into dynamics of DUX4 transcriptional network in FSHD patient myocytes.Significance StatementFSHD is the third most common muscular dystrophy and is associated with upregulation ofDUX4, a transcription factor, and its target genes. Although target genes are easily detectable in FSHD, low frequencyDUX4upregulation in patient myocytes is difficult to detect, and examining the relationship and dynamics ofDUX4and target gene expression without artificial overexpression ofDUX4has been challenging. Using RNAScope with highly specific probes, we detect the endogenousDUX4and target gene transcriptsin situin patient skeletal myotubes during differentiationin vitro. Our study reveals a uniqueDUX4expression pattern and its relationship to the expression of target genes, and evidence for self-sustainability of the target gene network. The study provides important new insights into the FSHD disease mechanism.
Physical activity shapes the intestinal microbiome and immunity of healthy mice but has no protective effects against colitis in MUC2-/- mice
Authors: Estaki Mehrbod , Morck Douglas W. , Quin Candice , Pither Jason , Barnett Jacqueline A. , Gill Sandeep K. , Gibson Deanna L. 
Published: May 2020

AbstractThe interactions among humans, their environment, and the trillions of microbes residing within the human intestinal tract form a tripartite relationship that is fundamental to the overall health of the host. Disruptions in the delicate balance between the intestinal microbiota and their host immunity are implicated in various chronic diseases including inflammatory bowel disease (IBD). There is no known cure for IBD, therefore, novel therapeutics targeting prevention and symptoms management are of great interest. Recently, physical activity in healthy mice was shown to be protective against chemically-induced colitis, however the benefits of physical activity during or following disease onset is not known. In this study, we examine whether voluntary wheel running is protective against primary disease symptoms in a mucin 2 deficient (Muc2-/-) life-long model of murine colitis. We show that 6 weeks of wheel running in healthy C57BL/6 mice leads to distinct changes in fecal bacteriome, increased butyrate production, and modulation in colonic gene expression of various cytokines, suggesting an overall primed anti-inflammatory state. However, these physical activity-derived benefits are not present in Muc2-/- mice harboring a dysfunctional mucosal layer from birth, ultimately showing no improvements in clinical signs. We extrapolate from our findings that while physical activity in healthy individuals may be an important preventative measure against IBD, for those with a compromised intestinal mucosa, a commonality in IBD patients, these benefits are lost.
The use of hybrid data-dependent and -independent acquisition spectral libraries empower dual-proteome profiling
Authors: Willems Patrick , Fels Ursula , Staes An , Gevaert Kris , Damme Petra Van 
Published: May 2020

ABSTRACTIn the context of bacterial infections, it is imperative that physiological responses can be studied in an integrated manner, meaning a simultaneous analysis of both the host and the pathogen responses. To improve the sensitivity of detection, data-independent acquisition (DIA) based proteomics was found to outperform data-dependent acquisition (DDA) workflows in identifying and quantifying low abundant proteins. Here, by making use of representative bacterial pathogen/host proteome samples, we report an optimized hybrid library generation workflow for data-independent acquisition mass spectrometry relying on the use of data-dependent andin silicopredicted spectral libraries. When compared to searching DDA experiment-specific libraries only, the use of hybrid libraries significantly improved peptide detection to an extent suggesting that infection relevant host-pathogen conditions could be profiled in sufficient depth without the need of a priori bacterial pathogen enrichment when studying the bacterial proteome.GRAPHICAL ABSTRACT
Discovery of a novel simian pegivirus in common marmosets (Callithrix jacchus) with lymphocytic enterocolitis
Authors: Heffron Anna S. , Lauck Michael , Somsen Elizabeth D. , Townsend Elizabeth C. , Bailey Adam L. , Sosa Megan , Eickhoff Jens , Capuano Saverio , Newman Christina M. , Kuhn Jens H. , Mejia Andres , Simmons Heather A. , O’Connor David H. 
Published: May 2020

AbstractFrom 2010 to 2015, 73 common marmosets (Callithrix jacchus) housed at the Wisconsin National Primate Research Center (WNPRC) were diagnosed postmortem with lymphocytic enterocolitis. We used unbiased deep-sequencing to screen the blood of deceased enterocolitis-positive marmosets for the presence of RNA viruses. In five out of eight marmosets with lymphocytic enterocolitis, we discovered a novel pegivirus that was not present in ten subsequently deep-sequenced matched, clinically-normal common marmosets with no evidence of lymphocytic enterocolitis. The novel virus, which we have named Southwest bike trail virus (SOBV), is most closely related (68% nucleotide identity) to a strain of simian pegivirus A that was previously isolated from a three-striped night monkey (Aotus trivirgatus). To determine the prevalence of this novel virus within the WNPRC marmoset colony, we screened 146 living animals and found an overall prevalence of 34% (50/146). Over the next four years, 85 of the 146 screened marmosets died or were euthanized and were examined histologically for lymphocytic enterocolitis. Out of these 85 animals, 27 SOBV-positive common marmosets had developed lymphocytic enterocolitis, compared to 42 SOBV-negative common marmosets, indicating no evidence of an association between this virus and development of enterocolitis in this cohort (p=0.0798). The novel pegivirus was also found in two of 32 (6%) clinically-normal common marmosets screened while in quarantine during the transfer from the New England Primate Research Center to the WNPRC, suggesting SOBV has different prevalence at different centers and could exert confounding influences on the comparison of marmoset studies from multiple centers.ImportanceCommon marmosets (Callithrix jacchus) are a valuable model species. We discovered two variants of a novel simian pegivirus, which we named the Southwest bike trail virus (SOBV), in common marmosets which had postmortem histologic diagnosis of lymphocytic enterocolitis. The virus was not present in ten matched, clinically-normal controls. We screened 146 live healthy common marmosets in the Wisconsin National Primate Research Center colony and found 34% (50/146) of the animals were SOBV-positive. SOBV was also present in two of 32 (6%) clinically-normal common marmosets from the New England Primate Research Center. These findings could have confounding effects in animal studies, especially those in which infection-free animals are desired, and they demonstrate the need for further investigations into SOBV transmission, the length of time of SOBV persistence, and SOBV prevalence at other primate centers, in order to increase understanding of the effects of SOBV and of this viral genus.