bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of early scientific literature in response to COVID-19: a scientometric perspective
Authors: Golinelli Davide , Nuzzolese Andrea Giovanni , Boetto Erik , Rallo Flavia , Greco Manfredi , Toscano Fabrizio , Fantini Maria Pia 
Published: April 2020

AbstractBackgroundIn the early phases of a new pandemic, identifying the most relevant evidence and quantifying which studies are shared the most can help researchers and policy makers. The aim of this study is to describe and quantify the impact of early scientific production in response to COVID-19 pandemic.MethodsThe study consisted of: 1) review of the scientific literature produced in the first 30 days since the first COVID-19 paper was published; 2) analysis of papers’ metrics with the construction of a “Computed-Impact-Score” (CIS) that represents a unifying score over heterogeneous bibliometric indicators. In this study we use metrics and alternative metrics collected into five separate categories. On top of those categories we compute the CIS. Highest CIS papers are further analyzed.Results239 papers have been included in the study. The mean of citations, mentions and social media interactions resulted in 1.63, 10 and 1250, respectively. The paper with highest CIS resulted “Clinical features of patients[…]” by Chaolin Huang et al., which rated first also in citations and mentions. This is the first paper describing patients affected by the new disease and reporting data that are clearly of great interest to both the scientific community and the general population.ConclusionsThe early response of scientific literature during an epidemic does not follow a pre-established pattern. Being able to monitor how communications spread from the scientific world toward the general population using both traditional and alternative metric measures is essential, especially in the early stages of a pandemic.
Faecal immunochemical testing (FIT): Sources of analytical variation based on three years of routine testing in the context of DG30
Authors: James Tim , Nicholson Brian D , Marr Rhiannon , Paddon Maria , East James E , Justice Steve , Oke Jason L , Shine Brian 
Published: April 2020

AbstractAimsTo determine analytical capabilities of a commonly used faecal immunochemical test (FIT) to detect haemoglobin (Hb) in the context of NICE guidance DG30, and the likely use of FIT to reprioritise patients delayed by the COVID-19 pandemic.MethodsData obtained from independent verification studies and clinical testing of the HM-JACKarc FIT method in routine primary care practice were analysed to derive analytical performance characteristics.ResultsDetection capabilities for the FIT method were 0.5 µg/g (limit of blank), 1.1 (limit of detection) and 15.0 µg/g (limit of quantification). 31 of 33 (94%) non-homogenised specimens analysed in triplicate were consistently categorised relative to 10 µg/g compared to all 33 (100%) homogenised specimens. Imprecision in non-homogenised specimens was higher (median 27.8%, (range 20.5% - 48.6%)) than in homogenised specimens (10.2%, (7.0 to 13.5%)). Considerable variation was observed in sequential clinical specimens from individual patients but no positive or negative trend in specimen degradation was observed (p=0.26).ConclusionsThe FIT method is capable of detecting Hb at concentrations well below the DG30 threshold of 10 µg/g. However, total imprecision is considerable when including sampling variation. Binary categorisation against a single defined threshold above and below 10 µg/g was more consistent and improved following specimen homogenisation. This approach may be more appropriate when reporting results for symptomatic patients tested in primary care, including those who have had definitive investigation delayed by the COVID-19 pandemic and need to be re-prioritised.Key MessagesFaecal immunochemical testing (FIT) is increasingly used to detect blood at low haemoglobin (Hb) concentrations in specimens from symptomatic primary care patients but the analytical characteristics in this context have not been fully documented.A commonly used FIT method showed good capability in a routine UK clinical setting to detect Hb at the NICE recommended threshold of 10µg/g. Imprecision estimates were considerable when sampling was considered, even above the limit of quantification of 15 µg/g.Analytical variability appears too high for reliable reporting of quantitative Hb concentrations: reporting positive or negative results around a threshold of 10µg/g appears more appropriate after sample homogenisation.Dichotomous FIT reporting is likely to be an important tool to risk stratify patients with lower GI cancer symptoms who have had their test deferred due to the COVID-19 pandemic
Serum anti-NMDA-receptor antibodies and cognitive function after ischemic stroke (PROSCIS-B)
Authors: Sperber Pia S. , Gebert Pimrapat , Broersen Leonie H.A. , Huo Shufan , Piper Sophie K. , Prüss Harald , Heuschmann Peter U. , Endres Matthias , Liman Thomas G. , Siegerink Bob 
Published: April 2020

ABSTRACTObjectiveWe aimed to investigate whether serum anti-N-Methyl-D-Aspartate-receptor GluN1 antibodies (NMDAR1-abs) are associated with worse cognitive function over three years after first ischemic stroke.MethodsData were used from the PROSpective Cohort with Incident Stroke-Berlin (PROSCIS-B;NCT01363856). NMDAR1-abs (IgM/IgA/IgG) were measured with cell-based assays from serum obtained within seven days after first-ever stroke. Seropositivity was defined as titers ≥1:10, low titers as ≤1:100 and high titers as >1:100. We assessed cognitive status annually up to three years after stroke with the Telephone Interview for Cognitive Status – modified (TICS–m) and used crude and adjusted linear mixed models to estimate the impact of NMDAR1-abs exposure on TICS-m over time.ResultsData on NMDAR1-abs (median day of sampling=4[IQR=2–5]) were available in 583 of 621 PROSCIS-B patients (39% female; median NIHSS=2[IQR=1–4]; median MMSE=28[IQR:26–30]; median mRS=2[IQR=1–3]) of whom 76(13%) were seropositive (IgM:n=48/IgA:n=43/IgG:n=2). TICS-m over time was not different in NMDAR1-abs seropositive compared to seronegative patients (βCrude=0.38[95%CI=-1.00 to 1.76]; adjusted βModel3=0.30[95%CI=-1.14 to 1.73]). In subgroups, TICS-m over time was not different in patients with low titers (βCrude=1.53[95%CI=-0.06 to 3.11]; adjusted βModel3=1.42[95%CI=-0.23 to 3.08]), however, in patients with high titers TICS-m was lower in the crude model (β=-2.54[95%CI=-4.99 to -0.08]), with a similar effect size after confounder adjustment (βModel3=-2.30[95%CI=-4.82 to 0.21]). All groups were compared to seronegative patients, respectively.ConclusionOverall NMDAR1-abs seropositivity was not associated with cognitive function over time after first-ever mild-to-moderate ischemic stroke. Our data suggest that high titers associate with impaired cognitive function after stroke, warranting larger studies.
Association between dopamine receptor D2 genetic polymorphism TaqIA1 (C t) and susceptibility to alcohol dependence
Authors: Choudhary Amrita , Yadav Upendra , Kumar Pradeep , Rai Vandana 
Published: April 2020

AbstractSeveral studies are published, which investigated dopamine receptor 2 (DRD2) gene TaqIA polymorphism as ris factor for alcohol dependence (AD) with positive and negative association. To derive a more precise estimation of the relationship, a meta-analysis of case-control studies that examined the association between DRD2 gene Taq1A polymorphism and alcohol dependence were performed. Eligible articles were identified through search of databases including PubMed, Science Direct, Springer link and Google Scholar. The association between the DRD2 TaqIA polymorphism and AD susceptibility was conducted using odds ratios (ORs) and 95 % confidence intervals (95 % CIs) as association measure.A total of 69 studies with 9,125 cases and 9,123 healthy controls were included in current meta-analysis. Results of present analysis showed significant association between DRD2 TaqIA polymorphism and AD risk using a five genetic modes (allele contrast model -OR=1.22, 95% CI=1.13-1.32, p<0.0001; homozygote model -OR= 1.35, 95%CI= 1.18-1.55; p= <0.0001; dominant model -OR= 1.29; 95%CI= 1.20-1.39; p<0.0001; recessive model-OR= 1.21; 95%CI= 1.08-1.36; p= 0.0006). There was no significant association found between In subgroup analysis, TaqIA polymorphism was not significantly associated with AD risk in Asian population under all genetic models, but in Caucasian population TaqIA polymorphism was significantly associated with AD risk.Overall, results support the hypothesis that DRD2 Taq1A polymorphism plays a role in alcohol dependence.
Community Needs Assessments in a Student-Run Clinic serving a West Philadelphia Neighborhood
Authors: Arenas Daniel J. , Hallak Dania D. , Noche Rommell , Vila-Arroyo Gilberto , Raman Swathi , Thomas Arthur , Zhou Sara , Richmond Adriana , Rauf Raisa , Su Irene , Beltrán Sourik , Lee Tim , Abelman Rebecca , Baginski Casey , Klusaritz Heather A. 
Published: April 2020

ABSTRACTBackgroundWhile Community Needs Assessments (CNAs) are an important tool for Student-Run Clinics (SRCs) to understand local communities’ healthcare needs, few studies have evaluated CNAs and their impact on care provided at SRCs.ObjectiveEvaluate results from two CNAs of an SRC in East Parkside, Philadelphia to better comprehend (1) community awareness and opinions regarding the SRC and (2) local healthcare concerns and access.Methods58 and 105 East Parkside residents were surveyed in 2011 and 2015 respectively. The results were analyzed to quantify various health-related measures in the community.ResultsResults showed high rates of hypertension, asthma, and diabetes. Rates of pap-smear and hypertension screening matched national averages while mammograms and colonoscopies were below national rates. Both CNAs showed that less than 40% of community members were aware of the clinic’s existence.ConclusionsCNAs can provide valuable insights regarding local health needs which can inform future healthcare interventions.
Meteorological factors and domestic new cases of coronavirus disease (COVID-19) in nine Asian cities: A time-series analysis
Authors: He Zonglin , Chin Yiqiao , Huang Jian , He Yi , Akinwunmi Babatunde O. , Yu Shinning , Zhang Casper JP , Ming Wai-kit 
Published: April 2020

AbstractAIMTo investigate the associations of meteorological factors and the daily new cases of coronavirus disease (COVID-19) in nine Asian cities.METHODPearson’s correlation and generalized additive modeling were performed to assess the relationships between daily new COVID-19 cases and meteorological factors (daily average temperature and relative humidity) with the most updated data currently available.RESULTSThe Pearson correlation showed that daily new confirmed cases of COVID-19 were more correlated with the average temperature than with relative humidity. Daily new confirmed cases were negatively correlated with the average temperature in Beijing (r=-0.565, P<0.01), Shanghai (r=-0.471, P<0.01), and Guangzhou (r=-0.530, P<0.01), yet in contrast, positively correlated with that in Japan (r=0.441, P<0.01). In most of the cities (Shanghai, Guangzhou, Hong Kong, Seoul, Tokyo, and Kuala Lumpur), generalized additive modeling analysis showed the number of daily new confirmed cases was positively associated with both average temperature and relative humidity, especially in lagged 3d model, where a positive influence of temperature on the daily new confirmed cases was discerned in 5 cities except in Beijing, Wuhan, Korea, and Malaysia. Nevertheless, the results were inconsistent across cities and lagged time, suggesting meteorological factors were unlikely to greatly influence the COVID-19 epidemic.CONCLUSIONThe associations between meteorological factors and the number of COVID-19 daily cases are inconsistent across cities and lagged time. Large-scale public health measures and expanded regional research are still required until a vaccine becomes available and herd immunity is established.Significance statementWith increasing COVID-19 cases across China and the world, and previous studies showing that meteorological factors may be associated with infectious disease transmission, the saying has it that when summer comes, the epidemic of COVID-19 may simultaneously fade away. We demonstrated the influence of meteorological factors on the daily domestic new cases of coronavirus disease (COVID-19) in nine Asian cities. And we found that the associations between meteorological factors and the number of COVID-19 daily cases are inconsistent across cities and time. We think this important topic may give better clues on prevention, management, and preparation for new events or new changes that could happen in the COVID-19 epidemiology in various geographical regions and as we move towards Summer.
A cross-sectional study of patients presenting for hospital-based screening for COVID-19: risk of disease, and healthcare access preferences
Authors: Rojek Amanda , Dutch Martin , Peyton Daniel , Pelly Rachel , Putland Mark , Hiscock Harriet , Knott Jonathan 
Published: April 2020

AbstractIntroductionEarly during the SARS-CoV-2 pandemic, Australian emergency departments (EDs) have experienced an unprecedented surge in patients seeking screening for COVID-19. Understanding what proportion of these patients require screening, who can be safely screened in community based models of care, and who requires an emergency departments to care for them is critical for workforce and infrastructure planning across the healthcare system, as well as public messaging campaigns.MethodssIn this cross sectional survey, we screened patients presenting to a SARS-CoV-2 screening clinic in a tertiary hospital Emergency Department in Melbourne, Australia. We assessed the proportion of patients who met screening criteria; self-reported symptom severity; reasons why they came to the ED for screening; views on community-based models of care; and sources of information accessed about COVID-19.ResultsWe included findings from 1846 patients who presented to the Emergency Department (ED) for COVID-19 screening from 18th to 30th March 2020. Most patients (55.3%) did not meet criteria for screening and most (57.6%) had mild or no (13.4%) symptoms. The main reason for coming to the ED was being referred by a telephone health service (31.3%) and 136 (7.4%) said they tried to contact their GP but could not get an appointment. Only 47 (2.6%) said they thought the disease was too specialized for their GP to manage. Patients accessed numerous information sources, commonly government websites (68.4%) and other websites (51.3%) for COVID-19 information.Conclusionsif we are to ensure that emergency departments can cope with the likely surge in presentations requiring resuscitation or inpatient care COVID-19, we should strengthen access to alternative services to triage patients to prevent unnecessary presentations at health services, and to direct those who are well but require screening away from EDs.
A Heuristic Model for Spreading of COVID 19 in Singapore
Authors: Lee Fook Hou 
Published: April 2020

ABSTRACTThis paper presents a simple heuristic model for COVID 19 spreading. The model is based on a propagation unit of time. The state of the epidemic at the end of the time unit is then related to that at the start through recurrence relationships. By propagating these relationships over the required number of time units, a projection can be made over time. The model is readily implemented on a spreadsheet and is therefore potentially widely accessible. It can serve as a useful tool for scenario planning and forecasting not just for an entire population, but also for a specific community within a population.
Meta-transcriptomic analysis reveals the gene expression and novel conserved sub-genomic RNAs in SARS-CoV-2 and MERS-CoV
Authors: Lyu Lin , Feng Ru , Zhang Mingnan , Gong Qiyu , Liao Yinjing , Zhou Yanjiao , Guo Xiaokui , Su Bing , Dorsett Yair , Chen Lei 
Published: April 2020

ABSTRACTBackgroundFundamental to viral biology is identification and annotation of viral genes and their function. Determining the level of coronavirus gene expression is inherently difficult due to the positive stranded RNA genome and the identification of sub-genomic RNAs (sgRNAs) that are required for expression of most viral genes. In the COVID-19 epidemic so far, few genomic studies have looked at viral sgRNAs and none have systematically examined the sgRNA profiles of large numbers of SARS-CoV2 datasets in conjuction with data for other coronaviruses.ResultsWe developed a bioinformatic pipeline to analyze the sgRNA profiles of coronaviruses and applied it to 588 individual samples from 20 independent studies, covering more than 10 coronavirus species. Our result showed that SARS-CoV, SARS-CoV-2 and MERS-CoV each had a core sgRNA repertoire generated via a canonical mechanism. Novel sgRNAs that encode peptides with evolutionarily conserved structures were identified in several coronaviruses and were expressed in vitro and in vivo. Two novel peptides may have direct functional relevance to disease, by alluding interferon responses and disrupting IL17E (IL25) signaling. Relevant to coronavirus infectivity and transmission, we also observed that the level of Spike sgRNAs were significantly higher in-vivo than in-vitro, while the opposite held true for the Nucleocapside protein.ConclusionsOur results greatly expanded the predicted number of coronaviruses proteins and identified potential viral peptide suggested to be involved in viral virulence. These methods and findings shed new light on coronavirus biology and provides a valuable resource for future genomic studies of coronaviruses.
Leigh Syndrome-inducing Mutations Affect LRPPRC / SLIRP Complex Formation
Authors: Coquille Sandrine , Thore Stéphane 
Published: April 2020

ABSTRACTMitochondria are essential organelles carrying their own genetic information which require specific gene expression processes. The leucine rich pentatricopeptide protein (LRPPRC) and its partner the SRA stem-loop interacting RNA binding protein (SLIRP) form a stable complex implicated in mRNA stability and polyadenylation. LRPPRC/SLIRP complex formation is still poorly characterized. We demonstrate that SLIRP interacts with the N-terminal region of LRPPRC in a RNA independent manner. We further show that the complex is stable in presence of high salt concentration. Point mutation and deletions found in the LRPPRC protein and responsible for the French-Canadian Leigh Syndrome (LSFC) are shown to affect complex formationin vitro. Our data are identifying the key region of LRPPRC involved in SLIRP association and showing the direct consequence of various LSFC mutations on the complex formation. Further experiments aiming at deciphering LRPPRC/SLIRP function(s)in vivowill benefit from our functional domain characterization.
The scRNA-seq expression profiling of the receptor ACE2 and the cellular protease TMPRSS2 reveals human organs susceptible to COVID-19 infection
Authors: Qi Jing , Zhou Yang , Hua Jiao , Zhang Liying , Bian Jialin , Liu Beibei , Zhao Zicen , Jin Shuilin 
Published: April 2020

SummaryBackgroundCOVID-19 caused by SARA-CoV-2 is a disaster sweeping over 200 countries, and more than 2,150,000 people are suffering from the disease and 140,000 people died. ACE2 is a receptor protein of SARS- CoV-2, and TMPRSS2 promotes virus proliferation and transmission. Some patients developed multiple organ dysfunction syndromes other than lungs. Therefore, studying the viral susceptibility of other organs is important for a deeper understanding of viral pathogenesis.MethodsThe advantage of scRNA-seq data is the identification of cell types by clustering the gene expression of cells. ACE2 and TMPRSS2 are highly expressed in AT2 of lungs, we compared the ACE2 and TMPRSS2 expression levels of cell types from 31 organs, with AT2 of lungs to evaluate the risk of the viral infection using scRNA-seq data.FindingsFor the first time, we found the brain, gall bladder, and fallopian tube are vulnerable to COVID-19 infection. Besides, the nose, heart, small intestine, large intestine, esophagus, testis and kidney are also identified to be high-risk organs with high expression levels of ACE2 and TMPRSS2. Moreover, the susceptible organs are grouped into three risk levels based on the TMPRSS2 expression. As a result, the respiratory system, digestive system and reproductive system are at the top-risk level to COVID-19 infection.InterpretationThis study provides evidence for COVID-19 infection in the human nervous system, digestive system, reproductive system, respiratory system, circulatory system and urinary system using scRNA-seq data, which helps for the clinical diagnosis and treatment of patients.
Potential microenvironment of SARS-CoV-2 infection in airway epithelial cells revealed by Human Protein Atlas database analysis
Authors: Leng Ling , Ma Jie , Zhang Leike , Li Wei , Zhao Lei , Zhu Yunping , Wu Zhihong , Cao Ruiyuan , Zhong Wu 
Published: April 2020

AbstractThe outbreak of COVID-19 has caused serious epidemic events in China and other countries. With the rapid spread of COVID-19, it is urgent to explore the pathogenesis of this novel coronavirus. However, the foundational research of COVID-19 is very weak. Although angiotensin converting enzyme 2 (ACE2) is the reported receptor of SARS-CoV-2, information about SARS-CoV-2 invading airway epithelial cells is very limited. Based on the analysis of the Human Protein Atlas database, we compared the virus-related receptors of epithelial-derived cells from different organs and found potential key molecules in the local microenvironment for SARS-CoV-2 entering airway epithelial cells. In addition, we found that these proteins were associated with virus reactive proteins in host airway epithelial cells, which may promote the activation of the immune system and the release of inflammatory factors. Our findings provide a new research direction for understanding the potential microenvironment required by SARS-CoV-2 infection in airway epithelial, which may assist in the discovery of potential drug targets against SARS-CoV-2 infection.