bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased hazard of mortality in cases compatible with SARS-CoV-2 variant of concern 202012/1 - a matched cohort study
Authors: Challen Robert , Brooks-Pollock Ellen , Read Jonathan M , Dyson Louise , Tsaneva-Atanasova Krasimira , Danon Leon 
Published: February 2021

AbstractObjectivesTo establish whether there is any change in mortality associated with infection of a new variant of SARS-CoV-2, designated a Variant of Concern in December 2020 (VOC-202012/1) compared to that associated with infection with circulating SARS-CoV-2 variants.DesignMatched cohort study. Cases are matched by age, gender, ethnicity, index of multiple deprivation, lower tier local authority region, and sample date of positive specimen, and differing only by detectability of the spike protein gene using the TaqPath assay - a proxy measure of VOC-202012/1 infection.SettingUnited Kingdom, community - based (Pillar 2) COVID-19 testing centres using the TaqPath assay.Participants54,906 pairs of participants testing positive for SARS-CoV-2 in Pillar 2 between 1st October 2020 and 29th January 2021, followed up until the 12th February 2021.Main outcome measuresDeath within 28 days of first positive SARS-CoV-2 test.ResultsThere is a high probability that the risk of mortality is increased by infection with VOC-202012/01 (p <0.001). The mortality hazard ratio associated with infection with VOC-202012/1 compared to infection with previously circulating variants is 1.64 (95% CI 1.32 - 2.04) in patients who have tested positive for COVID-19 in the community. In this comparatively low risk group, this represents an increase from 2.5 to 4.1 deaths per 1000 detected cases.ConclusionsIf this finding is generalisable to other populations, VOC-202012/1 infections have the potential to cause substantial additional mortality compared to previously circulating variants. Healthcare capacity planning, national and international control policies are all impacted by this finding, with increased mortality lending weight to the argument that further coordinated and stringent measures are justified to reduce deaths from SARS-CoV-2.
Investigation and public health response to a COVID-19 outbreak in a rural resort community — Blaine County, Idaho, 2020
Authors: Dunne Eileen M. , Maxwell Tanis , Dawson-Skuza Christi , Burns Matthew , Ball Christopher , Turner Kathryn , Hahn Christine G. , Bowyer Melody , Carter Kris K. , Hudson Logan 
Published: February 2021

AbstractBlaine County, Idaho, a rural area with a renowned resort, experienced an outbreak of novel coronavirus disease (COVID-19). We undertook an epidemiologic investigation to describe the outbreak and guide public health action. Confirmed cases of COVID-19 were identified from reports of SARS-CoV-2-positive laboratory test results to South Central Public Health District.Information on symptoms, hospitalization, recent travel, healthcare worker status, and close contacts was obtained by medical record review and patient interviews. Viral sequence analysis was conducted on a subset of available specimens. During March 13–April 10, 2020, a total of 451 COVID-19 cases occurred among Blaine County residents (1,959 cases per 100,000 population). An additional 37 cases occurred in out-of-state residents. Among the 451 COVID-19 patients, the median age was 51 years (Interquartile range [IQR]: 37–63), 52 (11.5%) were hospitalized, and 5 (1.1%) died. The median duration between specimen collection and a positive laboratory result was 9 days (IQR: 4–10). Forty-four (9.8%) patients reported recent travel. Healthcare workers comprised 56 (12.4%) cases; 33 of whom worked at the only hospital in the county, leading to a 15-day disruption of hospital services. Of 562 close contacts monitored by public health authorities, 22 (3.9%) had laboratory-confirmed COVID-19 and an additional 29 (5.2%) experienced compatible symptoms. Sequencing results from 34 Idaho specimens supported epidemiologic findings indicating travel as a source of SARS-CoV-2, and identified multiple lineages among hospital workers. Community mitigation strategies included school and resort closure, stay-at-home orders, and restrictions on incoming travelers. COVID-19 outbreaks in rural communities can disrupt health services. Lack of local laboratory capacity led to long turnaround times for COVID-19 test results. Rural communities frequented by tourists should consider implementing restrictions on incoming travelers among other mitigation strategies to reduce COVID-19 transmission.
Use of convalescent plasma in patients with coronavirus disease (Covid-19): Systematic review and meta-analysis
Authors: Tortosa Fernando , Carrasco Gabriela , Ragusa Martin , Haluska Pedro , Izcovich Ariel 
Published: February 2021

AbstractObjetivesTo assess the effects of convalescent plasma treatment in patients with coronavirus disease (COVID-19).Study designSystematic review and Meta-analysisData sourcesA systematic search was carried out on the L · OVE (Living OVerview of Evidence) platform for COVID-19 until October 31, 2020Study selectionRandomized clinical trials in which people with probable or confirmed COVID-19 were randomized to drug treatment, standard care, or placebo. Pairs of reviewers independently screened potentially eligible articles.MethodsThe PRISMA guidelines were followed for conducting a systematic review and meta-analysis. The risk of bias of the included studies was assessed using the Cochrane risk of bias tool 2.0, and the certainty of the evidence using the recommendation assessment, development and evaluation (GRADE) approach. For each outcome, the interventions were classified into groups, from most to least beneficial or harmful.ResultsWe identified 10 RCTs (randomized controlled trials) involving 11854 patients in which convalescent plasma was compared with standard of care or other treatments. The results of five RCTs that evaluated the use of convalescent plasma in patients with COVID-19 did not show significant differences in the effect on mortality and the need for invasive mechanical ventilation.ConclusionsCurrent evidence is insufficient to recommend the use of convalescent plasma in the treatment of moderate or severe COVID-19.Contribution of the authors
Evaluating the effect of COVID-19 on dispensing patterns: a national cohort analysis
Authors: Torabi Fatemeh , Akbari Ashley , North Laura , Harris Daniel , Davies Gareth , Gravenor Mike , Griffiths Rowena , Lyons Jane , Jenkins Neil , Morris Andrew , Halcox Julian , Lyons Ronan A. 
Published: February 2021

AbstractBackgroundMedication prescribing and dispensing often regarded as one of the most effective ways to manage and improve population health. Prescribed and dispensed medications can be monitored through data linkage for each patient. We hypothesised that changes in patient care resulting from COVID-19, changed the way patients access their prescribed medication.ObjectiveTo develop an efficient approach for evaluation of the impact of COVID-19 on drug dispensing patterns.MethodsRetrospective observational study using national patient-level dispensing records in Wales-UK. Total dispensed drug items between 01-Jan-2016 and 31-Dec-2019 (counterfactual pre-COVID-19) were compared to 2020 (COVID-19 year). We compared trends of dispensed items in three main British National Formulary (BNF) sections(Cardiovascular system, Central Nervous System, Immunological & Vaccine) using European Age-Standardized rates. We developed an online tool to enable monitoring of changes in dispensing as the pandemic evolves.ResultAmongst all BNF chapters, 52,357,639 items were dispensed in 2020 compared to 49,747,141 items in 2019 demonstrating a relative increase of 5.25% in 2020(95%CI[5.21,5.29]). Comparison of monthly patterns of 2020 and 2019 dispensed items showed a notable difference between the total number of dispensed drug items each month, with an average difference (D) of +290,055 and average Relative Change (RC) of +5.52%. The greatest RC was observed in a substantial March-2020 increase (D=+1,501,242 and RC=+28%), followed by second peak in June (D=+565,004, RC=+10.97%). May was characterised by lower dispensing (D=-399,244, RC=-5.9%). Cardiovascular categories were characterised, across all age groups, by dramatic March-2020 increases, at the epidemic peak, followed by months of lower than expected dispensing, and gradual recovery by September. The Central Nervous System category was similar, but with only a short decline in May, and quicker recovery. A stand-out grouping was Immunological and Vaccine, which dropped to very low levels across all age groups, and all months (including the March dispensing peak).ConclusionsAberration in clinical service delivery during COVID-19 led to substantial changes in community pharmacy drug dispensing. This change may contribute to a long-term burden of COVID-19, raising the importance of a comprehensive and timely monitoring of changes for evaluation of the potential impact on clinical care and outcomes
Predictors of suicidal thoughts and behavior in children: results from penalized logistic regression analyses in the ABCD study
Authors: van Velzen Laura S. , Toenders Yara J. , Avila-Parcet Aina , Dinga Richard , Rabinowitz Jill A. , Campos Adrián I. , Jahanshad Neda , Rentería Miguel E. , Schmaal Lianne 
Published: February 2021

AbstractDespite numerous efforts to predict suicide risk in children, the ability to reliably identify youth that will engage in suicide thoughts or behaviors (STB) has remained remarkably unsuccessful. To further knowledge in this area, we apply a novel machine learning approach and examine whether children with STB could be differentiated from children without STB based on a combination of sociodemographic, physical health, social environmental, clinical psychiatric, cognitive, biological and genetic characteristics. The study sample included 5,885 unrelated children (50% female, 67% white) between 9 and 11 years old from the Adolescent Brain Cognitive Development (ABCD) study. Both parents and youth reported on children’s STB and based on these reports, we divided children into three subgroups: 1. children with current or past STB, 2. children with psychiatric disorder but no STB (clinical controls) and 3. healthy control children. We performed binomial penalized logistic regression analysis to distinguish between groups. The analyses were performed separately for child-reported STB and parent-reported STB. Results showed that we were able to distinguish the STB group from healthy controls and clinical controls (area under the receiver operating characteristics curve (AUROC) range: 0.79-0.81 and 0.70-0.78 respectively). However, we could not distinguish children with suicidal ideation from those who attempted suicide (AUROC range 0.49-0.59). Factors that differentiated the STB group from the clinical control group included family conflict, prodromal psychosis symptoms, impulsivity, depression severity and a history of mental health treatment. Future research is needed to determine if these variables prospectively predict subsequent suicidal behavior.
Magnetic resonance imaging of the gastrointestinal tract shows reduced small bowel motility and altered chyme in cystic fibrosis compared to controls
Authors: Dellschaft Neele S , Ng Christabella , Hoad Caroline , Marciani Luca , Spiller Robin , Stewart Iain , Menys Alex , Barr Helen , Gowland Penny A , Major Giles , Smyth Alan R 
Published: February 2021

AbstractCystic fibrosis (CF) is a genetic disease affecting mucosal secretions. Most patients experience digestive symptoms, but the mechanisms are incompletely understood. Here we explore causes and consequences of slower gastrointestinal transit using magnetic resonance imaging (MRI).Twelve people with CF and 12 healthy controls, matched for age and gender, underwent MRI scans both fasted and after standardised meals over a period of 6.5 hours. Images were assessed for small bowel motility, longitudinal relaxation time (T1) of ascending colon chyme, chyme texture and appearance of the colon wall.Small bowel motility scores were significantly lower in CF than in healthy controls in the fasting state (CF median 40 arbitrary units IQR [31, 46] vs Control 86 a.u. [52, 106],P=0.034). This difference was less pronounced postprandially. Furthermore, ascending colon chyme T1was lower in CF than in controls (CF 0.59 s [0.38, 0.77] vs Control 0.79 s [0.55, 1.31],P=0.010). The difference in texture between small bowel and colon chyme, seen in health, was diminished in CF (difference in Haralick contrast 0.90 a.u. [0.38, 1.67] vs Control 2.11 a.u. [0.71, 3.30],P=0.010). Ascending colon mucosa in CF participants had an abnormal appearance compared to controls (Score 1-3, CF 2 [1, 3] vs Controls 1 [1, 1],P=0.019).Reduced small bowel motility and water content of ascending colon chyme are consistent with slower transit and constipation. MRI provides unique insights into chyme texture in the small bowel (suggesting bacterial overgrowth) and the appearance of the colon mucosa (suggesting altered mucus) in CF.Key point summary-People with cystic fibrosis (CF) have intrusive digestive symptoms and severe gut complications, but mechanisms are incompletely understood.-In this study, 12 people with CF were compared to healthy controls, undergoing repeated MRI scans before and after standardised meals.-Fasted small bowel motility is reduced in people with CF, consistent with slower transit. In addition, a reduced colonic chyme water content and abnormal appearance of small bowel and colonic chyme as well as colonic mucosa suggest small bowel bacterial overgrowth, fat malabsorption and abnormal mucus production-These MRI outcomes hold promise in the assessment of therapeutic interventions.
Clustering of Countries for COVID-19 Cases based on Disease Prevalence, Health Systems and Environmental Indicators
Authors: Rizvi Syeda Amna , Umair Muhammad , Cheema Muhammad Aamir 
Published: February 2021

ABSTRACTThe coronavirus has a high basic reproduction number (R0) and has caused the global COVID-19 pandemic. Governments are implementing lockdowns that are leading to economic fallout in many countries. Policy makers can take better decisions if provided with the indicators connected with the disease spread. This study is aimed to cluster the countries using social, economic, health and environmental related metrics affecting the disease spread so as to implement the policies to control the widespread of disease. Thus, countries with similar factors can take proactive steps to fight against the pandemic. The data is acquired for 79 countries and 18 different feature variables (the factors that are associated with COVID-19 spread) are selected. Pearson Product Moment Correlation Analysis is performed between all the feature variables with cumulative death cases and cumulative confirmed cases individually to get an insight of relation of these factors with the spread of COVID-19. Unsupervised k-means algorithm is used and the feature set includes economic, environmental indicators and disease prevalence along with COVID-19 variables. The learning model is able to group the countries into 4 clusters on the basis of relation with all 18 feature variables. We also present an analysis of correlation between the selected feature variables, and COVID-19 confirmed cases and deaths. Prevalence of underlying diseases shows strong correlation with COVID-19 whereas environmental health indicators are weakly correlated with COVID-19.
Public Covid-19 X-ray datasets and their impact on model bias - a systematic review of a significant problem
Authors: Cruz Beatriz Garcia Santa , Bossa Matías Nicolás , Sölter Jan , Husch Andreas Dominik 
Published: February 2021

ABSTRACTComputer-aided-diagnosis for COVID-19 based on chest X-ray suffers from weak bias assessment and limited quality-control. Undetected bias induced by inappropriate use of datasets, and improper consideration of confounders prevents the translation of prediction models into clinical practice. This study provides a systematic evaluation of publicly available COVID-19 chest X-ray datasets, determining their potential use and evaluating potential sources of bias.Only 5 out of 256 identified datasets met at least the criteria for proper assessment of risk of bias and could be analysed in detail. Remarkably almost all of the datasets utilised in 78 papers published in peer-reviewed journals, are not among these 5 datasets, thus leading to models with high risk of bias. This raises concerns about the suitability of such models for clinical use.This systematic review highlights the limited description of datasets employed for modelling and aids researchers to select the most suitable datasets for their task.
Worries about COVID-19 infection and psychological distress at work and while commuting
Authors: Uehara Masamichi , Ishimaru Tomohiro , Ando Hajime , Tateishi Seiichiro , Eguchi Hisashi , Tsuji Mayumi , Mori Koji , Matsuda Shinya , Fujino Yoshihisa 
Published: February 2021

AbstractObjectiveThis study examined the relationship between worry about COVID-19 infection in the workplace and while commuting to work and psychological distress in Japan.MethodsAn internet monitor study was conducted. Out of a total of 33,302 participants, 26,841 people were included. The subjects were asked single-item questions about whether they were worried about COVID-19 infection in general, at work and while commuting to work. Kessler 6 (K6) was used to assess psychological distress.ResultsThe OR was significantly higher in association with worry about infection in the workplace at 1.71 (95%CI 1.53–1.92) and worry about infection while commuting at 1.49 (95%CI 1.32–1.67).ConclusionsThis study suggests the need for psychological intervention to reduce worry about infection in response to public mental health challenges associated with the COVID-19 pandemic.
SARS-CoV-2 detection by rRT-PCR on self-collected anterior nares swabs or saliva compared with clinician-collected nasopharyngeal swabs — Denver and Atlanta, August – November, 2020
Authors: Marx Grace E. , Smith-Jeffcoat Sarah E. , Biggerstaff Brad J. , Koh Mitsuki , Nawrocki Courtney C. , Travanty Emily A. , Totten Sarah E. , Scott Tracy , De Hey Jesse Chavez-Van , Carlson Jesse J. , Wendel Karen A. , Burakoff Alexis W. , Hoffman Adam , Rebolledo Paulina A. , Schechter Marcos C. , Wang Yun F. , Moore Brooks L. , Atallah Hany Y. , Sexton D. Joseph , Hartloge Claire , Paulick Ashley , Miller Halie K. , Sleweon Sadia , Rosetti Rebecca , Shragai Talya , O’Laughlin Kevin , Stewart Rebekah J. , da Silva Juliana , Biedron Caitlin ,   CDPHE COVID-19 Laboratory Response Team,   CDC COVID-19 Response GA-10 Team,   CDC COVID-19 Response Lab Task Force, Thomas Jennifer D. , Kirking Hannah L. , Tate Jacqueline E. , Rowan Sarah E. 
Published: February 2021

AbstractNasopharyngeal swabs (NPS) collected by trained healthcare professionals are the preferred specimen for SARS-CoV-2 testing. Self-collected specimens might decrease patient discomfort, conserve healthcare resources, and be preferred by patients. During August – November 2020, 1,806 adults undergoing SARS-CoV-2 testing in Denver, Colorado and Atlanta, Georgia, provided self-collected anterior nares swabs (ANS) and saliva specimens before NPS collection. Compared to NPS, sensitivity for SARS-CoV-2 detection by rRT-PCR appeared higher for saliva than for ANS (85% versus 80% in Denver; 67% versus 58% in Atlanta) and higher among participants reporting current symptoms (94% and 87% in Denver; 72% and 62% in Atlanta, for saliva and ANS, respectively) than among those reporting no symptoms (29% and 50% in Denver; 50% and 44% in Atlanta, for saliva and ANS, respectively). Compared to ANS, saliva was more challenging to collect and process. Self-collected saliva and ANS are less sensitive than NPS for SARS-CoV-2 detection; however, they offer practical advantages and might be most useful for currently symptomatic patients.
Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated individuals
Authors: Kissler Stephen M. , Fauver Joseph R. , Mack Christina , Tai Caroline G. , Breban Mallery I. , Watkins Anne E. , Samant Radhika M. , Anderson Deverick J. , Metti Jessica , Khullar Gaurav , Baits Rachel , MacKay Matthew , Salgado Daisy , Baker Tim , Dudley Joel T. , Mason Christopher E. , Ho David D. , Grubaugh Nathan D. , Grad Yonatan H. 
Published: February 2021

AbstractBackgroundThe alpha and delta SARS-CoV-2 variants have been responsible for major recent waves of COVID-19 despite increasing vaccination rates. The reasons for the increased transmissibility of these variants and for the reduced transmissibility of vaccine breakthrough infections are unclear.MethodsWe quantified the course of viral proliferation and clearance for 173 individuals with acute SARS-CoV-2 infections using longitudinal quantitative RT-PCR tests conducted using anterior nares/oropharyngeal samples (n = 199,941) as part of the National Basketball Association’s (NBA) occupational health program between November 28th, 2020, and August 11th, 2021. We measured the duration of viral proliferation and clearance and the peak viral concentration separately for individuals infected with alpha, delta, and non-variants of interest/variants of concern (non-VOI/VOC), and for vaccinated and unvaccinated individuals.ResultsThe mean viral trajectories of alpha and delta infections resembled those of non-VOI/VOC infections. Vaccine breakthrough infections exhibited similar proliferation dynamics as infections in unvaccinated individuals (mean peak Ct: 20.5, 95% credible interval [19.0, 21.0] vs. 20.7 [19.8, 20.2], and mean proliferation time 3.2 days [2.5, 4.0] vs. 3.5 days [3.0, 4.0]); however, vaccinated individuals exhibited faster clearance (mean clearance time: 5.5 days [4.6, 6.6] vs. 7.5 days [6.8, 8.2]).ConclusionsAlpha, delta, and non-VOI/VOC infections feature similar viral trajectories. Acute infections in vaccinated and unvaccinated people feature similar proliferation and peak Ct, but vaccinated individuals cleared the infection more quickly. Viral concentrations do not fully explain the differences in infectiousness between SARS-CoV-2 variants, and mitigation measures are needed to limit transmission from vaccinated individuals.
Healthcare-associated COVID-19 in England: a national data linkage study
Authors: Bhattacharya Alex , Collin Simon M , Stimson James , Thelwall Simon , Nsonwu Olisaeloka , Gerver Sarah , Robotham Julie , Wilcox Mark , Hopkins Susan , Hope Russell 
Published: February 2021

AbstractObjectivesNosocomial transmission was an important aspect of SARS-CoV-1 and MERS-CoV outbreaks. Healthcare-associated SARS-CoV-2 infection has been reported in single and multi-site hospital-based studies in England, but not nationally.MethodsAdmission records for all hospitals in England were linked to SARS-CoV-2 national test data for the period 01/03/2020 to 31/08/2020. Case definitions were: community-onset community-acquired (CO.CA), first positive test (FPT) <14 days pre-admission, up to day 2 of admission; hospital-onset indeterminate healthcare-associated (HO.iHA), FPT on day 3-7; hospital-onset probable healthcare-associated (HO.pHA), FPT on day 8-14; hospital-onset definite healthcare-associated (HO.HA), FPT from day 15 of admission until discharge; community-onset possible healthcare-associated (CO.pHA), FPT ≤14 days post-discharge.ResultsOne-third (34.4%, 100,859/293,204) of all laboratory-confirmed COVID-19 cases were linked to a hospital record. HO.pHA and HO.HA cases represented 5.3% (15,564/293,204) of all laboratory-confirmed cases and 15.4% (15,564/100,859) of laboratory-confirmed cases among hospital patients. CO.CA and CO.pHA cases represented 86.5% (253,582/293,204) and 5.1% (14,913/293,204) of all laboratory-confirmed cases, respectively.ConclusionsUp to 1 in 6 SARS-CoV-2 infections among hospitalised patients with COVID-19 in England during the first 6 months of the pandemic could be attributed to nosocomial transmission, but these represent less than 1% of the estimated 3 million COVID-19 cases in this period.