bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seasonal and Daytime Variation in Multiple Immune Parameters in Humans: Evidence from 329,261 Participants of the UK Biobank Cohort
Authors: Wyse Cathy , O’Malley G , Coogan Andrew N. , Smith Daniel J. 
Published: October 2020

AbstractBackgroundSeasonal disease outbreaks are perennial features of human infectious disease but the factors generating these patterns are unclear. In animal studies, seasonal and circadian (daily) rhythms in immune function generate periodicity in vulnerability to disease, although it is not known whether the same applies to humans. Making use of extensive data from the UK Biobank cohort, we investigate seasonal and daytime variability in multiple immune parameters (inflammatory markers, white blood cell counts and antibody titres), and test for associations with a wide range of environmental and lifestyle factors.Methods and FindingsMarkers of inflammation (CRP), and white blood cell counts were measured between 8am and 7pm over a 4-year time period in 329,261 participants in UK Biobank. Individual-level data were linked to other factors that vary over seasonal and daily cycles, including changes in day length, outdoor temperature and vitamin D at the time the blood sample was collected. Analyses were further adjusted for potentially confounding lifestyle factors. Seasonal patterns were evident in lymphocyte and neutrophil counts, and CRP, but not monocytes, and these were independent of lifestyle, demographic and environmental factors. All the immune parameters assessed demonstrated significant daytime variation that was independent of confounding factors.ConclusionsAt a population level, human immune parameters vary across season and across time of day, independent of multiple confounding factors. Both season and time of day are fundamental dimensions of immune function that should be considered in all studies of immuno-prophylaxis and disease transmission. Strategic alignment of human activities to seasons and times of the day when we are less susceptible to infection could be an important additional tool for limiting population-level impacts of infectious diseases.
Evaluation of User Experiences for the Clean Team Ghana Container-Based Sanitation Service in Kumasi, Ghana
Authors: Tidwell James B. , Nyarko Kwabena B. , Ross Ian , Dwumfour-Asare Bismark , Scott Pippa 
Published: October 2020

AbstractThere is a lack of affordable and acceptable sanitation solutions for dense, low-income urban settlements. One option that has been proposed is container-based sanitation, where a sealed cartridge installed in a free-standing toilet is regularly changed and adequately separates users from their excreta. Though container-based toilets are considered a safely managed sanitation solution that meets the Sustainable Development Goal for sanitation, little is known about user experiences to inform how such a solution should be viewed by governments. We conducted a longitudinal prospective cohort study of changes in objective and subjective measures of sanitation quality due to the Clean Team Ghana (CTG) container- based toilet service in Kumasi, Ghana from June to December 2019. We collected data immediately prior to installation of a toilet and 10 weeks afterwards for 292 customers. Most initially used public toilets with good structural quality, but sometimes had poor cleanliness, a lack of handwashing facilities, and required a 14.3 minute mean round trip time to use. The evaluation found that CTG delivers a high-quality service that positively impacts the quality of life of CTG customers, as well as saving them money, reducing gender gaps in quality of life, and addressing the needs of those with physical disabilities. Satisfaction with CTG toilet and service characteristics was high, with the largest increases for satisfaction with smell, comfort, disgust, and privacy. Women in particular were positively impacted both for explicitly gendered indicators like the ability to practice menstrual hygiene management, and other indicators where women scored lower than men at baseline, including ease of access, ease of use, and cleanliness. Use of the service also benefitted those who had been unable to use a toilet for physical or social reasons beforehand. Problems with the CTG service, such as leaking, filling, smelling, or not being replaced as scheduled, were reported by fewer than 10% of customers. While one product or service does not fit the needs of all customers, this evaluation supports the growing body of evidence that container-based sanitation provides a service valued by users and acceptable to policymakers in dense urban settlements.
COVID-19 Infections Following Physical School Reopening
Authors: Miron Oren , Yu Kun-Hsing , Wilf-Miron Rachel , Kohane Isaac S. , Davidovitch Nadav 
Published: October 2020

AbstractBackgroundSchool reopened in August-September 2020 and their effect on COVID-19 infections is unclear.MethodsWe examined Coronavirus Disease-19 incidence following school reopening in Florida.ResultsWe found that counties teaching physically had 1.2-fold incidence increase in elementary schools and 1.3-fold increase in high schools, while counties teaching remotely had no increase.ConclusionsOur results suggest that counties teaching physically could consider teaching remotely, especially in high school, until it is safe to teach physically.What was knownSchools reopened in August-September 2020, with some teaching remotely, since the effect of physical reopening on COVID-19 infections is unclear.What we addedcounties teaching physically had 1.2-fold incidence increase in elementary schools and 1.3-fold increase in high schools. This suggests that counties teaching physically could consider teaching remotely instead, especially at the high school level.
Preliminary Estimates of Years of Life Lost (YLL) Due to COVID-19 in India
Authors: Indrayan Abhaya , Mishra Aman , Pathak Mona 
Published: October 2020

AbstractObjectivesMore than 7 million cases of COVID have been detected in India by the middle of October 2020 and more than 100 thousand deaths have occurred. In this communication, we present an estimate of the years of life lost (YLL) due to COVID-19 so far and the projection for the full year so that the health damage by this new disease can be compared with some other ailments.DesignRecords based studyMethodThe YLL by one premature death is the expectation of life at that age. To calculate YLL, the age-wise distribution of COVID cases and deaths was obtained from the official sources of the government of India. Similar calculations were done for the general population from all causes for comparison.ResultsA total of more than 2 million years of life have already lost due to COVID-19 and the pattern indicates that we may end up with nearly 4 million YLL due to this disease in India. This is nearly 20 years lost per COVID death, 303 years lost per 1000 cases of COVID, and about 3 years lost per 1000 population in a full year. The age-group 50–59 years has been particularly affected. Other important findings are summarized as key messages.ConclusionThe years of life lost so far and anticipated in full-year are enormous but may still be lower compared with some other causes such as road injuries.
Clinical Presentation, Complication and Outcome of Black Stone (Paraphenylene Diamine) Poisoning
Authors: Abro Hakim Ali , Chandio Sultan Ahmed , Jalbani Azizullah , Buriro Sheeraz Ali , Saeed Aafia , Shaukat Faizan 
Published: October 2020

AbstractIntroductionIn recent time, developing countries of South Asia and Africa have seen significant increase in ingestion of Para-Phenylene Diamine (PPD), locally known as Kala Pathar, either accidental or for suicide. Through this study, we aim to study the clinical presentations and outcomes among patients who have ingested PPD.MethodThis retrospective case series study was conducted in a tertiary care hospital of Pakistan, from April 2013 to August 2017. Data of patients of PPD poisoning was archived from the hospital’s medical records. Around 174 consecutive cases were included in the study. Patients were evaluated based on self-administrated proforma.ResultOut of 174 cases of PPD poisoning that were identified, 57(32.8%) were males and 117(67.2%) were females. The mean age ± SD (range) of the patients was 24.16±9 (10 to 70) years. Approximately 170 (97.8%) patients used PPD for suicidal intention. The most common presentation was facial swelling which was present in 144(82.8%) patients followed by dysphagia in 143(82.2%) patients. Complications include metabolic acidosis in 50 (28.7%) patients and aspiration pneumonia in 36 (20.7%) patients. A total of 101 (58%) improved, while others were either referred or left against medical advice (LAMA).ConclusionIncreasing incidence of ingestion of PPD for suicide warrants the regulatory authorities to restrict the use of PPD in hair dyes and implement strict measures to educate masses and curtail the easy access of such poisonous substances among common people.
Low serum vitamin D level and COVID-19 infection and outcomes, a multivariate meta-analysis
Authors: Chen Jie , Xie Lixia , Yuan Ping , Ma Jianyong , Yu Peng , Zheng Chunhua , Liu Xiao 
Published: October 2020

AbstractObjectiveThis study aimed to determine whether serum vitamin D is independently associated with COVID-19 infection and outcomes in patients with COVID-19.MethodsWe identified relevant studies by searching the PubMed, Embase, and medRxiv databases from December 2019 to October 1, 2020. Odds ratios (ORs) were pooled using random-effects models. Only reports with multivariate adjusted results were included to avoid the impact of potential confounding factors.ResultsA total of six studies with 377,265 patients were identified. Overall, in the categorical analysis, a low serum vitamin D level was associated with an increased risk of COVID-19 infection (OR: 1.47, 95% CI: 1.09- 1.97, I2=81%), hospitalization (OR: 1.83, 95% CI: 1.22-2.74, I2=0%), but not in-hospital death (OR: 2.73, 95% CI: 0.27-27.61). Notably, when vitamin D level was analyzed as a continuous variable, each 5 ng/ml increase in vitamin D level was not associated with any increased risk of COVID-19 infection (OR: 1.04, 95% CI: 0.96-1.12, I2=74%) or in-hospital death (OR: 1.02, 95% CI: 0.93-1.12).ConclusionsLow serum vitamin D is associated with an increased risk of COVID-19 infection and hospitalization. In-hospital death showed a tendency to be increased in COVID-19 patients with low vitamin D levels. The ongoing clinical trials for evaluation of vitamin D supplementation will be key to the validation of this adjunctive treatment for COVID-19 patients.
Reducing Covid-19 risk in schools: a qualitative examination of staff and family views and concerns
Authors: Lorenc Ava , Kesten Joanna M , Kidger Judi , Langford Rebecca , Horwood Jeremy 
Published: October 2020

AbstractBackgroundThe Covid-19 pandemic has necessitated schools implementing Covid-19 risk-reduction measures.MethodsWe investigated young people, parent and school staff attitudes towards secondary school Covid-19 mitigation measures. Recruitment used school communication, community organisations and snowball sampling. Audio recorded online/phone individual/group interviews lasted 45 minutes. Interviews focused on social distancing, hand-hygiene and testing. Team framework analysis used interview notes and transcripts.ResultsParticipants were 13 school staff, 20 parents and 17 young people. Concerns about Covid-19 risk at school, especially to vulnerable individuals, were outweighed by perceived risks of not returning to school. Some teachers anticipated guilt around being a potential ‘spreader’. Participants saw school mitigation measures as an acceptable and pragmatic solution to the impossibility of social distancing, although anticipated challenges in changing habitual behaviour. Participants supported school Covid-19 testing but identified the need to consider data security and stigma. Staff were concerned about unintended consequences of risk-reduction strategies and widening inequalities.ConclusionFamilies and staff supported Covid-19 mitigation measures in schools. Clear messaging and engendering collective responsibility are important for compliance and success. However, schools and policy makers should consider unintended consequences of measures, supporting vulnerable individuals and those with additional needs, and avoiding widening inequalities.
Baseline phenotype and 30-day outcomes of people tested for COVID-19: an international network cohort including >3.32 million people tested with real-time PCR and >219,000 tested positive for SARS-CoV-2 in South Korea, Spain and the United States
Authors: Golozar Asieh , Lai Lana YH , Sena Anthony G. , Vizcaya David , Schilling Lisa M. , Huser Vojtech , Nyberg Fredrik , Duvall Scott L. , Morales Daniel R. , Alshammari Thamir M , Abedtash Hamed , Ahmed Waheed-Ul-Rahman , Alser Osaid , Alghoul Heba , Zhang Ying , Gong Mengchun , Guan Yin , Areia Carlos , Jonnagaddala Jitendra , Shah Karishma , Lane Jennifer C.E. , Prats-Uribe Albert , Posada Jose D. , Shah Nigam H. , Subbian Vignesh , Zhang Lin , Fernandes Abrahão Maria Tereza , Rijnbeek Peter R. , You Seng Chan , Casajust Paula , Roel Elena , Recalde Martina , Fernández-Bertolín Sergio , Andryc Alan , Thomas Jason A. , Wilcox Adam B. , Fortin Stephen , Blacketer Clair , DeFalco Frank , Natarajan Karthik , Falconer Thomas , Spotnitz Matthew , Ostropolets Anna , Hripcsak George , Suchard Marc , Lynch Kristine E. , Matheny Michael E. , Williams Andrew , Reich Christian , Duarte-Salles Talita , Kostka Kristin , Ryan Patrick B. , Prieto-Alhambra Daniel 
Published: October 2020

ABSTRACTEarly identification of symptoms and comorbidities most predictive of COVID-19 is critical to identify infection, guide policies to effectively contain the pandemic, and improve health systems’ response. Here, we characterised socio-demographics and comorbidity in 3,316,107persons tested and 219,072 persons tested positive for SARS-CoV-2 since January 2020, and their key health outcomes in the month following the first positive test. Routine care data from primary care electronic health records (EHR) from Spain, hospital EHR from the United States (US), and claims data from South Korea and the US were used. The majority of study participants were women aged 18-65 years old. Positive/tested ratio varied greatly geographically (2.2:100 to 31.2:100) and over time (from 50:100 in February-April to 6.8:100 in May-June). Fever, cough and dyspnoea were the most common symptoms at presentation. Between 4%-38% required admission and 1-10.5% died within a month from their first positive test. Observed disparity in testing practices led to variable baseline characteristics and outcomes, both nationally (US) and internationally. Our findings highlight the importance of large scale characterization of COVID-19 international cohorts to inform planning and resource allocation including testing as countries face a second wave.
Causes of death in mental health service users during the first wave of the COVID-19 pandemic: South London and Maudsley data from March to June 2020, compared with 2015-2019
Authors: Stewart Robert , Jewell Amelia , Broadbent Matthew , Bakolis Ioannis , Das-Munshi Jayati 
Published: October 2020

AbstractThe COVID-19 pandemic is likely to have had a particularly high impact on the health and wellbeing of people with pre-existing mental disorders. This may include higher than expected mortality rates due to severe infections themselves, due to other comorbidities, or through increased suicide rates during lockdown. However, there has been very little published information to date on causes of death in mental health service users. Taking advantage of a large mental healthcare database linked to death registrations, we describe numbers of deaths within specific underlying-cause-of-death groups for the period from 1st March to 30th June in 2020 and compare these with the same four-month periods in 2015-2019. In past and current service users, there were 2561 deaths in March-June 2020, compared to an average of 1452 for the same months in 2015-19: an excess of 1109. The 708 deaths with COVID-19 as the underlying cause in 2020 accounted for 63.8% of that excess. The remaining excess was accounted for by unnatural/unexplained deaths and by deaths recorded as due to neurodegenerative conditions, with no excess in those attributed to cancer, circulatory disorders, digestive disorders, respiratory disorders, or other disease codes. Of 295 unexplained deaths in 2020 with missing data on cause, 162 (54.9%) were awaiting a formal death notice (i.e. the group that included deaths awaiting a coroner’s inquest) – an excess of 129 compared to the average of previous years, accounting for 11.6% of the excess in total deaths.
Serologic SARS-CoV-2 testing in healthcare workers with positive RT-PCR test or Covid-19 related symptoms
Authors: Visci Giovanni , Lodi Vittorio , Bonfiglioli Roberta , Lazzarotto Tiziana , Violante Francesco S. , Boffetta Paolo 
Published: October 2020

AbstractBackgroundLimited information is available on prevalence and determinants of serologic response to SARS-CoV-2 infection among healthcare workers (HCWs).MethodsWe analyzed the results of serologic testing with chemiluminescence immunoassay analyzer (CLIA), lateral flow immunoassay (LFIA) and enzyme-linked immunosorbent assay (ELISA) test among 544 HCWs with at least one positive RT-PCR test and 157 HCWs with Covid-19 related symptoms without a positive RT-PCR test from public hospitals in Bologna, Northern Italy. Tests were performed between March and August 2020. We fitted multivariate logistic regression models to identify determinants of positive serology.ResultsThe sensitivity of SARS-CoV-2 was 75.2% (LFIA) and 90.6% (CLIA). No differences in seropositivity were observed by sex, while older HCWs had higher positivity than other groups, and nurses had higher positivity compared to physicians, but not other HCWs. An estimated 73.4% of HCWs with Covid-19 symptoms without RT-PCR test were not infected with SARS-CoV-2.ConclusionsOur study provides the best available data on sensitivity of serologic tests and on determinants of serologic response among HCWs positive for SARS-CoV-2, and provide evidence on the low specificity of Covid-19 related symptoms to identify infected HCWs.SummaryThe sensitivity of SARS-CoV-2 lateral flow immunoassay serology in healthcare workers (HCWs) was 75.2%. Older HCWs and nurses had higher positivity than other groups. An estimated 73.4% of HCWs with Covid-19 symptoms without RT-PCR test were not infected with SARS-CoV-2.
Gene validation and remodelling using proteogenomics ofPhytophthora cinnamomi, the causal agent of Dieback
Authors: Andronis Christina E. , Hane James K. , Bringans Scott , Hardy Giles E. S. , Jacques Silke , Lipscombe Richard , Tan Kar-Chun 
Published: October 2020

AbstractPhytophthora cinnamomiis a pathogenic oomycete that causes plant dieback disease across a range of natural ecosystems and in many agriculturally important crops on a global scale. An annotated draft genome sequence and annotation is publicly available (JGI Mycocosm) and suggests 26,131 gene models. In this study, soluble mycelial, extracellular (secretome) and zoospore proteins ofP. cinnamomiwere exploited to refine the genome by correcting gene annotations and discovering novel genes. By implementing the diverse set of sub-proteomes into a generated proteogenomics pipeline, we were able to improve theP. cinnamomigenome. Liquid chromatography mass spectrometry was used to obtain high confidence peptides with spectral matching to both the annotated genome and a generated 6-frame translation. 2,764 annotations from the draft genome were confirmed by spectral matching. Using a proteogenomic pipeline, mass spectra were used to edit theP. cinnamomigenome and allowed identification of 23 new gene models and 60 edited gene features using high confidence peptides obtained by mass spectrometry, suggesting a rate of incorrect annotations of 3% of the detectable proteome. The novel features were further validated by total peptide support, alongside functional analysis including the use of Gene Ontology and functional domain identification. We demonstrated the use of spectral data in combination with our proteogenomics pipeline can be used to improve the genome of important plant diseases and identify biologically relevant missed genes. This study presents the first use of spectral data to edit and manually annotate an oomycete pathogen.
A modular approach to integrating multiple data sources into real-time clinical prediction for pediatric diarrhea
Authors: Brintz Ben J. , Haaland Benjamin , Howard Joel , Chao Dennis L. , Proctor Joshua L. , Khan Ashraful I. , Ahmed Sharia M. , Keegan Lindsay T. , Greene Tom , Keita Adama Mamby , Kotloff Karen L. , Platts-Mills James A. , Nelson Eric J. , Levine Adam C. , Pavia Andrew T. , Leung Daniel T. 
Published: October 2020

AbstractTraditional clinical prediction models focus on parameters of the individual patient. For infectious diseases, sources external to the patient, including characteristics of prior patients and seasonal factors, may improve predictive performance. We describe the development of a predictive model that integrates multiple sources of data in a principled statistical framework using a post-test odds formulation. Our method enables electronic real-time updating and flexibility, such that components can be included or excluded according to data availability. We apply this method to the prediction of etiology of pediatric diarrhea, where “pre-test” epidemiologic data may be highly informative. Diarrhea has a high burden in low-resource settings, and antibiotics are often over-prescribed. We demonstrate that our integrative method outperforms traditional prediction in accurately identifying cases with a viral etiology, and show that its clinical application, especially when used with an additional diagnostic test, could result in a 61% reduction in inappropriately prescribed antibiotics.
Plasmodium falciparum artemisinin-resistant K13 mutations confer a sexual-stage transmission advantage that can be overcome with atovaquone-proguanil
Authors: Pava Zuleima , Mok Sachel , Collins Katharine A. , Rebelo Maria , Watts Rebecca E. , Robinson Gregory J. , Wang Claire Y.T. , Mitchell Hayley , Lynch Sean , Gower Jeremy , Webb Lachlan , McEwan Sam , Odedra Anand , Barber Bridget , Marquart Louise , Dixon Matthew W.A. , Moehrle Joerg J. , Fidock David A. , McCarthy James S. 
Published: October 2020

ABSTRACTContaining the spread of artemisinin (ART)-resistant Plasmodium falciparum will be assisted by improved understanding of its human-to-mosquito transmission. We compared gametocyte dynamics among field isolates containing K13 mutations conferring ART resistance and K13 wild-type parasites. In Pailin, Cambodia, the male to female gametocyte ratio was higher among K13 mutant infections compared to K13 wild-type infections. We also investigated the effects of artesunate and atovaquone-proguanil on the transmissibility of an ART-resistant K13 mutant strain, Cam3.IIR539T, in a volunteer infection study. Gametocyte production was higher after a single dose of artesunate (2 mg/kg) in volunteers infected with ART-resistant compared to ART-sensitive parasites. Despite the presence of gametocytes in volunteers infected with ART-resistant parasites, there was no infection observed in Anopheles stephensi mosquitoes after atovaquone-proguanil treatment. We report transmission determinants of ART-resistant infections that could be advantageous over ART-sensitive infections. Moreover, we show additional benefits of treating ART-resistant infections with atovaquone-proguanil treatment.