bluuebunny/crossref_metadata_2025_split huggingface dataset:
Higher Native Peruvian ancestry proportion is associated with tuberculosis progression risk
Authors: Asgari Samira , Luo Yang , Slowikowski Kamil , Huang Chuan-Chin , Calderon Roger , Jimenez Judith , Yataco Rosa , Contreras Carmen , Galea Jerome T. , Lecca Leonid , Jones David , Moody D. Branch , Murray Megan B. , Raychaudhuri Soumya 
Published: September 2020

AbstractThe global burden of pulmonary tuberculosis (TB) remains a major public health problem that is particularly severe among and disproportionately affects indigenous populations. We aimed to investigate whether genetic factors related to indigeneity affect TB progression risk in a cohort of admixed Peruvians with active TB and their latently infected household contacts. Our results show that Native Peruvian ancestry is positively associated with TB progression risk: a 10% increase in native ancestry tracks with a 25% increased risk of TB progression. This risk is independent of the potentially confounding socio-demographic and environmental factors that we tested here. Our results demonstrate that the genetic contribution to TB risk varies among populations and brings new insight to the long-standing debate on the role of genetic ancestry in susceptibility to TB. Additionally, our study highlights the value of including diverse populations in genetic studies of infectious diseases and other complex phenotypes, and provides a road map for future similar studies where it is important to account for confounding non-genetic risk factors to identify genetic risk factors.
Estimation and Removal of spurious echo Artifacts in single-voxel MRS using Sensitivity Encoding
Authors: Berrington Adam , Považan Michal , Barker Peter B 
Published: September 2020

AbstractPurposeIn localized MR spectroscopy, spurious echo artifacts commonly occur when unsuppressed signal outside the volume-of-interest is exicted and refocused. In the spectral domain, these signals often overlap with metabolite resonances and hinder accurate quantification. Since the artifacts orginate from regions separate from the target MRS voxel, this work proposes that sensitivity encoding based on receive coil sensitivity profiles may be used to separate these signal contributions.MethodsNumerical simulations were performed to explore the effect of sensitivity encoded separation for unknown artifact regions. An imaging-based approach was developed to identify regions that may contribute to spurious echo artifacts, and tested for sensitivity-based unfolding of signal contribution on 6 datasets from 3 brain regions. Spectral data reconstructed using the proposed method (‘ERASE’) were compared to standard coil combination.ResultsThe method was able to fully separate metabolite and artifact signals if regions were known a priori. Mismatch between estimated and actual artifact locations reduced the efficiency of artifact removal. Water suppression imaging (WSI) was able to identify unsuppressed signal remote from the MRS voxel in all cases, and ERASE reconstruction (of up to 8 distinct locations) led to improvements in spectral quality and reduced fitting errors for the major metabolites compared to standard reconstruction, without significant degradation of spectral SNR.ConclusionThe ERASE reconstruction tool was demonstrated to reduce spurious echo artifacts in single voxel MRS. ERASE may be incorporated into standard MRS workflows to improve spectral quality when scanner hardware limitations or other factors result in out-of-voxel signal contamination.
Analysis of twenty-week time-series of confirmed cases of New Coronavirus COVID-19 and their simple short-term prediction for Georgia and Neighboring Countries (Armenia, Azerbaijan, Turkey, Russia) in amid of a global pandemic
Authors: Amiranashvili Avtandil G. , Khazaradze Ketevan R. , Japaridze Nino D. 
Published: September 2020

AbstractResults of a comparative statistical analysis of the daily data associated with New coronavirus COVID-19 infection of confirmed cases (Č) of the population in Georgia (GEO), Armenia (ARM), Azerbaijan (AZE), Turkey (TUR) and Russia (RUS) amid a global pandemic (WLD) in the period from March 14 to July 31, 2020 are presented.The analysis of data is carried out with the use of the standard statistical analysis methods of random events and methods of mathematical statistics for the non-accidental time-series of observations.In particular, a correlation and autocorrelation analysis of the observational data was carried out, the periodicity in the time- series of Č were revealed, the calculation of the interval prediction values of Č taking into account the periodicity in the time-series of observations from August 1 to 31, 2020 (ARM, AZE) and from August 1 to September 11, 2020 (WLD, GEO, TUR, RUS) were carried out.Comparison of real and calculated predictions data on Č in the study sites from August 1 to August 31, 2020 is carried out. It was found that daily, monthly and mean weekly real values of Č for all the studied locations practically fall into the 99% confidence interval of the predicted values of Č for the specified time period.A dangerous situation with the spread of coronavirus infection may arise when the mean weekly values of Č of the 99% upper level of the forecast confidence interval are exceeded within 1–2 weeks. Favorable – when the mean weekly values of Č decrease below 99% of the lower level of the forecast confidence interval.
Where has democracy helped the poor? Democratic transitions and early-life mortality at the country level
Authors: Pedro Ramos Antonio , Jose Flores Martiniano , Ross Michael L. 
Published: September 2020

AbstractThe effects of democracy on living conditions among the poor are disputed. Previous studies have addressed this question by estimating the average effect of democracy on early-life mortality across all countries. We revisit this debate using a research design that distinguishes between the aggregated effects of democracy across all countries and their individual effects within countries. Using Interrupted Time Series methodology and estimating model parameters in a Bayesian framework, we find the average effect of democracy on early-life mortality to be close to zero, but with considerable variation at the country-level. Democratization was followed by fewer child deaths in 21 countries, an increase in deaths in eight, and no measurable changes in the remaining 32 cases. Transitions were usually beneficial in Europe, neutral or beneficial in Africa and Asia, and neutral or harmful in Latin America. The distribution of country-level effects is not consistent with common arguments about the conditional effects of democratic transitions. Our results open a new line of research into the sources of theses heterogeneous effects.
Use of Unofficial Newspaper Data for COVID-19 Death Surveillance
Authors: Ahamad Mazbahul G. , Ahmed Monir U. , Talukder Byomkesh , Tanin Fahian 
Published: September 2020

AbstractObjectiveTo highlight the critical importance of unofficially reported newspaper-based deaths from coronavirus disease 2019 (COVID-19)–like illness (CLI) together with officially confirmed death counts to support improvements in COVID-19 death surveillance.MethodsBoth hospital-based official COVID-19 and unofficial CLI death counts were collected from daily newspapers between March 8 and August 22, 2020. We performed both exploratory and time-series analyses to understand the influence of combining newspaper-based CLI death counts with confirmed hospital death counts on the trends and forecasting of COVID-19 death counts. An autoregressive integrated moving average–based approach was used to forecast the number of weekly death counts for six weeks ahead.ResultsBetween March 8 and August 22, 2020, 2,156 CLI deaths were recorded based on newspaper reporting for a count that was 55% of the officially confirmed death count (n = 3,907). This shows that newspaper reports tend to cover a significant number of COVID-19 related deaths. Our forecast also indicates an approximate total of 406 CLI expected for the six weeks ahead, which could contribute to a total of 2,413 deaths including 2,007 confirmed deaths expected from August 23 to October 3, 2020.ConclusionsAnalyzing existing trends in and forecasting the expected number of newspaper-based CLI deaths indicates yet-unreported COVID-19 death counts, which could be a critical source to estimate provisional COVID-19 death counts and mortality surveillance.Public Health ImplicationsConsidering unofficial newspaper-based CLI death counts is essential to identify COVID-19 death severity and surveillance needs to advance public health research efforts to prepare appropriate response strategies for low- and middle-income countries.
The influence of pH on SARS-CoV-2 infection and COVID-19 severity
Authors: Jimenez Leandro , Codo Ana Campos , de Souza Sampaio Vanderson , Oliveira Antonio E.R. , Ferreira Lucas Kaoru Kobo , Davanzo Gustavo Gastão , de Brito Monteiro Lauar , Virgilio-da-Silva João Victor , Borba Mayla Gabriela Silva , de Souza Gabriela Fabiano , Zini Nathalia , de Andrade Gandolfi Flora , Murano Stéfanie Primon , Proença-Modena José Luiz , Val Fernando Almeida , Melo Gisely Cardoso , Monteiro Wuelton Marcelo , Nogueira Maurício Lacerda , Lacerda Marcus Vinícius Guimarães , Moraes-Vieira Pedro M. , Nakaya Helder I 
Published: September 2020

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect a broad range of human tissues by using the host receptor angiotensin-converting enzyme 2 (ACE2). Individuals with comorbidities associated with severe COVID-19 display higher levels ofACE2in the lungs compared to those without comorbidities, and conditions such as cell stress, elevated glucose levels and hypoxia may also increase the expression ofACE2. Here we showed that patients with Barrett’s esophagus (BE) have a higher expression ofACE2in BE tissues compared to normal squamous esophagus, and that the lower pH associated with BE may drive this increase in expression. Human primary monocytes cultured in reduced pH displayed increasedACE2expression and viral load upon SARS-CoV-2 infection. We also showed in two independent cohorts of COVID-19 patients that previous use of proton pump inhibitors is associated with 2- to 3-fold higher risk of death compared to those not using the drugs. Our work suggests that pH has a great influence on SARS-CoV-2 Infection and COVID-19 severity.
High COVID-19 transmission potential associated with re-opening universities can be mitigated with layered interventions
Authors: Brooks-Pollock Ellen , Christensen Hannah , Trickey Adam , Hemani Gibran , Nixon Emily , Thomas Amy , Turner Katy , Finn Adam , Hickman Matt , Relton Caroline , Danon Leon 
Published: September 2020

AbstractBackgroundRe-opening universities while controlling COVID-19 transmission poses unique challenges. UK universities typically host 20,000 to 40,000 undergraduate students, with the majority moving away from home to attend. In the absence of realistic mixing patterns, previous models suggest that outbreaks associated with universities re-opening are an eventuality.MethodsWe developed a stochastic transmission model based on realistic mixing patterns between students. We evaluated alternative mitigation interventions for a representative university.ResultsOur model predicts, for a set of plausible parameter values, that if asymptomatic cases are half as infectious as symptomatic cases then 5,760 (3,940 – 7,430) out of 28,000 students, 20% (14% – 26%), could be infected during the first term, with 950 (656 – 1,209) cases infectious on the last day of term. If asymptomatic cases are as infectious as symptomatic cases then three times as many cases could occur, with 94% (93% – 94%) of the student population getting infected during the first term. We predict that one third of infected students are likely to be in their first year, and first year students are the main drivers of transmission due to high numbers of contacts in communal residences. We find that reducing face-to-face teaching is likely to be the single most effective intervention, and this conclusion is robust to varying assumptions about asymptomatic transmission. Supplementing reduced face-to-face testing with COVID-secure interactions and reduced living circles could reduce the percentage of infected students by 75%. Mass testing of students would need to occur at least fortnightly, is not the most effective option considered, and comes at a cost of high numbers of students requiring self-isolation. When transmission is controlled in the student population, limiting imported infection from the community is important.ConclusionsPriority should be given to understanding the role of asymptomatic transmission in the spread of COVID-19. Irrespective of assumptions about asymptomatic transmission, our findings suggest that additional outbreak control measures should be considered for the university setting. These might include reduced face-to-face teaching, management of student mixing and enhanced testing. Onward transmission to family members at the end of term is likely without interventions.
High efficacy of face masks explained by characteristic regimes of airborne SARS-CoV-2 virus abundance
Authors: Cheng Yafang , Ma Nan , Witt Christian , Rapp Steffen , Wild Philipp , Andreae Meinrat O. , Pöschl Ulrich , Su Hang 
Published: September 2020

AbstractAirborne transmission by droplets and aerosols is important for the spread of viruses and face masks are a well-established preventive measure, but their effectiveness for mitigating COVID-19 is still under debate. We show that variations in mask efficacy can be explained by different regimes of virus abundance. For SARS-CoV-2, the virus load of infectious individuals can vary by orders of magnitude, but we find that most environments and contacts are in a virus-limited regime where simple surgical masks are highly effective on individual and population-average levels, whereas more advanced masks and other protective equipment are required in potentially virus-rich indoor environments such as medical centers and hospitals. Due to synergistic effects, masks are particularly effective in combination with other preventive measures like ventilation and distancing.One Sentence SummaryFace masks are highly effective due to prevailing virus-limited environments in airborne transmission of COVID-19.
Profiling Genome-Wide DNA Methylation Patterns in Human Aortic and Mitral Valves
Authors: Halawa Sarah , Latif Najma , Tseng Yuan-Tsan , Ibrahim Ayman M. , Chester Adrian H. , Moustafa Ahmed , Aguib Yasmine , Yacoub Magdi 
Published: September 2020

AbstractCardiac valves exhibit highly complex structures and specialized functions that include dynamic interactions between cells, extracellular matrix (ECM) and their hemodynamic environment. Valvular gene expression is tightly regulated by a variety of mechanisms including epigenetic factors such as histone modifications, RNA-based mechanisms and DNA methylation. To date, methylation fingerprints of non-diseased human aortic and mitral valves have not been studied. In this work we analyzed the differential methylation profiles of 12 non-diseased aortic and mitral valve tissue samples (in matched pairs). Analysis of methylation data (reduced representation bisulfite sequencing (RRBS)) of 1601 promoters genome-wide revealed 584 differentially methylated (DM) promoters, of which 13 were reported in endothelial mesenchymal trans-differentiation (EMT), 37 in aortic and mitral valve disease and 7 in ECM remodeling. Both functional classification as well as network analysis showed that the genes associated with the DM promoters were enriched for WNT-, Cadherin-, Endothelin-, PDGF- and VEGF-signaling implicated in valvular physiology and pathophysiology. Additional enrichment was detected for TGFB-, NOTCH- and Integrin-signaling involved in EMT as well as ECM remodeling. This data provides the first insight into differential regulation of human aortic and mitral valve tissue and identifies candidate genes linked to DM promoters. Our work will improve the understanding of valve biology, valve tissue engineering approaches and contributes to the identification of relevant drug targets.
The impact of asthma on mental health & wellbeing during COVID-19 lockdown
Authors: Higbee Daniel H , Nava George , Kwong Alex S F , Dodd James W , Granell Raquel 
Published: September 2020

AbstractIntroductionThe global SARS CoV2 pandemic resulted in social isolation measures with unintended negative impacts, particularly on mental health. We hypothesised that people with asthma are likely to be more vulnerable to worse mental health during lockdown.MethodsWe examined COVID-19 surveys (completed April/May 2020), nested within two generations of the Avon Longitudinal Study of Parents and Children (ALSPAC): index-generation ALSPAC-G1 (n= 2942, mean age=28) and the parent’s generation ALSPAC-G0 (n=3737, mean age=59). We used Poisson and logistic regression models to estimate the effect of asthma on wellbeing, anxiety and depression, and factors related to COVID-19 and lockdown. Models were adjusted for validated pre-pandemic measures of mental health and socio-economic factors.ResultsAsthma was associated with a 13% increase in depression score in ALSPAC-G1 (p=0.005) and 15% increase in ALSPAC-G0 (p=0.05) compared to participants without asthma, anxiety scores increased by 14% in ALSPAC-G1 (p=0.005) and by 16% in ALSPAC-G0 (p=0.02). Asthma was associated with a similar increase of anxiety and depression scores during COVID-19 in both generations (Z test p values >0.80).DiscussionPeople with asthma have worse mental health & wellbeing during lockdown compared to people without asthma. Although the effect of asthma on mental health is of similar magnitude between the generations, younger participants with asthma declined to lower levels of mental health despite reporting less symptoms, COVID-19 infection and self-isolation. This has important implications given repeated lockdowns. Young people with asthma should be closely monitored and supported to mitigate the impact of lockdown on their mental health.Key MessagesWhat is the question?What is the impact of asthma on mental health & wellbeing during COVID-19 pandemic?What is the bottom line?People living with asthma report worse wellbeing, anxiety and depression in lockdown compared to those without asthma, the effect is not entirely explained by pre-existing mental health problems, physical symptoms or COVID-19 infections.Why read on?Young people living with asthma are more likely to report concerns about susceptibility to COVID 19 and job security. The negative impact of asthma on length of self-isolation, suspected COVID and symptoms appears greater in older people with asthma.
SARS-CoV-2 detection by extraction-free qRT-PCR for massive and rapid COVID-19 diagnosis during a pandemic
Authors: Avetyan Diana , Chavushyan Andranik , Ghazaryan Hovsep , Melkonyan Ani , Stepanyan Ani , Zakharyan Roksana , Hayrapetyan Varduhi , Atshemyan Sofi , Martirosyan Gevorg , Melik-Andreasyan Gayane , Sargsyan Shushan , Ghazazyan Armine , Aleksanyan Naira , Yin Xiushan , Arakelyan Arsen 
Published: September 2020

AbstractCOVID-19 pandemic severely impacted the healthcare and economy on a global scale. It is widely recognized that mass testing is an efficient way to contain the infection spread as well as the development of informed policies for disease management. However, the current COVID-19 worldwide infection rates increased demand in the rapid and reliable screening of SARS-CoV-2 infection.We compared the performance of qRT-PCR in direct heat-inactivated, heat-inactivated/pelleted samples against RNA in a group of 74 subjects (44 positive and 30 negative). In addition, we compared the sensitivity of heat-inactivated/pelleted in another group of 196 COVID-19 positive samples.Our study suggests that swab sample heat-inactivation and pelleting show higher accuracy for SARS-CoV-2 detection PCR assay compared to heat-inactivation only (89% vs 83% of the detection in RNA). The accuracy of detection using direct samples varied depending on the sample transport and storage media as well as the concentration of viral particles.Our study suggests that purified RNA provides more accurate results, however, direct qRT-PCR may help to significantly increase testing capacity. Switching to the direct sample testing is justified if the number of tests is doubled at least.
Mental health as a mediator of the association between educational inequality and cardiovascular disease: A Mendelian randomisation study
Authors: Jones Daniel P , Wootton Robyn E , Gill Dipender , Carter Alice R , Gunnell David , Munafò Marcus R , Sallis Hannah M 
Published: September 2020

AbstractBackgroundEducation is inversely associated with cardiovascular disease. Several mediators for this association have been established but a significant proportion of the protective effect remains unaccounted for. Mental health is a proposed mediator, but current evidence is mixed and subject to bias from confounding factors and reverse causation. Mendelian randomisation (MR) is an instrumental variable technique that uses genetic proxies for exposures and mediators to reduce such bias.Methods and ResultsWe used logistic regression and two-step MR analyses to investigate whether educational attainment affects risk of mental health disorders. We then performed observational and MR mediation analyses to explore whether mental health disorders mediate the association between educational attainment and risk of cardiovascular disease. Higher levels of educational attainment were associated with reduced depression, anxiety and cardiovascular disease in observational analyses [Odds Ratio (95% Confidence interval) 0.79 (0.77-0.81), 0.76 (0.73-0.79) and 0.79 (0.78-0.81) respectively], and MR analyses provided support for these reflecting causal effects [OR (95% CI) 0.72 (0.67-0.77), 0.50 (0.42-0.59) and 0.62 (0.58-0.66) respectively]. Both anxiety and depression were associated with cardiovascular disease in observational analyses [OR (95% CI) 1.63 (1.49-1.79) and OR (95% CI) 1.70 (1.59-1.82) respectively] but only depression was associated in the MR analyses [OR (95% CI) 1.09 (1.03-1.15)]. Roughly 6% of the total protective effect of education on cardiovascular disease was mediated by depression.ConclusionsHigher levels of educational attainment protect against mental health disorders and reduced depression accounts for a small proportion of the total protective effect of education on cardiovascular disease.
The King’s College London Coronavirus Health and Experiences of Colleagues at King’s Study: SARS-CoV-2 antibody response in an occupational sample
Authors: Leightley Daniel , Vitiello Valentina , Bergin-Cartwright Gabriella , Wickersham Alice , Davis Katrina A.S. , Stevelink Sharon A.M , Hotopf Matthew , Razavi Reza 
Published: September 2020

AbstractWe report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at King’s College London. Between June and July 2020, antibody testing kits were sent to n = 2296 participants; n = 2004 (86.3%) responded, of whom n = 1882 (93.9%) returned valid test results. Of those that returned valid results, n = 124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.