bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Aberration Detection-Based Approach for Sentinel Syndromic Surveillance of COVID-19 and Other Novel Influenza-Like Illnesses
Authors: Wen Andrew , Wang Liwei , He Huan , Liu Sijia , Fu Sunyang , Sohn Sunghwan , Kugel Jacob A. , Kaggal Vinod C. , Huang Ming , Wang Yanshan , Shen Feichen , Fan Jungwei , Liu Hongfang 
Published: June 2020

AbstractCoronavirus Disease 2019 (COVID-19) has emerged as a significant global concern, triggering harsh public health restrictions in a successful bid to curb its exponential growth. As discussion shifts towards relaxation of these restrictions, there is significant concern of second-wave resurgence. The key to managing these outbreaks is early detection and intervention, and yet there is significant lag time associated with usage of laboratory confirmed cases for surveillance purposes. To address this, syndromic surveillance can be considered to provide a timelier alternative for first-line screening. Existing syndromic surveillance solutions are however typically focused around a known disease and have limited capability to distinguish between outbreaks of individual diseases sharing similar syndromes. This poses a challenge for surveillance of COVID-19 as its active periods are tend to overlap temporally with other influenza-like illnesses. In this study we explore performing sentinel syndromic surveillance for COVID-19 and other influenza-like illnesses using a deep learning-based approach. Our methods are based on aberration detection utilizing autoencoders that leverages symptom prevalence distributions to distinguish outbreaks of two ongoing diseases that share similar syndromes, even if they occur concurrently. We first demonstrate that this approach works for detection of outbreaks of influenza, which has known temporal boundaries. We then demonstrate that the autoencoder can be trained to not alert on known and well-managed influenza-like illnesses such as the common cold and influenza. Finally, we applied our approach to 2019-2020 data in the context of a COVID-19 syndromic surveillance task to demonstrate how implementation of such a system could have provided early warning of an outbreak of a novel influenza-like illness that did not match the symptom prevalence profile of influenza and other known influenza-like illnesses.
Evidence for ethnic inequalities in mortality related to COVID-19 infections: Findings from an ecological analysis of England and Wales
Authors: Nazroo James , Bécares Laia 
Published: June 2020

AbstractBackgroundIn the absence of direct data on ethnic inequalities in COVID-19 related mortality in the UK, we examine the relationship between ethnic composition of an area and rate of mortality in the area.MethodsEcological analysis using COVID-19 related mortality rates occurring by 24thApril 2020, and ethnic composition of the population, across local authorities in England and Wales. Account is taken of age, population density, area deprivation and pollution.ResultsFor every 1% rise in proportion of the population who are ethnic minority, COVID-19 related deaths increased by 5·10 (3·99 to 6·21) per million. This rise is present for each ethnic minority category examined. The size of this increase is a little reduced in a fully adjusted model, suggesting that some of the association results from ethnic minority people living in more densely populated, more polluted and more deprived areas.This estimate suggests that the average England and Wales COVID-19 related death rate would rise by 25% in a local authority with twice the average number of ethnic minority people.DiscussionWe find clear evidence that rates of COVID-19 related mortality within a local authority increase as the proportion of the population who are ethnic minority increases. We suggest that this is a consequence of social and economic inequalities, including among key workers, driven by entrenched structural and institutional racism and racial discrimination. We argue that these factors should be central to any investigation of ethnic inequalities in COVID-19 outcomes.
Estimating weekly excess mortality at sub-national level in Italy during the COVID-19 pandemic
Authors: Blangiardo Marta , Cameletti Michela , Pirani Monica , Corsetti Gianni , Battaglini Marco , Baio Gianluca 
Published: June 2020

AbstractObjectivesTo provide a sub-national analysis of excess mortality during the COVID-19 pandemic in Italy.DesignPopulation-based on all-cause mortality official data, available as counts by age and sex.SettingThe 7,904 municipalities in Italy.ParticipantsAll residents in Italy in the years 2016 to 2020.Main outcome measuresAll-cause mortality weekly rates for each municipality, based on the first four months of 2016 – 2019. Predicted all-cause weekly deaths and mortality rates at municipality level for 2020, based on the modelled spatio-temporal trends.ResultsThere was strong evidence of excess mortality for Northern Italy; Lombardia showed higher mortality rates than expected from the end of February, with 23,946 (23,013 to 24,786) total excess deaths. North-West and North-East regions showed higher mortality from the beginning of March, with 6,942 (6,142 to 7,667) and 8,033 (7,061 to 9,044) total excess deaths respectively. After discounting for the number of COVID-19-confirmed deaths, Lombardia still registered 10,197 (9,264 to 11,037) excess deaths, while regions in the North-West and North-East had 2,572 (1,772 to 3,297) and 2,047 (1,075 to 3,058) extra deaths, respectively. We observed marked geographical differences at municipality level. The city of Bergamo (Lombardia) showed the largest percent excess 88.9% (81.9% to 95.2%) at the peak of the pandemic. An excess of 84.2% (73.8% to 93.4%) was also estimated at the same time for the city of Pesaro (Central Italy), in stark contrast with the rest of the region, which does not show evidence of excess deaths.ConclusionsOur study gives a comprehensive picture of the evolution of all-cause mortality in Italy from 2016 to 2020 and describes the spatio-temporal differences in excess mortality during the COVID-19 pandemic. Our model shows heterogeneous impact of COVID-19, and it can be used to help policy- makers target measures to limit the burden on the health-care system as well as reducing social and economic consequences. Our probabilistic methodology is useful for real-time mortality surveillance, continuously monitoring local temporal trends and flagging where and when mortality rates deviate from the expected range, which might suggest a second wave of the pandemic.
Effects of Tocilizumab on Mortality in Hospitalized Patients with COVID-19: A Multicenter Cohort Study
Authors: Martínez-Sanz Javier , Muriel Alfonso , Ron Raquel , Herrera Sabina , Pérez-Molina José A. , Moreno Santiago , Serrano-Villar Sergio 
Published: June 2020

ABSTRACTBackgroundWhile there are no treatments with proven efficacy for patients with severe coronavirus disease 2019 (COVID-19), tocilizumab has been proposed as a candidate therapy, especially among patients with higher systemic inflammation.MethodsWe conducted a cohort study of patients hospitalized with COVID-19 in Spain. The primary outcome was time to death and the secondary outcome time to intensive care unit admission (ICU) or death. We used inverse-probability weighting to fit marginal structural models adjusted for time-varying covariates to determine the causal relationship between tocilizumab use and the outcomes.ResultsA total of 1,229 and 10,673 person/days were analyzed. In the adjusted marginal structural models, a significant interaction between tocilizumab use and high C- reactive protein (CRP) levels was detected. Tocilizumab was associated with decreased risk of death (aHR 0.34, 95% CI 0.16–0.72, p=0.005) and ICU admission or death (aHR 0.38, 95% CI 0.19–0.81, p=0.011) among patients with baseline CRP >150 mg/L, but not among those with CRP ≤150 mg/L. Exploratory subgroup analyses yielded point estimates that were consistent with these findings.ConclusionsIn this large observational study, tocilizumab was associated with a lower risk of death or ICU or death in patients with higher CRP levels. While the results of ongoing clinical trials of tocilizumab in patients with COVID-19 will be important to establish its safety and efficacy, our findings have implications for the design of future clinical trials and support the use of tocilizumab among subjects with higher CRP levels.
Examine the impact of weather and ambient air pollutant parameters on daily case of COVID-19 in India
Authors: Das Kousik , Chatterjee Nilanjana Das 
Published: June 2020

AbstractThe present study presents a view on exploring the relationship pattern between COVID 19 daily cases with weather parameters and air pollutants in mainland India. We consider mean temperature, relative humidity, solar radiation, rainfall, wind speed, PM2.5, PM10, SO2, NO2and CO as independent variable and daily COVID 19 cases as dependent variable for 18 states during 18thmarch to 30thApril, 2020.After dividing the dataset for 0 to 10 day, 10 to 25 days and 0 to 44 days, the current study applied Akaike s Information Criteria (AIC) and Generalized Additive Model (GAM) to examine the kind of relationship between independent variables with COVID 19 cases. Initially GAM model result shows variables like temperature and solar radiation has positive relation (p<0.05) in 0 to 10 days study with daily cases. In 25 days dataset it significantly shows that temperature has positive relation above 23 degree centigrade, SO2has a negative relationship and relative humidity has negative (between 30% to 45% and > 60%) and a positive relationship (45% to 60%) with COVID 19 cases (p=0.05). 44 days dataset has six parameters includes temperature as positive, relative humidity as negative (between 0 to 45%) and then positive (after >45%), NO2as Positive (0 to 35 microgram/m3) followed by negative trend (after > 40 microgram/m3), SO2and rainfall as negative relation. After sensitive analysis, it is found that weather variables like relative humidity, solar radiation and rainfall are more sensitive than temperature and wind speed. Whereas pollutants like NO2, PM2.5, PM10and CO are more sensitive variables than SO2in this study. In summary this study finds temperature, relative humidity, solar radiation, wind speed, SO2, PM2.5, and CO may be important factors associated with COVID 19 pandemic.Graphical AbstractHighlights➢There was a significant relationship between daily positive COVID-19 case with weather and pollution factors➢We found PM2.5and CO positively associated with transmission of positive cases where as NO2and SO2have a negative relation after sensitive analysis.➢We have found temperature and wind speed have positive relation whereas, relative humidity and solar radiation have negative relation after sensitive analysis.➢Weather variables like relative humidity and solar radiation and rainfall are more sensitive than temperature and wind speed. Pollutants like NO2, PM2.5, PM10and CO are more sensitive variables than SO2in this study.
Return of Results in a Global Sample of Psychiatric Genetics Researchers: Practices, Attitudes, and Knowledge
Authors: Lázaro-Muñoz Gabriel , Torgerson Laura , Pereira Stacey 
Published: June 2020

AbstractPurposePatient-participants in psychiatric genetics research may be at an increased risk for negative psychosocial impacts related to the return of genetic research results. Examining psychiatric genetics researchers’ return of results practices and perspectives can aid the development of empirically-informed and ethically-sound guidelines.MethodsA survey of 407 psychiatric genetics researchers from 39 countries was conducted to examine current return of results practices, attitudes, and knowledge.ResultsMost respondents (61%) reported that their studies generated medically relevant genomic findings. Although 24% have returned results to individual participants, 52% of those involved in decisions about return of results plan to return or continue to return results. Respondents supported offering medically actionable results related to psychiatric disorders (82%), and the majority agreed non-medically actionable risks for Huntington’s (71%) and Alzheimer’s disease (64%) should be offered. About half (49%) of respondents supported offering reliable polygenic risk scores for psychiatric conditions. Despite plans to return, only 14% of researchers agreed there are adequate guidelines for returning results, and 59% rated their knowledge about how to manage the process for returning results as poor.ConclusionPsychiatric genetics researchers support returning a wide range of results to patient-participants, but they lack adequate knowledge and guidelines.
SARS-CoV-2 triggered neutrophil extracellular traps (NETs) mediate COVID-19 pathology
Authors: Veras Flavio , Pontelli Marjorie , Silva Camila , Toller-Kawahisa Juliana , Lima Mikhael de , Nascimento Daniele , Schneider Ayda , Caetité Diego , Rosales Roberta , Colón David , Martins Ronaldo , Castro Italo , Almeida Glaucia , Lopes Maria Isabel , Benatti Maíra , Bonjorno Letícia , Giannini Marcela , Luppino-Assad Rodrigo , de Almeida Sérgio , Vilar Fernando , Santana Rodrigo , Bollela Valdes , Martins Maria , Miranda Carlos , Borges Marcos , Pazin-Filho Antônio , Cunha Larissa , Zamboni Dario , Dal-Pizzol Felipe , Leiria Luiz , Siyuan Li , Batah Sabrina , Fabro Alexandre , Mauad Thais , Dolhnikoff Marisa , Duarte-Neto Amaro. , Saldiva Paulo , Cunha Thiago , Alves-Filho José , Arruda Eurico , Louzada-Junior Paulo , de Oliveira Renê , Cunha Fernando 
Published: June 2020

AbstractSevere COVID-19 patients develop acute respiratory distress syndrome that may progress to respiratory failure. These patients also develop cytokine storm syndrome, and organ dysfunctions, which is a clinical picture that resembles sepsis. Considering that neutrophil extracellular traps (NETs) have been described as an important factors of tissue damage in sepsis, we investigated whether NETs would be produced in COVID-19 patients and participate in the lung tissue damage. A cohort of 32 hospitalized patients with a confirmed diagnosis of COVID-19 and respective healthy controls were enrolled. NETs concentration was assessed by MPO-DNA PicoGreen assay or by confocal immunofluorescence. The cytotoxic effect of SARS-CoV-2-induced NETs was analyzed in human epithelial lung cells (A549 cells). The concentration of NETs was augmented in plasma and tracheal aspirate from COVID-19 patients and their neutrophils spontaneously released higher levels of NETs. NETs were also found in the lung tissue specimens from autopsies of COVID-19 patients. Notably, viable SARS-CoV-2 can directly induce in vitro release of NETs by healthy neutrophils in a PAD-4-dependent manner. Finally, NETs released by SARS-CoV-2-activated neutrophils promote lung epithelial cell death in vitro. These results unravel a possible detrimental role of NETs in the pathophysiology of COVID-19. Therefore, the inhibition of NETs represent a potential therapeutic target for COVID-19.
Sequence analysis of travel-related SARS-CoV-2 cases in the Greater Geelong region, Australia
Authors: Bhatta Tarka Raj , Chamings Anthony , Liew Kwee-Chin , Langham Freya , Gasser Rudi , Harris Owen , Gador-Whyte Andrew , Stenos John , Athan Eugene , Alexandersen Soren 
Published: June 2020

AbstractThis study reports the sequence analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from infected individuals within the Greater Geelong region, Victoria, Australia. All but one individual had recently returned from travelling abroad, and all had clinical signs consistent with SARS-CoV-2 infection. SARS-CoV-2 belonging to three lineages were detected and represent separate introductions of the virus into the region. Sequence data were consistent with the recent travel history of each case. Full virus genome sequencing can play an important role in supporting local epidemiological tracing and monitoring for community transmission. Quality of the SARS-CoV-2 sequences obtained was highly dependent on appropriate sample collection and handling.
Longitudinal Surveillance for SARS-CoV-2 RNA Among Asymptomatic Staff in Five Colorado Skilled Nursing Facilities: Epidemiologic, Virologic and Sequence Analysis
Authors: Quicke Kendra , Gallichotte Emily , Sexton Nicole , Young Michael , Janich Ashley , Gahm Gregory , Carlton Elizabeth J. , Ehrhart Nicole , Ebel Gregory D. 
Published: June 2020

AbstractSARS-CoV-2 emerged in 2019 and has become a major global pathogen in an astonishingly short period of time. The emergence of SARS-CoV-2 also has been notable due to its impacts on individuals residing within skilled nursing facilities (SNFs) such as rehabilitation centers and nursing homes. SNF residents tend to possess several risk factors for the most severe outcomes of SARS-CoV-2 infection, including advanced age and the presence of multiple comorbidities. Indeed, residents of long-term care facilities represent approximately 40 percent of US SARS-CoV-2 deaths. To assess the prevalence and incidence of SARS-CoV-2 among SNF workers, determine the extent of asymptomatic infection by SARS-CoV-2, and provide information on the genomic epidemiology of the virus within these unique care settings, we sampled workers weekly at five SNFs in Colorado using nasopharyngeal swabs, determined the presence of viral RNA and infectious virus among these workers, and sequenced 48 nearly complete genomes. This manuscript reports results from the first five to six weeks of observation. Our data reveal a strikingly high degree of asymptomatic infection, a strong correlation between RNA detection and the presence of infectious virus in NP swabs, persistent RNA in a subset of individuals, and declining incidence over time. Our data suggests that asymptomatic individuals infected by SARS-CoV-2 may contribute to virus transmission within the workplace.
COVID-19 related mortality and spread of disease in long-term care: a living systematic review of emerging evidence
Authors: Salcher-Konrad Maximilian , Jhass Arnoupe , Naci Huseyin , Tan Marselia , El-Tawil Yousef , Comas-Herrera Adelina 
Published: June 2020

AbstractBackgroundPolicy responses to mitigate the impact of the COVID-19 pandemic on long-term care (LTC) require robust and timely evidence on mortality and spread of the disease in these settings. The aim of this living systematic review is to synthesise early international evidence on mortality rates and incidence of COVID-19 among people who use and provide LTC.MethodsWe report findings of a living systematic review (CRD42020183557), including studies identified through database searches up to 26 June 2020. We searched seven databases (MEDLINE; Embase; CINAHL Plus; Web of Science; Global Health; WHO COVID-19 Research Database; medRxiv) to identify all studies reporting primary data on COVID-19 related mortality and incidence of disease among LTC users and staff. We excluded studies not focusing on LTC. Included studies were critically appraised and results on number of deaths and COVID-19 related mortality rates, case fatality rates, and excess deaths (co-primary outcomes), as well as incidence of disease, hospitalisations, and ICU admissions were synthesised narratively.FindingsA total of 54 study reports for 49 unique primary studies or outbreak reports were included. Outbreak investigations in LTC facilities found COVID-19 incidence rates of between 0.0% and 71.7% among residents and between 0.4% and 64.0% among staff at affected facilities. Mortality rates varied from 0.0% to 17.1% of all residents at outbreak facilities, with case fatality rates between 0.0% and 33.7%. In included studies of outbreaks, no LTC staff members had died.Studies of wider LTC populations found that between 0.4% and 40.8% of users, and between 4.0% and 23.8% of staff were infected, although the generalisability of these studies is limited.There was limited information on the impact of COVID-19 on LTC in the community.InterpretationLong-term care users have been particularly vulnerable to the COVID-19 pandemic. However, we found wide variation in spread of disease and mortality rates between outbreaks at individual LTC facilities. Further research into the factors determining successful prevention and containment of COVID-19 outbreaks is needed to protect long-term care users and staff.FundingThis work was partially conducted as part of the “Strengthening responses to dementia in developing countries” (STRiDE) project, supported by the UK Research and Innovation’s Global Challenges Research Fund (ES/P010938/1). The funders had no role in the design and execution of this study, interpretation of its results, and decision to submit this work to be published.
Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing
Authors: Grädel C. , Miani M.A. Terrazos , Baumann C. , Barbani MT , Neuenschwander S. , Leib S.L. , Suter-Riniker F. , Ramette A. 
Published: June 2020

AbstractEnteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, those viruses are identified by PCR based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. Results of the approach were complemented with those obtained by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. The identification of the enterovirus sequences in the sample was confirmed by the short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94-97%. Here we show that nanopore DRS can be used to correctly identify the genotypes of enteroviruses from patient stool samples with high viral load.
Saturation and self-absorption effects in the angle-dependent 2p3d resonant inelastic X-ray scattering spectra of Co3+
Authors: Wang Ru-Pan , Elnaggar Hebatalla , Titus Charles J. , Tomiyasu Keisuke , Geessinck Jaap , Koster Gertjan , Frati Federica , Okamoto Jun , Huang Di-Jing , de Groot Frank M. F. 
Published: June 2020

Angle-dependent 2p3d resonant inelastic X-ray scattering spectra of a LaCoO3 single crystal and a 55 nm LaCoO3 film on a SrTiO3 substrate are presented. Theoretical calculation shows that, with ∼20 meV resolved Co 2p3d resonant inelastic X-ray scattering (RIXS), the excited states of the isotropic 1A1g
(O
h
) ground state are split by 3d spin–orbit coupling, which can be distinguished via their angular dependence. However, strong self-absorption and saturation effects distort the spectra of the LaCoO3 single crystal and limit the observation of small angular dependence. In contrast, the RIXS on 55 nm LaCoO3 shows less self-absorption effects and preserves the angular dependence of the excited states.