bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innate lymphoid cell composition associates with COVID-19 disease severity
Authors: García Marina , Kokkinou Efthymia , García Anna Carrasco , Parrot Tiphaine , Palma Medina Laura M. , Maleki Kimia T. , Christ Wanda , Varnaitė Renata , Filipovic Iva , Ljunggren Hans-Gustaf , Björkström Niklas K. , Folkesson Elin , Rooyackers Olav , Eriksson Lars I. , Sönnerborg Anders , Aleman Soo , Strålin Kristoffer , Gredmark-Russ Sara , Klingström Jonas , Mjösberg Jenny ,   the Karolinska KI/K COVID-19 Study Group
Published: October 2020

ABSTRACTObjectivesThe role of innate lymphoid cells (ILCs) in coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is unknown. Understanding the immune response in COVID-19 could contribute to unravel the pathogenesis and identification of treatment targets. To describe the phenotypic landscape of circulating ILCs in COVID-19 patients and to identify ILC phenotypes correlated to serum biomarkers, clinical markers, and laboratory parameters relevant in COVID-19.MethodsBlood samples collected from moderately (n=11) and severely ill (n=12) COVID-19 patients as well as healthy control donors (n=16), were analyzed with 18-parameter flow cytometry. Using supervised and unsupervised approaches, we examined the ILC activation status and homing profile. Clinical and laboratory parameters were obtained from all COVID-19 patients and serum biomarkers were analyzed with multiplex immunoassays.ResultsILCs were largely depleted from the circulation of COVID-19 patients compared with healthy controls. Remaining circulating ILCs from patients revealed increased frequencies of ILC2 in moderate COVID-19, with a concomitant decrease of ILC precursors (ILCp), as compared with controls. ILC2 and ILCp showed an activated phenotype with increased CD69 expression, whereas expression levels of the chemokine receptors CXCR3 and CCR4 were significantly altered in ILC2 and ILCp, and ILC1, respectively. The activated ILC profile of COVID-19 patients was associated with soluble inflammatory markers, while frequencies of ILC subsets were correlated with laboratory parameters that reflect the disease severity.ConclusionThis study provides insights into the potential role of ILCs in immune responses against SARS-CoV-2, particularly linked to the severity of COVID-19.
Dynamic dysregulation of IL-6 and genes functional in NETosis, complement and coagulation in severe COVID-19 illness
Authors: Mukhopadhyay Samanwoy , Sinha Subrata , Mohapatra Saroj Kant 
Published: October 2020

AbstractComprehensive and unbiased re-analysis of published blood transcriptome data from patients of COVID-19 reveals significant up-regulation of the gene set functional in NETosis, but no evidence of general “cytokine storm”. In severe COVID-19 illness, there is significant up-regulation of complement and coagulation pathway, and negative correlation between NETosis and respiratory function (oxygen saturation). Interestingly, there is an early spike in the level of IL-6 gene expression in severe illness compared to moderate illness. With passing days post-onset, the level of IL-6 expression in severe illness approaches that in moderate illness. The data are consistent with IL-6 acting as a driver of NETosis in the early phase of severe COVID-19 illness, that results in a vicious cycle of NETosis-complement/coagulation-respiratory dysfunction. This has important consequence for timing of rational therapy with anti-IL-6 and NETosis inhibitors in severe COVID-19 illness.
Antivenom accessibility impacts mortality and severity of Brazilian snake envenomation: a geospatial information systems analysis
Authors: Ye Jinny Jing , Scheidt João Felipe Hermann Costa , de Andrade Luciano , Rocha Thiago Augusto Hernandes , Fan Hui Wen , Monteiro Wuelton , Palacios Ricardo , Staton Catherine Ann , Nickenig Vissoci João Ricardo , Gerardo Charles John 
Published: October 2020

AbstractBackgroundIn 2017, the World Health Organization declared the snakebite envenomation as a neglected tropical disease. Annually, snakebite envenomation causes approximately 400,000 permanent disabilities and 95,000 deaths worldwide. People with the greatest risk of envenomation lack access to adequate health care, including treatment with antivenom. We developed an analysis of accessibility to antivenom in Brazil in order to verify the impacts on mortality.Methods and FindingsInformation about number of accidents, deaths, antivenom, medical assistance, and species, were retrieved from the Brazilian Health Informatics Department (DATASUS) from 2010 to 2015 and analyzed using geostatistics to evaluate the association between snakebite accidents and mortality. An Spatial analysis using Global Moran’s I was performed in order to verify the presence of spatiality as an independent variable to the distribution of the accidents. In addition, we also tested three different analysis of regression using Ordinary Least Square (OLS), Spatial Error, and Geographically Weighed Regression (GWR), together with the information obtained from the DATASUS and sociodemographic indicators, to verify the spatial-temporal distribution of envenomation cases and time to reach the healthcare centers. The regression presenting the lowest Akaike Criterion Information (AIC), highest adjusted R2, and variables with p < 0.05 was selected to represent our model. Lastly, the accessibility index was performed using 2-step floating catchment area based on the amount of hospital beds and inhabitants. This study revealed 141,039 cases of snakebites, 598 deaths, and mortality rate of 3.13 per 1,000,000 inhabitants. Moreover, GWR presented the best fit (AIC = 55477.56; adjusted R2 = 0.55) and showed that illiteracy, income, percentage of urban population, percentage of antivenom, accessibility index for hospital beds with antivenom, proportion of cases with more than 3 hours to reach healthcare are correlated with the mortality rate by snakebite (p < 0.05).ConclusionThis study identified regions affected by snakebite and how the accessibility to antivenom treatment plays an important role in the mortality in Brazil. Public interventions can located to those most vulnerable regions in order to improve the accident outcome.
Precautionary breaks: planned, limited duration circuit breaks to control the prevalence of COVID-19
Authors: Keeling Matt J. , Guyver-Fletcher Glen , Holmes Alex , Dyson Louise , Tildesley Michael J. , Hill Edward M. , Medley Graham F. 
Published: October 2020

AbstractThe COVID-19 pandemic in the UK has been characterised by periods of exponential growth and decline, as different non-pharmaceutical interventions (NPIs) are brought into play. During the early uncontrolled phase of the outbreak (early March 2020) there was a period of prolonged exponential growth with epidemiological observations such as hospitalisation doubling every 3-4 days (growth rate r ≈ 0.2). The enforcement of strict lockdown measures led to a noticeable decline in all epidemic quantities (r ≈ −0.06) that slowed during the summer as control measures were relaxed (r ≈ −0.02). Since August, infections, hospitalisations and deaths have been rising (precise estimation of the current growth rate is difficult due to extreme regional heterogeneity and temporal lags between the different epidemiological observations) and various NPIs have been applied locally throughout the UK in response.Controlling any rise in infection is a compromise between public health and societal costs, with more stringent NPIs reducing cases but damaging the economy and restricting freedoms. Currently, NPI imposition is made in response to the epidemiological state, are of indefinite length and are often imposed at short notice, greatly increasing the negative impact. An alternative approach is to consider planned, limited duration periods of strict NPIs aiming to purposefully reduce prevalence before such emergency NPIs are required. These “precautionary breaks” may offer a means of keeping control of the epidemic, while their fixed duration and the forewarning may limit their society impact. Here, using simple analysis and age-structured models matched to the unfolding UK epidemic, we investigate the action of precautionary breaks. In particular we consider their impact on the prevalence of infection, as well as the total number of predicted hospitalisations and deaths. We find that precautionary breaks provide the biggest gains when the growth rate is low, but offer a much needed brake on increasing infection when the growth rate is higher, potentially allowing other measures (such as contact tracing) to regain control.
Measurement of small droplet aerosol concentrations in public spaces using handheld particle counters
Authors: Somsen G. Aernout , van Rijn Cees , Kooij Stefan , Bem Reinout A. , Bonn Daniel 
Published: October 2020

AbstractWe investigate the role of aerosols in the transmission of SARS-CoV-2 in public spaces. Direct measurement of aerosol concentrations however has proven technically difficult; we propose the use of handheld particle counters as a novel and easily applicable method to measure aerosol concentrations. This allow us to perform measurements in typical public spaces, each differing in volume, number of people and ventilation rate. These data are used to estimate the relation between aerosol persistence time and the risk of infection with SARS-CoV-2.
Real World SOF/VEL/VOX Retreatment Outcomes and Viral Resistance Analysis for HCV Patients with Prior Failure to DAAs
Authors: Smith David A , Bradshaw Daniel , Mbisa Jean , Manso Carmen F , Bibby David , Singer Josh , Thomson Emma , Filipe Ana , Aranday-Cortes Elihu , Ansari M. Azim , Brown Anthony , Hudson Emma , Benselin Jennifer , Healy Brendan , Troke Phil ,   STOP-HCV Consortium,   HCV Research UK, McLauchlan John , Barnes Eleanor , Irving William L 
Published: October 2020

AbstractSustained viral response (SVR) rates to first-line Direct Acting Antiviral (DAA) therapy for hepatitis C virus (HCV) infection routinely exceed 95%. However, a small number of patients require retreatment. Sofosbuvir, velpatasvir and voxilaprevir (SOF/VEL/VOX) is a potent DAA combination primarily used for the retreatment of patients failed by first line DAA therapies. Here we evaluate retreatment outcomes and the effects of resistance associated substitutions (RAS) in a real-world cohort, including the largest number of genotype (GT)3 infected patients, to date. 144 patients from the UK were retreated with SOF/VEL/VOX following virologic failure with first-line DAA treatment regimens. Full-length HCV genome, next-generation sequencing was performed prior to retreatment with SOF/VEL/VOX. HCV subtypes were assigned and RAS relevant to each genotype were identified (15% read cut-off). GT1a and GT3a were the two most common subtypes in the cohort, each making up 38% (GT1a n=55, GT3a n=54) of the cohort. 40% (n=58) of patients had liver cirrhosis of whom 7% (n=4) were decompensated, 10% (n=14) had hepatocellular carcinoma (HCC) and 8% (n=12) had received a liver transplant prior to retreatment. The overall re-treatment SVR12 rate was 90% (129/144). On univariate analysis, GT3 infection (50/62; SVR=81%, p=0.009), cirrhosis (47/58; SVR=81%, p=0.01) and prior treatment with SOF/VEL(12/17; SVR=71%, p=0.02) or SOF + DCV (14/19; SVR=74%, p=0.012) were all significantly associated with retreatment failure, but existence of pre retreatment RAS was not when the genotype of the virus is taken into account. The lower SVR rates achieved in patients retreated with SOF/VEL/VOX for patients with GT3 infection, cirrhosis and prior treatment with SOF/VEL or SOF/DCV has important implications for both patients and HCV elimination strategies.
Does autism protect against COVID quarantine effects?
Authors: Guidotti Marco , Gateau Adrien , Malvy Joelle , Bonnet-Brilhault Frédérique 
Published: October 2020

AbstractIntroductionCOVID-19 outbreak has imposed an eight-week confinement in France. During this period, children and their families were exposed to a full-time home life. The aim of this study was to assess the emotional experience and tolerance of children with autism spectrum disorder (ASD) in this particular context.MethodA clinical survey was proposed to parents and rated by professionals once a week during the quarantine period in France. 95 autistic children followed by the child and adolescent psychiatry department of Tours university hospital were assessed from the 18th of March to the 8th of May. The following clinical points were investigated: child anxiety, family anxiety, behavior problems, impact on sleep, impact on appetite, impact on school work, family tension, confinement intolerance, difficulties to follow a schedule, isolation behavior.ResultsDespite minor changes in family anxiety and school work, no difference was highlighted between clinical scores collected at the beginning and at the end of this period. ASD children with or without intellectual disability had non-significant clinical changes during quarantine. This evolution was also independent of the accommodation type (house or apartment) and the parental status (relationship, separated or isolated).ConclusionThe sameness dimension in autism and parents’ adaptation may be involved in this clinical stability during COVID confinement. Moreover, specialized tools and support provided by professionals could have participated to these outcomes and must be regularly promoted in order to help families in this still difficult period.
Epidemiologial Analysis of Patients Presenting to a West London District General Hospital Requiring Admission with Covid-19
Authors: Heald E , Ring N , Vatvani D , Shackleton D 
Published: October 2020

AbstractBackgroundCoronavirus has lead to significant morbidity and mortality both within the UK and worldwide. We hypothesise there are local clusters of coronavirus which would therefore be amenable to targeted public health measures.MethodsThis is a retrospective, observational case series conducted in a West London District General Hospital. All patients admitted to hospital with a radiological or microbiological diagnosis of Covid-19 were included (children under 16 years were excluded). Consecutive sampling was used and baseline characteristics including age, sex, postcode and final patient outcome were collected from the electronic health records. Patient origin postcode was plotted to a map of the local area and an online cloud based mapping analysis system was used to generate heat maps and case density maps which were compared to living base layers. The primary outcome was identification of local clusters of cases of coronavirus. Secondary outcome was identification of population characteristics that may provide evidence for more targetted public health intervention in a second wave.ResultsLocal clusters of infection were identified within the target population. These appeared to correlate with higher indices of deprivation, poorer overall health and high household occupancy suggesting a role for public health measures to target these areas.ConclusionThere is a role for targeted public health measures in tackling the spread of coronavirus, paying particular attention to those who live in more deprived areas.
A comparative study of infection and mortality in COVID-19 across countries: A scaling analysis
Authors: Das Ranjan , Hossain Akmal , Mandal Sayak , Pariari Debasmita , Rohj Rohit Kumar , Shukla Swapnil , Varma Rahul Mahavir , Sarma D. D. 
Published: October 2020

AbstractAnalysing infection and mortality data for COVID-19 as a function of days for 54 countries across all continents, we show that there is a simple scaling behaviour connecting these two quantities for any given nation when the data is segmented over few ranges of dates covering the most rapid spread of the pandemic and the recovery, wherever achieved. This scaling is described by two parameters, one representing a shift along the time axis and the other is a normalisation factor, providing a reliable definition of the mortality rate for each country in a given period. The number of segments for any country required in our analyses turns out to be surprisingly few with as many as 16 out of 54 countries being described by a single segment and no country requiring more than three segments. Estimates of the shift and mortality for these 54 countries in different periods show large spreads ranging over 0-16 days and 0.45-19.96%, respectively. Shift and mortality are found to be inversely correlated. Analyses of number of tests carried out for detecting COVID-19 and the number of infections detected due to such tests suggest that an effective way to increase the shift, and therefore, decrease mortality, is to increase number of tests per infection detected. This points to the need of a dynamic management of testing that should accelerate with the rise of the pandemic; it also suggests a basis for adjusting variations in the testing patterns in different geographical locations within a given country.
Quantifying year-round nocturnal bird migration with a fluid dynamics model
Authors: Nussbaumer Raphaël , Bauer Silke , Benoit Lionel , Mariethoz Grégoire , Liechti Felix , Schmid Baptiste 
Published: October 2020

AbstractThe movements of migratory birds constitute huge biomass flows that influence ecosystems and human economy, agriculture and health through the transport of energy, nutrients, seeds, and parasites. To better understand the influence on ecosystems and the corresponding services and disservices, we need to characterize and quantify the migratory movements at various spatial and temporal scales.Representing the flow of birds in the air as a fluid, we applied a flow model to interpolated maps of bird density and velocity retrieved from the European weather radar network, covering almost a full year. Using this model, we quantified how many birds take-off, fly, and land across Western Europe, (1) to track waves of bird migration between nights, (2) cumulate the number of bird on the ground and (3) quantify the seasonal flow into and out of the study area through several regional transects.Our results show that up to 188 million (M) birds take-off over a single night. Exemplarily, we tracked a migration wave in spring, in which birds crossed the study area in 4 days with nocturnal flights of approximately 300 km. Over the course of a season, we estimated that 494 million (M) birds entered through the southern transects and, at the same time, 251 M left in the northern transects, creating a surplus of 243 M birds within the study area. Similarly, in autumn, 544 M more birds departed than arrived: 314 M birds entered through the northern transects while 858 M left through the southern transects.Our study show-cases the potential of combining interdisciplinary data and methods to elucidate the dynamics of avian migration from nightly to seasonal and yearly time-scales and from regional to continental spatial scales.
Multi-modal Single-molecule Imaging with Continuously Controlled Spectral-resolution (CoCoS) Microscopy
Authors: Jeffet Jonathan , Michaeli Yael , Torchinsky Dmitry , Israel-Elgali Ifat , Shomron Noam , Craggs Timothy D. , Ebenstein Yuval 
Published: October 2020

AbstractColor is a fundamental contrast mechanism in fluorescence microscopy, providing the basis for numerous imaging and spectroscopy techniques. The ever-growing need to acquire high-throughput, dynamic data from multicolor species is driving the development of optical schemes that optimize the achievable spectral, temporal, and spatial resolution needed in order to follow biological, chemical and physical processes. Here we introduce Continuously Controlled Spectral-resolution (CoCoS) microscopy, an imaging scheme that encodes color into spatial read-out in the image plane, with continuous control over the spectral resolution. The concept enables single-frame acquisition of multiple color channels, allowing simultaneous, single-molecule colocalization for barcoding and Förster resonance energy transfer (FRET) experiments. The simple control over the spectral dispersion allows switching between imaging modalities at a click of a button. We demonstrate the utility of CoCoS for multicolor localization microscopy of microRNA barcodes in clinical samples, single-molecule FRET measurements, and single-molecule spectroscopy. CoCoS may be integrated as a simple add-on to existing microscopes and will find use in applications that aim to record dynamic, multicolor localization events such as in multiplex FRET and tracking of multi-component, interacting complexes.
Massive genome decay and insertion sequence expansion drive the evolution of a novel host-restricted bacterial pathogen
Authors: Yebra Gonzalo , Haag Andreas F , Neamah Maan M , Wee Bryan A , Richardson Emily J , Horcajo Pilar , Granneman Sander , Tormo-Más María Ángeles , de la Fuente Ricardo , Fitzgerald J Ross , Penadés José R 
Published: October 2020

AbstractBackgroundThe emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as those associated with a switch in host or disease tropism are often accompanied by genetic adaptation.Staphylococcus aureusis a multi-host bacterial species comprising strains with distinct tropisms for human and livestock species. A microaerophilic subspecies,Staphylococcus aureussubsp.anaerobius, is responsible for outbreaks of Morel’s disease, a lymphadenitis in small ruminants. However, the evolutionary history ofS. aureussubsp.anaerobiusand its relatedness toS. aureusare unknown.ResultsEvolutionary genomic analyses of clinicalS. aureussubsp.anaerobiusisolates revealed a highly conserved clone that descended from aS. aureusprogenitor about 1000 years ago before differentiating into distinct lineages representing African and European isolates.S. aureussubsp.anaerobiushas undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower thanS. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, several large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes resulting in a highly fastidious metabolism. Importantly, expansion of ∼87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, representing a novel concept of the IS regulon.ConclusionsOur findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of theS. aureusgenome through an array of parallel mechanisms.