bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outward and inward protections of different mask designs for different respiratory activities
Authors: Koh Xue Qi , Sng Anqi , Chee Jing Yee , Sadovoy Anton , Luo Ping , Daniel Dan 
Published: April 2021

We evaluate the outward and inward protections of different mask types (N95, surgical and two cloth mask designs) taking into account the imperfect fit on the wearer. To this end, we built a manikin to simulate exhaling, coughing and inhaling of aerosol droplets 0.3–5.0 µm in diameters. The outward and inward protections depend on many factors, including the droplet size, the mask fit and the presence of a filter layer. Here, we show that cloth and surgical masks with a non-woven filter layer can achieve a combined outward and inward protections between 50% and 90%. Removing the filter layer greatly reduces the protection efficiency to below 20% for the smallest droplet size. While a well-fitted N95 masks offer protection efficiency close to 100%, a poorly fitted N95 mask with gaps offers less protection than a well-fitted surgical/cloth mask. We also found that double masking—the wearing of cloth mask on top of a surgical mask—is only effective at reducing outward droplet emissions when coughing, while offering no additional protection when exhaling/inhaling as compared to a single cloth/surgical mask. The results of our work can inform the implementation of mask mandates to minimize airborne transmissions of coronavirus disease of 2019 (COVID-19).Practical implicationsA single cloth/surgical mask with non-woven filter layer offers significant protection against airborne transmissions.Filtering facepiece masks such as N95 respirators are unlikely to achieve the advertised high protection for the general public due to poor mask fit.Double-masking offers little to no additional protection over a single cloth/surgical mask.
Invasive airway “Intubation” in COVID-19 patients :statistics, causes and recommendations
Authors: Mohammadi Mostafa , Pour Khamseh Alireza Khafaee , Varpaei Hesam Aldin 
Published: April 2021

AbstractBackgroundSevere COVID-19 disease could induce acute respiratory distress which is characterized by tachypnea, hypoxia, and dyspnea. Intubation and mechanical ventilation are a strategic treatment of COVID-19 distress or hypoxia.MethodsWe searched PubMed, Embase, and Scopus databases through April 1, 2021, to identify relevant randomized control trials, observational studies, and case series.Results24 studies were included in this review. Studies were conducted in the USA, China, Spain, South Korea, Italy, Iran, and Brazil. Most patients were intubated in the intensive care unit. Rapid sequence induction was mostly used for intubation. ROX index might be utilized for the predictor of the necessity of intubation in COVID-19 patients. According to the previous studies the rate of intubation reported 5 to 88%. It was revealed that 1.4 - 44.5% of patients might be extubated. Yet obesity and age (elderly) are the only risk factors of delayed or difficult extubation.Discussion and conclusionAcute respiratory distress in COVID-19 patients could require endotracheal intubation and mechanical ventilation. Severe respiratory distress, loss of consciousness, and hypoxia were the most important reasons for intubation. Also, increased levels of ferritin, d-dimer, and lipase in common with hypoxia are correlated with intubation and ICU admission Mortality following intubation is reported to be 15 to 36%. Awake-prone positioning in comparison to high-flow nasal oxygen therapy did not reduce the risk of intubation and mechanical ventilation. There was no association between intubation timing and mortality of infected patients. noninvasive ventilation may have survival benefits.
North West London Covid-19 Vaccination Programme: Real-world evidence for Vaccine uptake and effectiveness
Authors: Glampson B , Brittain J , Kaura Amit , Mulla A , Mercuri L , Brett S , Aylin P , Sandall T , Goodman I , Redhead J , Saravanakumar K , Mayer E K 
Published: April 2021

AbstractObjectiveTo assess the early vaccine administration coverage and vaccine effectiveness and outcome data across an integrated care system of eight CCGs leveraging a unique population-level care datasetDesignRetrospective cohort study.SettingIndividuals eligible for COVID 19 vaccination in North West London based on linked primary and secondary care data.Participants2,183,939 individuals eligible for COVID 19 vaccinationResultsDuring the NWL vaccine programme study time period 5.88% of individuals declined and did not receive a vaccination. Black or black British individuals had the highest rate of declining a vaccine at 16.14% (4,337). There was a strong negative association between deprivation and rate of declining vaccination (r=-0.94, p<0.01) with 13.5% of individuals declining vaccination in the most deprived postcodes compared to 0.98% in the least deprived postcodes.In the first six days after vaccination 344 of 389587 individuals tested positive for COVID-19 (0.09%). The rate increased to 0.13% (525/389,243) between days 7 and 13, before then gradually falling week on week.At 28 days post vaccination there was a 74% (HR 0.26 (0.19-0.35)) and 78% (HR 0.22 (0.18-0.27)) reduction in risk of testing positive for COVID-19 for individuals that received the Oxford/Astrazeneca and Pfizer/BioNTech vaccines respectively, when compared with unvaccinated individuals.After vaccination very low rates of hospital admission were seen in individuals testing positive for COVID-19 (0.01% of all patients vaccinated).ConclusionsThis study provides further evidence that a single dose of either the Pfizer/BioNTech vaccine or the Oxford/Astrazeneca vaccine is effective at reducing the risk of testing positive for COVID-19 up to 60 days across all adult age groups, ethnic groups, and risk categories in an urban UK population. There was no difference in effectiveness up to 28 days between the Oxford/Astrazeneca and Pfizer/BioNtech vaccines.In those declining vaccination higher rates were seen in those living in the most deprived areas and in Black and Black British groups.There was no definitive evidence to suggest COVID-19 was transmitted as a result of vaccination hubs during vaccine the administration roll-out in NWL, and the risk of contracting COVID-19 and/or becoming hospitalised after vaccination has been demonstrated to be very low in the vaccinated population.
Emergence of multiple SARS-CoV-2 antibody escape variants in an immunocompromised host undergoing convalescent plasma treatment
Authors: Chen Liang , Zody Michael C , Mediavilla Jose R , Cunningham Marcus H , Composto Kaelea , Chow Kar Fai , Kordalewska Milena , Corvelo André , Oschwald Dayna M , Fennessey Samantha , Zetkulic Marygrace , Dar Sophia , Kramer Yael , Mathema Barun , Maniatis Tom , Perlin David S , Kreiswirth Barry N 
Published: April 2021

AbstractSARS-CoV-2 Variants of Concerns (VOC), e.g., B.1.351 (20H/501Y.V2) and P1 (20J/501Y.V3), harboring N-terminal domain (NTD) or the receptor-binding domain (RBD) (e.g., E484K) mutations, exhibit reduced in vitro susceptibility to convalescent serum, commercial antibody cocktails, and vaccine neutralization, and have been associated with reinfection. The accumulation of these mutations could be the consequence of intra-host viral evolution due to prolonged infection in immunocompromised hosts. In this study, we document the microevolution of SARS-CoV-2 recovered from sequential tracheal aspirates from an immunosuppressed patient on tacrolimus, steroids and convalescent plasma therapy, and identify the emergence of multiple NTD and RBD mutations associated with reduced antibody neutralization as early as three weeks after infection. SARS-CoV-2 genomes from the first swab (Day 0) and three tracheal aspirates (Day 7, 21 and 27) were compared at the sequence level. We identified five different S protein mutations at the NTD or RBD regions from the second tracheal aspirate sample (21 Day). The S:Q493R substitution and S:243-244LA deletion had ∼70% frequency, while ORF1a:A138T, S:141-144LGVY deletion, S:E484K and S:Q493K substitutions demonstrated ∼30%, ∼30%, ∼20% and ∼10% mutation frequency, respectively. However, the third tracheal aspirate sample collected one week later (Day 27) was predominated by the haplotype of ORF1a:A138T, S:141-144LGVY deletion and S:E484K (> 95% mutation frequency). Notably, S protein deletions (141-144LGVY and 243-244LA deletions in NTD region) and substitutions (Q493K/R and E484K in the RBD region) previously showed reduced susceptibly to monoclonal antibody or convalescent plasma. The observation supports the hypothesis that VOCs can independently arise and that immunocompromised patients on convalescent plasma therapy are potential breeding grounds for immune-escape mutants.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThe study was in part supported by Center for Discovery and Innovation and Hackensack Meridian Health Foundation.
Development of a tool to prioritize the monitoring of COVID-19 patients by public health teams
Authors: Vecino-Ortiz Andres I. , Guzman-Tordecilla Nicolás , Ruiz Yenny Fernanda Guzmán , Peñaloza-Quintero Rolando Enrique , Fernández-Niño Julián A. , Gomez Fernando Ruiz , Trujillo Antonio J. 
Published: April 2021

AbstractBackgroundIn the context of the COVID-19 pandemic, public health teams have struggled to conduct monitoring for confirmed or suspicious COVID-19 patients. However, monitoring these patients is critical to improving the chances of survival, and therefore, a prioritization strategy for these patients is warranted. This study developed a monitoring algorithm for COVID-19 patients for the Colombian Ministry of Health and Social Protection (MOH).MethodsThis work included 1) a literature review, 2) consultations with MOH and National Institute of Health officials, and 3) data analysis of all positive COVID-19 cases and their outcomes. We used clinical and socioeconomic variables to develop a set of risk categories to identify severe cases of COVID-19.ResultsThis tool provided four different risk categories for COVID-19 patients. As soon as the time of diagnosis, this tool can identify 91% of all severe and fatal COVID-19 cases within the first two risk categories.ConclusionThis tool is a low-cost strategy to prioritize patients at higher risk of experiencing severe COVID-19. This tool was developed so public health teams can focus their scarce monitoring resources on individuals at higher mortality risk. This tool can be easily adapted to the context of other lower and middle-income countries. Policymakers would benefit from this low-cost strategy to reduce COVID-19 mortality, particularly during outbreaks.
DNA methylation and brain dysmaturation in preterm infants
Authors: Wheater Emily N. W. , Galdi Paola , McCartney Daniel L. , Blesa Manuel , Sullivan Gemma , Stoye David Q. , Lamb Gillian , Sparrow Sarah , Murphy Lee , Wrobel Nicola , Quigley Alan J. , Semple Scott , Thrippleton Michael J. , Wardlaw Joanna M. , Bastin Mark E. , Marioni Riccardo E. , Cox Simon R. , Boardman James P. 
Published: April 2021

AbstractPreterm birth is associated with dysconnectivity of structural brain networks and is a leading cause of neurocognitive impairment in childhood. Variation in DNA methylation (DNAm) is associated with early exposure to extrauterine life but there has been little research exploring its relationship with brain development.Using genome-wide DNA methylation data from saliva of 258 neonates, we investigated the impact of gestational age on the methylome and performed functional analysis to identify enriched gene sets from probes that contributed to differentially methylated probes (DMPs) or regions (DMRs). We tested the hypothesis that variation in DNAm could underpin the association between preterm birth and atypical brain development by linking DMPs with measures of white matter connectivity derived from diffusion MRI metrics: peak width of skeletonised mean diffusivity (PSMD), fractional anisotropy (PSFA) and neurite density index (PSNDI).Gestational age at birth was associated with widespread differential methylation, with genome-wide significant associations observed for 8,870 CpG probes (p<3.6×10−8) and 1,767 differentially methylated regions. Functional analysis identified 14 enriched gene ontology terms pertaining to cell-cell contacts and cell-extracellular matrix contacts. Principal component analysis of probes with genome-wide significance revealed a first principal component (PC1) that explained 23.5% of variance in DNAm, and this was negatively associated with gestational age at birth. PC1 was associated with PSMD (β=0.349, p=8.37×10−10) and PSNDI (β=0.364, p=4.15×10−5), but not with PSFA (β=−0.035, p=0.510); these relationships mirrored the imaging metrics’ associations with gestational age at birth.Gestational age at birth has a profound and widely distributed effect on the neonatal saliva methylome. Enriched gene ontology terms related to cell-cell contacts reveal pathways that could mediate the effect of early life environmental exposures on development. Finally, associations between differential DNAm and image markers of white matter tract microstructure suggest that variation in DNAm may provide a link between preterm birth and the dysconnectivity of developing brain networks that characterises atypical brain development in preterm infants.
Estimating COVID-19 infection fatality rate in Mumbai during 2020
Authors: Banaji Murad 
Published: April 2021

AbstractThe aim of this piece is to provide estimates of the infection fatality rate (IFR) of COVID-19 in Mumbai during 2020, namely the fraction of SARS-CoV-2 infections which resulted in death. Estimates are presented for slums and nonslum areas, and for the city as a whole. These are based largely on the city’s official COVID-19 fatality data, seroprevalence data, and all-cause mortality data. Using recorded COVID-19 fatalities in the numerator, we obtain IFR estimates of 0.13%-0.17%. On the other hand, using excess deaths we obtain IFR estimates of 0.28%-0.40%. The estimates based on excess deaths are broadly consistent with the city’s age structure, and meta-analyses of COVID-19 age-stratified IFR. If excess deaths were largely from COVID-19, then only around half of COVID-19 deaths were officially recorded in the city. The analysis indicates that levels of excess mortality in excess deaths per 1000 population were similar in the city’s slums and nonslum areas. On the other hand the estimated ratio of excess deaths to official COVID-19 deaths in the slums was much higher than in nonslum areas, suggesting much weaker COVID-19 death reporting from the slums.
Public health impacts of an imminent Red Sea oil spill
Authors: Huynh Benjamin Q , Kwong Laura H , Kiang Mathew V , Chin Elizabeth T , Mohareb Amir M , Jumaan Aisha O , Basu Sanjay , Geldsetzer Pascal , Karaki Fatima M , Rehkopf David H 
Published: April 2021

AbstractThe possibility of a massive oil spill in the Red Sea is increasingly likely. The Safer, a deteriorating oil tanker containing 1.1 million barrels of oil, has been deserted near the coast of Yemen since 2015, and threatens environmental catastrophe to a country presently in a humanitarian crisis. Here, we model the immediate public health impacts of a simulated spill. We estimate all of Yemen’s imported fuel through its key Red Sea ports would be disrupted, and that the anticipated spill could disrupt clean water supply equivalent to the daily use of 9 to 9.9 million people, food supply for 5.7 to 8.4 million people, and 93% to 100% of Yemen’s Red Sea fisheries. We also estimate an increased risk of cardiovascular hospitalization from pollution ranging from 5.8% to 42.0% over the duration of the spill. The spill and its potentially disastrous impacts remain entirely preventable through offloading the oil. Our results stress the need for urgent action to avert this looming disaster.
Accuracy of antigen and nucleic acid amplification testing on saliva and naopharyngeal samples for detection of SARS-CoV-2 in ambulatory care
Authors: Kernéis Solen , Elie Caroline , Fourgeaud Jacques , Choupeaux Laure , Delarue Séverine Mercier , Alby Marie-Laure , Quentin Pierre , Pavie Juliette , Brazille Patricia , Néré Marie Laure , Minier Marine , Gabassi Audrey , Gibaud Aurélien , Gauthier Sébastien , Leroy Chrystel , Voirin-Mathieu Etienne , Poyart Claire , Vidaud Michel , Parfait Béatrice , Delaugerre Constance , Tréluyer Jean-Marc , Le Goff Jérôme 
Published: April 2021

AbstractBackgroundNasopharyngeal sampling for nucleic acid amplification testing (NAAT) is the current standard diagnostic test for of coronavirus disease 2019 (COVID-19). However, the NAAT technique is lengthy and nasopharyngeal sampling requires trained personnel. Saliva NAAT represents an interesting alternative but diagnostic performances vary widely between studies.ObjectiveTo assess the diagnostic accuracy of a nasopharyngeal point-of-care antigen (Ag) test and of saliva NAAT for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), as compared to nasopharyngeal NAAT.DesignProspective participant enrollment from 19 October through 18 December 2020.SettingTwo community COVID-19 screening centers in Paris, France.Participants1452 ambulatory children and adults referred for SARS-CoV-2 testing.InterventionsNAAT on a saliva sample (performed with three different protocols for pre-processing, amplification and detection of SARS-CoV-2) and Ag testing on a nasopharyngeal sample.MeasurementsPerformance of saliva NAAT and nasopharyngeal Ag testing.ResultsOverall, 129/1443 (9%) participants tested positive on nasopharyngeal NAAT (102/564 [18%] in symptomatic and 27/879 [3%] in asymptomatic participants). Sensitivity was of 94% (95% CI, 86% to 98%), 23% (CI, 14% to 35%), 94% (CI, 88% to 97%) and 96% (CI, 91% to 99%) for the nasopharyngeal Ag test and the three different protocols of saliva NAAT, respectively. Estimates of specificity were above 95% for all methods. Diagnostic accuracy was similar in symptomatic and asymptomatic individuals.LimitationsFew children (n=122, 8%) were included.ConclusionIn the ambulatory setting, diagnostic accuracy of nasopharyngeal Ag testing and of saliva NAAT seems similar to that of nasopharyngeal NAAT, subject to strict compliance with specific pre-processing and amplification protocols.Registration numberNCT04578509Funding SourcesFrench Ministry of Health and the Assistance Publique-Hôpitaux de Paris Foundation.
Predation by protists influences the temperature response of microbial communities
Authors: Rocca Jennifer D. , Yammine Andrea , Simonin Marie , Gibert Jean P. 
Published: April 2021

AbstractTemperature strongly influences microbial community structure and function, which in turn contributes to the global carbon cycle that can fuel further warming. Recent studies suggest that biotic interactions amongst microbes may play an important role in determining the temperature responses of these communities. However, how microbial predation regulates these communities under future climates is still poorly understood. Here we assess whether predation by one of the most important bacterial consumers globally – protists – influences the temperature response of a freshwater microbial community structure and function. To do so, we exposed these microbial communities to two cosmopolitan species of protists at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to shifts in microbial community structure, these responses changed over time and in the presence of protist predators. Protists influenced microbial biomass and function through effects on community structure, and predation actually reduced microbial respiration rate at elevated temperature. Indicator species and threshold indicator taxa analyses showed that these predation effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities, but also demonstrates that predation can mediate these responses to warming, with important consequences for the global carbon cycle and future warming.
Neural Potts Model
Authors: Sercu Tom , Verkuil Robert , Meier Joshua , Amos Brandon , Lin Zeming , Chen Caroline , Liu Jason , LeCun Yann , Rives Alexander 
Published: April 2021

AbstractWe propose the Neural Potts Model objective as an amortized optimization problem. The objective enables training a single model with shared parameters to explicitly model energy landscapes across multiple protein families. Given a protein sequence as input, the model is trained to predict a pairwise coupling matrix for a Potts model energy function describing the local evolutionary landscape of the sequence. Couplings can be predicted for novel sequences. A controlled ablation experiment assessing unsupervised contact prediction on sets of related protein families finds a gain from amortization for low-depth multiple sequence alignments; the result is then confirmed on a database with broad coverage of protein sequences.
The Expression Pattern of miR-17, −24, −124 and −145 as Diagnostic Factor for Metastatic Gastric Cancer; a Lesson from Gastric Cancer Stem cells
Authors: Yasavoli-Sharahi Hamed , Jahangiri-Tazehkand Soheil , Iranmehr Zahra , Eslahchi Changiz , Razavi Amirnader Emami , Moradi Sharif , Asl Niloofar Shayan , Memari Fereidoon , Ebrahimi Marzieh 
Published: April 2021

AbstractBackgroundDistant metastasis of Gastric Cancer (GC) causes more than 700 000 deaths worldwide. Cancer Stem Cells (CSCs) are a subpopulation of cancer cells responsible for aggressiveness and chemoresistance in clinical settings. MicroRNAs (miRNAs) emerge as important players in regulating self-renewal and metastasis in CSCs. Understanding the role of miRNAs in CSCs offer a potential diagnostic tool for GC patients. This study is aimed to identify miRNAs that target both stemness and metastasis in gastric cancer stem cells (GCSCs) and differentially expressed in metastatic GC patients as diagnostic biomarkers for GC metastasis.MethodsWe investigate the gene expression profile of patients using the GEO database and Rstudio software. To obtain the regulatory networks and miRNAs, the STRING and miRwalk database used. The gastric cancer tissues were obtained from Iranian National Tumor Bank (INTB) to validate the results.ResultsOur results indicated three important regulatory cores affecting the immune system’s regulation, tumor progress, and metastasis. Based on the bioinformatics results, four miRNAs miR-17-5p, miR-24-3p, miR-124-3p, and miR-145-5p, were selected, and their expression pattern was evaluated in 10 patients’ metastatic tumors compared to 10 nonmetastatic tumors by real-time PCR. The expression level of mir-17, −24, and −124 was upregulated about 8, 10, 60 folds, respectively, and miR-145 was down-regulated 4.5 folds in metastatic tumors compared to nonmetastatic tumors.Conclusionthe high expression level of miR-17, −24, −124, and low level of miR-145 in GC patients’ samples could be a potential biomarker for the presence of GCSCs and the diagnosis of metastasis.