bluuebunny/crossref_metadata_2025_split huggingface dataset:
High seroprevalence but short-lived immune response to SARS-CoV-2 infection in Paris
Authors: Anna François , Goyard Sophie , Lalanne Ana Ines , Nevo Fabien , Gransagne Marion , Souque Philippe , Louis Delphine , Gillon Véronique , Turbiez Isabelle , Bidard François-Clément , Gobillion Aline , Savignoni Alexia , Guillot-Delost Maude , Dejardin François , Dufour Evelyne , Petres Stéphane , Goff Odile Richard-Le , Choucha Zaineb , Helynck Olivier , Janin Yves L. , Escriou Nicolas , Charneau Pierre , Perez Franck , Rose Thierry , Lantz Olivier 
Published: October 2020

ABSTRACTAlthough the COVID-19 pandemic peaked in March/April 2020 in France, the prevalence of infection is barely known. Herein, we assessed using high-throughput methods the serological response against the SARS-CoV-2 virus of 1847 participants working in one institution in Paris.In May-July 2020, 11% (95% CI: 9.7-12.6) of serums were positive for IgG against the SARS-CoV-2 N and S proteins and 9.5% (CI:8.2-11.0) were pseudo-neutralizer. The prevalence of immunization was 11.6% (CI:10.2-13.2) considering positivity in at least one assays. In 5% (CI:3.9-7.1) of RT-qPCR positive individuals, no systemic IgGs were detected. Among immune individuals, 21% had been asymptomatic. Anosmia and ageusia occurred in 52% of the IgG-positive individuals and in 3% of the negative ones. In contrast, 30% of the anosmia-ageusia cases were seronegative suggesting that the true prevalence of infection may reach 16.6%. In sera obtained 4-8 weeks after the first sampling anti-N and anti-S IgG titers and pseudo-neutralization activity declined by 31%, 17% and 53%, respectively with half-life of 35, 87 and 28 days, respectively.The population studied is representative of active workers in Paris. The short lifespan of the serological systemic responses suggests an underestimation the true prevalence of infection.
PUBLIC TRANSIT RIDERSHIP ANALYSIS DURING THE COVID-19 PANDEMIC
Authors: Ahangari Samira , Chavis Celeste , Jeihani Mansoureh 
Published: October 2020

ABSTRACTThis study investigates the effect of the coronavirus (COVID-19) pandemic on public transport ridership in Baltimore and nine other U.S. cities similar to Baltimore, in terms of population and service area, during the first five months of 2020. The analysis is based on ridership numbers, vehicle revenue hours, and vehicles operated in maximum service. A compliance analysis was done between 2020 and 2019, as well as a monthly analysis of 2020 by mode and type of services. In comparison to 2019, the ridership decreases from March, the start of the pandemic, while all ten cities experienced the most decrease in ridership in April.
StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence
Authors: Gemayel Karl , Lomsadze Alexandre , Borodovsky Mark 
Published: October 2020

AbstractAlgorithms of ab initio gene finding were shown to make sufficiently accurate predictions in prokaryotic genomes. Nonetheless, for up to 15-25% of genes per genome the gene start predictions might differ even when made by the supposedly most accurate tools. To address this discrepancy, we have introduced StartLink+, an approach combining ab initio and multiple sequence alignment based methods. StartLink+ makes predictions for a majority of genes per genome (73% on average); in tests on sets of genes with experimentally verified starts the StartLink+ accuracy was shown to be 98-99%. When StartLink+ predictions made for a large set of prokaryotic genomes were compared with the database annotations we observed that on average the gene start annotations deviated from the predictions for ~5% of genes in AT-rich genomes and for 10-15% of genes in GC-rich genomes.
A controlled clinical effectiveness trial of multimodal cognitive rehabilitation on episodic memory functioning in older adults with traumatic brain injury (TBI)
Authors: Cisneros Eduardo , de Guise Elaine , Belleville Sylvie , McKerral Michelle 
Published: October 2020

AbstractObjectivesThis study aimed to evaluate the impact of a multimodal cognitive intervention, the Cognitive Enrichment Program (CEP), on episodic memory in traumatic brain injured (TBI) older adults, as compared to an active control group that received usual care in the form of holistic rehabilitation.MethodsThe CEP’s Memory module consisted in memory strategies to promote encoding. Effectiveness was evaluated by psychometric tests (Face-name association, Word list recall, Text memory), while generalization was measured through self-reported questionnaires about daily memory functioning (Self-Evaluation Memory Questionnaire) and psychological well-being (Psychological General Well-Being Index). Measures were obtained before and after intervention, and six months later.ResultsBoth groups showed improvement on most measures, but the experimental group showed greater statistically significant improvement. ANCOVA mixed model repeated measures analysis showed a strong group-by-time interaction for theFace-name associationtest, with a large effect size. A significant group-by-time interaction was obtained on three generalization self-report measures, including increased memorization of the content ofConversations, reducedSlips of attention, and increased memory ofPolitical & social Events, with moderate to large effect sizes. Clinically significant improvements were found forPsychological well-beingin the experimental group, where 50% of participants improved to the well-being category and remained stable six months later (9/17; 53%). Also, the number of experimental participants showing severe distress before CEP training (9) was reduced after intervention (5) and remained relatively stable at 6 months.ConclusionsThe CEP is a promising cognitive rehabilitation program that showed high satisfaction in participants and that can not only improve episodic memory in terms of psychometric scores, but also in daily life situations, as well as enhance psychological well-being in older individuals having sustained a TBI.
The Impact of the Affordable Care Act on Colorectal Cancer Incidence and Mortality: the case of Kaiser Permanente of Northern California
Authors: Lee Catherine , Eldridge Elizabeth H. , Reed Mary E. , Lee Jeffrey K. , Kushi Lawrence H. , Spiegelman Donna 
Published: October 2020

AbstractBackgroundThe Patient Protection and Affordable Care Act (ACA) eliminated cost sharing for preventive services, including colorectal cancer (CRC) screening for individuals aged 50 to 75 with private health insurance. The present study is the first to examine the impact of the no-cost CRC screening due to the ACA on CRC incidence and mortality.MethodsWe modeled trends in CRC incidence and CRC-related mortality in an open cohort of 2,113,283 Kaiser Permanente Northern California (KPNC) members aged 50 years and older between 2003 and 2016 using an interrupted time series design. Individual-level data were analyzed at the month-level. Analyses were adjusted for age, race/ethnicity and sex. As a sensitivity analysis, we considered a controlled approach, with a comparison group of KPNC members covered by health plans with pre-ACA zero cost-sharing for CRC screening.ResultsA total of 178,582,512 person-months were used in the analysis of CRC incidence, of which 48% occurred in the period before the ACA was passed into law (1/1/2003-3/31/2010) and 52% after (4/1/2010-12/31/2016). In primary analyses, the model for CRC incidence indicated a drop in the trend coinciding with the passage of the ACA (change in level incidence rate ratio, IRR: 0.83, 95% CI: 0.77-0.90, p-value < 0.0001), followed by a decrease in trend (change in slope IRR: 0.97/year, 95% CI: 0.93-1.00, p-value = 0.05). Results for CRC-related mortality were similar. Our controlled results indicate that free screening due to the ACA was associated with greater improvements in CRC outcomes among members previously covered by health plans with out-of-pocket costs for screening, compared to health plans with zero cost sharing for screening before the ACA went into effect.ConclusionsWe found that free CRC screening due to the ACA was associated with a decrease in age-, race/ethnicity- and sex-adjusted CRC incidence and CRC-related mortality, after accounting for contemporaneous competing interventions. Furthermore, these findings were robust to the addition of a comparison group with zero cost sharing both pre- and post-ACA.
Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis
Authors: Huang Ni , Perez Paola , Kato Takafumi , Mikami Yu , Okuda Kenichi , Gilmore Rodney C. , Domínguez Conde Cecilia , Gasmi Billel , Stein Sydney , Beach Margaret , Pelayo Eileen , Maldonado Jose , LaFont Bernard , Padilla Ricardo , Murrah Valerie , Maile Robert , Lovell Will , Wallet Shannon , Bowman Natalie M. , Meinig Suzanne L , Wolfgang Matthew C , Choudhury Saibyasachi N. , Novotny Mark , Aevermann Brian D , Scheuermann Richard , Cannon Gabrielle , Anderson Carlton , Marchesan Julie , Bush Mandy , Freire Marcelo , Kimple Adam , Herr Daniel L. , Rabin Joseph , Grazioli Alison , French Benjamin N. , Pranzatelli Thomas , Chiorini John A. , Kleiner David E. , Pittaluga Stefania , Hewitt Stephen , Burbelo Peter D. , Chertow Daniel ,   NIH COVID-19 Autopsy Consortium,   HCA Oral and Craniofacial Biological Network, Frank Karen , Lee Janice , Boucher Richard C. , Teichmann Sarah A. , Warner Blake M. , Byrd Kevin M. 
Published: October 2020

ABSTRACTDespite signs of infection, the involvement of the oral cavity in COVID-19 is poorly understood. To address this, single-cell RNA sequencing data-sets were integrated from human minor salivary glands and gingiva to identify 11 epithelial, 7 mesenchymal, and 15 immune cell clusters. Analysis of SARS-CoV-2 viral entry factor expression showed enrichment in epithelia including the ducts and acini of the salivary glands and the suprabasal cells of the mucosae. COVID-19 autopsy tissues confirmed in vivo SARS-CoV-2 infection in the salivary glands and mucosa. Saliva from SARS-CoV-2-infected individuals harbored epithelial cells exhibitingACE2expression and SARS-CoV-2 RNA. Matched nasopharyngeal and saliva samples found distinct viral shedding dynamics and viral burden in saliva correlated with COVID-19 symptoms including taste loss. Upon recovery, this cohort exhibited salivary antibodies against SARS-CoV-2 proteins. Collectively, the oral cavity represents a robust site for COVID-19 infection and implicates saliva in viral transmission.
Disruptions to schistosomiasis programmes due to COVID-19: an analysis of potential impact and mitigation strategies
Authors: Kura Klodeta , Ayabina Diepreye , Toor Jaspreet , Hollingsworth T. Deirdre , Anderson Roy M. 
Published: October 2020

AbstractBackgroundThe 2030 goal for schistosomiasis is elimination as a public health problem (EPHP), with mass drug administration (MDA) of praziquantel to school-aged children (SAC) a central pillar of the strategy. However, due to COVID-19, many mass treatment campaigns for schistosomiasis have been halted with uncertain implications for the programmes.MethodWe use mathematical modelling to explore how postponement of MDA and various mitigation strategies affect achievement of the EPHP goal for Schistosoma mansoni and S. haematobium.ResultsIn moderate and some high prevalence settings, the disruption may delay the goal by up to two years. In some high prevalence settings EPHP is not achievable with current strategies, and so the disruption will not impact this. Here, increasing SAC coverage and treating adults can achieve the goal.The impact of MDA disruption and the appropriate mitigation strategy varies according to the baseline prevalence prior to treatment, the burden of infection in adults and stage of the programme.ConclusionsSchistosomiasis MDA programmes in medium and high prevalence areas should restart as soon as is feasible, and mitigation strategies may be required in some settings.
Impact of the COVID-19 pandemic on remote mental healthcare and prescribing in psychiatry
Authors: Patel Rashmi , Irving Jessica , Brinn Aimee , Broadbent Matthew , Shetty Hitesh , Pritchard Megan , Downs Johnny , Stewart Robert , Harland Robert , McGuire Philip 
Published: October 2020

AbstractObjectivesThe recent COVID-19 pandemic has disrupted mental healthcare delivery, with many services shifting from in- person to remote patient contact. We investigated the impact of the pandemic on the use of remote consultation and on the prescribing of psychiatric medications.Design and settingThe Clinical Record Interactive Search tool (CRIS) was used to examine de-identified electronic health records (EHRs) of people receiving mental healthcare from the South London and Maudsley (SLaM) NHS Foundation Trust. Data from the period before and after the onset of the pandemic were analysed using linear regression, and visualised using locally estimated scatterplot smoothing (LOESS).ParticipantsAll patients receiving care from SLaM between 7th January 2019 and 20th September 2020 (around 37,500 patients per week).Outcome measuresThe number of clinical contacts (in-person, remote or non-attended) with mental healthcare professionals per weekPrescribing of antipsychotic and mood stabiliser medications per weekResultsFollowing the onset of the pandemic, the frequency of in-person contacts was significantly reduced compared to that in the previous year (β coefficient: −5829.6 contacts, 95% CI −6919.5 to −4739.6, p<0.001), while the frequency of remote contacts significantly increased (β coefficient: 3338.5 contacts, 95% CI 3074.4 to 3602.7, p<0.001). Rates of remote consultation were lower in older adults than in working age adults, children and adolescents. Despite this change in the type of patient contact, antipsychotic and mood stabiliser prescribing remained at similar levels.ConclusionsThe COVID-19 pandemic has been associated with a marked increase in remote consultation, particularly among younger patients. However, there was no evidence that this has led to changes in psychiatric prescribing. Nevertheless, further work is needed to ensure that older patients are able to access mental healthcare remotely.
The spatio-temporal landscape of lung pathology in SARS-CoV-2 infection
Authors: Rendeiro André Figueiredo , Ravichandran Hiranmayi , Bram Yaron , Salvatore Steven , Borczuk Alain , Elemento Olivier , Schwartz Robert Edward 
Published: October 2020

SummaryRecent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19)1–8. However thorough interrogation of the interplay between infected cells and the immune system at sites of infection is lacking. We use high parameter imaging mass cytometry9targeting the expression of 36 proteins, to investigate at single cell resolution, the cellular composition and spatial architecture of human acute lung injury including SARS-CoV-2. This spatially resolved, single-cell data unravels the disordered structure of the infected and injured lung alongside the distribution of extensive immune infiltration. Neutrophil and macrophage infiltration are hallmarks of bacterial pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells and induces a localized hyper-inflammatory cell state associated with lung damage. By leveraging the temporal range of COVID-19 severe fatal disease in relation to the time of symptom onset, we observe increased macrophage extravasation, mesenchymal cells, and fibroblasts abundance concomitant with increased proximity between these cell types as the disease progresses, possibly as an attempt to repair the damaged lung tissue. This spatially resolved single-cell data allowed us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. This spatial single-cell landscape enabled the pathophysiological characterization of the human lung from its macroscopic presentation to the single-cell, providing an important basis for the understanding of COVID-19, and lung pathology in general.
Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults
Authors: Ward Helen , Cooke Graham , Atchison Christina , Whitaker Matthew , Elliott Joshua , Moshe Maya , Brown Jonathan C , Flower Barney , Daunt Anna , Ainslie Kylie , Ashby Deborah , Donnelly Christl , Riley Steven , Darzi Ara , Barclay Wendy , Elliott Paul ,   for the REACT study team
Published: October 2020

AbstractBackgroundThe prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity.MethodsPrevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed.ResultsThere were 17,576 positive tests over the three rounds. Antibody prevalence, adjusted for test characteristics and weighted to the adult population of England, declined from 6.0% [5.8, 6.1], to 4.8% [4.7, 5.0] and 4.4% [4.3, 4.5], a fall of 26.5% [-29.0, −23.8] over the three months of the study. There was a decline between rounds 1 and 3 in all age groups, with the highest prevalence of a positive result and smallest overall decline in positivity in the youngest age group (18-24 years: −14.9% [-21.6, −8.1]), and lowest prevalence and largest decline in the oldest group (75+ years: −39.0% [-50.8, −27.2]); there was no change in antibody positivity between rounds 1 and 3 in healthcare workers (+3.45% [-5.7, +12.7]).The decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (−64.0% [-75.6, −52.3]), compared to −22.3% ([-27.0, −17.7]) in those with SARS-CoV-2 infection confirmed on PCR.DiscussionThese findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.
A quantitative exploration of symptoms in COVID-19 patients: an observational cohort study
Authors: Qu Gaojing , Chen Junwen , Huang Guoxin , Zhang Meiling , Yu Hui , Zhu Haoming , Chen Lei , Wang Dengru , Pei Bin 
Published: October 2020

AbstractBackgroundAs the spreading of the COVID-19 around the global, we investigated the characteristics and changes of symptoms in COVID-19 patients.MethodsThis was an ambispective observational cohort study, and 133 confirmed COVID-19 patients were included and all symptoms over the course were analyzed qualitatively. The symptoms, their changes over the course in the cohort and in the different clinical types, etc. were illustrated. Differences in different periods and severities were analyzed through Chi square test, association with severity was analyzed through LASSO binomial logistic regression analysis. Inter-correlation and classification of symptoms were completed. Major symptoms were screened and their changes were illustrated.ResultsA total of 43 symptoms with frequencies as 6067 in this cohort. Differences of symptoms in different stages and clinical types were significant. Expectoration, shortness of breath, dyspnea, diarrhea, poor appetite were positively but vomiting, waist discomfort, pharyngeal discomfort, acid reflux were negatively correlated with the combined-severe and critical type; dyspnea was correlated with the critical type. The 17 major symptoms were identified. The average daily frequency of symptoms per case was decreased continuously before the transition into the severe type and increased immediately one day before the transition and then decreased. It was decreased continuously before the transition date of the critical type and increased from the transition into the critical type to the next day and decreased thereafter. Dyspnea (P<0.001), shortness of breath (P<0.01) and chest distress (P<0.05) were correlated with death and their corresponding coefficient was 0.393, 0.258, 0.214, respectively.ConclusionThe symptoms of COVID-19 patients mainly related to upper respiratory tract infection, cardiopulmonary function, and digestive system. The mild type and the early stage in other types mainly related to upper respiratory tract infection. The cardiopulmonary function and digestive system associated symptoms were found in all other types and stages. Dyspnea was correlated with critical type and dyspnea, shortness of breath, and chest distress were correlated with death. Respiratory dysfunction (or incompleteness) associated symptoms were the characteristic symptoms. The changes of symptoms did not synchronously with the changes of severity before the transition into the severe or critical type.
RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction
Authors: Ramos Thaís A. R. , Galindo Nilbson R. O. , Arias-Carrasco Raúl , da Silva Cecília F. , Maracaja-Coutinho Vinicius , do Rêgo Thaís G. 
Published: October 2020

ABSTRACTNon-coding RNAs (ncRNAs) are important players in the cellular regulation of organisms from different kingdoms. One of the key steps in ncRNAs research is the ability to distinguish coding/non-coding sequences. We applied 7 machine learning algorithms (Naive Bayes, SVM, KNN, Random Forest, XGBoost, ANN and DL) through 15 model organisms from different evolutionary branches. Then, we created a stand-alone and web server tool (RNAmining) to distinguish coding and noncoding sequences, selecting the algorithm with the best performance (XGBoost). Firstly, we used coding/non-coding sequences downloaded from Ensembl (April 14th, 2020). Then, coding/non-coding sequences were balanced, had their tri-nucleotides counts analysed and we performed a normalization by the sequence length. Thus, in total we built 180 models. All the machine learning algorithms tests were performed using 10-folds cross-validation and we selected the algorithm with the best results (XGBoost) to implement at RNAmining. Best F1-scores ranged from 97.56% to 99.57% depending on the organism. Moreover, we produced a benchmarking with other tools already in literature (CPAT, CPC2, RNAcon and Transdecoder) and our results outperformed them, opening opportunities for the development of RNAmining, which is freely available athttps://rnamining.integrativebioinformatics.me/.