bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Commercial SARS-CoV-2 Antibody Assays, Jamaica
Authors: Butterfield Tiffany R. , Bruce-Mowatt Alrica , Phillips Yakima Z. R. , Brown Nicole , Francis Keisha , Brown Jabari , Taylor Devon , Bruce Carl A. , McGrowder Donovan , Wharfe Gilian , Sandiford Simone L. , Thompson Tamara K. , Anzinger Joshua J. 
Published: September 2020

AbstractThe performance of the Roche Elecsys® Anti-SARS-CoV-2, Abbott Architect SARS-CoV-2 IgG, Euroimmun SARS-CoV-2 IgA, Euroimmun SARS-CoV-2 IgG ELISA, and Trillium IgG/IgM rapid assays was evaluated in Jamaica, the largest country of the English-speaking Caribbean. Diagnostic sensitivities of the assays were assessed by testing serum samples from SARS-CoV-2 PCR-confirmed persons. Serum samples collected ≥14 days after onset of symptoms, or ≥14 days after an initial SARS-CoV-2 RT-PCR positive test for asymptomatics, showed diagnostic sensitivities ranging from 67.9-75.0% when including all possible disease severities and increased to 90.0-95.0% when examining those with moderate to critical disease. Grouping moderate to critical disease showed a significant association with a SARS-CoV-2 antibody positive result for all assays. Diagnostic specificity, assessed by testing serum samples collected during 2018-2019 from healthy persons and from persons with antibodies to a wide range of viral infections, ranged from 96.7-100.0%. For all assays examined, SARS-CoV-2 real-time PCR cycle threshold (Ct) values of the initial nasopharyngeal swab sample testing positive were significantly different for samples testing antibody positive versus negative. These data from a predominantly African descent Caribbean population shows comparable diagnostic sensitivities and specificities for all testing platforms assessed and limited utility of these tests for persons with asymptomatic and mild infections.
T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses
Authors: Ogbe Ane , Kronsteiner Barbara , Skelly Donal T. , Pace Matthew , Brown Anthony , Adland Emily , Adair Kareena , Akhter Hossain Delowar , Ali Mohammad , Ali Serat-E , Angyal Adrienn , Ansari M. Azim , Arancibia-Cárcamo Carolina V , Brown Helen , Chinnakannan Senthil , Conlon Christopher , de Lara Catherine , de Silva Thushan , Dold Christina , Dong Tao , Donnison Timothy , Eyre David , Flaxman Amy , Fletcher Helen , Gardner Joshua , Grist James T. , Hackstein Carl-Philipp , Jaruthamsophon Kanoot , Jeffrey Katie , Lambe Teresa , Lee Lian , Li Wenqin , Lim Nicholas , Matthews Philippa C. , Mentzer Alexander J. , Moore Shona C. , Naisbitt Dean J , Ogese Monday , Ogg Graham , Openshaw Peter , Pirmohamed Munir , Pollard Andrew J. , Ramamurthy Narayan , Rongkard Patpong , Rowland-Jones Sarah , Sampson Oliver , Screaton Gavin , Sette Alessandro , Stafford Lizzie , Thompson Craig , Thomson Paul J , Thwaites Ryan , Vieira Vinicius , Weiskopf Daniela , Zacharopoulou Panagiota ,   Oxford Immunology Network Covid-19 Response T cell Consortium,   Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team, Turtle Lance , Klenerman Paul , Goulder Philip , Frater John , Barnes Eleanor , Dunachie Susanna 
Published: September 2020

AbstractA major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.
Heat-based N95 mask decontamination and reuse in a large hospital setting
Authors: Vora Tushar , Bhattacharya Arnab , Ghosh Shankar , Gowda Kiran , Dhanaki Nandita , Gala Rajul , Dubey Nitin , Raut Vandana , Singh Vikas Kumar , Prakash Gagan , Laskar Sarbani Ghosh , Sengar Manju , Chinnaswamy Girish , Pramesh C S 
Published: September 2020

AbstractThe shortage of N95 masks have spurred efforts on developing safe and scientifically-validated decontamination and reuse protocols that are easily scalable and universally applicable even in low-resource settings. We report on the development and implementation of a heat-based N95 mask decontamination system in a large hospital setting (Tata Memorial Hospital, Mumbai, India) with over 8000 N95 masks from about 1400 individual users decontaminated and in reuse till date. We describe the challenges and constraints in choosing a proven, scalable, and easy-to-implement decontamination solution. We discuss the heat treatment and particle filtration efficiency measurement experiments done to validate a decontamination treatment protocol at a target temperature of 70oC for a duration of 60 minutes, and the scaling up of this method using a standard hot drying cabinet at the hospital. The logistics of ensuring optimal utilization of the decontamination facility without compromising on basic safety principles are detailed. Our method relies on equipment available in standard hospitals, is simple to set-up, scalable, and can be easily replicated in low-resource settings. We further believe such limited reuse strategies, even in times of abundant N95 mask availability, would not only be cost-saving but also be environmentally responsible in reducing the amount of medical waste.
DeepCOVID: An Operational Deep Learning-driven Framework for Explainable Real-time COVID-19 Forecasting
Authors: Rodríguez Alexander , Tabassum Anika , Cui Jiaming , Xie Jiajia , Ho Javen , Agarwal Pulak , Adhikari Bijaya , Prakash B. Aditya 
Published: September 2020

AbstractHow do we forecast an emerging pandemic in real time in a purely data-driven manner? How to leverage rich heterogeneous data based on various signals such as mobility, testing, and/or disease exposure for forecasting? How to handle noisy data and generate uncertainties in the forecast? In this paper, we present DeepCovid, an operational deep learning frame-work designed for real-time COVID-19 forecasting. Deep-Covid works well with sparse data and can handle noisy heterogeneous data signals by propagating the uncertainty from the data in a principled manner resulting in meaningful uncertainties in the forecast. The deployed framework also consists of modules for both real-time and retrospective exploratory analysis to enable interpretation of the forecasts. Results from real-time predictions (featured on the CDC website and FiveThirtyEight.com) since April 2020 indicates that our approach is competitive among the methods in the COVID-19 Forecast Hub, especially for short-term predictions.
Comparison of infection control strategies to reduce COVID-19 outbreaks in homeless shelters in the United States: a simulation study
Authors: Chapman Lloyd A.C. , Kushel Margot , Cox Sarah N. , Scarborough Ashley , Cawley Caroline , Nguyen Trang , Rodriguez-Barraquer Isabel , Greenhouse Bryan , Imbert Elizabeth , Lo Nathan C. 
Published: September 2020

AbstractBackgroundCOVID-19 outbreaks have occurred in homeless shelters across the US, highlighting an urgent need to identify the most effective infection control strategy to prevent future outbreaks.MethodsWe developed a microsimulation model of SARS-CoV-2 transmission in a homeless shelter and calibrated it to data from cross-sectional polymerase-chain-reaction (PCR) surveys conducted during COVID-19 outbreaks in five shelters in three US cities from March 28 to April 10, 2020. We estimated the probability of averting a COVID-19 outbreak when an exposed individual is introduced into a representative homeless shelter of 250 residents and 50 staff over 30 days under different infection control strategies, including daily symptom-based screening, twice-weekly PCR testing and universal mask wearing.ResultsThe proportion of PCR-positive residents and staff at the shelters with observed outbreaks ranged from 2.6% to 51.6%, which translated to basic reproduction number (R0) estimates of 2.9–6.2. The probability of averting an outbreak diminished with higher transmissibility (R0) within the simulated shelter and increasing incidence in the local community. With moderate community incidence (~30 confirmed cases/1,000,000 people/day), the estimated probabilities of averting an outbreak in a low-risk (R0=1.5), moderate-risk (R0=2.9), and high-risk (R0=6.2) shelter were, respectively: 0.35, 0.13 and 0.04 for daily symptom-based screening; 0.53, 0.20, and 0.09 for twice-weekly PCR testing; 0.62, 0.27 and 0.08 for universal masking; and 0.74, 0.42 and 0.19 for these strategies combined.ConclusionsIn high-risk homeless shelter environments and locations with high community incidence of COVID-19, even intensive infection control strategies (incorporating daily symptom-screening, frequent PCR testing and universal mask wearing) are unlikely to prevent outbreaks, suggesting a need for non-congregate housing arrangements for people experiencing homelessness. In lower-risk environments, combined interventions should be employed to reduce outbreak risk.
Young adults with recurrent low back pain demonstrate altered trunk coordination during gait independent of pain status and attentional demands
Authors: Shih Hai-Jung Steffi , Winstein Carolee J. , Kulig Kornelia 
Published: September 2020

AbstractPain influences both attention and motor behavior. We used a dual-task interference paradigm to investigate 1) alterations in attentional performance, 2) the ability to switch task prioritization, and 3) the effect of attentional demand on trunk coordination during narrow-based walking in and out of a painful episode in individuals with recurrent low back pain (LBP). We tested twenty young adults with LBP both in and out of a painful episode and compared them to twenty matched back-healthy individuals. Participants simultaneously performed a narrow step width matching task and an arithmetic task, with and without instructions to prioritize either task. A motion capture system was used to record kinematic data, and frontal plane trunk coordination was analyzed using vector coding on the thorax and pelvis angles. Single task performance, dual-task effect, dual-task performance variability, task prioritization switch, and trunk coordination were analyzed using paired t-tests or repeated measures two-way ANOVAs. Results indicated that active pain has a detrimental effect on attentional processes, indicated by poorer single task performance and increased dual-task performance variability for individuals with recurrent LBP. Individuals with LBP, regardless of pain status, were able to switch task prioritization to a similar degree as their back-healthy counterparts. Compared to the control group, individuals with recurrent LBP exhibited a less in-phase, more pelvis-dominated trunk coordination during narrow-based walking, independent of pain status and regardless of attentional manipulations. Thus, altered trunk coordination in persons with LBP appears to be habitual, automatic, and persists beyond symptom duration.
Two Color Single Molecule Sequencing on GenoCare™ 1600 Platform to Facilitate Clinical Applications
Authors: Chen Fang , Liu Bin , Chen Meirong , Jiang Zefei , Zhou Zhiliang , Wu Ping , Zhang Meng , Jin Huan , Li Linsen , Lu Liuyan , Wang Qi , Shang Huan , Xie Bing , Liu Lei , Lin Xia , Chen Weiyue , Xu Jianfeng , Sun Ruitao , Wang Guangming , Zheng Jiao , Qi Jifang , Yang Bo , Chen Dexia , Zeng Lidong , Li Gailing , Li Yan , Lv Hui , Zhao Nannan , Zhou Bo , Wang Wen , Cai Jinsen , Liu Siyu , Luo Weiwei , Zhang Juan , Zhang Yanhua , Lu Yongyi , Fan Jicai , Dan Haitao , He Xuesen , Liu Lichun , Feng Yan , Chen Jianglin , Huang Wei , Sun Lei , Yan Qin 
Published: September 2020

AbstractWith the rapid development of precision medicine industry, DNA sequencing becomes increasingly important as a research and diagnosis tool. For clinical applications, medical professionals require a platform which is fast, easy to use, and presents clear information relevant to definitive diagnosis. We have developed a single molecule desktop sequencing platform, GenoCare™ 1600. Fast library preparation (without amplification) and simple instrument operation make it friendlier for clinical use. Here we presented sequencing data of E. coli sample from GenoCare™ 1600 with consensus accuracy reaches 99.99%. We also demonstrated sequencing of microbial mixtures and COVID-19 samples from throat swabs. Our data show accurate quantitation of microbial, sensitive identification of SARS-CoV-2 virus and detection of variants confirmed by Sanger sequencing.
Efficacy of Famotidine for COVID-19: A Systematic Review and Meta-analysis
Authors: Sethia Rahul , Prasad Manya , Mahapatra Soumya Jagannath , Nischal Neeraj , Soneja Manish , Garg Pramod , Shalimar  
Published: September 2020

AbstractBackgroundCoronavirus Disease 2019 (COVID-19) pandemic continues unabated in many parts of the world. In the absence of any definite antiviral therapy except some benefit of remdesivir, there is an ongoing search for effective therapy. Famotidine has been shown to reduce mortality in hospitalized patients in a few studies. We conducted a systematic review on the use of famotidine in COVID-19.MethodsWe searched the databases Medline, Embase, Cochrane CENTRAL and Medrxiv. Title/abstract screening, full text screening and data abstraction were carried out in by two reviewers. Case series, cohort studies and randomized trials were included.ResultsFive studies were eligible for inclusion: all were retrospective cohort or case series. Low quality evidence suggests a likely clinical benefit for the use of famotidine in decreasing mortality in hospitalized patients with moderate to severe COVID-19. A meta-analysis of two cohort studies showed a statistically significant decrease in the composite outcome for death and intubation with famotidine (HR 0.44, 95% CI 0.27 to 0.73).ConclusionFurther evidence from RCTs is required for famotidine to treat COVID 19.
Association study of BDNF Val66Met gene polymorphism with bipolar disorder and lithium treatment response in Indian population
Authors: Paul Pradip , Nadella Ravi Kumar , Sen Somdatta , Ithal Dhruva , Mahadevan Jayant , Reddy Y C Janardhan , Jain Sanjeev , Purushottam Meera , Viswanath Biju 
Published: September 2020

AbstractBackgroundThe association of the Val66Met (rs6265) polymorphism in the brain derived neurotrophic factor (BDNF) gene with bipolar disorder (BD) and response to lithium treatment has been suggested, though inconsistently. The considerable diversity of allele frequency across different populations contributes to this. There is no data from South Asia till date. Hence, we examined the association of this polymorphism in BD cases from India, and its correlation with lithium treatment response.MethodsBD patients (N=301) were recruited from the clinical services of National Institute of Mental Health and Neurosciences (NIMHANS), India. Lithium treatment response for 190 BD subjects was assessed using Alda scale by NIMH life charts. Patients with total score ≥ 7 were defined as lithium responders (N=115) and patients with score <7 were defined as lithium non-responders (N=75). Healthy controls (N = 484) with no lifetime history of neuropsychiatric illness, or a family history of mental illness were recruited as control set. Genotyping was performed by TaqMan genotyping assay.ResultsGenotype and allele frequency of BDNF Val66Met SNP was significantly different (χ2 = 7.78, p=0.02) in cases compared to controls, and the Val(G) allele was more frequent (χ2 = 7.08, p=0.008) in BD patients. Although there was trend towards significance for greater occurrence of Val(G) allele among lithium non-responders, this difference did not persist in an analysis of extreme response groups.ConclusionsThe Val(G) allele of BDNF Val66Met polymorphism is associated with risk of BD in this sample, but is not related to response to lithium.
EPI Distortion Correction is Easy and Useful, and You Should Use It: A case study with toddler data
Authors: Roopchansingh Vinai , French Jerry J. , Nielson Dylan M. , Reynolds Richard C. , Glen Daniel R. , D’ Souza Precilla , Taylor Paul A. , Cox Robert W. , Thurm Audrey E. 
Published: September 2020

AbstractTask, resting state, and diffusion MRI data are usually acquired from subjects using echo-planar based imaging techniques. These techniques are highly susceptible to B0homogeneity effects that result in geometric distortions in the reconstructed images. As researchers work to link the information from these scans back to various developmental stages, or to conditions and diseases in specific regions or structures of the brain, it becomes critical to have accurate correspondence between more geometrically distorted echo-planar images and less geometrically distorted anatomical images. A variety of techniques and tools have been developed to improve this correspondence. The basic premise behind most techniques used to mitigate geometric distortion is to acquire enough information to inform software tools how echo-planar images are warped, then have them undo that warping. Here, we investigate the application of two common methods: B0correction, and reverse-polarity phase-encoding (or reverse blip) correction. We implement each of these in two separate, widely used software packages in the field: AFNI and FSL. We find that using either technique in either software package results in reduced geometric distortions in the EPI images. We discuss the practical implementations of these methods (e.g., increased scan and processing time). In general, however, both methods possess readily available data acquisition schemes, and are highly efficient to include in processing streams. Due to the overall data improvement, we strongly recommend that researchers include one of these methods in their standard protocols.
The composition of the microbiota in the full-term fetal gut and amniotic fluid: a bovine caesarean section study
Authors: Husso Aleksi , Lietaer Leen , Pessa-Morikawa Tiina , Grönthal Thomas , Govaere Jan , Van Soom Ann , Iivanainen Antti , Opsomer Geert , Niku Mikael 
Published: September 2020

AbstractThe fetal development of the intestinal immune system is stimulated by the maternal microbiota, but it is still unclear whether viable bacteria exist in the healthy fetus. Analysis of such low microbial biomass environments are challenging due to contamination issues. The aims of the current study were to assess the bacterial load and characterize the bacterial composition of the amniotic fluid and meconium of full-term calves, leading to a better knowledge of prenatal bacterial seeding of the fetal intestine. Amniotic fluid and rectal meconium samples were collected during and immediately after elective caesarean section, performed in 25 Belgian Blue cow-calf couples. The samples were analyzed by qPCR, bacterial culture using GAM agar and 16S rRNA gene amplicon sequencing. To minimize the effects of contaminants, we included multiple technical controls and stringently filtered the 16S rRNA gene sequencing data to exclude putative contaminant sequences. The meconium samples contained a significantly higher amount of bacterial DNA than the negative controls and 5 of 24 samples contained culturable bacteria. In the amniotic fluid, the amount of bacterial DNA was not significantly different from the negative controls and all samples were culture negative. Bacterial sequences were identified in both sample types and were primarily of phyla Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria, with some individual variation. We conclude that most calves encounterin uteromaternal-fetal transmission of bacterial DNA, but the amount of bacterial DNA is low and viable bacteria are rare.
Prime-boost vaccination of mice and Rhesus macaques with two novel adenovirus vectored COVID-19 vaccine candidates
Authors: Luo Shengxue , Zhang Panli , Liu Bochao , Yang Chan , Liang Chaolan , Wang Qi , Zhang Ling , Tang Xi , Li Jinfeng , Hou Shuiping , Zeng Jinfeng , Fu Yongshui , Allain Jean-Pierre , Li Tingting , Zhang Yuming , Li Chengyao 
Published: September 2020

ABSTRACTCOVID-19 vaccines are being developed urgently worldwide, among which single-shot adenovirus vectored vaccines represent a major approach. Here, we constructed two novel adenovirus vectored COVID-19 vaccine candidates on simian adenovirus serotype 23 (Sad23L) and human adenovirus serotype 49 vectors (Ad49L) carrying the full-length gene of SARS-CoV-2 spike protein (S), designated Sad23L-nCoV-S and Ad49L-nCoV-S vaccines, respectively. The immunogenicity elicited by these two vaccine strains was individually evaluated in mice. Specific humoral and cellular immune responses were proportionally observed in a dose-dependent manner, and stronger response was obtained by boosting. Furthermore, five rhesus macaques were intramuscularly injected with a dose of 5×109PFU Sad23L-nCoV-S vaccine for prime vaccination, followed by boosting with 5×109PFU of Ad49L-nCoV-S vaccine at 4-week interval. Three macaques were injected with Sad23L-GFP and Ad49L-GFP vectorial viruses as negative controls. Both mice and macaques tolerated well the vaccine inoculations without detectable clinical or pathologic changes. In macaques, prime-boost vaccination regimen induced high titers of 103.16S-binding antibody (S-BAb), 102.75cell receptor binding domain (RBD)-BAb and 102.38neutralizing antibody (NAb) to pseudovirus a week after boosting injection, followed by sustained high levels over 10 weeks of observation. Robust IFN-γ secreting T-cell response (712.6 SFCs/106cells), IL-2 secreting T-cell response (334 SFCs/106cells) and intracellular IFN-γ expressing CD4+/CD8+T cell response (0.39%/0.55%) to S peptides were detected in the vaccinated macaques. It was concluded that prime-boost immunization with Sad23L-nCoV-S and Ad49L-nCoV-S vaccines can safely elicit strong immunity in animals in preparation of clinical phase 1/2 trials.