bluuebunny/crossref_metadata_2025_split huggingface dataset:
A citizen science initiative for open data and visualization of COVID-19 outbreak in Kerala, India
Authors: Ulahannan Jijo Pulickiyil , Narayanan Nikhil , Thalhath Nishad , Prabhakaran Prem , Chaliyeduth Sreekanth , Suresh Sooraj P , Mohammed Musfir , Rajeevan E , Joseph Sindhu , Balakrishnan Akhil , Uthaman Jeevan , Karingamadathil Manoj , Thomas Sunil Thonikkuzhiyil , Sureshkumar Unnikrishnan , Balan Shabeesh , Vellichirammal Neetha Nanoth 
Published: May 2020

ABSTRACTObjectiveIndia reported its first COVID-19 case in the state of Kerala and an outbreak initiated subsequently. The Department of Health Services, Government of Kerala, initially released daily updates through daily textual bulletins for public awareness to control the spread of the disease. However, this unstructured data limits upstream applications, such as visualization, and analysis, thus demanding refinement to generate open and reusable datasets.Materials and MethodsThrough a citizen science initiative, we leveraged publicly available and crowd-verified data on COVID-19 outbreak in Kerala from the government bulletins and media outlets to generate reusable datasets. This was further visualized as a dashboard through a frontend web application and a JSON repository, which serves as an API for the frontend.ResultsFrom the sourced data, we provided real-time analysis, and daily updates of COVID-19 cases in Kerala, through a user-friendly bilingual dashboard (https://covid19kerala.info/) for non-specialists. To ensure longevity and reusability, the dataset was deposited in an open-access public repository for future analysis. Finally, we provide outbreak trends and demographic characteristics of the individuals affected with COVID-19 in Kerala during the first 138 days of the outbreak.DiscussionWe anticipate that our dataset can form the basis for future studies, supplemented with clinical and epidemiological data from the individuals affected with COVID-19 in Kerala.ConclusionWe reported a citizen science initiative on the COVID-19 outbreak in Kerala to collect and deposit data in a structured format, which was utilized for visualizing the outbreak trend and describing demographic characteristics of affected individuals.
Analytical performance of lateral flow immunoassay for SARS-CoV-2 exposure screening on venous and capillary blood samples
Authors: Black Margaret A. , Shen Guomiao , Feng Xiaojun , Garcia Beltran Wilfredo F. , Feng Yang , Vasudevaraja Varshini , Allison Douglas , Lin Lawrence H. , Gindin Tatyana , Astudillo Michael , Yang Diane , Murali Mandakolathur , Iafrate A. John , Jour George , Cotzia Paolo , Snuderl Matija 
Published: May 2020

AbstractObjectivesNumerous serologic immunoassays have been launched to detect antibodies to SARS-CoV-2, including rapid tests. Here, we validate use of a lateral flow immunoassay (LFI) intended for rapid screening and qualitative detection of anti-SARS-CoV-2 IgM and IgG in serum, plasma, and whole blood, and compare results with ELISA. We also seek to establish the value of LFI testing on blood obtained from a capillary blood sample.MethodsSamples collected by venous blood draw and capillary finger stick were obtained from patients with SARS-CoV-2 detected by RT-qPCR and control patients negative for SARS-CoV-2. Samples were tested with the 2019-nCoV IgG/IgM Detection Kit (Colloidal Gold) lateral flow immunoassay, and antibody calls were compared with results obtained by ELISA.ResultsThe Biolidics LFI kit shows clinical sensitivity of 92% at 7 days after PCR diagnosis of SARS-CoV-2 on venous blood. Test specificity was 92% for IgM and 100% for IgG. There was no significant difference in detecting IgM and IgG with Biolidics LFI and ELISA at D0 and D7 (p=1.00), except for detection of IgM at D7 (p=0.04). Finger stick whole blood of SARS-CoV-2 patients showed 93% sensitivity for antibody detection.ConclusionsClinical performance of Biolidics 2019-nCoV IgG/IgM Detection Kit (Colloidal Gold) is comparable to ELISA and showed consistent results across different sample types. Furthermore, we show that capillary blood obtained by finger stick shows similar sensitivity for detecting anti-SARS-CoV-2 IgM and IgG antibodies as venous blood samples. This provides an opportunity for decentralized rapid testing in the community and may allow point-of-care and longitudinal self-testing for the presence of anti-SARS-CoV-2 antibodies.
Transmission of aerosols through pristine and reprocessed N95 respirators
Authors: Chen Paul Z. , Ngan Aldrich , Manson Niclas , Maynes Jason T. , Borschel Gregory H. , Rotstein Ori D. , Gu Frank X. 
Published: May 2020

AbstractDuring the Covid-19 pandemic, pristine and reprocessed N95 respirators are crucial equipment towards limiting nosocomial infections. The NIOSH test certifying the N95 rating, however, poorly simulates aerosols in healthcare settings, limiting our understanding of the exposure risk for healthcare workers wearing these masks, especially reprocessed ones. We used experimental conditions that simulated the sizes, densities and airflow properties of infectious aerosols in healthcare settings. We analyzed the penetration and leakage of aerosols through pristine and reprocessed N95 respirators. Seven reprocessing methods were investigated. Our findings suggest that pristine and properly reprocessed N95 respirators effectively limit exposure to infectious aerosols, but that care must be taken to avoid the elucidated degradation mechanisms and limit noncompliant wear.
Diffuse correlation spectroscopy used to monitor cerebral blood flow during adult hypothermic circulatory arrests
Authors: Zavriyev Alexander I. , Kaya Kutlu , Farzam Parisa , Farzam Parya Y. , Sunwoo John , Orihuela-Espina Felipe , Jassar Arminder S. , Cameron Duke E. , Sundt Thoralf M. , Melnitchouk Serguei , Carp Stefan A. , Franceschini Maria Angela , Qu Jason Z. 
Published: May 2020

AbstractReal-time noninvasive monitoring of cerebral blood flow during surgery could improve the morbidity and mortality rates associated with hypothermic circulatory arrests (HCA) in adult cardiac patients. In this study, we used a combined frequency domain near-infrared spectroscopy (FDNIRS) and diffuse correlation spectroscopy (DCS) system to measure cerebral oxygen saturation (SO2) and an index of blood flow (CBFi) in 12 adults going under cardiac surgery with HCA. Our measurements revealed that a negligible amount of blood is delivered to the brain during HCA with retrograde cerebral perfusion (RCP), indistinguishable from HCA-only cases (CBFi drops of 91% ± 3% and 96% ± 2%, respectively) and that CBFi drops for both are significantly higher than drops during HCA with antegrade cerebral perfusion (ACP) (p = 0.003). We conclude that FDNIRS-DCS can be a powerful tool to optimize cerebral perfusion, and that RCP needs to be further examined to confirm its efficacy, or lack thereof.
Heg.IA: An intelligent system to support diagnosis of Covid-19 based on blood tests
Authors: de Freitas Barbosa Valter Augusto , Gomes Juliana Carneiro , de Santana Maíra Araújo , de Almeida Albuquerque Jeniffer Emidio , de Souza Rodrigo Gomes , de Souza Ricardo Emmanuel , dos Santos Wellington Pinheiro 
Published: May 2020

AbstractA new kind of coronavirus, the SARS-Cov2, started the biggest pandemic of the century. It has already killed more than 250,000 people. Because of this, it is necessary quick and precise diagnosis test. The current gold standard is the RT-PCR with DNA sequencing and identification, but its results takes too long to be available. Tests base on IgM/IgG antibodies have been used, but their sensitivity and specificity may be very low. Many studies have been demonstrating the Covid-19 impact in hematological parameters. This work proposes an intelligent system to support Covid-19 diagnosis based on blood testing. We tested several machine learning methods, and we achieved high classification performance: 95.159% ± 0.693 of overall accuracy, kappa index of 0.903 ± 0.014, sensitivity of 0.968 ± 0.007, precision of 0.938 ± 0.010 and specificity of 0.936 ± 0.011. These results were achieved using classical and low computational cost classifiers, with Bayes Network being the best of them. In addition, only 24 blood tests were needed. This points to the possibility of a new rapid test with low cost. The desktop version of the system is fully functional and available for free use.
Immunosurveillance of CCR6+ T-cells predicts treatment response to dimethyl-fumarate: implications for personalized treatment strategies in multiple sclerosis
Authors: Alifieris Constantinos , Schultze Seunghee Kim , Sand Ilana Katz , Casaccia Patrizia , Ntranos Achilles 
Published: May 2020

AbstractObjectiveThe field of multiple sclerosis (MS) has seen a tremendous expansion of treatments in the past decade. However, treatment response in individual patients can currently be determined only by waiting for breakthrough disease activity to occur. This highlights a critical need for biomarkers that can predict treatment response and stratify the risk of impeding disease activity before damage is inflicted to the CNS. Here we show that CCR6+CD3+ T-cell surveillance in peripheral blood can be used to discriminate responders and non-responders to dimethyl-fumarate.MethodsA cohort of 101 treatment-naïve, dimethyl-fumarate (DMF) treated MS patients and healthy controls was immunophenotyped and then responders and non-responders were determined retrospectively after clinical and radiographic follow up. Receiver operating characteristic (ROC) curve, linear and logistic regression, mixed effects models, and cox proportional hazards were used for the analysis.ResultsAmong various clinical and immunophenotypic metrics, the percentage of CCR6+CD3+ T-cells was the most significant predictor of impending disease activity. This immunophenotypic metric was able to discriminate responders and non-responders to DMF with an area under the ROC of 0.85 (95% CI: 0.71–0.99), which was higher than that achieved using surrogate metrics for T-helper-1-like T-helper-17 or T-cytotoxic-17 cells. DMF-treated patients with the highest percentage of CCR6+CD3+ T-cells had a significantly higher risk of impending disease activity compared to patients with a low percentage.InterpretationChanges in CCR6+CD3+ T-cells in the periphery could precede disease activity by many months and potentially serve as an early biomarker of treatment response, at least for DMF. These results have implications for novel personalized treatment strategies in MS.
The differential impact of physical distancing strategies on social contacts relevant for the spread of COVID-19: Evidence from a multi-country survey
Authors: Del Fava Emanuele , Cimentada Jorge , Perrotta Daniela , Grow André , Rampazzo Francesco , Gil-Clavel Sofia , Zagheni Emilio 
Published: May 2020

AbstractPhysical distancing measures are intended to mitigate the spread of COVID-19, even though their impact on social contacts and disease transmission remains unclear. Obtaining timely data on social contact patterns can help to assess the impact of such protective measures. We conducted an online opt-in survey based on targeted Facebook advertising campaigns across seven European countries (Belgium, France, Germany, Italy, Netherlands, Spain, United Kingdom (UK)) and the United States (US), achieving a sample of 53,708 questionnaires in the period March 13–April 13, 2020. Post-stratification weights were produced to correct for biases. Data on social contact numbers, as well as on protective behaviour and perceived level of threat were collected and used to the expected net reproduction number by week,Rt, with respect to pre-pandemic data. Compared to social contacts reported prior to COVID-19, in mid-April daily social contact numbers had decreased between 49% in Germany and 83% in Italy, ranging from below three contacts per day in France, Spain, and the UK up to four in Germany and the Netherlands. Such reductions were sufficient to bringRtto one or even below in all countries, except Germany. Evidence from the US and the UK showed that the number of daily social contacts mainly decreased after governments issued the first physical distancing guidelines. Finally, although contact numbers decreased uniformly across age groups, older adults reported the lowest numbers of contacts, indicating higher levels of protection. We provided a comparable set of statistics on social contact patterns during the COVID-19 pandemic for eight high-income countries, disaggregated by week. As these estimates offer a more grounded alternative to the theoretical assumptions often used in epidemiological models, the scientific community could draw on this information for developing more realistic epidemic models of COVID-19.
Impact of relaxing Covid-19 social distancing measures on rural North Wales: a simulation analysis
Authors: Hughes Rhodri P , Hughes Dyfrig A 
Published: May 2020

AbstractBackgroundSocial distancing policies aimed to limit Covid–19 are gradually being relaxed as nationally reported peaks in incident cases are passed. Population density is an important driver of national incidence rates; however peak incidences in rural regions may lag national figures by several weeks. We aimed to forecast the impact of relaxed social distancing rules on rural North Wales.MethodsDaily data on the deaths of people with a positive test for Covid–19 were obtained from Public Health Wales and the UK Government. Sigmoidal growth functions were fitted by non-linear least squares and model averaging used to extrapolate mortality over time. The dates of peak mortality incidences for North Wales, Wales and the UK; and the percentage predicted maximum mortality (as of 7th May 2020) were estimated.ResultsThe peak daily death rates in Wales and the UK were estimated to have occurred on the 14/04/2020 and 15/04/2020, respectively. For North Wales, this occurred on the 07/05/2020, corresponding to the date of analysis. The number of deaths reported in North Wales represents 31% of the predicted total cumulative number, compared with 71% and 60% for Wales and the UK, respectively.ConclusionPolicies governing the movement of people in the gradual release from lockdown are likely to impact significantly on areas –principally rural in nature– where cases of Covid–19, deaths and immunity are likely to be much lower than in populated areas. This is particularly difficult to manage across jurisdictions, such as between England and Wales, and in popular holiday destinations.
The effect of ambient temperature on worldwide COVID-19 cases and deaths – an epidemiological study
Authors: Sethwala Anver , Akbarally Mohamed , Better Nathan , Lefkovits Jeffrey , Grigg Leeanne , Akbarally Huzefa 
Published: May 2020

AbstractBackgroundThe role of ambient temperature in the spread of SARS-CoV-2 infections and subsequent deaths due to COVID-19 remains contentious. Coronaviruses such as the 2003 SARS-CoV showed an increased risk of transmission during cooler days. We sought to analyse the effects of ambient temperature on SARS-COV-2 transmission and deaths related to the virus.MethodsThe world population of COVID-19 cases and attributable deaths from the 23rd January 2020 to 11th April 2020 were analysed. Temperature 5 days before cases and 23 days prior to deaths (to account for the time lag of incubation period and time from symptoms to death) was compared to the average temperature experienced by the world population.ResultsThe total number of cases during this period was 1,605,788 and total number of deaths was 103,471. The median temperature at the time of COVID-19 infection was 9.12°C (10–90th percentile 4.29–17.97°C) whilst the median temperature of the world population for the same period was 9.61°C warmer at 18.73°C (10–90th percentile 4.09-28.49°C) with a notional p-value =5.1 x10−11. The median temperature at the time of a COVID-19 death was 9.72°C (10–90th percentile 5.39–14.11°C) whilst the median temperature of the world population was 7.55°C warmer at 17.27°C (10–90th percentile 2.57°C-27.76°C) with a notional p-value = 1.1 x10−10. 80% of all COVID-19 related cases and deaths occurred between 4.29°C and 17.97°C.ConclusionA definitive association between infection rate and death from COVID-19 and ambient temperature exists, with the highest risk occurring around 9°C. Governments should maintain vigilance with containment strategies when the ambient temperatures correspond to this highest risk.
Perceptions and Attitudes Towards Shoulder Padding and Shoulder Injury in Rugby Union
Authors: Hughes Angus , Carré Prof. Matt , Driscoll Dr. Heather 
Published: May 2020

ABSTRACTObjectiveTo develop an understanding of the role of shoulder padding in preventing injuries in rugby by investigating player perceptions and attitudes towards shoulder padding and extending previous research into the nature of shoulder injuries in rugby.MethodsA survey was distributed to current rugby players over 13 years old. Questions related to the participants’ demographic, attitudes to shoulder padding and shoulder injury history.Results616 rugby players responded to the survey. 66.1% of respondents had worn shoulder padding at some point during their career. Youth players (13–17 years old) and the older demographic (36+ years old) perceived shoulder padding to be more effective. 37.1% of respondents considered shoulder padding to be effective at preventing cuts and abrasions with 21.9% finding it very effective. 50.3% considered it to be effective at preventing contusion injury with 9.7% finding it very effective. 45.5% wore padding for injury prevention, while 19.2% wore padding to protect from reoccurring injury. 38.6% did not wear shoulder padding because they felt it was not needed for the game of rugby. Sprain/ ligament damage (57.5%) and bruising (55.5%) to the shoulder were the most commonly reported injury.ConclusionsResearch should focus on quantifying the injury preventive capabilities while also educating the rugby community on shoulder padding. Bruising, cuts and abrasion injuries to the shoulder are prevalent. The ability of shoulder padding to protect from these injuries should be further explored.
Chromosome scale reference genome of Cluster bean (Cyamopsis tetragonoloba(L.) Taub.)
Authors: Gaikwad Kishor , Ramakrishna G. , Srivastava Harsha , Saxena Swati , Kaila Tanvi , Tyagi Anshika , Sharma Priya , Sharma Sandhya , Sharma R , Mahla HR , Amitha Mithra SV , Solanke Amol , Kalia Pritam , Rao AR , Rai Anil , Sharma TR , Singh NK 
Published: May 2020

AbstractClusterbean (Cyamopsis tetragonoloba(L.) Taub.), also known as Guar is a widely cultivated dryland legume of Western India and parts of Africa. Apart from being a vegetable crop, it is also an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan which is widely used in cosmetics, pharmaceuticals, food processing, shale gas drilling etc. Here, for the first time we are reporting a chromosome-scale reference genome assembly of clusterbean, from a high galactomannan containing popular guar cultivar, RGC-936, by combining sequenced reads from Illumina, 10x Chromium and Oxford Nanopore technologies. The initial assembly of 1580 scaffolds with an N50 value of 7.12 Mbp was generated. Then, the final genome assembly was obtained by anchoring these scaffolds to a high density SNP map. Finally, a genome assembly of 550.31 Mbp was obtained in 7 pseudomolecules corresponding to 7 chromosomes with a very high N50 of 78.27 Mbp. We finally predicted 34,680 protein-coding genes in the guar genome. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted breeding of superior cultivars.
EFF-1 promotes muscle fusion, paralysis and retargets infection by AFF-1-coated viruses inC. elegans
Authors: Meledin Anna , Li Xiaohui , Matveev Elena , Gildor Boaz , Katzir Ofer , Podbilewicz Benjamin 
Published: May 2020

A hallmark of muscle development is that myoblasts fuse to form myofibers. However, smooth muscles and cardiomyocytes do not generally fuse. InC. elegans, the body wall muscles (BWMs), the physiological equivalents of skeletal muscles, are mononuclear. Here, to determine what would be the consequences of fusing BWMs, we express the cell-cell fusogen EFF-1 in these cells. We find that EFF-1 induces paralysis and dumpy phenotypes. To determine whether EFF-1-induced muscle fusion results in these pathologies we injected viruses pseudotyped with AFF-1, a paralog of EFF-1, into the pseudocoelom ofC. elegans. When these engineered viruses encounter cells expressing EFF-1 or AFF-1 they are able to infect them as revealed by GFP expression from the viral genome. We find that AFF-1 viruses can fuse to EFF-1-expressing muscles revealing multinucleated fibers that cause paralysis and abnormal muscle morphogenesis. Thus, aberrant fusion of otherwise non-syncytial muscle cells may lead to pathological conditions.Graphical abstractSignificance statementMost cells are individual units that do not mix their cytoplasms. However, some cells fuse to become multinucleated in placenta, bones and muscles. In most animals, muscles are formed by myofibers that originate by cell-cell fusion. In contrast, inC. elegansthe body wall muscles are mononucleated cells that mediate worm-like movement. EFF-1 and AFF-1 fusogens mediate physiological cell fusion inC. elegans. By ectopically expressing EFF-1 in body wall muscles we induce their fusion resulting in behavioral and morphological deleterious effects, revealing possible causes of congenital myopathies in humans. Using AFF-1-coated pseudoviruses we infect EFF-1-expressing muscle cells retargeting viral infection into these cells. We suggest that virus retargeting can be utilized to study myogenesis, neuronal regeneration, gamete fusion and screens for new fusogens in different organisms. In addition, our virus retargeting system can be used in gene-therapy, viral-based oncolysis and to study viral-host interactions.