bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2: Proof of recombination between strains and emergence of possibly more virulent ones
Authors: Haddad Dania , John Sumi Elsa , Mohammad Anwar , Hammad Maha M , Hebbar Prashantha , Channanath Arshad , Nizam Rasheeba , Al-Qabandi Sarah , Madhoun Ashraf Al , Alshukry Abdullah , Ali Hamad , Thanaraj Thangavel Alphonse , Al-Mulla Fahd 
Published: November 2020

AbstractCOVID-19 is challenging healthcare preparedness, world economies, and livelihoods. The infection and death rates associated with this pandemic are strikingly variable in different countries. To elucidate this discrepancy, we analyzed 2431 early spread SARS-CoV-2 sequences from GISAID. We estimated continental-wise admixture proportions, assessed haplotype block estimation, and tested for the presence or absence of strains recombination. Herein, we identified 1010 unique missense mutations and seven different SARS-CoV-2 clusters. In samples from Asia, a small haplotype block was identified; whereas, samples from Europe and North America harbored large and different haplotype blocks with nonsynonymous variants. Variant frequency and linkage disequilibrium varied among continents, especially in North America. Recombination between different strains was only observed in North American and European sequences. Additionally, we structurally modeled the two most common mutations D614G and P314L which suggested that these linked mutations may enhance viral entry and stability. Overall, we propose that COVID-19 virulence may be more severe in Europe and North America due to coinfection with different SARS-CoV-2 strains leading to genomic recombination which might be challenging for current treatment regimens and vaccine development. Furthermore, our study provides a possible explanation for the more severe second wave of COVID-19 that many countries are currently experiencing presented as higher rates of infection and death.
Automatic Head and Neck Tumor Segmentation in PET/CT with Scale Attention Network
Authors: Yuan Yading 
Published: November 2020

AbstractAutomatic segmentation is an essential but challenging step for extracting quantitative imaging bio-markers for characterizing head and neck tumor in tumor detection, diagnosis, prognosis, treatment planning and assessment. The HEad and neCK TumOR Segmentation Challenge 2020 (HECKTOR 2020) provides a common platform for comparing different automatic algorithms for segmentation the primary gross target volume (GTV) in the oropharynx region on FDG-PET and CT images. We participated in the image segmentation challenge by developing a fully automatic segmentation network based on encoder-decoder architecture. In order to better integrate information across different scales, we proposed a dynamic scale attention mechanism that incorporates low-level details with high-level semantics from feature maps at different scales. Our framework was trained using the 201 challenge training cases provided by HECKTOR 2020, and achieved an average Dice Similarity Coefficient (DSC) of 0.7505 with cross validation. By testing on the 53 testing cases, our model achieved an average DSC, precision and recall of 0.7318, 0.7851, and 0.7319 respectively, which ranked our method in the fourth place in the challenge (id: deepX).
Modelling the positive testing rate of COVID-19 in South Africa Using A Semi-Parametric Smoother for Binomial Data
Authors: Owokotomo Olajumoke Evangelina , Manda Samuel , Kasim Adetayo , Claesen Jurgen , Shkedy Ziv , Reddy Tarylee 
Published: November 2020

AbstractThe current outbreak of COVID-19 is a major pandemic that has shaken up the entire world in a short time. South Africa has the highest number of COVID-19 cases in Africa and understanding the country’s disease trajectory is important for government policy makers to plan the optimal COVID-19 intervention strategy. The number of cases is highly correlated with the number of COVID-19 tests undertaking. Thus, current methods of understanding the COVID-19 transmission process in the country based only on the number of cases can be misleading. In light of this, we propose to estimate both the probability of positive cases per tests conducted (the positive testing rate) and the rate in which the positive testing rate changes over time (its derivative) using a flexible semi-parametric model.We applied the method to the observed positive testing rate in South Africa with data obtained from March 5th to September 2nd 2020. We found that the positive testing rate was declining from early March when the disease was first observed until early May where it kept on increasing. In the month of July 2020, the infection reached its peak then its started to decrease again indicating that the intervention strategy is effective. From mid August, 2020, the rate of change of the positive testing rate indicates that decline in the positive testing rate is slowing down, suggesting that a less effective intervention is currently implemented.
Neurobiological Underpinnings of Social-Emotional Impairments in Adolescents with Non-Suicidal Self-Injury
Authors: Lutz Nina , Villa Luca , Jassim Nazia , Goodyer Ian , Suckling John , Wilkinson Paul 
Published: November 2020

ObjectiveFew studies have investigated the neurological underpinnings of social-emotional processing among individuals with non-suicidal self-injury (NSSI), despite the range of interpersonal impairments associated with the behavior. This study aims to identify NSSI-specific patterns of resting state functional connectivity (RSFC) and neural activation during an emotional facial expression task.MethodsParticipants were currently depressed, antidepressant-free adolescents with and without lifetime history of NSSI. Left and right amygdala were specified as seed regions for RSFC analysis (n=43 NSSI, n=9 clinical controls). The emotional faces task presented participants with neutral, happy, and sad faces. Whole-brain analyses examined neural activation during the task, and groups were compared on post-scan ratings of facial emotional intensity (n=39 NSSI, n=9 clinical controls).ResultsGroups did not differ in RSFC analyses. Adolescents with NSSI showed attenuated neural activation to happy (versus neutral) faces in areas of the occipital lobe and cerebellum, and rated neutral and sad faces as more negative than clinical controls.ConclusionsWhile groups did not differ in baseline limbic connectivity, neurological and behavioral findings revealed NSSI-specific alterations in processing of social-emotional stimuli. Depressed adolescents with NSSI interpreted ambiguous or negative social stimuli more negatively than depressed controls, and had an attenuated neural response to positive social stimuli. This negative bias likely contributes to the myriad interpersonal difficulties associated with NSSI. Adolescents with NSSI may benefit from treatments which combat these negative social interpretations and improve control over emotional responses to interpersonal stress.
The iHealth-T2D study: Statistical analysis plan for a cluster randomised controlled trial with intensive family-based lifestyle modification programme to reduce type 2 diabetes risk amongst South Asians
Authors: Muilwijk Mirthe , Loh Marie , Mahmood Sara , Palaniswamy Saranya , Siddiqui Samreen , Silva Wnurinham , Frost Gary S. , Gage Heather M. , Jarvelin Marjo-Riitta , Rannan-Eliya Ravindra P. , Ahmed Sajjad , Jha Sujeet , Kasturiratne Anuradhani , Katulanda Prasad , Khawaja Khadija I. , Kooner Jaspal S. , Wickremasinghe Ananda R. , van Valkengoed Irene G.M. , Chambers John C. 
Published: November 2020

AbstractBackgroundSouth Asians are at high risk of type 2 diabetes (T2D). Lifestyle modification is effective at preventing T2D amongst South Asians, but the approaches to screening and intervention are limited by high-costs, poor scalability and thus low impact on T2D burden. An intensive family-based lifestyle modification programme for prevention of T2D was developed. The aim of the iHealth-T2D trial is to compare the effectiveness of this programme with usual care.MethodsThe iHealth-T2D trial is designed as a cluster randomised controlled trial (RCT) conducted at 120 locations across India, Pakistan, Sri Lanka and the UK. A total of 3,682 South Asian men and women with age between 40-70 years without T2D but at elevated risk for T2D [defined by central obesity (waist circumference ≥95cm in Sri Lanka, or ≥100cm in India, Pakistan and UK) and/or prediabetes (HbA1c ≥6.0%)] were included in the trial. Here we describe in detail the statistical analysis plan (SAP), which was finalised before outcomes were available to the investigators. The primary outcome will be evaluated after three years of follow-up after enrolment to the study, and is defined as T2D incidence in the intervention arm compared to usual care. Secondary outcomes are evaluated both after one and three years of follow-up and include biochemical measurements, anthropometric measurements, behavioural components and treatment compliance.DiscussionThe iHealth-T2D trial will provide evidence whether an intensive family-based lifestyle modification programme in South Asians who are at high risk for T2D is effective in the prevention of T2D. The data from the trial will be analysed according to this pre-specified SAP.Ethics and disseminationThe trial was approved by the international review board of each participating study site. Study findings will be disseminated through peer-reviewed publications and in conference presentations.Trial registrationEudraCT 2016-001350-18. Registered 14 April 2016https://www.hra.nhs.uk/planning-and-improving-research/application-summaries/research-summaries/ihealth-t2d/;ClinicalTrials.govNCT02949739. Registered 31 October 2016,https://clinicaltrials.gov/ct2/show/NCT02949739, First posted 31/10/2016.
Mobile consulting (mConsulting) as an option for accessing healthcare services for communities in remote rural areas and urban slums in low- and middle- income countries: A mixed methods study
Authors: Harris Bronwyn , Ajisola Motunrayo , Alam Raisa , Watkins Jocelyn Antsley , Arvanitis Theodoros N , Bakibinga Pauline , Chipwaza Beatrice , Choudhury Nazratun , Fayhun Olufunke , Kibe Peter , Omigbodun Akinyinka , Owoaje Eme , Pemba Senga , Potter Rachel , Rizvi Narjis , Sturt Jackie , Cave Jonathan , Iqbal Romaina , Kabaria Caroline , Kalolo Albino , Kyobutungi Catherine , Lilford Richard , Mashanya Titus , Ndegese Sylvester , Rahman Omar , Sayani Saleem , Yusuf Rita , Griffiths Frances 
Published: November 2020

AbstractObjectiveRemote or mobile consulting (mConsulting) is being promoted to strengthen health systems, deliver universal health coverage and facilitate safe clinical communication during COVID-19 and beyond. We explored whether mConsulting is a viable option for communities with minimal resources in low- and middle-income countries (LMICs).MethodsWe reviewed evidence published since 2018 about mConsulting in LMICs and undertook a scoping study (pre-COVID) in two rural settings (Pakistan, Tanzania) and five urban slums (Kenya, Nigeria, Bangladesh), using policy/document review, secondary analysis of survey data (from the urban sites), and thematic analysis of interviews/workshops with community members, healthcare workers, digital/telecommunications experts, mConsulting providers, local and national decision-makers. Project advisory groups guided the study in each country.ResultsWe reviewed five empirical studies and seven reviews, analysed data from 5,219 urban slum households and engaged with 419 stakeholders in rural and urban sites. Regulatory frameworks are available in each country. mConsulting services are operating through provider platforms (n=5-17) and, at community-level, some direct experience of mConsulting with healthcare workers using their own phones was reported - for emergencies, advice and care follow-up. Stakeholder willingness was high, provided challenges are addressed in technology, infrastructure, data security, confidentiality, acceptability and health system integration. mConsulting can reduce affordability barriers and facilitate care-seeking practices.ConclusionsThere are indications of readiness for mConsulting in communities with minimal resources. However, wider system strengthening is needed to bolster referrals, specialist services, laboratories and supply-chains to fully realise the continuity of care and responsiveness that mConsulting services offer, particularly during/beyond COVID-19.
Protective behaviours and secondary harms from non-pharmaceutical interventions during the COVID-19 epidemic in South Africa: a multisite prospective longitudinal study
Authors: Harling Guy , Gómez-Olivé Francesc Xavier , Tlouyamma Joseph , Mutevedzi Tinofa , Kabudula Chodziwadziwa Whiteson , Mahlako Ruth , Singh Urisha , Ohene-Kwofie Daniel , Buckland Rose , Ndagurwa Pedzisai , Gareta Dickman , Gunda Resign , Mngomezulu Thobeka , Nxumalo Siyabonga , Wong Emily B. , Kahn Kathleen , Siedner Mark J. , Maimela Eric , Tollman Stephen , Collinson Mark , Herbst Kobus 
Published: November 2020

ABSTRACTBackgroundIn March 2020 South Africa implemented strict non-pharmaceutical interventions (NPIs) to contain Covid-19. Over the subsequent five months NPIs were eased in stages according to national strategy. Covid-19 spread throughout the country heterogeneously, reaching rural areas by July and peaking in July-August. Data on the impact of NPI policies on social and economic wellbeing and access to healthcare is limited. We therefore analysed how rural residents of three South African provinces changed their behaviour during the first epidemic wave.MethodsThe South African Population Research Infrastructure Network (SAPRIN) nodes in Mpumalanga (Agincourt), KwaZulu-Natal (AHRI) and Limpopo (DIMAMO) provinces conducted longitudinal telephone surveys among randomly sampled households from rural and peri-urban surveillance populations every 2-3 weeks. Interviews included questions on: Covid-19 knowledge and behaviours; health and economic impact of NPIs; and mental health.Results2262 households completed 10,966 interviews between April and August 2020. By August, self-reported satisfaction with Covid-19 knowledge had risen from 48% to 85% and facemask use to over 95%. As selected NPIs were eased mobility increased, and economic losses and anxiety and depression symptoms fell. When Covid-19 cases spiked at one node in July, movement dropped rapidly, and missed daily medication rates doubled. Economic concerns and mental health symptoms were lower in households receiving a greater number of government-funded old-age pensions.ConclusionsSouth Africans reported complying with stringent Covid-19 NPIs despite the threat of substantial social, economic and health repercussions. Government-supported social welfare programmes appeared to buffer interruptions in income and healthcare access during local outbreaks. Epidemic control policies must be balanced against impacts on wellbeing in resource-limited settings and designed with parallel support systems where they threaten income and basic service access.
What is the Status of Elderly Abuse in India: A Systematic Review Protocol
Authors: Nagi Raunaq Singh , Sembiah Sembagamuthu , Chatterjee Anirban , Negi Rudresh 
Published: November 2020

AbstractElder abuse has been identified as one of the major problems of public health globally. Many types of mistreatment practices contribute to elder abuse. Also, the event has been known to occur in community as well as institutional settings such as hospitals and nursing homes. Elder abuse has been shown to affect the quality of life of individuals and increase premature mortality of the elderly. However, majority of elder abuse remains undocumented due to reasons such as fear and lack of awareness of one’s rights among others. Furthermore, the social construct of Indian societies makes the identification and acknowledgement of elder abuse challenging. Although, there have been studies and reports regarding the prevalence of elder abuse in India from various geographical regions, the strength of this evidence is unknown and a general view of prevalence of elder abuse in India is missing.We propose to undertake a systematic review and metanalysis of the published literature from India regarding the prevalence of elder abuse in any setting. For the purpose we will scan various indexing databases for identification of relevant studies and follow standard protocols and guidelines for formulation of evidence. The results of this study will give an entrusted overview of the status of elder abuse in India and aid policy-making initiatives and interventions to be directed accordingly.
Correlation of Body Mass Index (BMI), initial neutralizing antibodies (nAb), ABO group and kinetics of nAb and anti-nucleocapsid (NP) SARS-CoV-2 antibodies in convalescent plasma (CCP) donors – A longitudinal study with proposals for better quality of CCP collections
Authors: Wendel S , Fontão-Wendel R , Fachini R , Candelaria G , Scuracchio P , Achkar R , Brito MA , Reis LFL , Camargo A , Amano M , Machado RRG , Araujo D , Soares CP , Durigon E 
Published: November 2020

AbstractIntroductionA cohort of COVID-19 convalescent volunteers allowed the study of neutralizing (nAb) and ligand antibodies kinetics by providing sequential samples during a median of 100 days after onset of disease.Material and MethodsA cohort of previously RT-PCR+ve (detected by nasopharyngeal swab during the acute phase), male convalescent patients, all with mild symptoms, were enrolled on serial blood sample collection for evaluation of longitudinal nAb titers and anti-nucleocapsid (NP) antibodies (IgM, IgG and IgA). Nabs were detected by a cytopathic effect-based virus neutralization test (CPE-based VNT), carried out with SARS-CoV-2 (GenBank: MT350282)ResultsA total of 78 male volunteers provided 316 samples, spanning a total of 4820 days of study. Although only 25% of donors kept nAb titers ≥160, after a median of 100 days after the onset of disease, there was a high probability of sustaining nAB titers ≥160 in volunteers whose initial nAb titer was ≥1280, weight ≥ 90kg or BMI classified as overweight or obese, evidenced by Kaplan-Meier estimates and Cox hazard regression. There was no correlation between ABO group, ABO antibody titers and persistent high nAb titers. High IgG anti-NP (S/CO ≥5.0) is a good surrogate for detecting nAB ≥160, defined by ROC curve (sensitivity = 90.5%; CI95% 84.5-94.7%)ConclusionSelection of CCP donors for multiple collections based on initial high nAb titers (≥1280) or overweight/obese (BMI) provides a simple strategy to achieve higher quality in CCP programs. High IgG anti-NP levels can also be used as surrogate markers for high nAb screening.
Early Prediction of Hemodynamic Shock in the Intensive Care Units with Deep Learning on Thermal Videos
Authors: Vats Vanshika , Nagori Aditya , Singh Pradeep , Dutt Raman , Bandhey Harsh , Wason Mahika , Lodha Rakesh , Sethi Tavpritesh 
Published: November 2020

AbstractShock is one of the major killers in Intensive Care Units and early interventions can potentially reverse it. In this study, we advance a non-contact thermal imaging modality to continuous monitoring of hemodynamic shock working on 103,936 frames from 406 videos recorded longitudinally upon 22 patients. Deep learning was used to preprocess and extract the Center-to-Peripheral Difference (CPD) in temperature values from the videos. This time-series data along with heart rate was finally analyzed using Long-Short Term Memory models to predict the shock status up to the next 6 hours. Our models achieved the best area under the receiver operating characteristics curve of 0.81 ± 0.06 and area under the precision-recall curve of 0.78 ± 0.05 at 5 hours, providing sufficient time to stabilize the patient. Our approach, thus, provides a reliable shock prediction using an automated decision pipeline, that can provide better care and save lives.
Estimating the cumulative incidence of SARS-CoV-2 infection and the infection fatality ratio in light of waning antibodies
Authors: Shioda Kayoko , Lau Max SY , Kraay Alicia NM , Nelson Kristin N , Siegler Aaron J , Sullivan Patrick S , Collins Matthew H , Weitz Joshua S , Lopman Benjamin A 
Published: November 2020

AbstractBackgroundSerology tests can identify previous infections and facilitate estimation of the number of total infections. However, immunoglobulins targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported to wane below the detectable level of serological assays. We estimate the cumulative incidence of SARS-CoV-2 infection from serology studies, accounting for expected levels of antibody acquisition (seroconversion) and waning (seroreversion), and apply this framework using data from New York City (NYC) and Connecticut.MethodsWe estimated time from seroconversion to seroreversion and infection fatality ratio (IFR) using mortality data from March-October 2020 and population-level cross-sectional seroprevalence data from April-August 2020 in NYC and Connecticut. We then estimated the daily seroprevalence and cumulative incidence of SARS-CoV-2 infection.FindingsThe estimated average time from seroconversion to seroreversion was 3-4 months. The estimated IFR was 1.1% (95% credible interval: 1.0-1.2%) in NYC and 1.4% (1.1-1.7%) in Connecticut. The estimated daily seroprevalence declined after a peak in the spring. The estimated cumulative incidence reached 26.8% (24.2-29.7%) and 8.8% (7.1-11.3%) at the end of September in NYC and Connecticut, higher than maximum seroprevalence measures (22.1% and 6.1%), respectively.InterpretationThe cumulative incidence of SARS-CoV-2 infection is underestimated using cross-sectional serology data without adjustment for waning antibodies. Our approach can help quantify the magnitude of underestimation and adjust estimates for waning antibodies.FundingThis study was supported by the US National Science Foundation and the National Institute of Allergy and Infectious Diseases.