bluuebunny/crossref_metadata_2025_split huggingface dataset:
Medical laboratory waste generation rate, management practices and associated factors in Addis Ababa, Ethiopia
Authors: Endris Salem , Tamir Zemenu , Sisay Abay 
Published: August 2021

AbstractBackgroundBiomedical wastes (BMW) generated from medical laboratories are hazardous and can be deleterious to humans and the environment. Highly infectious types of biomedical wastes are commonly generated at an unacceptably high rate from health laboratories of developing countries with a poor management system like Ethiopia. This study was aimed to evaluate the generation rate of biomedical wastes, management practices and associated factors among public healthcare medical laboratories in Addis Ababa, Ethiopia.Materials and methodsHealth institution based cross-sectional study was conducted from July 13 to September 25, 2020 in 6 hospital laboratories and 20 health center laboratories in Addis Ababa, Ethiopia.Data on socio-demographic characteristics, knowledge and practice of biomedical wast managment of the health facilities, Biomedical waste generation rate were collected using data collection tools. Data were managed using SPSS version 20 software. Descriptive statistcs,Pearson correlation, linear and logistic regression analysis were computed to identify indepedent predictors of the dependent variable. Odds ratio with 95% confidence interval was used to determine the strength of association.ResultsThe finding revealed that the mean ± SD of the daily generation rate of biomedical wastes was 4.9 ± 3.13 kg/day per medical laboratory. Nineteen (74.3%) medical laboratories had a proper practice of biomedical waste management which is significantly associated with knowledge of professsionals on biomedical waste management policies and guidelines, availability of separate financial sources for biomedical waste management and training level of professionals.ConclusionThe study showed high generation of biomedical waste from medical laboratories in public healthcare of Addis Ababa,Ethiopia. Near two-thirds of health facilities had a proper practice of waste segregation, collection, storage, and treatment of biomedical wastes generated from their laboratory. However, there was a poor practice of transportation and disposal. Hence, due attention and practicing as per the current national guidelines of biomedical waste management is recoomended.
Development and validation of a deep learning algorithm based on fundus photographs for estimating the CAIDE dementia risk score
Authors: Hua Rong , Xiong Jianhao , Li Gail , Zhu Yidan , Ge Zongyuan , Ma Yanjun , Fu Meng , Li Chenglong , Wang Bin , Dong Li , Zhao Xin , Ma Zhiqiang , Chen Jili , He Chao , Wang Zhaohui , Wei Wenbin , Wang Fei , Gao Xiangyang , Chen Yuzhong , Zeng Qiang , Xie Wuxiang 
Published: August 2021

AbstractThe Cardiovascular Risk Factors, Aging, and Incidence of Dementia (CAIDE) dementia risk score is a recognized tool for dementia risk stratification. However, its application is limited due to the requirements for multidimensional information and fasting blood draw. Consequently, effective, convenient and noninvasive tool for screening individuals with high dementia risk in large population-based settings is urgently needed. A deep learning algorithm based on fundus photographs for estimating the CAIDE dementia risk score was developed and internally validated by a medical check-up dataset included 271,864 participants in 19 province-level administrative regions of China, and externally validated based on an independent dataset included 20,690 check-up participants in Beijing. The performance for identifying individuals with high dementia risk (CAIDE dementia risk score ≥10 points) was evaluated by area under the receiver operating curve (AUC) with 95% confidence interval (CI). We found that the algorithm achieved an AUC of 0.944 (95% CI 0.939–0.950) in the internal validation group and 0.926 (95% CI, 0.913–0.939) in the external group, respectively. Besides, the estimated CAIDE dementia risk score derived from the algorithm was significantly associated with both comprehensive cognitive function and specific cognitive domains. In conclusion, this algorithm trained via fundus photographs could well identify individuals with high dementia risk in a population setting. Therefore, it has potential to be utilized as a noninvasive and more expedient method for dementia risk stratification. It might also be adopted in dementia clinical trials, incorporated as inclusion criteria to efficiently select eligible participants.
Avoiding bias in Mendelian randomization when stratifying on a collider
Authors: Coscia Claudia , Gill Dipender , Benítez Raquel , Pérez Teresa , Malats Núria , Burgess Stephen 
Published: August 2021

AbstractBackgroundMendelian randomization (MR) uses genetic variants as instrumental variables to investigate the causal effect of a risk factor on an outcome. A collider is a variable influenced by two or more other variables. Naive calculation of MR estimates in strata of the population defined by a variable affected by the risk factor can result in collider bias.MethodsWe propose an approach that allows MR estimation in strata of the population while avoiding collider bias. This approach constructs a new variable, the residual collider, as the residual from regression of the collider on the genetic instrument, and then calculates causal estimates in strata defined by quantiles of the residual collider. Estimates stratified on the residual collider will typically have an equivalent interpretation to estimates stratified on the collider, but they are not subject to collider bias. We apply the approach in several simulation scenarios considering different characteristics of the collider variable and strengths of the instrument. We then apply the proposed approach to investigate the causal effect of smoking on bladder cancer in strata of the population defined by bodyweight.ResultsThe new approach generated unbiased estimates in all the simulation settings. In the applied example, we observed a trend in the stratum-specific MR estimates at different bodyweight levels that suggested stronger effects of smoking on bladder cancer among individuals with lower bodyweight.ConclusionsThe proposed approach can be used to perform MR studying heterogeneity among subgroups of the population while avoiding collider bias.
Dynamics of the Third wave, modelling COVID-19 pandemic with an outlook towards India
Authors: Basak Ayanava , Rahaman Sayanur , Guha Abhishek , Sanyal Tanmay 
Published: August 2021

AbstractSince 2020, the COVID-19 pandemic has devastated human civilization throughout the earth. The pandemic is returning in different waves because of constant changes in the genetic components of the virus. Had we been able to predict the nature and timing of these waves earlier, numerous lives could, in essence, have been saved. It is evident that the situation has spiraled out of control in several countries for want of proper preventive measures. In this article, we described a comprehensive mathematical approach to understand the nature of the pandemic waves. Also, we determined the probable timing of the third wave that will help the concerned government(s) to take the necessary steps to better prepare for the unforeseen situation.
Inexpensive workflow for simultaneous monitoring of HIV viral load and detection of SARS-CoV-2 infection
Authors: Gulati Gaurav K , Panpradist Nuttada , Stewart Samuel W A , Beck Ingrid A , Boyce Ceejay , Oreskovic Amy K , García-Morales Claudia , Avila-Ríos Santiago , Han Peter D. , Reyes-Terán Gustavo , Starita Lea M. , Frenkel Lisa M , Lutz Barry R , Lai James J 
Published: August 2021

AbstractBackgroundCOVID-19 pandemic interrupted routine care for individuals living with HIV, putting them at risk of becoming virologically unsuppressed and ill. Often they are at high risk for exposure to SARS-CoV-2 infection and severe disease once infected. For this population, it is urgent to closely monitor HIV plasma viral load (VL) and screen for SARS-COV-2 infection.MethodWe have developed a non-proprietary method to isolate RNA from plasma, nasal secretions (NS), or both. HIV, SARS-CoV-2, and human RP targets in extracted RNA are then RT-qPCR to estimate the VL and classify HIV/SARS-CoV-2 status (i.e., HIV as VL failure or suppressed; SARS-CoV-2 as positive, presumptive positive, negative, or indeterminate). We evaluated this workflow on 133 clinical specimens: 40 plasma specimens (30 HIV-seropositive), 67 NS specimens (31 SARS-CoV-2-positive), and 26 pooled plasma/NS specimens (26 HIV-positive with 10 SARS-CoV-2-positive), and compared the results obtained using the in-house extraction to those using a commercial extraction kit.ResultsIn-house extraction had a detection limit of 200-copies/mL for HIV and 100-copies/mL for SARS-CoV-2. In-house and commercial methods yielded positively correlated HIV VL (R2: 0.98 for contrived samples; 0.81 for seropositive plasma). SARS-CoV-2 detection had 100% concordant classifications in contrived samples, and in clinical NS extracted by in-house method, excluding indeterminate results, was 95% concordant (25 positives, 6 presumptive positives, and 31 negatives) to those using the commercial method. Analysis of pooled plasma/NS showed R2of 0.91 (contrived samples) and 0.71 (clinical specimens) for HIV VL correlations obtained by both extraction methods, while SARS-CoV-2 detection showed 100% concordance in contrived and clinical specimens.InterpretationOur low-cost workflow for molecular testing of HIV and SARS-CoV-2 could serve as an alternative to current standard assays for laboratories in low-resource settings.
Vaccine Effectiveness against Referral to Hospital and Severe Lung Injury Associated with COVID-19: A Case-Control Study in St. Petersburg, Russia
Authors: Barchuk Anton , Cherkashin Mikhail , Bulina Anna , Berezina Natalia , Rakova Tatyana , Kuplevatskaya Darya , Stanevich Oksana , Skougarevskiy Dmitriy , Okhotin Artemiy 
Published: August 2021

BackgroundResults of a randomised trial showed the safety and efficacy of Gam-COVID-Vac against COVID-19. However, compared to other vaccines used across the globe, the real-world data on the effectiveness of Gam-COVID-Vac, especially against the disease caused by Delta variant of concern, was not available. We aimed to assess the effectiveness of vaccination mainly conducted with Gam-COVID-Vac in St. Petersburg, Russia.MethodsWe designed a case-control study to assess the vaccine effectiveness (VE) against lung injury and referral to hospital. Self-reported vaccination status was collected for individuals with confirmed SARS-CoV-2 infection who were referred for initial low-dose computed tomography triage in two outpatient centres in July 3 – August 9, 2021 in St. Petersburg, Russia. We used logistic regression models to estimate the adjusted (for age, sex, and triage centre) VE for complete (>14 days after the second dose) vaccination. We estimated the VE against referral for hospital admission, COVID-19-related lung injury assessed with LDCT, and decline in oxygen saturation.ResultsIn the final analysis, 13,893 patients were included, 1,291 (9.3%) of patients met our criteria for complete vaccination status, and 495 (3.6%) were referred to hospital. In the primary analysis, the adjusted VE against referral to hospital was 81% (95% CI: 68–88) for complete vaccination. The VE against referral to hospital was more pronounced in women (84%, 95% CI: 66–92) compared to men (76%, 95% CI: 51–88). Vaccine protective effect increased with increasing lung injury categories, from 54% (95% CI: 48–60) against any sign of lung injury to 76% (95% CI: 59–86) against more than 50% lung involvement. A sharp increase was observed in the probability of hospital admission with age for non-vaccinated patients in relation to an almost flat relationship for the completely vaccinated group.ConclusionsCOVID-19 vaccination was effective against referral to hospital in patients with symptomatic SARS-CoV-2 infection in St. Petersburg, Russia. This protection is probably mediated through VE against lung injury associated with COVID-19.
Measuring the digital divide among people with Severe Mental Ill Health using the Essential Digital Skills framework
Authors: Panagiotis Spanakis , Ruth Wadman , Lauren Walker , Paul Heron , Alice Mathers , John Baker , Gordon Johnston , Simon Gilbody , Emily Peckham 
Published: August 2021

AbstractAimsAmidst the vast digitalisation of health and other services during the pandemic, people with no digital skills are at risk for digital exclusion. This risk might not abide by the end of the pandemic. This paper seeks to understand whether people with severe mental ill health (SMI) have the necessary digital skills to adapt to these changes and avoid digital exclusion.Methods249 adults with SMI across England completed a survey online or offline. They provided information on their digital skills based on the Essential Digital Skills (EDS) framework, sociodemographic information, and digital access. This is the first time the EDS is benchmarked in people with SMI.Results42.2% had no Foundation Skills and 46.2% lacked skills for daily life (lacking Foundation or Life Skills). 23.0% of those working lacked skills for professional life (lacking Foundation or Work Skills). The most commonly missing skills were handling passwords and using the device settings (Foundation Skills) and online problem solving (Skills for Life). People were interested in learning more about approximately half of the skills they did not have. People were more likely to lack Foundation Skills if they were older, not in employment, had a psychosis-spectrum disorder, or had no Internet access at home.ConclusionA significant portion of people with SMI lacked Foundation Skills in this objective and benchmarked survey. This points to a high risk for digital exclusion and the need for focused policy and tailored health sector support, to ensure people retain access to key services and develop digital skills and confidence. To our knowledge this is the first time this has been described using the Essential Digital Skills (EDS) framework. Services, including the NHS, need to be aware and mitigate the risks.
Communicating risk to patients: developing an “Efficiency Index” for diagnostic and screening tests
Authors: Larner Andrew J 
Published: August 2021

AbstractDiagnostic and screening tests may have risks such as misdiagnosis, as well as the potential benefits of correct diagnosis. Effective communication of this risk to both clinicians and patients can be problematic. The purpose of this study was to develop a metric called the “efficiency index” (EI), defined as the ratio of test accuracy and inaccuracy, or the number needed to misdiagnose divided by number needed to diagnose. This was compared with a previously described “likelihood to be diagnosed or misdiagnosed” (LDM), also based on “numbers needed” metrics. Datasets from prospective pragmatic test accuracy studies examining four brief cognitive screening instruments (Mini-Mental State Examination; Montreal Cognitive Assessment; Mini-Addenbrooke’s Cognitive Examination, MACE; and Free-Cog) were analysed to calculate values for EI and LDM, and to examine their variation with test cut-off for MACE. EI values were also calculated using a modification of McGee’s heuristic for the simplification of likelihood ratios to estimate percentage change in diagnostic probability. The findings indicate that EI is easier to calculate than LDM and, unlike LDM, may be classified either qualitatively or quantitatively in a manner similar to likelihood ratios. EI shows the utility or inutility of diagnostic and screening tests, illustrating the inevitable trade-off between diagnosis and misdiagnosis. It may be a useful metric to communicate risk in a way that is easily intelligible for both clinicians and patients.
Association of COVID-19 vaccines ChAdOx1 and BNT162b2 with major venous, arterial, or thrombocytopenic events: whole population cohort study in 46 million adults in England
Authors:   CVD-COVID-UK consortium,   Writing committee, Whiteley William N , Ip Samantha , Cooper Jennifer A , Bolton Thomas , Keene Spencer , Walker Venexia , Denholm Rachel , Akbari Ashley , Omigie Efosa , Hollings Sam , Di Angelantonio Emanuele , Denaxas Spiros , Wood Angela , Sterne Jonathan A C , Sudlow Cathie 
Published: August 2021

ABSTRACTBackgroundThromboses in unusual locations after the COVID-19 vaccine ChAdOx1-S have been reported. Better understanding of population-level thrombotic risks after COVID-19 vaccination is needed.MethodsWe analysed linked electronic health records from adults living in England, from 8th December 2020 to 18th March 2021. We estimated incidence rates and hazard ratios (HRs) for major arterial, venous and thrombocytopenic outcomes 1-28 and >28 days after first vaccination dose for ChAdOx1-S and BNT162b2 vaccines. Analyses were performed separately for ages <70 and ≥70 years, and adjusted for age, sex, comorbidities, and social and demographic factors.ResultsOf 46,162,942 adults, 21,193,814 (46%) had their first vaccination during follow-up. Adjusted HRs 1-28 days after ChAdOx1-S, compared with unvaccinated rates, at ages <70 and ≥70 respectively, were 0.97 (95% CI: 0.90-1.05) and 0.58 (0.53–0.63) for venous thromboses, and 0.90 (0.86-0.95) and 0.76 (0.73-0.79) for arterial thromboses. Corresponding HRs for BNT162b2 were 0.81 (0.74–0.88) and 0.57 (0.53–0.62) for venous thromboses, and 0.94 (0.90-0.99) and 0.72 (0.70-0.75) for arterial thromboses. HRs for thrombotic events were higher at younger ages for venous thromboses after ChAdOx1-S, and for arterial thromboses after both vaccines.Rates of intracranial venous thrombosis (ICVT) and thrombocytopenia in adults aged <70 years were higher 1-28 days after ChAdOx1-S (adjusted HRs 2.27, 95% CI:1.33– 3.88 and 1.71, 1.35–2.16 respectively), but not after BNT162b2 (0.59, 0.24–1.45 and 1.00, 0.75–1.34) compared with unvaccinated. The corresponding absolute excess risks of ICVT 1-28 days after ChAdOx1-S were 0.9–3 per million, varying by age and sex.ConclusionsIncreases in ICVT and thrombocytopenia after ChAdOx1-S vaccination in adults aged <70 years were small compared with its effect in reducing COVID-19 morbidity and mortality, although more precise estimates for adults <40 years are needed. For people aged ≥70 years, rates of arterial or venous thrombotic, events were generally lower after either vaccine.
White Matter Abnormalities in Body Integrity Dysphoria
Authors: Saetta Gianluca , Ruddy Kathy , Zapparoli Laura , Gandola Martina , Salvato Gerardo , Sberna Maurizio , Bottini Gabriella , Brugger Peter , Lenggenhager Bigna 
Published: August 2021

Abstract“Body integrity dysphoria” (BID) is a severe condition affecting non-psychotic individuals where a limb may be experienced as not being part of the body, despite normal anatomical development and intact sensorimotor functions. Limb amputation is desired for restoring their own identity. We previously demonstrated altered brain structural (gray matter) and functional connectivity in 16 men with a long-lasting and exclusive desire for left leg amputation. Here we aimed to identify in the same sample altered patterns of white matter structural connectivity. Fractional anisotropy (FA), derived from Diffusion Tensor Imaging data, was considered as a measure of structural connectivity. Results showed reduced structural connectivity of: i) the right superior parietal lobule (rSPL) with the right cuneus, superior occipital and posterior cingulate gyri ii) the pars orbitalis of the right middle frontal gyrus (rMFGOrb) with the putamen iii) the left middle temporal gyrus (lMTG) with the pars triangularis of the left inferior frontal gyrus. Increased connectivity was observed between the right paracentral lobule (rPLC) and the right caudate nucleus. By using a complementary method of investigation, we confirmed and extended previous results showing alterations in areas tuned to the processing of the sensorimotor representations of the affected leg (rPCL), and to higher-order components of bodily representation such as the body image (rSPL). Alongside this network for bodily awareness, other networks such as the limbic (rMFGOrb) and the mirror (lMTG) systems showed structural alterations as well. These findings consolidate current understanding of the neural correlates of BID, which might in turn guide diagnostics and rehabilitative treatments.
Integrated immune networks in SARS-CoV-2 infected pregnant women reveal differential NK cell and unconventional T cell activation
Authors: Habel Jennifer R , Chua Brendon Y , Kedzierski Lukasz , Selva Kevin J , Damelang Timon , Haycroft Ebene R , Nguyen Thi HO , Koay Hui-Fern , Nicholson Suellen , McQuilten Hayley , Jia Xiaoxiao , Allen Lilith F , Hensen Luca , Zhang Wuji , van de Sandt Carolien E , Neil Jessica A , Amanat Fatima , Krammer Florian , Wragg Kathleen , Juno Jennifer A , Wheatley Adam K , Tan Hyon-Xhi , Pell Gabrielle , Audsley Jennifer , Thevarajan Irani , Denholm Justin , Subbarao Kanta , Godfrey Dale I , Cheng Allen C , Tong Steven YC , Bond Katherine , Williamson Deborah A , James Fiona , Holmes Natasha E , Smibert Olivia C , Trubiano Jason A , Gordon Claire L , Chung Amy W , Whitehead Clare L , Kent Stephen J , Lappas Martha , Rowntree Louise C , Kedzierska Katherine 
Published: August 2021

ABSTRACTAlthough pregnancy poses a greater risk for severe COVID-19, the underlying immunological changes associated with SARS-CoV-2 infection during pregnancy are poorly understood. We defined immune responses to SARS-CoV-2 in pregnant and non-pregnant women during acute and convalescent COVID-19 up to 258 days post symptom onset, quantifying 217 immunological parameters. Additionally, matched maternal and cord blood were collected from COVID-19 convalescent pregnancies. Although serological responses to SARS-CoV-2 were similar in pregnant and non-pregnant women, cellular immune analyses revealed marked differences in key NK cell and unconventional T cell responses during COVID-19 in pregnant women. While NK cells, γδ T cells and MAIT cells displayed pre-activated phenotypes in healthy pregnant women when compared to non-pregnant age-matched women, activation profiles of these pre-activated NK and unconventional T cells remained unchanged at acute and convalescent COVID-19 in pregnancy. Conversely, activation dynamics of NK and unconventional T cells were prototypical in non-pregnant women in COVID-19. In contrast, activation of αβ CD4+and CD8+T cells, T follicular helper cells and antibody-secreting cells was similar in pregnant and non-pregnant women with COVID-19. Elevated levels of IL-1β, IFN-γ, IL-8, IL-18 and IL-33 were also found in pregnant women in their healthy state, and these cytokine levels remained elevated during acute and convalescent COVID-19. Collectively, our study provides the first comprehensive map of longitudinal immunological responses to SARS-CoV-2 infection in pregnant women, providing insights into patient management and education during COVID-19 pregnancy.