bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the transparency of reporting in two-sample summary data Mendelian randomization studies
Authors: Woolf Benjamin , Cara Nina Di , Moreno-Stokoe Christopher , Skrivankova Veronika , Drax Katie , Higgins Julian P.T. , Hemani Gibran , Munafò Marcus R. , Smith George Davey , Yarmolinsky James , Richmond Rebecca C. 
Published: October 2021

AbstractBackgroundTwo-sample Mendelian randomization (2SMR) is an increasingly popular epidemiological method that uses genetic variants as instruments for making causal inferences. Clear reporting of methods employed in such studies is important for evaluating their underlying quality. However, the quality of methodological reporting of 2SMR studies is currently unclear.ObjectivesWe aimed to assess the reporting quality of studies that used MR-Base, one of the most popular platforms for implementing 2SMR analysis.MethodsWe created a bespoke reporting checklist to evaluate reporting quality of 2SMR studies. We then searched Web of Science Core Collection, PsycInfo, MEDLINE, EMBASE and Google Scholar citations of the MR-Base descriptor paper to identify published MR studies that used MR-Base for any component of the MR analysis. Study screening and data extraction were performed by at least two independent reviewers.Results87 studies were included in the primary analysis. Reporting quality was generally poor across studies with a mean of 53% (SD = 14%) of items reported in each study. Many items required for evaluating the validity of key assumptions made in MR were poorly reported: only 44% of studies provided sufficient details for assessing if the genetic variant associates with the exposure (‘relevance’ assumption), 31% for assessing if there are any variant-outcome confounders (‘independence’ assumption), 89% for the assessing if the variant causes the outcome independently of the exposure (‘exclusion restriction’ assumption), and 32% for assumptions of falsification tests. We did not find evidence of a change in reporting quality over time or a difference in reporting quality between studies that used MR-Base and a random sample of MR studies that did not use this platform.DiscussionThe quality of reporting of two-sample Mendelian randomization studies in our sample was generally poor. Journals and researchers should implement the STROBE-MR guidelines to improve reporting quality.Other: FundingESRC, CRUK, MRC, John Climax Benevolent Fund, University of Bristol, and the Wellcome Trust. Registration: This study pre-registered on the OSF, and the protocol can be found at DOI 10.17605/OSF.IO/NFM27
Efficacy and safety of a third SARS-CoV-2 vaccination in multiple sclerosis vaccine non-responders
Authors: König Marton , Torgauten Hilde Marie , Øverås Mathias Herstad , Chopra Adity , Rudjord Lorentzen Åslaug , Tran The Trung , Mjaaland Siri , Aaberge Ingeborg Sundsvalen , Myhr Kjell-Morten , Wergeland Stig , Berge Tone , Harbo Hanne Flinstad , Fredvik Torkildsen Øivind , Holmøy Trygve , Celius Elisabeth Gulowsen , Munthe Ludvig Andre , Vaage John Torgils , Lund-Johansen Fridtjof , Nygaard Gro Owren 
Published: October 2021

AbstractImportanceVaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to protect against coronavirus disease of 2019 (COVID-19) is recommended for patients with multiple sclerosis (pwMS). However, approximately 80% of all pwMS treated with anti-CD20 therapy (rituximab, ocrelizumab) or fingolimod have low or absent humoral immunity after vaccination with two doses of SARS-CoV-2 mRNA vaccines. The efficacy and safety of a third vaccine dose in this group is largely unknown.ObjectiveTo characterize the humoral immunogenicity and the safety of a third dose of mRNA-COVID-19 vaccine in anti-CD20-or fingolimod-treated pwMS with low or absent humoral immunity (i.e., anti-SARS-CoV-2 IgG <70 arbitrary units (AU) and <5 AU, respectively) after two vaccinations.Design, setting and participants130 anti-CD20- or fingolimod-treated pwMS with low or absent humoral immunity despite full vaccination against SARS-CoV-2, received a third dose of SARS-CoV-2 mRNA vaccine. Humoral immunity (i.e., antibody response against SARS-CoV-2) and the frequency and characteristics of side-effects were analyzed in all participants.ExposuresA third vaccine dose against SARS-CoV-2 with BNT162b2- or mRNA-1273-COVID-19 vaccine.Main outcomes and measuresPatient- and treatment-specific variables were acquired using a digital questionnaire, the Norwegian Immunization Registry and hospital journals. Humoral immunity was assessed by measuring SARS-CoV-2 SPIKE receptor-binding domain (RBD) IgG response. Low/absent humoral immunity was assumed in cases of AU<70 after anti-SPIKE protein-based serology 3-5 weeks after revaccination.ResultsA third dose of SARS-CoV-2 mRNA vaccine increased anti-SARS-CoV-2 SPIKE RBD IgG levels significantly. The proportion of patients with assumed protective humoral immunity (anti-SARS-CoV-2 SPIKE RBD IgG > 70 AU) were 25% among patients using anti-CD20 therapy and 7% among those treated with fingolimod. No adverse events were registered during the study period.Conclusion and relevanceA third dose of mRNA-COVID-19 vaccine was associated with significantly increased levels of anti-SARS-CoV-2 SPIKE RBD IgG, – and hence assumed protective humoral immunity - in anti-CD20- or fingolimod-treated pwMS with low or absent humoral immunity despite full vaccination. The effect of a third vaccine dose was limited and more prominent among those treated with anti-CD20 therapy.
VIKING II, a Worldwide Observational Cohort of Volunteers with Northern Isles Ancestry
Authors: Kerr Shona M. , Edwards Rachel , Buchanan David , Dean John , Miedzybrodzka Zosia , Wilson James F. 
Published: October 2021

AbstractIntroductionThe purpose of VIKING II is to create an observational cohort of volunteers with ancestry from the Northern Isles of Scotland, primarily for identifying genetic variants influencing disease. The new online protocol is separate to, but follows on from, earlier genetic epidemiological clinic-based studies in the isolated populations of Orkney and Shetland. These populations are favourable for the study of rarer genetic variants due to genetic drift, the large number of relatives, and availability of pedigree information.Methods and AnalysisOnline methods are being used to recruit ∼4,000 people who have Northern Isles ancestry, living anywhere in the world. The option for participants to have actionable genetic results returned is offered. Broad consent will be taken electronically. Data will be collected at baseline through an online questionnaire and longitudinally through linkage to NHS data in the electronic health record. The questionnaire collects a variety of phenotypes including personal and family health. DNA will be extracted from saliva samples then genome-wide genotyped and exome sequenced. VIKING II aims to capitalise on the special features of the Northern Isles populations to create a research cohort that will facilitate the analysis of genetic variants associated with a broad range of traits and disease endpoints.Ethics and DisseminationThe South East Scotland Research Ethics Committee gave the study a favourable opinion. VIKING II is sponsored by the University of Edinburgh and NHS Lothian. Summary research findings will be disseminated to participants and funding bodies, presented at conferences and reported in peer-reviewed publications.Article SummaryStrengths and limitations of this studyDetailed data and biological sample collection of research volunteers with unique ancestry.Consent for access to routinely collected clinical EHR data and for future re-contact, providing a longitudinal component.Optional consent for return of actionable genetic results.4,000 participants is a relatively small number for certain types of genetic analyses, so the cohort is underpowered on its own, in some study designs.Resources to maintain the cohort, and to store data and DNA samples, are significant, with sustainability dependent on infrastructure support and continued funding.
Extent of cord pathology in the lumbosacral enlargement in non-traumatic versus traumatic spinal cord injury
Authors: David Gergely , Vallotton Kevin , Hupp Markus , Curt Armin , Freund Patrick , Seif Maryam 
Published: October 2021

AbstractObjectivesThis study compares remote neurodegenerative changes caudal to a cervical injury in degenerative cervical myelopathy (DCM) (i.e. non-traumatic) and incomplete traumatic spinal cord injury (tSCI) patients, using MRI-based tissue area measurements and diffusion tensor imaging (DTI).MethodsEighteen mild to moderate DCM patients with sensory impairments (mean mJOA score: 16.2), 14 incomplete tetraplegic tSCI patients (AIS C&D), and 20 healthy controls were recruited. All participants received DTI and T2*-weighted scans in the lumbosacral enlargement (caudal to injury) and at C2/C3 (rostral to injury). MRI readouts included DTI metrics in the white matter (WM) columns and cross-sectional WM and gray matter area. One-way ANOVA with Tukey post-hoc comparison (p<0.05) was used to assess group differences.ResultsIn the lumbosacral enlargement, compared to DCM, tSCI patients exhibited decreased fractional anisotropy in the lateral (tSCI vs. DCM, −11.9%, p=0.007) and ventral WM column (−8.0%, p=0.021), and showed trend toward lower values in the dorsal column (−8.9%, p=0.068). At C2/C3, no differences in DTI metrics were observed between DCM and tSCI, but compared to controls, fractional anisotropy was lower in both groups in the dorsal (DCM vs. controls, −7.9%, p=0.024; tSCI vs. controls, −10.0%, p=0.007) and in the lateral column (DCM: −6.2%, p=0.039; tSCI: −13.3%, p<0.001). WM areas were not different between patient groups, but were significantly lower compared to healthy controls both in the lumbosacral enlargement (DCM: −16.9%, p<0.001; tSCI, −10.5%, p=0.043) and at C2/C3 (DCM: −16.0%, p<0.001; tSCI: −18.1%, p<0.001).ConclusionIn conclusion, mild to moderate DCM and incomplete tSCI lead to similar degree of degeneration of the dorsal and lateral columns at C2/C3, but tSCI results in more widespread white matter damage in the lumbosacral enlargement. These remote changes are likely to contribute to the impairment and recovery of the patients. Diffusion MRI is a sensitive tool to assess remote pathological changes in DCM and tSCI patients.
Signed Distance Correlation (SiDCo): A network analysis application of distance correlation for identifying metabolic networks disrupted in Dementia with Lewy Bodies
Authors: Čuperlović-Culf Miroslava , Yilmaz Ali , Stewart David , Surendra Anuradha , Akyol Sumeyya , Vishweswaraiah Sangeetha , Shao Xiaojian , Alecu Irina , Nguyen-Tran Thao , McGuinness Bernadette , Passmore Peter , Kehoe Patrick G. , Maddens Michael E. , Green Brian D. , Graham Stewart F. , Bennett Steffany A.L. 
Published: October 2021

AbstractMotivationIdentifying pathological metabolic changes in complex disease such as Dementia with Lewy Bodies (DLB) requires a deep understanding of functional modifications in the context of metabolic networks. Network determination and analysis from metabolomics and lipidomics data remains a major challenge due to sparse experimental coverage, a variety of different functional relationships between metabolites and lipids, and only sporadically described reaction networks.ResultsDistance correlation, measuring linear and non-linear dependences between variables as well as correlation between vectors of different lengths, e.g. different sample sizes, is presented as an approach for data-driven metabolic network development. Additionally, novel approaches for the analysis of changes in pair-wise correlation as well as overall correlations for metabolites in different conditions are introduced and demonstrated on DLB data. Distance correlation and signed distance correlation was utilized to determine metabolic network in brain in DLB patients and matching controls and results for the two groups are compared in order to identify metabolites with the largest functional change in their network in the disease state. Novel correlation network analysis showed alterations in the metabolic network in DLB brains relative to the controls, with the largest differences observed in O-phosphocholine, fructose, propylene-glycol, pantothenate, thereby providing novel insights into DLB pathology only made apparent through network investigation with presented methods.
Co-administration of treatment for rifampicin-resistant tuberculosis and chronic hepatitis C virus infection: a TBnet and ESGMYC study
Authors: Tunesi Simone , Dû Damien Le , Gualano Gina , Millet Joan-Pau , Skrahin Aliaksandr , Bothamley Graham , Casas Xavier , Goletti Delia , Lange Christoph , Musso Maria , Palmieri Fabrizio , Pourcher Valérie , Rioux Christophe , Skrahina Alena , Veziris Nicolas , Viatushka Dzmitry , Jachym-Fréchet Mathilde , Guglielmetti Lorenzo ,   for the TBnet,   the ESGMYC,   the French MDR-TB Group
Published: October 2021

ABSTRACTConcomitant treatment for chronic hepatitis C virus infection and multidrug-resistant tuberculosis is safe and effective.
Durability of antibody responses and frequency of clinical and subclinical SARS-CoV-2 infection six months after BNT162b2 COVID-19 vaccination in healthcare workers
Authors: Laing Eric D. , Weiss Carol D. , Samuels Emily C. , Coggins Si’Ana A. , Wang Wei , Wang Richard , Vassell Russell , Sterling Spencer L. , Tso Marana A. , Conner Tonia , Goguet Emilie , Moser Matthew , Jackson-Thompson Belinda M. , Illinik Luca , Davies Julian , Ortega Orlando , Parmelee Edward , Hollis-Perry Monique , Maiolatesi Santina E. , Wang Gregory , Ramsey Kathleen F. , Reyes Anatalio E. , Alcorta Yolanda , Wong Mimi A. , Lindrose Alyssa R. , Duplessis Christopher A. , Tribble David R. , Malloy Allison M.W. , Burgess Timothy H. , Pollett Simon D. , Olsen Cara H. , Broder Christopher C. , Mitre Edward 
Published: October 2021

AbstractAntibodies against SARS-CoV-2 decay but persist six months post-vaccination, with lower levels of neutralizing titers against Delta than wild-type. Only 2 of 227 vaccinated healthcare workers experienced outpatient symptomatic breakthrough infections despite 59 of 227 exhibiting serological evidence of exposure to SARS-CoV-2 as defined by development of anti-nucleocapsid protein antibodies.
Can infrared camera images be used for screening in Adolescent Idiopathic Scoliosis?
Authors: Ka Natalie Lam Oi , Peng James Cheng , Zhang Teng , Yip Joanne , Fok Queenie , Lee Maple , Wong Charlotte , Kwan Kenny , Cheung Kenneth MC 
Published: October 2021

Introduction/Background contextAdolescent idiopathic scoliosis (AIS) is the most common type of scoliosis, and affects up to 4% of adolescents in early stages1. The deformity can develop during any of the rapid periods of growth in children2, and the time of pubertal growth spurt also plays a role in spinal curve progression3. Hence it is crucial to detect the disease early, to provide timely intervention.Detection of scoliosis when it is mild or before the growth spurt can be conducted via various screening methods. Adam’s forward bend test (FBT) and scoliometer measurement of the angle of trunk rotation (ATR) are commonly used4, to observe lateral bending and rotation of the spine, causing a visible rib hump. Moiré topography can also be used, but is reserved for second tier due to some degree of ambiguity5. X-rays (XR) remain the best way to diagnose scoliosis, as it provides a clear image of the spine and allows measurement of Cobb angle; however it has risks associated including requirement of the use of ionising radiation6.Infrared (IR) thermography can be used to measure surface temperature and is performed with an IR camera. The temperature distribution and data matrix can be visualised into a thermal map, which has previously been studied and associated with the thermal asymmetry in paraspinal muscles7, as well as significant temperature differences between the convex and concave side of the spinal curvature for idiopathic scoliotic patients8. We hypothesize that such asymmetry and temperature differences may produce a detectable pattern on IR thermography, which would prompt further confirmatory investigations to reach a fast and non-radiation screening of AIS.Aims and ObjectivesFor the purposes of this study, the hypothesised thermal pattern detected by IR thermography will be compared to the spinal deformities observed on XR, the ground truth as labelled by specialists. This will allow us to establish a paired dataset comparing spine visualisation between the two imaging modalities. Thus, the compared dataset would enable the generation of a machine learning model capable of automated classification of the deformity severities. The predictive accuracy of the model will be evaluated by the specialists’ assessment results. The aim of the project is to use IR to predict the severity of the scoliotic curve, opening up the possibility of using IR thermography with no radiation exposure and fully automated analytical pipeline for the screening of AIS.
Computer skills of health workers in rural Ghana and their use of social media: Implications for increased use of information technology in service delivery
Authors: Ofori Sylvia K , Akowuah Emmanuel A , Babatunde Doyinsola , Cowan Logan , Baiden Frank 
Published: October 2021

AbstractBackgroundInformation and Communication Technologies (ICTs) have improved the delivery of healthcare worldwide especially in disease control, patient management, and health data analysis. However, access to infrastructure like computers and knowledge of ICT is a major problem to various digital health initiatives among health professionals.ObjectiveThe aim of the present study was, to assess healthcare workers’ basic computer skills and use of social media and identify specific deficiencies that require training to help them function effectively.MethodsWe conducted a cross-sectional study among 51 healthcare workers in seven health centers in a region in Ghana over three months using a self-administered pre-tested questionnaire.ResultsHalf of the participants had adequate basic computer skills, of which 60.87% were women (P=0.0205). Only 15.69%, who were all males, of participants used computer software at least once a month. Most participants also used Facebook and WhatsApp.ConclusionHealth professionals in the health centers need to be trained on basic computer skills and, information technology should be incorporated into the health systems for efficient health delivery.
HEAT SHOCK FACTOR BINDING PROTEIN limits meiotic crossovers by repressing HEI10 transcription
Authors: Kim Juhyun , Park Jihye , Kim Heejin , Son Namil , Lambing Christophe , Kim Eun-Jung , Kim Jaeil , Byun Dohwan , Lee Youngkyung , Park Yeong Mi , Nageswaran Divyashree C. , Kuo Pallas , Dang Tuong Vi T. , Hwang Ildoo , Henderson Ian R. , Choi Kyuha 
Published: October 2021

AbstractThe number of meiotic crossovers is tightly controlled and most depend on pro-crossover ZMM proteins, such as the E3 ligase HEI10. Despite the importance of HEI10 dosage for crossover formation, how HEI10 transcription is controlled remains unexplored. In a forward genetic screen using a sensitive fluorescent seed crossover reporter in Arabidopsis thaliana we identify heat shock factor binding protein (HSBP) as a repressor of HEI10 transcription and crossover numbers. Using genome-wide crossover mapping and cytogenetics, we show that hsbp mutations or meiotic HSBP knockdowns increase ZMM-dependent crossovers towards the telomeres, mirroring the effects of HEI10 overexpression. Through RNA sequencing, DNA methylome and chromatin immunoprecipitation analysis, we reveal that HSBP directly represses HEI10 transcription by binding with heat shock factors (HSFs) at the HEI10 promoter and maintaining DNA methylation over the HEI10 5′ untranslated region. Our findings provide insights into how the temperature response regulator HSBP restricts meiotic HEI10 transcription and crossover number by attenuating HSF activity.
Plant-based production of SARS-CoV-2 antigens for use in a subunit vaccine
Authors: Demone Jordan , Nourimand Maryam , Maltseva Mariam , Nasr-Sharif Mina , Galipeau Yannick , Langlois Marc-André , MacLean Allyson M. 
Published: October 2021

AbstractThe COVID-19 pandemic has brought to the forefront an urgent need for the rapid development of highly efficacious vaccines, particularly in light of the ongoing emergence of multiple variants of concern. Plant-based recombinant protein platforms are emerging as cost-effective and highly scalable alternatives to conventional protein production. Viral glycoproteins, however, are historically challenging to produce in plants. Herein, we report the production of plant-expressed wild-type glycosylated SARS-CoV-2 Spike RBD (receptor-binding domain) protein that is recognized by anti-RBD antibodies and exhibits high-affinity binding to the SARS-CoV-2 receptor ACE2 (angiotensin-converting enzyme 2). Moreover, our plant-expressed RBD was readily detected by IgM, IgA, and IgG antibodies from naturally infected convalescent, vaccinated, or convalescent and vaccinated individuals. We further demonstrate that RBD binding to the ACE2 receptor was efficiently neutralized by antibodies from sera of SARS-CoV-2 convalescent and partially and fully vaccinated individuals. Collectively, these findings demonstrate that recombinant RBD produced in planta exhibits suitable biochemical and antigenic features for use in a subunit vaccine platform.
Outsourced hearing in an orb-weaving spider that uses its web as an auditory sensor
Authors: Zhou Jian , Lai Junpeng , Menda Gil , Stafstrom Jay A. , Miles Carol I. , Hoy Ronald R. , Miles Ronald N. 
Published: October 2021

AbstractHearing is a fundamental sense of many animals, including all mammals, birds, some reptiles, amphibians, fish, and arthropods. The auditory organs of these animals are extremely diverse in anatomy after hundreds of millions of years of evolution, yet all are made up of cellular tissues and are morphologically part of bodies of animals. Here we show hearing in the orb-weaving spider, Larinioides sclopetarius is not constrained by the organism’s body but is extended through outsourcing hearing to its extended phenotype, the proteinaceous, self-manufactured orb-web. We find the wispy, wheel-shaped orb-web acts as a hyperacute acoustic “antenna” to capture the sound-induced air particle movements that approach the maximum physical efficiency, better than the acoustic responsivity of all previously known eardrums. By sensing the motion of web threads, the spider remotely detects and localizes the source of an incoming airborne acoustic wave such as those emitted by approaching prey or predators. By outsourcing its acoustic sensors to its web, the spider is released from body size constraints and permits the araneid spider to increase its sound-sensitive surface area enormously, up to 10,000 times greater than the spider itself. The spider also enables the flexibility to functionally adjust and regularly regenerate its “external eardrum” according to its needs. The “outsourcing” and “supersizing” of auditory function in spiders provides unique features for studying extended and regenerative sensing, and designing novel acoustic flow detectors for precise fluid dynamic measurement and manipulation.