bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collaborative Case Review: A Systems-Based Approach to Patient Safety Event Investigation and Analysis
Authors: Lacson Ronilda , Khorasani Ramin , Fiumara Karen , Kapoor Neena , Curley Patrick , Boland Giles W. , Eappen Sunil 
Published: May 2021

Objectives
The aims of the study were to assess a system-based approach to event investigation and analysis—collaborative case reviews (CCRs)—and to measure impact of clinical specialty on strength of action items prescribed.

Methods
A fully integrated CCR process, co-led by radiology and an institutional patient safety program, was implemented on November 1, 2017, at our large academic medical center for evaluating adverse events involving radiology. Quality and safety teams performed reviews for events identified with other departments who maintained their existing processes. This institutional review board–approved study describes the program, including percentage of CCR from an institutional Electronic Safety Reporting System, percentage of CCR per specialty, and action item completion rates and strength (e.g., stronger) based on a Veterans Administration–designed hierarchy. χ2 analysis assessed impact of clinical specialty on strength of action prescribed.

Results
Seventy-three CCR in 2018 generated 260 action items from 10 specialties. Seventy percent (51/73) were adverse events identified through Electronic Safety Reporting System. The specialty most frequently associated with CCR was radiology (16/73, 22%). Most action items (204/260, 78%) were completed in 1 year; stronger action items were completed in 71 (27%) of 260. Radiology was responsible for 61 action items; 25 (41%) of 61 were strong versus all other specialties with strong action items in 46 (23%) of 199 (P < 0.01).

Conclusions
An integrated multispecialty CCR co-led by the radiology department and an institutional patient safety program was associated with a higher proportion of CCR, stronger action items, and higher action item completion rate versus other hospital departments. Active engagement in CCR can provide insights into addressing adverse events and promote patient safety.
The Efficacy of Memantine for the Treatment of Migraine: A Meta-Analysis of Randomized Controlled Studies
Authors: Xu Zhili , Chen Linglong , Jin Shuang , Chen Xinguo , Yang Baohua 
Published: May 2021

Introduction
The efficacy of memantine for migraine remains controversial. We conduct a systematic review and meta-analysis to explore the influence of memantine versus placebo on treatment in migraine patients.

Methods
We search PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases through February 2020 for randomized controlled trials assessing the effect of memantine versus placebo on treatment efficacy in migraine patients. This meta-analysis is performed using the random-effect model.

Results
Three randomized controlled trials are included in the meta-analysis. Overall, compared with control group in migraine patients, memantine treatment is associated with substantially reduced monthly attack frequency (mean difference [MD], −2.14; 95% confidence interval [CI], −2.83 to −1.46; P < 0.00001), number of migraine days (MD, −4.17; 95% CI, −6.40 to −1.93; P = 0.0003) and Migraine Disability Assessment (MD, −5.63; 95% CI, −6.46 to −4.79; P < 0.00001), but demonstrates no obvious influence on acute pain medications (MD, −1.23; 95% CI, −4.63 to 2.17; P = 0.48).

Conclusions
Memantine treatment may benefit to the control of migraine.
The Use of Motor-Evoked Potentials in Clinical Trials in Multiple Sclerosis
Authors: Fernández Victoria 
Published: May 2021

Summary:
Motor-evoked potentials (MEPs) can be used to assess the integrity of the descending corticospinal tract in the laboratory. Evoked potentials (EPs) have been widely used in the past for the diagnosis of multiple sclerosis (MS), but they are now becoming more useful in assessing the prognosis of the disease. Motor-evoked potentials have been included in EP scales that have demonstrated good correlations with clinical disability. Soon after the onset of MS, it is possible to detect an ongoing process of neurodegeneration and axonal loss. Axonal loss is probably responsible for the disability and disease progression that occurs in MS. Given the good correlations of EPs in detecting disease progression in MS, they have been used to monitor the effects of drugs used to treat the disease. Several clinical trials used MEPs as part of their EP evaluation, but MEPs have never been used as a measure of efficacy in clinical trials testing neuroprotective agents, although MEPs could be a very promising tool to measure neuroprotection and remyelination resulting from these drugs. To be used in multicenter clinical trials, MEP readings should be comparable between centers. Standardized multicenter EP assessment with central reading has been demonstrated to be feasible and reliable. Although MEP measurements have been correlated with clinical scores and other measures of neurodegeneration, further validation of MEP amplitude measurements is needed regarding their validity, reliability, and sensitivity before they can be routinely used in clinical drug trials in MS.
Effect of storage conditions on SARS-CoV-2 RNA quantification in wastewater solids
Authors: Simpson Adrian , Topol Aaron , White Bradley , Wolfe Marlene K. , Wigginton Krista , Boehm Alexandria B. 
Published: May 2021

AbstractSARS-CoV-2 RNA in wastewater settled solids is associated with COVID-19 incidence in sewersheds and therefore, there is a strong interest in using these measurements to augment traditional disease surveillance methods. A wastewater surveillance program should provide rapid turn around for sample measurements (ideally within 24 hours), but storage of samples is necessary for a variety of reasons including biobanking. Here we investigate how storage of wastewater solids at 4°C, -20°C, and -80°C affects measured concentrations of SARS-CoV-2 RNA. We find that short term (7-8 d) storage of raw solids at 4°C has little effect on measured concentrations of SARS-CoV-2 RNA, whereas longer term storage at 4°C (35-122 d) or freezing reduces measurements by 60%, on average. We show that normalizing SARS-CoV-2 RNA concentrations by concentrations of pepper mild mottle virus (PMMoV) RNA, an endogenous wastewater virus, can correct for changes during storage as storage can have a similar effect on PMMoV RNA as on SARS-CoV-2 RNA. The reductions in SARS-CoV-2 RNA in solids during freeze thaws is less than those reported for the same target in liquid influent by several authors.
Meta-Analysis of Risk of Vaccine-Induced Immune Thrombotic Thrombocytopenia Following ChAdOx1-S Recombinant Vaccine
Authors: Chan Benjamin TB , Bobos Pavlos , Odutayo Ayodele , Pai Menaka 
Published: May 2021

AbstractContextVaccine-induced immune thrombotic thrombocytopenia (VITT) has been reported after administering ChAdOx1-S recombinant COVID-19 vaccine (marketed as Vaxzevira™ by Astra-Zeneca, Covishield™). Estimates of incidence vary between countries, due to different age distributions chosen, case definitions and choice of denominator (persons vaccinated vs immunizations given). This study clarifies these estimates by pooling data from ten countries and examining differences by age group.MethodsWe examined case reports, press releases and immunization data and calculated pooled estimates of VITT incidence using random effects models. Sensitivity analyses considered different combinations of countries and varying assumptions on time between vaccination and reporting of cases.ResultsPooling all countries, VITT incidence was 0.73 per 100,000 persons receiving first dose of Covishield/Vaxzevira [95% CI .43,1.23]. Incidence for age 65 and over was 0.11 per 100,000 persons [95% CI .05-.26], and significantly higher among those under age 55: 1.67 per 100,000 persons [95% CI 1.30-2.14] in the UK, 5.06 per 100,000 persons in Norway [95% CI 2.16, 11.86]. The latter had the best data on counts of persons vaccinated. Incidence for age 55 to 64 years was 0.34 [95% CI 0.13, 0.85] in the UK, lower than for under age 55.ConclusionVITT is a rare vaccine-associated adverse event. Incidence estimates vary between jurisdictions. However, even the highest reported incidence from Norway is low – and in settings with high community transmission, lower than risk of serious outcomes associated with Covid-19. Policymakers and individuals can use these data to calculate risk-benefit ratios and better target vaccine distribution.EssentialsThis paper measures risk of vaccine-induced immune thrombotic thrombocytopenia (VITT) after ChAdOx1-S recombinant COVID-19 vaccinePooled estimates of incidence were calculated with a random effects model based on data from 10 countriesOverall risk is 1 in 139,000; for age 65 and over, about 1 in 1,000,000; for age under 55, between 1 in 20,000 to 60,000VITT risk is low and varies by age. These data can inform policies around vaccination distribution.
Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples
Authors: de Vries Jutte J.C. , Brown Julianne R. , Fischer Nicole , Sidorov Igor A. , Morfopoulou Sofia , Huang Jiabin , Oude Munnink Bas B. , Sayiner Arzu , Bulgurcu Alihan , Rodriguez Christophe , Gricourt Guillaume , Keyaerts Els , Beller Leen , Bachofen Claudia , Kubacki Jakub , Cordey Samuel , Laubscher Florian , Schmitz Dennis , Beer Martin , Hoeper Dirk , Huber Michael , Kufner Verena , Zaheri Maryam , Lebrand Aitana , Papa Anna , van Boheemen Sander , Kroes Aloys C.M. , Breuer Judith , Lopez-Labrador F. Xavier , Claas Eric C.J. 
Published: May 2021

AbstractMetagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.MethodsMetagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analysed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analysed.ResultsOverall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection.ConclusionA wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.
LACK OF ASSOCIATION BETWEEN CONVALESCENT PLASMA ADMINISTRATION AND LENGTH OF HOSPITAL STAY: A HOSPITAL-DAY STRATIFIED MULTI-CENTER RETROSPECTIVE COHORT STUDY
Authors: Alamgir Joy , Abid M. Ruhul , Garibaldi Brian , Munir Naved , Setoguchi Soko , Hong Stephanie S. , Chen Xinci , Kocis Paul T. , Yajima Masanao , Alexander G. Caleb , Mehta Hemalkumar B. , Madhira Vithal , Ergas Rosa , O’Brien Thomas R. , Bozzette Sam 
Published: May 2021

ABSTRACTBackgroundEffects of timing of Convalescent plasma (CP) administration on hospitalized COVID-19 patients are not established.MethodsWe used the National COVID Cohort Collaborative data to perform a retrospective cohort study of hospitalized COVID-19 patients in the United States between 07-01-2020 and 12-19-2020. We stratified patients based on day of CP administration (Day 0, 1, 2, 3 and 4) from COVID-19 diagnosis. We used 35 predictors to frame matched cohorts accounting for clinical and sociodemographic characteristics. We used competing risk survival models to examine the association between CP administration and length of hospital stay with in-hospital death as a competing risk performing Gray’s test on the cumulative incidence function and Cox’s regression on cause specific hazard ratios.ResultsIn a cohort of 4,003 hospitalized COVID-19 patients, 197 (4.9%) received CP within the first 5 days following COVID-19 diagnosis. After adjusting for potential confounding variables, there were no statistically significant associations between day of CP administration and length of hospital stay. Day 0 CP administration signallled lower mortality but was not statistically significant (HR 0.45 [0.19-1.03]).ConclusionsWe found no association between the timing of CP administration and length of stay among hospitalized COVID-19 patients.
Integrative lipidomics and metabolomics for system-level understanding of the metabolic syndrome in long-term treated HIV-infected individuals
Authors: Villumsen Sofie Olund , Benfeitas Rui , Dehlbæk Knudsen Andreas , Gelpi Marco , Høgh Julie , Thomsen Magda Teresa , Murray Daniel , Ullum Henrik , Neogi Ujjwal , Nielsen Susanne Dam 
Published: May 2021

AbstractPeople living with HIV (PLWH) require life-long anti-retroviral treatment and often present with comorbidities such as metabolic syndrome (MetS). A systematic lipidomic characterization and its association with metabolism is currently missing. In this study, we included 100 PLWH with MetS and 100 without MetS from the Copenhagen comorbidity in HIV infection (COCOMO) cohort to examine whether and how lipidome profiles associated with MetS in PLWH. We combined several standard biostatistical, machine learning, and network analysis techniques to investigate the lipidome systematically and comprehensively. Our observations indicate an increased abundance of the glycerolipids and an association between structural composition patterns of glycerolipids in PLWH with MetS. Further integration of the key metabolites identified earlier in the same population and clinical data with lipidomics suggest disruption of the glutamate and fatty acid metabolism. suggest their involvement in pathogenesis of PLWH with MetS.
A prospective diagnostic study to measure the accuracy of detection of SARS-CoV-2 Variants Of Concern (VOC) utilising a novel RT-PCR GENotyping algorithm in an In silico Evaluation (VOC-GENIE)
Authors: Borley Daryl , Trevor R.A. , Richter Alex , Kidd Stephen , Cortes Nick , Moore Nathan , Goring Alice , Templeton Kate , Teltumbde Prachi , Grippon Seden , Oladimeji Paul , Sanchez-Bretano Aida , Dawson Andrew , Martin Joanne E 
Published: May 2021

AbstractBackgroundSARS-CoV-2 variants of concern (VOCs) have been associated with higher rate of transmission, and evasion of immunisation and antibody therapeutics. Variant sequencing is widely utilized in the UK. However, only 0.5% (~650k) of the 133 million cumulative positive cases worldwide were sequenced (in GISAID) on 08 April 2021 with 97% from Europe and North America and only ~0.25% (~320k) were variant sequences. This may be due to the lack of availability, high cost, infrastructure and expert staff required for sequencing.Public health decisions based on a non-randomised sample of 0.5% of the population may be insufficiently powered, and subject to sampling bias and systematic error. In addition, sequencing is rarely available in situ in a clinically relevant timeframe and thus, is not currently compatible with diagnosis and treatment patient care pathways. Therefore, we investigated an alternative approach using polymerase chain reaction (PCR) genotyping to detect the key single nucleotide polymorphisms (SNPs) associated with increased transmission and immune evasion in SARS-CoV-2 variants.MethodsWe investigated the utility of SARS-CoV-2 SNP detection with a panel of PCR-genotyping assays in a large data set of 640,482 SARS-CoV-2 high quality, full length sequences using a prospective in silico trial design and explored the potential impact of rapid in situ variant testing on the COVID-19 diagnosis and treatment patient pathway.ResultsFive SNPs were selected by screening the published literature for a reported association with increased transmission and / or immune evasion. 344881 sequences contained one or more of the five SNPs. This algorithm of SNPs was found to be able to identify the four variants of concern (VOCs) and sequences containing the E484K and L452R escape mutations.InterpretationThe in silico analysis suggest that the key mutations and variants of SARS-CoV-2 may be reliably detected using a focused algorithm of biologically relevant SNPs. This highlights the potential for rapid in situ PCR genotyping to compliment or replace sequencing or to be utilized instead of sequences in settings where sequencing is not feasible, accessible or affordable. Rapid detection of variants with in situ PCR genotyping may facilitate a more effective COVID-19 diagnosis and treatment patient pathway.FundingThe study was funded by Primer Design (UK), with kind contributions from all academic partners.
The impact of COVID-19 on the provision of respectful maternity care: findings from a global survey of health workers
Authors: Asefa Anteneh , Semaan Aline , Delvaux Therese , Huysmans Elise , Galle Anna , Sacks Emma , Bohren Meghan A. , Morgan Alison , Sadler Michelle , Vedam Saraswathi , Benova Lenka 
Published: May 2021

AbstractBackgroundSignificant adjustments to the provision of maternity care in response to the COVID-19 pandemic and the direct impacts of COVID-19 can compromise the quality of maternal and newborn care.AimTo explore how the COVID-19 pandemic affected frontline health workers’ ability to provide respectful maternity care globally.MethodsWe conducted a global online survey of health workers to assess the provision of maternal and newborn healthcare during the COVID-19 pandemic. We collected quantitative and qualitative data between July and December 2020 and conducted a qualitative content analysis to explore open-ended responses.FindingsHealth workers (n=1,127) from 71 countries participated; and 120 participants from 33 countries provided qualitative data. The COVID-19 pandemic negatively affected the provision of respectful maternity care in multiple ways. Six central themes were identified: less family involvement, reduced emotional and physical support for women, compromised standards of care, increased exposure to medically unjustified caesarean section, and staff overwhelmed by rapidly changing guidelines and enhanced infection prevention measures. Further, respectful care provided to women and newborns with suspected or confirmed COVID-19 infection was severely affected due to health workers’ fear of getting infected and measures taken to minimise COVID-19 transmission.DiscussionMultidimensional and contextually-adapted actions are urgently needed to mitigate the impacts of the COVID-19 pandemic on the provision and continued promotion of respectful maternity care globally in the long-term.ConclusionsThe measures taken during the COVID-19 pandemic disrupted the quality of care provided to women during labour and childbirth generally, and respectful maternity care specifically.
COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland
Authors: de la Fuente Garcia Sofia , Haider Fasih , Luz Saturnino 
Published: May 2021

AbstractThe COVID-19 pandemic has led to unprecedented restrictions in people’s lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring people’s psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.Clinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.
The evidence on transmission dynamics of COVID-19 from pre- and asymptomatic cases: protocol for a systematic review (Version 2)
Authors: Jefferson T , Plüddemann A , Spencer EA , Brassey J , Rosca EC , Onakpoya I , Evans DH , Conly JM , Heneghan C 
Published: May 2021

AbstractBackgroundThe role of forward transmission of infection from cases of SARS-CoV-2 who remain without symptoms and signs throughout the active phase of the disease (asymptomatic) and those who have not developed symptoms or signs when surveyed (presymptomatic) is at present unclear, despite the important role that they may play in transmission dynamics.MethodsWe will search LitCovid, medRxiv, Google Scholar and the WHO Covid-19 database using Covid-19, SARS-CoV-2, transmission, and appropriate synonyms as search terms. We will also search the reference lists of included studies for additional relevant studies. We will include studies of people exposed to SARS-CoV-2 within 2-14 days of close contact or suspected community or institutional exposure to index asymptomatic or pre-symptomatic infected individuals, as defined in each study along with secondary case(s) infected. We will include only studies that provide proof of transmission outcome using culturable virus and /or genetic sequencing. The inclusion of this higher-quality evidence aims to overcome the methodological shortcomings of lower quality studies. We will assess the microbiologic or genetic sequencing evidence in an effort to inform the quality of the chain of transmission evidence and adequacy of follow up of sign and symptom monitoring.Expected resultsWe intend to present the evidence in three distinct packages: study description, methodological quality assessment and data extracted. We intend on summarising the evidence and drawing conclusions as to the quality of the evidence.