bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Post-Acute Sequelae of COVID-19 (PASC) Symptom Lexicon Using Electronic Health Record Clinical Notes
Authors: Wang Liqin , Foer Dinah , MacPhaul Erin , Lo Ying-Chih , Bates David W. , Zhou Li 
Published: August 2021

ABSTRACTObjectiveTo develop a comprehensive post-acute sequelae of COVID-19 (PASC) symptom lexicon from clinical notes to support PASC symptom identification and research.MethodsWe identified 26,117 COVID-19 positive patients from the Mass General Brigham’s electronic health records (EHR) and extracted 328,879 clinical notes from their post-acute infection period (day 51-110 from first positive COVID-19 test). The PASC symptom lexicon incorporated Unified Medical Language System® (UMLS) Metathesaurus concepts and synonyms based on selected semantic types. The MTERMS natural language processing (NLP) tool was used to automatically extract symptoms from a development dataset. The lexicon was iteratively revised with manual chart review, keyword search, concept consolidation, and evaluation of NLP output. We assessed the comprehensiveness of the lexicon and the NLP performance using a validation dataset and reported the symptom prevalence across the entire corpus.ResultsThe PASC symptom lexicon included 355 symptoms consolidated from 1,520 UMLS concepts. NLP achieved an averaged precision of 0.94 and an estimated recall of 0.84. Symptoms with the highest frequency included pain (43.1%), anxiety (25.8%), depression (24.0%), fatigue (23.4%), joint pain (21.0%), shortness of breath (20.8%), headache (20.0%), nausea and/or vomiting (19.9%), myalgia (19.0%), and gastroesophageal reflux (18.6%).Discussion and ConclusionPASC symptoms are diverse. A comprehensive PASC symptom lexicon can be derived using a data-driven, ontology-driven and NLP-assisted approach. By using unstructured data, this approach may improve identification and analysis of patient symptoms in the EHR, and inform prospective study design, preventative care strategies, and therapeutic interventions for patient care.
Age-specific rate of severe and critical SARS-CoV-2 infections estimated with multi-country seroprevalence studies
Authors: Herrera-Esposito Daniel , de los Campos Gustavo 
Published: August 2021

AbstractKnowing the age-specific rates at which individuals infected with SARS-CoV-2 develop severe and critical disease is essential for designing public policy, for epidemic modeling, and for individual risk evaluation. In this study, we present the first estimates of these rates using multi-country serology studies, and data on hospital admissions and mortality from early to mid-2020. We integrated data from those sources using a Bayesian model that accounts for the high heterogeneity between data sources and for the uncertainty associated to the estimates reported from each data source. Our results show that the risk of severe and critical disease increases exponentially with age, but much less steeply than the risk of fatal illness. Importantly, the estimated rate of severe disease outcome in adolescents is between one and two orders of magnitude larger than the reported rate of vaccine side-effects, showing how these estimates are relevant for health policy. Finally, we validate our results by showing that they are in close agreement with the estimates obtained from an indirect method that uses reported infection fatality rates estimates and hospital mortality data.
Decline in pneumococcal disease in young children during the COVID-19 pandemic associated with suppression of seasonal respiratory viruses, despite persistent pneumococcal carriage: A prospective cohort study
Authors: Danino Dana , Ben-Shimol Shalom , van der Beek Bart Adriaan , Givon-Lavi Noga , Avni Yonat Shemer , Greenberg David , Weinberger Daniel M. , Dagan Ron 
Published: August 2021

AbstractBackgroundInvasive pneumococcal disease (IPD) declined during the COVID-19 pandemic. Previous studies hypothesized that this was due to reduced pneumococcal transmission resulting from non-pharmacological interventions. We used multiple ongoing cohort surveillance projects in children <5 years to test this hypothesis.MethodsThe first SARS-CoV-2 cases were detected in February-2020, resulting in a full lockdown, followed by several partial restrictions. Data from ongoing surveillance projects captured the incidence dynamics of community-acquired alveolar pneumonia (CAAP), non-alveolar lower respiratory infections necessitating chest X-rays (NA-LRI), nasopharyngeal pneumococcal carriage in non-respiratory visits, nasopharyngeal respiratory virus detection (by PCR), and nationwide invasive pneumococcal disease (IPD). Monthly rates (January-2020 through February-2021 vs. mean monthly rates 2016-2019 [expected rates]) adjusted for age and ethnicity, were compared.FindingsCAAP and bacteremic pneumococcal pneumonia were strongly reduced (incidence rate ratios, [IRRs] 0η07 and 0η19, respectively); NA-LRI and non-pneumonia IPD were also reduced, with a lesser magnitude (IRRs, 0η46 and 0η42, respectively). In contrast, pneumococcal carriage prevalence was only slightly reduced and density of colonization and pneumococcal serotype distributions were similar to previous years. The pneumococcus-associated disease decline was temporally associated with a full suppression of RSV, influenza viruses, and hMPV, often implicated as co-pathogens with pneumococcus. In contrast, adenovirus, rhinovirus, and parainfluenza activities were within or above expected levels.InterpretationReductions in pneumococcal and pneumococcus-associated diseases occurring during the COVID-19 pandemic were not predominantly related to reduced pneumococcal transmission and carriage but were strongly associated with the complete disappearance of specific respiratory viruses.FundingPartially funded by Pfizer, Inc.
Rapid comparative evaluation of SARS-CoV-2 rapid point-of-care antigen tests
Authors: Denzler Anna , Jacobs Max L. , Witte Victoria , Schnitzler Paul , Denkinger Claudia M. , Knop Michael 
Published: August 2021

AbstractBackgroundCurrently, more than 500 different AgPOCTs for SARS-CoV-2 diagnostics are on sale (July 2021), for many of which no data about sensitivity other than self-acclaimed values by the manufacturers are available. In many cases these do not reflect real-life diagnostic sensitivities. Therefore, manufacturer-independent quality checks of available AgPOCTs are needed, given the potential implications of false-negative results.ObjectiveThe objective of this study was to develop a scalable approach for direct comparison of the analytical sensitivities of commercially available SARS-CoV-2 antigen point-of-care tests (AgPOCTs) in order to rapidly identify poor performing products.MethodsWe present a methodology for quick assessment of the sensitivity of SARS-CoV-2 lateral flow test stripes suitable for quality evaluation of many different products. We established reference samples with high, medium and low SARS-CoV-2 viral loads along with a SARS-CoV-2 negative control sample. Test samples were used to semi-quantitatively assess the analytical sensitivities of 32 different commercial AgPOCTs in a head-to-head comparison.ResultsAmong 32 SARS-CoV-2 AgPOCTs tested, we observe sensitivity differences across a broad range of viral loads (∼7.0*108to ∼1.7*105SARS-CoV-2 genome copies per ml). 23 AgPOCTs detected the Ct25 test sample (∼1.4*106copies/ ml), while only five tests detected the Ct28 test sample (∼1.7*105copies/ ml). In the low range of analytical sensitivity we found three saliva spit tests only delivering positive results for the Ct21 sample (∼2.2*107copies/ ml). Comparison with published data support our AgPOCT ranking. Importantly, we identified an AgPOCT offered in many local drugstores and supermarkets, which did not reliably recognize the sample with highest viral load (Ct16 test sample with ∼7.0*108copies/ ml) leading to serious doubts in its usefulness in SARS-CoV-2 diagnostics.ConclusionThe rapid sensitivity assessment procedure presented here provides useful estimations on the analytical sensitivities of 32 AgPOCTs and identified a widely-spread AgPOCT with concerningly low sensitivity.
BIOCHEMICAL AND HAEMATOLOGICAL CHANGES ASSOCIATED WITH TRANSPLACENTAL CONGENITAL MALARIA IN KOGI STATE, NORTHCENTRAL NIGERIA
Authors: Akor Shedrack Egbunu , Musa Dickson Achimugu , Akogu SPO , Matthew Akpa , Friday Emmanuel Titus , Idachaba Timothy , Onoja Patience , Abdul Ameh Simon 
Published: August 2021

ABSTRACTBackgroundTransplacental congenital malaria is a vertical transplacental transmission of malaria parasites from the mother to the baby in utero or perinatally during labor. Cord blood that conveyed oxygen and nutrients from mother to fetus and return with carbon dioxide and other waste materials can transmit malaria pathogen. This study is aim to establish early diagnosis of transplacental congenital malaria using cord blood biochemical and haematological indices. Cord blood from 164 babies delivered at three hospitals in Kogi State between January and December, 2020 were microscopically investigated for malaria parasite. Biochemical and Haematological analyses were done using SYSMEX XP-300, Roche 9180 and VIS Spectrophotometer model 721. The data obtained were expressed as mean ±standard deviation using SPSS 23. The indicator level of statistical significance was set at p<0.05. The results showed significant (p<0.05) decreased in values of WBC, platelet, sodium, potassium, urea, creatinine, RBC, PCV, haemoglobin and MCHC in malaria infected cord blood in comparison to malaria negative control group. Significant (P<0.05) increased activities of liver enzymes (AST, ALT, ALP), total protein, bicarbonate and chloride in malaria infected cord blood when compared with malaria negative group. However, no statistically significant difference in lymphocyte, MCV, MCH, neutrophil and mixed of both malaria infected and malaria negative cord blood. This study suggests that cord blood biochemical and haematological indices can be used to diagnose and manage transplacental congenital malaria in fetus and neonates.
What is the suitability of clinical vignettes in benchmarking the performance of online symptom checkers? An audit study
Authors: El-Osta Austen , Webber Iman , Alaa Aos , Bagkeris Emmanouil , Mian Saba , Sharabiani Mansour , Majeed Azeem 
Published: August 2021

ABSTRACTObjectiveTo assess the suitability of primary care vignettes in benchmarking the performance of online symptom checkersDesignObservational study using publicly available, free online symptom checkersParticipantsThree symptom checkers (Healthily, Ada and Babylon) that provided consultations in English. 139 standardized patient vignettes were compiled by RCGP. Three independent GPs interpreted the vignettes to arrive at a “Gold Standard” consisting of 3 dispositions and divided into one of three categories of triage urgency: (1) emergency care required, (2) primary care required and (3) self-care.Main outcome measuresSix professional non-medical and lay inputters simulated 2774 standardized patient evaluations using 3 online symptom checkers (OSC). We recorded when OSC provided a triage recommendation and whether it correctly recommended the appropriate triage recommendation across three categories of triage urgency (emergency care, primary care or self-care). We collected data on whether the solution appeared within the first 3 dispositions in each of the standards across 2774 standardized patient evaluations.ResultsWhen benchmarked against the Gold Standard, Healthily provided an appropriate triage recommendation 61.9% of the time compared to 45.3% and 42.4% of the time for Babylon and Ada respectively. There was poor agreement between OSC consultation outcome and Gold Standard dispositions. When compared to the Gold Standard, Healthily gave an unsafe “under-triage” recommendation 28.6% of the time overall across the three categories compared to 43.3% for Ada and 47.5% for Babylon (P<0.001).ConclusionsOSCs recommended ‘very unsafe’ triages only <4% of the time suggesting that the online consultation tools are generally working at a safe level of risk. Primary care vignettes are a helpful tool to support development of OSC, but not ideally suited to benchmark the performance of different OSC. Real-world evidence studies involving general practice are recommended to benchmark the performance of OSC in the community setting.Strengths and limitations of this study139 independently created primary care vignettes covering 18 subcategories of primary care were used to benchmark the performance of three online symptom checkers using 2774 unique patient simulationsA gold standard for each primary care vignette was derived using GP roundtables and single blinded testingWe investigated the extent that different inputters using the same vignette and online symptom checker received differing consultation outcomes and triage recommendationsWe developed an accuracy matrix to objectively monitor online symptom checker consultation outcome and the safety of the triage recommendationLimitations included a different number of inputters to simulate patients across the three online symptom checkers tested
Comparison of reported main COVID-19 information sources in national and culturally and linguistically diverse communities in Australia
Authors: Ayre J , Muscat DMM , Mac O , Batcup C , Cvejic E , Pickles K , Dolan H , Bonner C , Mouwad D , Zachariah D , Turalic U , Santalucia Y , Chen T , Vasic G , McCaffery K 
Published: August 2021

AbstractBackgroundTo manage the COVID-19 pandemic effectively, governments need clear and effective communication. This is a challenge for culturally diverse communities as groups may have different informational needs and information-seeking behaviours. In this paper we present the frequency of information sources for COVID-19 in a culturally diverse area of Sydney, Australia.MethodsThis study reports findings from two surveys. The first recruited participants across 10 languages between March 21 and July 9, 2021. The second provides a point of reference, and was an Australian, nationally-representative sample of English-speaking participants between November 4 – 18, 2020.ResultsFor the survey in culturally and linguistically diverse communities, of 708 participants, mean age was 45.4 years (SE 0.78), and 51% of respondents were female. Across all language groups, 54.7% of participants used Australian official or public broadcasters to find out about COVID-19 (n=421). Australian commercial information sources (54.1%, n=417), social media (51.6%, n=397), and family and friends in Australia (32.7%, n=252) were common sources. Patterns varied substantially across language groups. In the nationally representative survey (n=2313), 67% of participants (n=1540) used Australian official or public broadcasters, with lower proportions for social media (31.9%, n=738) and friends, family or other personal sources (23.1%; n=533).ConclusionAlmost 50% of participants from culturally and linguistically diverse communities did not report using Australian official or public broadcaster as main sources of information. Instead Australian commercial information sources, friends and family, overseas sources and social media were common. Though a crude comparison of the two datasets, this data can guide policy decisions for communication to different community groups. Further analysis is needed to interpret this data. Better understanding of how diverse communities seek and receive COVID-19 health information is imperative as we manage the current COVID-19 outbreak in the Sydney region.
Muscle microRNAs in the cerebrospinal fluid predict clinical response to nusinersen therapy in type II and type III spinal muscular atrophy patients
Authors: Magen Iddo , Aharoni Sharon , Yacovzada Nancy Sarah , Latzer Itay Tokatly , Alves Christiano R R , Sagi Liora , Fattal-Valevski Aviva , Swoboda Kathryn J , Katz Jacob , Bruckheimer Elchanan , Nevo Yoram , Hornstein Eran 
Published: August 2021

AbstractObjectiveThe antisense oligonucleotide nusinersen (spinraza) regulates splicing of thesurvival motor neuron 2(SMN2)messenger RNA to increase SMN protein expression and has improved ventilator free survival and motor function outcomes in infantile onset forms of SMA, treated early in the course of the disease. However, the response in later onset forms of SMA is highly variable and dependent on symptom severity and disease duration at treatment initiation. Therefore, we aimed to identify novel noninvasive biomarkers that could predict the response to nusinersen in type II and III SMA patients.Methods34 SMA patients were included. We applied next-generation sequencing to identify microRNAs in the cerebrospinal fluid (CSF) as candidate biomarkers predicting response to nusinersen. Hammersmith Functional Motor Scale Expanded (HFMSE), was conducted at baseline and 6 months post initiation of nusinersen therapy to assess motor function. Patients changing by ≥ 3 or ≤0 points in the HFMSE total score were considered as responders or non-responders, respectively.ResultsLower baseline levels of two muscle microRNAs (miR-206 and miR-133), alone or in combination, predicted the pre-determined clinical response to nusinersen after 6 months therapy. Moreover, miR-206 levels were inversely correlated with the HFMSE score.ConclusionsLower miR-206 and miR-133 in the CSF predict more robust clinical response to nusinersen treatment in later onset SMA patients. These novel findings have high clinical relevance for identifying early treatment response to nusinsersen in later onset SMA patients and call to test the ability of miRNAs to predict more sustained long-term benefit.
Specialized interferon ligand action in COVID19
Authors: Galbraith Matthew D. , Kinning Kohl T. , Sullivan Kelly D. , Araya Paula , Smith Keith P. , Granrath Ross E. , Shaw Jessica R. , Baxter Ryan , Jordan Kimberly R. , Russell Seth , Dzieciatkowska Monika , Reisz Julie A. , Gamboni Fabia , Cendali Francesca , Ghosh Tusharkanti , Monte Andrew A. , Bennett Tellen D. , Hansen Kirk C. , Hsieh Elena W.Y. , D’Alessandro Angelo , Espinosa Joaquin M. 
Published: August 2021

ABSTRACTThe impacts of IFN signaling on COVID19 pathology are multiple, with protective and harmful effects being documented. We report here a multi-omics investigation of IFN signaling in hospitalized COVID19 patients, defining the biosignatures associated with varying levels of 12 different IFN ligands. Previously we showed that seroconversion associates with decreased production of select IFN ligands (Galbraith et al, 2021). We show now that the antiviral transcriptional response in circulating immune cells is strongly associated with a specific subset of ligands, most prominently IFNA2 and IFNG. In contrast, proteomics signatures indicative of endothelial damage associate with levels of IFNB and IFNA6. Differential IFN ligand production is linked to distinct constellations of circulating immune cells. Lastly, IFN ligands associate differentially with activation of the kynurenine pathway, dysregulated fatty acid metabolism, and altered central carbon metabolism. Altogether, these results reveal specialized IFN ligand action in COVID19, with potential diagnostic and therapeutic implications.IMPACT STATEMENTAnalysis of multi-omics signatures associated with 12 different IFN ligands reveals their specialized action in COVID19.
Unrestricted Online Sharing of High-frequency, High-resolution Data on SARS-CoV-2 in Wastewater to Inform the COVID-19 Public Health Response in Greater Tempe, Arizona
Authors: Bowes Devin A. , Driver Erin M. , Kraberger Simona , Fontenele Rafaela S. , Holland LaRinda A. , Wright Jillian , Johnston Bridger , Savic Sonja , Newell Melanie Engstrom , Adhikari Sangeet , Kumar Rahul , Goetz Hanah , Binsfeld Allison , Nessi Kaxandra , Watkins Payton , Mahant Akhil , Zevitz Jake , Deitrick Stephanie , Brown Philip , Dalton Richard , Garcia Chris , Inchausti Rosa , Holmes Wydale , Tian Xiao-Jun , Varsani Arvind , Lim Efrem S. , Scotch Matthew , Halden Rolf U. 
Published: August 2021

AbstractThe COVID-19 pandemic prompted a global integration of wastewater-based epidemiology (WBE) into public health surveillance. Among early pre-COVID practitioners was Greater Tempe (population ~200,000), Arizona, where high-frequency, high-resolution monitoring of opioids began in 2018, leading to unrestricted online data release. Leveraging an existing, neighborhood-level monitoring network, wastewater from eleven contiguous catchment areas was analyzed by RT-qPCR for the SARS-CoV-2 E gene from April 2020 to March 2021 (n=1,556). Wastewater data identified an infection hotspot in a predominantly Hispanic and Native American community, triggering targeted interventions. During the first SARS-CoV-2 wave (June 2020), spikes in virus levels preceded an increase in clinical cases by 8.5±2.1 days, providing an early-warning capability that later transitioned into a lagging indicator (−2.0±1.4 days) during the December/January 2020-21 wave of clinical cases. Globally representing the first demonstration of immediate, unrestricted WBE data sharing and featuring long-term, innovative, high-frequency, high-resolution sub-catchment monitoring, this successful case study encourages further applications of WBE to inform public health interventions.
NSTEMI Decide: Development of a Decision Aid for Older Adults with Non ST Elevation Myocardial Infarction
Authors: Summapund Jenny , Sibley Rachel A. , Iqbal Sohah , Kiefer Nicholas J. , Langford Aisha , Spatz Erica , Barnett Mallory , Rivers Joshua , Chaudhry Sarwat I. , Dickson Victoria V. , Sikand Nikhil V. , Matlock Daniel D. , Dodson John A. 
Published: August 2021

AbstractBackgroundMany patients hospitalized with non-ST elevation myocardial infarction (NSTEMI) are older adults (age ≥75), in whom invasive coronary angiography confers potential benefits but also higher risks than the general population. Our goal was to therefore develop a patient decision aid (PtDA) to assist with shared decision making (SDM) between cardiologists and older adults with this condition.MethodsWe followed International Patient Decision Aid Standards to develop the NSTEMI Decide PtDA. The initial prototype was based on structured interviews from 20 patients and 20 clinicians. Risks and benefits of invasive coronary angiography were derived from the available literature in older adults, with an emphasis on findings from randomized trials. The PtDA was then revised through an iterative, user-centered design approach with rapid prototyping using input from both clinician and patients to meet the needs of both stakeholders.ResultsThe PtDA went through 8 iterations. The final decision aid was 11 pages and included background information (6 pages), explanation of benefits and risks (4 pages), and a summary (1 page). Large font (≥26 point) was used to accommodate visual difficulties. Language was tailored to an 8th grade reading level. Based on the best available literature, we included benefits of invasive coronary angiography (recurrent myocardial infarction, repeat revascularization) and risks (stroke, bleeding, acute kidney injury). The final PtDA was converted to a mobile health application to increase usability on portable digital devices in the clinical setting.ConclusionsWe developed the first PtDA tailored to older adults hospitalized with NSTEMI. This PtDA will be prospectively tested to evaluate dimensions including feasibility of use, satisfaction with care, medical knowledge, and decisional conflict.