Miracle-dz/UniFAR-FTUs huggingface dataset:
Viral sequencing reveals US healthcare personnel rarely become infected with SARS-CoV-2 through patient contact

Background Healthcare personnel (HCP) are at increased risk of infection with the severe acute respiratory coronavirus 2019 virus (SARS-CoV-2). Between 12 March 2020 and 10 January 2021, >1,170 HCP tested positive for SARS-CoV-2 at a major academic medical institution in the Upper Midwest of the United States. We aimed to understand the sources of infections in HCP and to evaluate the efficacy of infection control procedures used at this institution to protect HCP from healthcare-associated transmission. Methods In this retrospective case series, we used viral genomics to investigate the likely source of SARS-CoV-2 infection in 96 HCP where epidemiological data alone could not be used to rule out healthcare-associated transmission. We obtained limited epidemiological data through informal interviews and review of the electronic health record. We combined viral sequence data and available epidemiological information to infer the most likely source of HCP infection. Findings We investigated 32 SARS-CoV-2 infection clusters involving 96 HCP, 140 possible patient contacts, and 1 household contact (total n = 237). Of these, 182 sequences met quality standards and were used for downstream analysis. We found the majority of HCP infections could not be linked to a patient or co-worker and therefore likely occurred in the outside community (58/96; 60.4%). We found a smaller percentage could be traced to a coworker (10/96; 10.4%) or were part of a patient-employee cluster (12/96; 12.5%). Strikingly, the smallest proportion of HCP infections could be clearly traced to a patient source (4/96; 4.2%). Interpretation Infection control procedures, consistently followed, offer significant protection to HCP caring for COVID-19 patients in a representative American academic medical institution. Rapid SARS-CoV-2 genome sequencing in healthcare settings can be used retrospectively to reconstruct the likely source of HCP infection when epidemiological data are not available or are inconclusive. Understanding the source of SARS-CoV-2 infection can then be used prospectively to adjust and improve infection control practices and guidelines.
Countries with high deaths due to flu and tuberculosis demonstrate lower COVID-19 mortality: roles of vaccinations

ABSTRACT Deaths due to the ongoing COVID-19 pandemic vary (3–1681 deaths/million and mortality rates 0.71–14.54%) and are far greater in some countries compared to others. This observation led us to perform epidemiological analysis, using data in the public domain, to study the correlation of COVID-19 with the prevalence and vaccination strategies for two respiratory pathogens: flu and tuberculosis (TB). Countries showing more than 1000 COVID-19 deaths were selected at three time points during the ongoing pandemic: 17 May, 1 October and 31 December 2020. The major findings of this study that are broadly consistent at all three time points are: First, countries with high flu deaths negatively correlate with COVID-19 deaths/million. Second, TB incidences and deaths negatively correlate with COVID-19 deaths/million. Countries displaying high TB and flu deaths (Nigeria, Ethiopia, Myanmar, Indonesia, India) display lower COVID-19 deaths/million compared to countries with low TB and flu deaths (Italy, Spain, USA, France). Third, countries with greater flu vaccination display lower flu incidences but higher COVID-19 deaths/million and mortality rates. On the other hand, Bacillus Calmette Guerin (BCG) vaccination negatively correlates with Covid-19 deaths/million. Fourth, countries with only BCG, but no flu, vaccination show delayed and lower number of COVID-19 deaths/million compared to countries with flu, but no BCG, vaccination. Fifth, countries with high BCG vaccination coverage as well as high TB deaths display the lowest COVID-19 deaths/million. The implications of this global study are discussed with respect to the roles of respiratory infections and vaccinations in lowering COVID-19 deaths.
miRNAs detection in equine plasma by qPCR for doping control: assessment of blood sampling and study of eca-miR-144 as potential ESA biomarker.

Short half-life doping substances are, quickly eliminated and therefore difficult to control with traditional analytical chemistry methods. Indirect methods targeting biomarkers constitute an alternative to extend detection time frames in doping control analyses. Gene expression analysis (i.e. transcriptomics) has already shown interesting results in both Humans and Equines for erythropoietin (EPO), Growth Hormone (GH) and Anabolic Androgenic Steroid (AAS) misuses. In Humans, circulating cell-free microRNAs in plasma were described as new potential biomarkers for control of Major Doping Agent (MDA) abuses. The development of a qPCR method allowing the detection of circulating miRNAs was carried out on equine plasma collected on different type of tubes (EDTA, Lithium-Heparin). Whereas analyzing plasma collected in EDTA tubes is a standard method in molecular biology, analyzing plasma collected in Lithium-Heparin (LiHep) tubes is challenging, as heparin is a RT-PCR inhibitor. Different strategies were considered and attention was paid on both miRNAs extraction quality and detection sensitivity. The detection of endogenous circulating miRNAs was performed and compared between the different types of tubes. In parallel, homologs of human miRNAs characterized as potential biomarkers of doping were sought in equine databases. The miRNA eca-miR-144, described as potential erythropoiesis stimulating agents (ESAs) administration candidate biomarker was retained and assessed in equine post-administration samples. The results about the qPCR method development and optimization are exposed as well as the equine miRNAs detection. To our knowledge, this work is the first study and the proof of concept of circulating miRNAs detection in plasma dedicated to equine doping control.
Reliable Deep Learning–Based Detection of Misplaced Chest Electrodes During Electrocardiogram Recording: Algorithm Development and Validation

Background A 12-lead electrocardiogram (ECG) is the most commonly used method to diagnose patients with cardiovascular diseases. However, there are a number of possible misinterpretations of the ECG that can be caused by several different factors, such as the misplacement of chest electrodes. Objective The aim of this study is to build advanced algorithms to detect precordial (chest) electrode misplacement. Methods In this study, we used traditional machine learning (ML) and deep learning (DL) to autodetect the misplacement of electrodes V1 and V2 using features from the resultant ECG. The algorithms were trained using data extracted from high-resolution body surface potential maps of patients who were diagnosed with myocardial infarction, diagnosed with left ventricular hypertrophy, or a normal ECG. Results DL achieved the highest accuracy in this study for detecting V1 and V2 electrode misplacement, with an accuracy of 93.0% (95% CI 91.46-94.53) for misplacement in the second intercostal space. The performance of DL in the second intercostal space was benchmarked with physicians (n=11 and age 47.3 years, SD 15.5) who were experienced in reading ECGs (mean number of ECGs read in the past year 436.54, SD 397.9). Physicians were poor at recognizing chest electrode misplacement on the ECG and achieved a mean accuracy of 60% (95% CI 56.09-63.90), which was significantly poorer than that of DL (P<.001). Conclusions DL provides the best performance for detecting chest electrode misplacement when compared with the ability of experienced physicians. DL and ML could be used to help flag ECGs that have been incorrectly recorded and flag that the data may be flawed, which could reduce the number of erroneous diagnoses.
Two new aromatic derivatives from Codonopsis pilosula and their α-glucosidase inhibitory activities

Abstract The ethanol extract of the roots of Codonopsis pilosula was subjected to chromatographic fractionation, which result in the isolation and characterization of two new aromatic derivatives 2,3-dihydroxypropyl 2,4-dihydroxy-3,6-dimethylbenzoate (1) and 2-oxopropyl 3-hydroxy-4-methoxybenzoate (2), along with three known compounds pilosulinene A (3), pollenfuran B (4) and (+)-pinoresinol (5). Their structures were demonstrated by HRESIMS and spectroscopic methods including NMR and IR. It is worth noting that compound 4 was isolated for the first time from the genus Codonopsis. The potential hypoglycemic properties of compounds 2–5 were evaluated by measuring their α-glucosidase inhibitory effects. As a result, compounds 2 and 3 showed weak α-glucosidase inhibitory activities with IC50 values of 154.8 ± 11.0 μM and 24.0 ± 2.2 μM, respectively.
Lipophilicity and Click Reactivity Determine the Performance of Bioorthogonal Tetrazine Tools in Pretargeted In Vivo Chemistry

The development of highly selective and fast biocompatible reactions for ligation and cleavage has paved the way for new diagnostic and therapeutic applications of pretargeted in vivo chemistry. The concept of bioorthogonal pretargeting has attracted considerable interest, in particular for the targeted delivery of radionuclides and drugs. In nuclear medicine, pretargeting can provide increased target-to-background ratios at early time-points compared to traditional approaches. This reduces the radiation burden to healthy tissue and, depending on the selected radionuclide, enables better imaging contrast or higher therapeutic efficiency. Moreover, bioorthogonally triggered cleavage of pretargeted antibody–drug conjugates represents an emerging strategy to achieve controlled release and locally increased drug concentrations. The toolbox of bioorthogonal reactions has significantly expanded in the past decade, with the tetrazine ligation being the fastest and one of the most versatile in vivo chemistries. Progress in the field, however, relies heavily on the development and evaluation of (radio)labeled compounds, preventing the use of compound libraries for systematic studies. The rational design of tetrazine probes and triggers has thus been impeded by the limited understanding of the impact of structural parameters on the in vivo ligation performance. In this work, we describe the development of a pretargeted blocking assay that allows for the investigation of the in vivo fate of a structurally diverse library of 45 unlabeled tetrazines and their capability to reach and react with pretargeted trans-cyclooctene (TCO)-modified antibodies in tumor-bearing mice. This study enabled us to assess the correlation of click reactivity and lipophilicity of tetrazines with their in vivo performance. In particular, high rate constants (>50 000 M–1 s–1) for the reaction with TCO and low calculated logD7.4 values (below −3) of the tetrazine were identified as strong indicators for successful pretargeting. Radiolabeling gave access to a set of selected 18F-labeled tetrazines, including highly reactive scaffolds, which were used in pretargeted PET imaging studies to confirm the results from the blocking study. These insights thus enable the rational design of tetrazine probes for in vivo application and will thereby assist the clinical translation of bioorthogonal pretargeting.
RNAi of the N‐glycosylation‐related genes confirms their importance in insect development and α‐1,6‐fucosyltransferase plays a role in the ecdysis event for the hemimetabolous pest insect Nilaparvata lugens

Recently N‐glycosylation was found to be required for the postembryonic development and metamorphosis of the holometabolous beetle Tribolium castaneum. However, the role of N‐glycosylation in the development of hemimetabolous insects is unknown. To further elucidate the role of N‐glycosylation in the development of insects, a functional characterization of the N‐glycosylation‐related genes (NGRGs) was performed in a model insect for hemimetabolous development, namely the brown planthopper Nilaparvata lugens. In this project, we report the effects of RNAi‐mediated silencing of 15 NGRGs on the postembryonic development of N. lugens. Two major observations were made. First, interruption of the early steps of N‐glycan processing led to a lethal phenotype during the transition from nymph to adult as was observed in T. castaneum. Second, we report here on an essential function for the α‐1,6‐fucosyl transferase in the ecdysis event of N. lugens between nymphal instars, since gene‐silencing by RNAi led to failure of ecdysis and subsequent mortality of the treated insect.
Potato Consumption and Risk of Site-Specific Cancers in Adults: A Systematic Review and Dose-Response Meta-Analysis of Observational Studies.

The etiology of cancer type may vary significantly due to anatomy, embryology, and physiology of the cancer site. Although the association between potato consumption and colorectal cancer (CRC) was summarized in a 2018 meta-analysis of 5 cohort studies, to the best of our knowledge, no meta-analysis has evaluated potato consumption in relation to multiple cancer sites in adults. Medline/PubMed, ISI Web of Knowledge, Scopus, and the Cochrane Database of Systematic Reviews were searched for relevant publications through August 2020. We selected cohort or case-control studies conducted in adults that reported risk estimates (relative risk [RRs], HRs, and ORs) of potato intake for any cancer type. Random effects meta-analyses compared high and low intake categories. Twenty prospective cohort studies (total n = 785,348) including 19,882 incident cases, and 36 case-control studies (21,822 cases; 66,502 controls) were included. Among cohort studies, we did not find an association between high versus low intake of total potato (white and yellow) consumption and overall cancers: 1.04 (95% CI: 0.96, 1.11; tau2 = 0.005, n = 18). We found no relation between total potato consumption (high compared with low intake) and risk of CRC, pancreatic cancer, colon, gastric, breast, prostate, kidney, lung, or bladder cancer in cohort or case-control studies. We did not find an association between high versus low consumption of potato preparations (boiled/fried/mashed/roasted/baked) and risk of gastrointestinal-, sex-hormone-, or urinary-related cancers in cohort or case-control studies. Certainty of the evidence was low for total cancer, CRC, colon, rectal, renal, pancreatic, breast, prostate, and lung cancer and very low for gastric and bladder cancer. In conclusion, potato intake or potato preparations were not associated with multiple cancer sites when comparing high and low intake categories. This finding was consistent with the findings from the 2018 meta-analysis regarding potato intake and risk of CRC.
Knowledge, attitudes, and practices towards COVID-19 among Venezuelans during the 2020 epidemic: An online cross-sectional survey

Background COVID-19 threatens health systems worldwide, but Venezuela’s system is particularly vulnerable. To prevent the spread of COVID-19, individuals must adopt preventive behaviors. However, to encourage behavior change, we must first understand current knowledge, attitudes, and practices (KAPs) that inform response to this health threat. Methods We explored KAPs among Venezuelans using a cross-sectional, internet-based questionnaire. The questionnaire explored individuals’ knowledge about COVID-19; their attitudes toward the world’s and the Venezuelan authorities’ abilities to control it; and their self-reported practices. We also collected demographic data. Binomial logistic regression analyses were used to predict the adoption of preventive behaviors based on demographic variables, individual knowledge level, and individual attitudes. Results 3122 individuals completed the questionnaire. Participants had a high level of knowledge about COVID-19. They expressed high levels of optimism that the world would eventually control COVID-19, but they were very pessimistic about the public authorities in Venezuela. Most participants adopted preventive practices. Binomial regression suggests younger people, less educated people, and manual laborers hold lower levels of knowledge, and these groups, as well as men, were less likely to adopt preventive practices. Knowledge, by itself, had no association with optimism and little association with self-reported practices. Conclusions As other KAP studies in Latin America found, knowledge is not sufficient to prompt behavior change. Venezuelans’ pessimism about their own country’s ability should be explored in greater depth. Health promotion in Venezuela may wish to target the most at risk groups: men, younger people, less educated people, and manual laborers.
Organizational empowerment and practice outcomes of acute care nurse practitioners in Taiwan: A national survey

ABSTRACT Background: Nurse practitioners (NPs) play an important role in addressing growing health care needs. Among NPs, organizational empowerment is positively associated with overall practice outcomes. Therefore, efforts to promote organizational empowerment in practice are necessary to increase job satisfaction among NPs as well as decrease the stress and intention to leave. Purpose: This study investigated the relationships of organizational empowerment and practice outcomes of job satisfaction, work stress, and intention to leave in acute care practices. Methodological orientation: This study was conducted as a cross-sectional design with a national survey of 946 acute care NPs. Questionnaires contained demographic and practice characteristics, Misener Nurse Practitioner Job Satisfaction Scale, Condition for Work Effectiveness Questionnaire II, and the work stress VAS scale. Hierarchical Linear Model (HLM) was used to investigate individual NP-level or organization-level effects on job satisfaction. The factors associated with job satisfaction were examined by stepwise multiple regression. Results: The organizational empowerment was low, work stress was moderately high, and job satisfaction was between slightly unsatisfied and slightly satisfied. The HLM results indicated that organization-level effects did not affect the job satisfaction of NPs. Nurse practitioners with greater formal power, resources, and informal power had higher job satisfaction. Conversely, NPs with an intention to leave and a higher level of stress showed lower job satisfaction. Conclusions: Organizational empowerment, intention to leave, and stress affect job satisfaction of acute care NPs in Taiwan. Implications for practic: To enhance the job satisfaction of NPs, health care administrators should empower NPs by providing access to opportunity, support, information, and resources in the health care delivery system.
Direct imaging of glymphatic transport using H217O MRI

The recently proposed glymphatic pathway for solute transport and waste clearance from the brain has been the focus of intense debate. By exploiting an isotopically enriched MRI tracer, H217O, we directly imaged glymphatic water transport in the rat brain in vivo. Our results reveal glymphatic transport that is dramatically faster and more extensive than previously thought and unlikely to be explained by diffusion alone. Moreover, we confirm the critical role of aquaporin-4 channels in glymphatic transport.
Intake of New Zealand Blackcurrant Powder Affects Skin-Borne Volatile Organic Compounds in Middle-Aged and Older Adults

Abstract Skin volatile organic compounds (VOCs) can cause body odor or reveal human disease and may result from lipid peroxidation or activity by skin bacteria. We examined the effect of intake of New Zealand blackcurrant (NZBC) powder for 77 skin VOCs in middle-aged and older adults in a crossover design. Fourteen adults (nine males, age: 55 ± 5 yrs) consumed NZBC powder for 7 days (6 g·day−1 with 138.6 mg anthocyanins). Two hours after the last intake, a passive flux sampler with trapping media was applied in the base of the neck for 1 hour. Gas chromatography-mass spectrometry was used for media analysis. Habitual anthocyanin intake was quantified using a food frequency questionnaire. Compared to control (i.e., no intake of NZBC powder), emission of six skin VOCs (i.e., 2-nonenal, acetic acid, 2-hexanone, 6-methyl-5-hepten-2-one, benzaldehyde, allyl methyl sulfide) were lower by more than 25%. Increases were observed for γ-octanolactone (+184%) and γ-decanolactone (+89%). A trend for a decrease for isovaleraldehyde, hexanal, and 2-pentanone, and an increase for heptanoic acid and γ-nonanolactone was observed. There was a significant correlation with daily habitual dietary anthocyanin intake for control values of hexanal and percentage change of γ-octanolactone. NZBC powder can change emanation of some VOCs in human skin. Analysis of skin VOCs following specific polyphenol intake may address the impact of dietary components to affect internal metabolic processes, body odor, and health.
Risk of HIV Diagnosis Following Bacterial Sexually Transmitted Infections in Tennessee, 2013–2017

A population-based, Southern statewide observational cohort study found that syphilis was associated with the highest risk of incident human immunodeficiency virus diagnosis overall as compared with chlamydia, regardless of self-reported sexual practices. Background Data on associations between sexually transmitted infections (STIs) and incident human immunodeficiency virus (HIV) diagnoses beyond men who have sex with men (MSM) are lacking. Identifying STIs associated with greatest risk of incident HIV diagnosis could help better target HIV testing and prevention interventions. Methods The STI and HIV surveillance data from individuals 13 years or older in Tennessee from January 2013 to December 2017 were cross-matched. Individuals without diagnosed HIV, but with reportable STIs (chlamydia, gonorrhea, syphilis) were followed up from first STI diagnosis until HIV diagnosis or end of study. Cox regression with time-varying STI exposure was used to estimate adjusted hazard ratios (aHRs) and 95% confidence intervals (CI) for subsequent HIV diagnosis; results were stratified by self-reported MSM. Results We included 148,465 individuals without HIV (3831 MSM; 144,634 non-MSM, including heterosexual men and women) diagnosed with reportable STIs; 473 had incident HIV diagnoses over 377,823 person-years (p-y) of follow-up (median, 2.6 p-y). Controlling for demographic and behavioral factors, diagnoses of gonorrhea, early syphilis, late syphilis, and STI coinfection were independently associated with incident HIV diagnosis compared with chlamydia. Early syphilis was associated with highest HIV diagnosis risk overall (aHR, 5.5; 95% CI, 3.5–5.8); this risk was higher for non-MSM (aHR, 12.3; 95% CI, 6.8–22.3) versus MSM (aHR, 2.9; 95% CI, 1.7–4.7). Conclusions While public health efforts often focus on MSM, non-MSM with STIs is also a subgroup at high risk of incident HIV diagnosis. Non-MSM and MSM with any STI, particularly syphilis, should be prioritized for HIV testing and prevention interventions.
Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France

Following the spread of the SARS-CoV-2 B.1. 1.7 variant, social distancing was strengthened in France in January 2021. Using a two-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalisations to plateau by decreasing transmission of the historical strains while B.1. 1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalisations is expected, despite the foreseen increase in vaccination rhythm.