Miracle-dz/UniFAR-FTUs huggingface dataset:
Teachers’ perceptions of teaching physical education using online learning during the COVID-19: A quantitative study in Turkey

Introduction This quantitative study aimed to determine physical education teachers’ (PETs) perceptions of online physical education (OLPE) during the COVID-19 pandemic in Turkey. Methods An OLPE teaching survey during the COVID-19 was used, comprising PETs’ opinions on OLPE teaching as well as the advantages, disadvantages, difficulties, and suggestions for OLPE teaching. Results A significant difference by gender was identified in the individual approach to student learning, greater student independence, and ongoing monitoring of student results for teachers, parents, and students. In addition, a significant difference was found by gender in the difficulty in implementing the core curriculum content as well as by school type in the lack of proper home equipment, absence of or limited Internet access, and problems with connecting the computer, tablet, or smartphone to the Internet. Moreover, PETs stated that OLPE teaching is not only the best way to transfer basic information, but it also gives them an opportunity to learn digital technology by devoting time for research for self-improvement. However, they stated that students do not perceive OLPE as a lesson, as student participation is lacking. Moreover, there are deficiencies in students’ social-emotional development. They also stated that the content of the lessons was insufficient, and they were unable to make the lesson interesting. Conclusion PETs’ suggested recommendations included enriching the course content, increasing the lesson time, developing a new curriculum, and creating a platform to access course resources.
Using haematophagous fly blood meals to study the diversity of blood‐borne pathogens infecting wild mammals

Many emerging infectious diseases originate from wild animals, so there is a profound need for surveillance and monitoring of their pathogens. However, the practical difficulty of sample acquisition from wild animals tends to limit the feasibility and effectiveness of such surveys. Xenosurveillance, using blood‐feeding invertebrates to obtain tissue samples from wild animals and then detect their pathogens, is a promising method to do so. Here, we describe the use of tsetse fly blood meals to determine (directly through molecular diagnostic and indirectly through serology), the diversity of circulating blood‐borne pathogens (including bacteria, viruses and protozoa) in a natural mammalian community of Tanzania. Molecular analyses of captured tsetse flies (182 pools of flies totalizing 1728 flies) revealed that the blood meals obtained came from 18 different vertebrate species including 16 non‐human mammals, representing approximately 25% of the large mammal species present in the study area. Molecular diagnostic demonstrated the presence of different protozoa parasites and bacteria of medical and/or veterinary interest. None of the six virus species searched for by molecular methods were detected but an ELISA test detected antibodies against African swine fever virus among warthogs, indicating that the virus had been circulating in the area. Sampling of blood‐feeding insects represents an efficient and practical approach to tracking a diversity of pathogens from multiple mammalian species, directly through molecular diagnostic or indirectly through serology, which could readily expand and enhance our understanding of the ecology and evolution of infectious agents and their interactions with their hosts in wild animal communities.
Use of Human Intestinal Enteroids to Evaluate Persistence of Infectious Human Norovirus in Seawater

Little data on the persistence of human norovirus infectivity are available to predict its transmissibility. Using human intestinal enteroids, we demonstrate that 2 human norovirus strains can remain infectious for several weeks in seawater. Such experiments can improve understanding of factors associated with norovirus survival in coastal waters and shellfish.
A myriad of posterior fossa cysts: A single center experience

Antenatal posterior fossa cystic lesions are intimidating due to overlapping imaging features of benign and severe malformations. Sonographic assessment of the posterior fossa with good resolution median sagittal and axial views, either primary or secondarily reconstructed, plays the lead role in antenatal evaluation, further enhanced when sequential assessments are added. We present 10 cases of fetal posterior fossa cystic lesions diagnosed in the first and second trimesters that were sequentially analyzed and followed up till delivery or termination. The ultrasound imaging appearance, evolution, and morphometry have been presented in this article.
The effect of an HIV preexposure prophylaxis panel management strategy to increase preexposure prophylaxis prescriptions

Objective: The HIV preexposure prophylaxis optimization intervention (PrEP-OI) study evaluated the efficacy of a panel management intervention using PrEP coordinators and a web-based panel management tool to support healthcare providers in optimizing PrEP prescription and ongoing PrEP care. Design: The PrEP-OI study was a stepped-wedge randomized clinical trial conducted across 10 San Francisco Department of Public Health primary care sites between November 2018 and September 2019. Each month, clinics one-by-one initiated PrEP-OI in random order until all sites received the intervention by the study team. Methods: The primary outcome was the number of PrEP prescriptions per month. Secondary outcomes compared pre- and postintervention periods on whether PrEP was discussed and whether PrEP-related counseling (e.g., HIV risk assessment, risk reduction counseling, PrEP initiation/continuation assessment) was conducted. Prescription and clinical data were abstracted from the electronic health records. We calculated incidence rate ratios (IRR) and risk ratios (RR) to estimate the intervention effect on primary and secondary outcomes. Results: The number of PrEP prescriptions across clinics increased from 1.85/month (standard deviation [SD] = 2.55) preintervention to 2.44/month (SD = 3.44) postintervention (IRR = 1.34; 95% confidence interval [CI] = 1.05–1.73; P = 0.021). PrEP-related discussions during clinic visits (RR = 1.13; 95% CI = 1.04–1.22; P = 0.004), HIV risk assessment (RR = 1.40; 95% CI = 1.14–1.72; P = 0.001), and risk reduction counseling (RR = 1.16; 95% CI = 1.03–1.30; P = 0.011) increased from the pre- to the postintervention period. Assessment of PrEP initiation/continuation increased over time during the postintervention period (RR = 1.05; 95% CI = 0.99–1.11; P = 0.100). Conclusions: A panel management intervention using PrEP coordinators and a web-based panel management tool increased PrEP prescribing and improved PrEP-related counseling in safety-net primary care clinics.
Clinical, radiologic, and physiologic features of idiopathic pulmonary fibrosis (IPF) with and without emphysema

ABSTRACT Background Idiopathic pulmonary fibrosis (IPF) can combine with emphysema, a condition termed as IPF with emphysema (IPFE). We compared the clinical, radiologic, and physiologic features of IPF and IPFE. Research design and methods Newly diagnosed IPF and IPFE patients were recruited between January 2018 and September 2020. Symptoms, high resolution computed tomography (HRCT), pulmonary function test (PFT) data, composite physiologic index (CPI), gender-age-physiology (GAP) scores, and follow-up data were obtained. Results The IPFE group had greater proportion of male smokers, and of lung cancer cases. The IPFE group had higher VC, FVC FEV1, and lower FEV1/FVC and DLCO and lower percent fibrosis on HRCT. Both groups had similar symptoms and mortality. Mortality rate was associated with inability to perform PFT, CPI, GAP scores, percent fibrosis, VC, FVC, FEV1, and DLCO, serum SCC-Ag and CA125, and anti-fibrotic therapy (≥12 months) in IPF, while it was associated with inability to perform PFT, CPI, percent fibrosis, DLCO, serum CEA, CYFRA21-1 and CA125, and anti-fibrotic therapy (≥12 months) in IPFE. Conclusion IPF and IPFE patients are different in smoking history, physiologic indices, HRCT patterns and prognostic factors, however, they have similar mortality. Anti-fibrotic therapy could improve the survival rate in both IPF and IPFE.
A healthy plant-based diet is favorably associated with cardiometabolic risk factors among participants of South Asian ancestry.

BACKGROUND Plant-based diets are recommended for chronic disease prevention, yet there has been little focus on plant-based diet quality among participants of South Asian ancestry who consume a predominantly plant-based diet. OBJECTIVE We evaluated cross-sectional and prospective associations between plant-based diet quality and cardiometabolic risk among participants of South Asian ancestry who are living in the US. DESIGN We included 891 participants of South Asian ancestry who completed the baseline visit in the Mediators of Atherosclerosis in South Asians Living in America (MASALA) study. The prospective analysis included 735 participants who completed exam 2 (∼5 y after baseline). Plant-based diet quality was assessed using 3 indices - an overall plant-based diet index (PDI) that summarizes the consumption of plant foods, a healthful PDI (hPDI) that measures consumption of healthy plant foods, and an unhealthful PDI (uPDI) that reflects consumption of less-healthy plant foods. RESULTS At baseline, the PDI was inversely associated with fasting glucose. We observed an inverse association between PDI and hPDI with HOMA-IR, LDL-C, weight, and BMI (all P<0.05). Higher scores on the hPDI, but not PDI, were associated with lower glycated hemoglobin, higher adiponectin, lower visceral fat area and pericardial fat volume. Each 5-unit higher hPDI was associated with a lower likelihood of fatty liver (odds ratio [OR] 0.76 [95% CI: 0.64, 0.90]), and obesity (OR 0.88 [95% confidence interval (CI): 0.80, 0.97]). There were no associations between uPDI and cardiometabolic risk. Prospectively, after covariate adjustment for baseline values, each 5-unit higher hPDI was associated with an 18% lower risk of incident type 2 diabetes (OR 0.82 [95% CI: 0.67, 1.00]). CONCLUSIONS A higher intake of healthful plant-based foods was associated with a favorable cardiometabolic risk profile. Dietary recommendations to lower chronic disease risk among participants of South Asian ancestry should focus on the quality of plant-based foods.
Occupational doses in interventional angiography after radiological protection training and use of a real-time direct display dosimeter

Vascular x-ray guided interventions are complex and may result in high occupational doses to ionising radiation if staff do not take appropriate actions to minimise their exposure. In this prospective intervention study, ten staff members wore an extra personal dosimeter on the upper body above their regular protective clothing during four consecutive periods. Between each period either additional practical radiological protection training was given or a real-time direct display dosimeter were provided to the staff. Each staff’s personal dose equivalent, Hp(10) normalised to the total air kerma-area product for the procedures where each staff were involved, KAPt, was used as the dependent variable. A focus-group interview with the staff were performed about the usefulness of the training and real-time dose rate display system. Our aim was to investigate if the interventions (practical training or real-time dose rate display) did affect the staff doses in the short and long term (five months later). Significant (p < 0.05) reductions of staff doses Hp(10)/KAPt were found after practical radiological protection training, but not after using real-time dose rate displays. Significant reductions were maintained after five months without additional interventions. The results from the focus-group interview indicated that making radiation ‘visible’, during practical training and usage of real-time direct display dosimeter, made it easier to understand how to act to lower occupational doses.
Associations between HIV viremia during antiretroviral therapy and cardiovascular disease

Objective: To investigate the association between HIV viremia exposure during antiretroviral therapy (ART) and cardiovascular disease (CVD) risk. Design: Nationwide observational cohort. Methods: Participants (age >15 years) from the Swedish nationwide InfCareHIV register initiating ART 1996–2017 were categorized in a time-updated manner into four viremia categories, starting from 12 months after ART initiation: suppression (<50 copies/ml), low-level viremia (50–199 copies/ml and 200–999 copies/ml, respectively), and high-level viremia (≥1000 copies/ml). In addition, cumulative viremia was estimated as the area under the log viral load (VL) curve. Proportional subhazard models adjusted for sex, age, pre-ART CD4 and VL, injection drug use, and country of birth were used to analyze the association between viremia exposure and CVD risk (ischemic heart disease, stroke, and heart failure; data obtained by linkage to national registers), accounting for the competing risk of non-CVD death. Results: In all, 337 cases of CVD were observed during 44 937 person-years of follow-up (n = 6562). Higher viremia exposure was associated with CVD, both when parameterized as cumulative viremia (adjusted subhazard ratio [aSHR] per 1 log10 copy × year/ml, 1.03; 95% confidence interval [CI], 1.01–1.05) and as viremia category (aSHR for high-level viremia versus suppression, 1.45; 95% CI, 1.03–2.05). We observed no association between CVD and low-level viremia compared with those with suppression. Conclusions: Higher exposure to HIV viremia was linked to CVD in ART recipients, whereas no increased risk was detected for people with low-level viremia compared with viral suppression. Causal inference is limited by the observational nature of this study.
Incidence, risk factors, and outcomes of pulmonary hyperten- sion in preterm infants with bronchopulmonary dysplasia

Objectives: To determine the incidence and risk factors for pulmonary hypertension (PH) in preterm infants with moderate to severe bronchopulmonary dysplasia (BPD) and to compare shortterm outcomes. Methods: Preterm infants <32 weeks gestation born August 2013 through July 2015 with moderate to severe BPD at 36 weeks postmenstrual age were categorized into BPD-PH (exposure) and BPDnoPH (control) groups. Results: Of 92 infants with BPD, 87 had echocardiographic assessment, of whom 24 (28%) had PH. On multiple logistic regression after adjustment for gestational age and sex, no significant risk factors for PH were identified based on data from this cohort. There were no differences in resource utilization or clinical outcomes including survival to discharge. Conclusion: Approximately one out of four patients with moderate to severe BPD were identified as having PH. No significant risk factors for PH were identified. No differences in outcomes were identified for those with and without PH.
Original Articles Temporal and Regional Expression of Glucose-Dependent Insulinotropic Peptide and Its Receptor in Spinal Cord Injured Rats

Spinal cord injury (SCI) results in loss of movement, sensibility, and autonomic control at the level of the lesion and at lower parts of the body. Several experimental strategies have been used in attempts to increase endogenous mechanisms of neuroprotection, neuroplasticity, and repair, but with limited success. It is known that glucose-dependent insulinotropic peptide (GIP) and its receptor (GIPR) can enhance synaptic plasticity, neurogenesis, and axonal outgrowth. However, their role in the injury has never been studied. The aim of this study was to evaluate the changes in expression levels of both GIP and GIPR in acute and chronic phases of SCI in rats. Following SCI (2 to 24 h after damage), the rat spinal cord showed a lesion in which the epicenter had a cavity with hemorrhage and necrosis. Furthermore, the lesion cavity also showed ballooned cells 14 and 28 days after injury. We found that SCI induced increases in GIPR expression in areas neighboring the site of injury at 6 h and 28 days after the injury. Moreover, higher GIP expression was observed in these regions on day 28. Neuronal projections from the injury epicenter showed an increase in GIP immunoreactivity 24 h and 14 and 28 days after SCI. Interestingly, GIP was also found in progenitor cells at the spinal cord canal 24 h after injury, whereas both GIP and GIPR were present in progenitor cells at the injury epicenter 14 days after in SCI animals. These results suggest that GIP and its receptor might be implicated with neurogenesis and the repair process after SCI.
Progression of Unifocal vs. Multifocal Geographic Atrophy in Age-related Macular Degeneration: A Systematic Review and Meta-analysis

Topic: Determining the natural history of unifocal versus multifocal geographic atrophy (GA) secondary to non-exudative age-related macular degeneration. Clinical Relevance: The association between GA focality (i.e., unifocal versus multifocal lesions) and enlargement rate is inconsistent in the literature, with some studies reporting a comparable growth rate between unifocal and multifocal GA, whereas others suggesting the growth rate varies widely between the 2 groups. Methods: We searched 5 literature databases up to May 3rd, 2019 for studies that classified treatment-naïve GA patients based on lesion focality. We performed random effects meta-analysis to determine the growth rates of GA. To account for different entry times among cohorts, we introduced a horizontal translation factor to the dataset of each cohort. Heterogeneity and study quality were assessed using I2 statistic and Quality In Prognosis Studies tool, respectively. Publication bias was evaluated by funnel plots and the Egger test. Results: We included 12 studies with 3489 eyes from 3001 patients. After the introduction of translation factors, the effective radius of unifocal and multifocal GA enlarged linearly over approximately 7 years. The effective radius growth rate of multifocal GA (0.199 ± 0.012 mm/year) was 46.3% higher than the growth rate of unifocal GA (0.136 ± 0.008 mm/years) (P < 0.001). Interestingly, unifocal and multifocal GA lesions with the same total baseline area grew at vastly different rates, with an estimated ratio of the growth rate as 1.46 (between 2 and 3). This difference disappeared after we accounted for different baseline total perimeter between unifocal and multifocal groups. The measured GA growth rate was consistent across studies using color fundus photography, fundus autofluorescence, or optical coherence tomography (P = 0.35–0.99). Corresponding author: Lucian V. Del Priore, MD, PhD, Robert R. Young Professor and Chair, Department of Ophthalmology and Visual Science, Yale University School of Medicine, 40 Temple Street, Suite 1B, New Haven, CT 06510 (lucian.delpriore@yale.edu). Conflict of Interest: L. L. Shen, None; M. Sun, None; H. K. Grossetta Nardini, None; L. V. Del Priore, Astellas Institute for Regenerative Medicine (Consultant). Address for reprints: 40 Temple Street, Suite 1B, New Haven, CT 06510. HHS Public Access Author manuscript Ophthalmol Retina. Author manuscript; available in PMC 2021 September 01. Published in final edited form as: Ophthalmol Retina. 2020 September ; 4(9): 899–910. doi:10.1016/j.oret. 2020.03. 020. A uhor M anscript
Genome analysis Bioinformatics pipeline using JUDI: Just Do It!

Summary: Large-scale data analysis in bioinformatics requires pipelined execution of multiple software. Generally each stage in a pipeline takes considerable computing resources and several workﬂow management systems (WMS), e.g. Snakemake, Nextﬂow, Common Workﬂow Language, Galaxy, etc. have been developed to ensure optimum execution of the stages across two invocations of the pipeline. However, when the pipeline needs to be executed with different settings of parameters, e.g. thresholds, underlying algorithms, etc. these WMS require signiﬁ-cant scripting to ensure an optimal execution. We developed JUDI on top of DoIt , a Python based WMS, to systematically handle parameter settings based on the principles of database management systems. Using a novel modular approach that encapsulates a parameter database in each task and ﬁle associated with a pipeline stage, JUDI simpliﬁes plug-and-play of the pipeline stages. For a typical pipeline with n parameters, JUDI reduces the number of lines of scripting required by a factor of O ( n ). With properly designed parameter databases, JUDI not only enables reproducing research under published values of parameters but also facilitates exploring newer results under novel parameter settings.
Hexokinase Regulates Susceptibility to Bax-Mediated Mitochondrial Membrane Injury after Ischemic Stress

Hexokinase (HK), the rate-limiting enzyme in glycolysis, regulates cell survival either by promoting metabolism and/or inhibiting apoptosis. HKI and HKII, isoforms with mitochondrial targeting sequences, were studied in renal epithelial cells after ATP depletion, an insult that activates GSK3β and Bax, induces mitochondrial membrane injury and causes apoptosis. Stress decreased total ATP content, caused HKII to dissociate from mitochondria, released mitochondrial apoptosis inducing factor (AIF) and cytochrome c, activated caspase-3 and reduced cell survival. Compared to control, HKI or II over-expression improved survival after stress without preventing GSK3β or Bax activation, increasing ATP content, or reducing mitochondrial fragmentation. HKI or HKII over-expression increased mitochondria-associated, isoform-specific HK content and decreased mitochondrial membrane injury and apoptosis. In vivo, HKII localized to the murine proximal tubule. Ischemia reduced total HKII content and caused mitochondrial HKII dissociation in proximal but not distal tubules. In HK over-expressing cells, HKII and Bax did not interact before or after stress. However, HK over-expression increased organelle-associated HK during stress and decreased mitochondrial Bax accumulation, outer membrane injury and apoptosis in a manner that appears to be independent of its effect on renal epithelial cell ATP content, suggesting that HK and Bax compete for similar mitochondrial membrane binding sites.
Comparing the Diagnostic Performance of QuantiFERON-TB Gold Plus to Other Tests of Latent Tuberculosis Infection: A Systematic Review and Meta-analysis

Received 22 June 2020; editorial decision 22 November 2020; published online 7 December 2020. Protocol registered at PROSPERO: CRD42019146546 Correspondence: Dick Menzies, Office 3D.58, 5252 Boulevard de Maisonneuve O, Montréal, QB H4A 3S5, Canada (dick.menzies@mcgill.ca). Clinical Infectious Diseases 2021;73(5):e1116–25 © The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com. DOI: 10.1093/cid/ciaa1822 Comparing the Diagnostic Performance of QuantiFERON-TB Gold Plus to Other Tests of Latent Tuberculosis Infection: A Systematic Review and Meta-analysis