Miracle-dz/UniFAR-FTUs huggingface dataset:
SARS-CoV-2 reinfections during the Delta and Omicron waves

BACKGROUND Increased SARS-CoV-2 reinfection rates have been reported recently, with some locations basing reinfection on a second positive PCR test at least 90 days after initial infection. In this study, we used Johns Hopkins SARS-CoV-2 genomic surveillance data to evaluate the frequency of sequencing-validated, confirmed, and inferred reinfections between March 2020 and July 2022. METHODS Patients who had 2 or more positive SARS-CoV-2 tests in our system, with samples sequenced as a part of our surveillance efforts, were identified as the cohort for our study. SARS-CoV-2 genomes of patients’ initial and later samples were compared. RESULTS A total of 755 patients (920 samples) had a positive test at least 90 days after the initial test, with a median time between tests of 377 days. Sequencing was attempted on 231 samples and was successful in 127. Rates of successful sequencing spiked during the Omicron surge; there was a higher median number of days from initial infection in these cases compared with those with failed sequences. A total of 122 (98%) patients showed evidence of reinfection; 45 of these patients had sequence-validated reinfection and 77 had inferred reinfections (later sequencing showed a clade that was not circulating when the patient was initially infected). Of the 45 patients with sequence-validated reinfections, 43 (96%) had reinfections that were caused by the Omicron variant, 41 (91%) were symptomatic, 32 (71%) were vaccinated prior to the second infection, 6 (13%) were immunosuppressed, and only 2 (4%) were hospitalized. CONCLUSION Sequence-validated reinfections increased with the Omicron surge but were generally associated with mild infections. FUNDING Funding was provided by the Johns Hopkins Center of Excellence in Influenza Research and Surveillance (HHSN272201400007C), CDC (75D30121C11061), Johns Hopkins University President’s Fund Research Response, Johns Hopkins Department of Pathology, and the Maryland Department of Health.
Effects of low and high intensity interval training exercises on VO2max and components of neuromuscular and vascular system in male volunteers

Abstract Objectives: To evaluate the effects of different intensity exercises on maximal oxygen consumption (VO2max and levels of components, namely brain-derived neurotrophic factor (BDNF), tyrosine kinase receptor B (TrKB), vascular endothelial growth factor (VEGF), peroxisome proliferator activated receptor-gamma coactivator (PGC-1α), and irisin. Methods: Thirty-six male participants were divided into control (CNT), low-intensity (LIIT), and high-intensity interval training (HIIT) groups. LIIT and HIIT groups consisted of 8 exercises (20 s work and rest in each repetition, respectively) conducted for 4 weeks. VO2max and protein component levels were determined pre- and post-training. VO2max capacity was also determined using the Yo Yo Intermittent Recovery Test-1 (Yo Yo IR-1). Statistical analysis was conducted to determine significance of the differences observed. Results: According to the YoYo IR-1, VO2max, serum BDNF, VEGF, PGC1α, irisin, and TrkB data obtained in the study, a statistically significant difference between the groups was observed (p<0.05). While the interaction effect was found to be statistically significant in the study using PGC1α, VEGF, and TrkB data (p<0.05), it was not found to be statistically significant using YoYo IR-1, VO2max, serum BDNF, or irisin data (p>0.05). Conclusion: HIIT and LIIT improved all study parameters, while HIIT showed a greater effect than LIIT.
International pediatric surgery partnerships in sub-Saharan Africa: a scoping literature review

ABSTRACT Background Sub-Saharan Africa (SSA) faces a critical shortage of pediatric surgical providers. International partnerships can play an important role in pediatric surgical capacity building but must be ethical and sustainable. Objective The purpose of this study is to perform a scoping literature review of international pediatric surgery partnerships in SSA from 2009 to 2019. We aim to categorize and critically assess past partnerships to aid in future capacity-building efforts. Methods We performed a scoping literature review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Scoping Reviews (PRISMA-ScR) guidelines. We searched the PubMed and Embase databases for articles published from 2009 to 2019 using 24 keywords. Articles were selected according to inclusion criteria and assessed by two readers. Descriptive analyses of the data collected were conducted in Excel. Results A total of 2376 articles were identified. After duplicates were removed, 405 articles were screened. In total, 83 articles were assessed for eligibility, and 62 were included in the review. The most common partnership category was short-term surgical trip (28 articles, 45%). A total of 35 articles (56%) included education of host country providers as part of the partnership. Only 45% of partnerships included follow-up care, and 50% included postoperative outcomes when applicable. Conclusions To increase sustainability, more partnerships must include education of local health-care providers, and short-term surgical trips must be integrated into long-term partnerships. More partnerships need to report postoperative outcomes and ensure follow-up care. Educating peri-operative providers, training general surgeons in common pediatric procedures, and increasing telehealth use are other goals for future partnerships.
A psychological flexibility perspective on well-being: Emotional reactivity, adaptive choices, and daily experiences.

According to psychological flexibility theory, fully experiencing one's emotions, even when they involve negative reactions, can enhance psychological well-being. In pursuit of this possibility, procedures capable of disentangling reaction intensities from reaction durations, in response to affective images, were developed and variations of this paradigm were applied in understanding variations in happiness and adaptive behavior. Consistent with psychological flexibility theory, three studies showed that more intense emotional reactions, irrespective of valence, were associated with higher levels of well-being. Two additional studies showed that happy individuals, relative to less happy individuals, exhibited more functional approach/avoidance behavior in behavior-focused tasks. Together, the results are consistent with the idea that adaptive emotion generation systems are those that flexibly adapt emotion output to concurrent emotion-related stimulation. The program of research adds to our understanding of the relationship between emotion reactivity and well-being while highlighting specific processes through which emotion and well-being interact. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
Psychometric properties of the English version of the Audio Processor Satisfaction Questionnaire (APSQ)

Objective The Audio Processor Satisfaction Questionnaire (APSQ) is a standardized tool to measure a user’s satisfaction with their audio processor(s). It was first developed and validated in the German language. The purpose of the current study was to validate the English version of the APSQ. Design The 15 items of the APSQ were translated into English. Item and scale analyses assessed the quality of individual items and of the questionnaire in its entirety. Study sample Sixty-seven adults with hearing implants participated. Forty-six of them completed the questionnaire twice within 2–4 weeks. Results High mean values were obtained with total scores and with scores of the comfort, social life, and usability domains, indicating that users are generally satisfied with their audio processors. The questionnaire achieved good test-retest reliability with high internal consistency. A significant positive correlation between time since implantation and user satisfaction was found. Conclusion Results of the item and reliability analyses suggest that the English version of the APSQ is a valid and reliable tool to assess user satisfaction with their audio processor(s).
Endothelial versus pronephron fate decision is modulated by the transcription factors Cloche/Npas4l, Tal1, and Lmo2

Endothelial specification is a key event during embryogenesis; however, when, and how, endothelial cells separate from other lineages is poorly understood. In zebrafish, Npas4l is indispensable for endothelial specification by inducing the expression of the transcription factor genes etsrp, tal1, and lmo2. We generated a knock-in reporter in zebrafish npas4l to visualize endothelial progenitors and their derivatives in wild-type and mutant embryos. Unexpectedly, we find that in npas4l mutants, npas4l reporter–expressing cells contribute to the pronephron tubules. Single-cell transcriptomics and live imaging of the early lateral plate mesoderm in wild-type embryos indeed reveals coexpression of endothelial and pronephron markers, a finding confirmed by creERT2-based lineage tracing. Increased contribution of npas4l reporter–expressing cells to pronephron tubules is also observed in tal1 and lmo2 mutants and is reversed in npas4l mutants injected with tal1 mRNA. Together, these data reveal that Npas4l/Tal1/Lmo2 regulate the fate decision between the endothelial and pronephron lineages.
HTT (huntingtin) and RAB7 co-migrate retrogradely on a signaling LAMP1-containing late endosome during axonal injury

ABSTRACT HTT (huntingtin) is a 350-kDa protein of unknown function. While HTT moves bidirectionally within axons and HTT loss/reduction causes axonal transport defects, the identity of cargo-containing vesicles that HTT helps move remain elusive. Previously, we found an axonal retrogradely moving HTT-Rab7 vesicle complex; however, its biological relevance is unclear. Using Drosophila genetics, in vivo microscopy, membrane isolation and pharmacological inhibition, here we identified that adaptors Hip1 and Rilpl aid the retrograde motility of LAMP1-containing HTT-Rab7 late endosomes, not autophagosomes. Reduction of Syx17 and chloroquine- or bafilomycin A1-mediated pharmacological inhibition, but not reduction of Atg5, disrupted the in vivo motility of these vesicles. Further, because HTT-Rab7 vesicles colocalized with long-distance signaling components (BMP signaling: tkv-wit, injury: wnd) and move in a retrograde direction after Drosophila nerve crush, we propose that these vesicles likely traffic damage signals following axonal injury. Together, our findings support a previously unknown role for HTT in the retrograde movement of a Rab7-LAMP1-containing signaling late endosome. Abbreviations Atg5: Autophagy-related 5; Atg8a: Autophagy-related 8a; AL: autolysosome; AP: autophagosome; BAF1: bafilomycin A1; BDNF: brain derived neurotrophic factor; BMP: bone morphogenetic protein; Cyt-c-p: Cytochrome c proximal; CQ: chloroquine; DCTN1: dynactin 1; Dhc: dynein heavy chain; EE: early endosome; DYNC1I1: dynein cytoplasmic 1 intermediate chain 1; HD: Huntington disease; HIP1/Hip1: huntingtin interacting protein 1; HTT/htt: huntingtin; iNeuron: iPSC-derived human neurons; IP: immunoprecipitation; Khc: kinesin heavy chain; KIF5C: kinesin family member 5C; LAMP1/Lamp1: lysosomal associated membrane protein 1; LE: late endosome; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K12/DLK: mitogen-activated protein kinase kinase kinase 12; MAPK8/JNK/bsk: mitogen-activated protein kinase 8/basket; MAPK8IP3/JIP3: mitogen-activated protein kinase 8 interacting protein 3; NGF: nerve growth factor; NMJ: neuromuscular junction; NTRK1/TRKA: neurotrophic receptor tyrosine kinase 1; NRTK2/TRKB: neurotrophic receptor tyrosine kinase 2; nuf: nuclear fallout; PG: phagophore; PtdIns3P: phosphatidylinositol-3-phosphate; puc: puckered; ref(2)P: refractory to sigma P; Rilpl: Rab interacting lysosomal protein like; Rip11: Rab11 interacting protein; RTN1: reticulon 1; syd: sunday driver; SYP: synaptophysin; SYT1/Syt1: synaptotagmin 1; STX17/Syx17: syntaxin 17; tkv: thickveins; VF: vesicle fraction; wit: wishful thinking; wnd: wallenda
The collateral damage of COVID-19 to cardiovascular services: a meta-analysis

Abstract Aims The effect of the COVID-19 pandemic on care and outcomes across non-COVID-19 cardiovascular (CV) diseases is unknown. A systematic review and meta-analysis was performed to quantify the effect and investigate for variation by CV disease, geographic region, country income classification and the time course of the pandemic. Methods and results From January 2019 to December 2021, Medline and Embase databases were searched for observational studies comparing a pandemic and pre-pandemic period with relation to CV disease hospitalisations, diagnostic and interventional procedures, outpatient consultations, and mortality. Observational data were synthesised by incidence rate ratios (IRR) and risk ratios (RR) for binary outcomes and weighted mean differences for continuous outcomes with 95% confidence intervals. The study was registered with PROSPERO (CRD42021265930). A total of 158 studies, covering 49 countries and 6 continents, were used for quantitative synthesis. Most studies (80%) reported information for high-income countries (HICs). Across all CV disease and geographies there were fewer hospitalisations, diagnostic and interventional procedures, and outpatient consultations during the pandemic. By meta-regression, in low-middle income countries (LMICs) compared to HICs the decline in ST-segment elevation myocardial infarction (STEMI) hospitalisations (RR 0.79, 95% confidence interval [CI] 0.66–0.94) and revascularisation (RR 0.73, 95% CI 0.62–0.87) was more severe. In LMICs, but not HICs, in-hospital mortality increased for STEMI (RR 1.22, 95% CI 1.10–1.37) and heart failure (RR 1.08, 95% CI 1.04–1.12). The magnitude of decline in hospitalisations for CV diseases did not differ between the first and second wave. Conclusions There was substantial global collateral CV damage during the COVID-19 pandemic with disparity in severity by country income classification.
Bezlotoxumab prevents extraintestinal organ damage induced by Clostridioides difficile infection

ABSTRACT Clostridioides difficile is the most common cause of infectious antibiotic-associated diarrhea, with disease mediated by two major toxins TcdA and TcdB. In severe cases, systemic disease complications may arise, resulting in fatal disease. Systemic disease in animal models has been described, with thymic damage an observable consequence of severe disease in mice. Using a mouse model of C. difficile infection, we examined this disease phenotype, focussing on the thymus and serum markers of systemic disease. The efficacy of bezlotoxumab, a monoclonal TcdB therapeutic, to prevent toxin mediated systemic disease complications was also examined. C. difficile infection causes toxin-dependent thymic damage and CD4+CD8+ thymocyte depletion in mice. These systemic complications coincide with changes in biochemical markers of liver and kidney function, including increased serum urea and creatinine, and hypoglycemia. Administration of bezlotoxumab during C. difficile infection prevents systemic disease and thymic atrophy, without blocking gut damage, suggesting the leakage of gut contents into circulation may influence systemic disease. As the thymus has such a crucial role in T cell production and immune system development, these findings may have important implications in relapse of C. difficile disease and impaired immunity during C. difficile infection. The prevention of thymic atrophy and reduced systemic response following bezlotoxumab treatment, without altering colonic damage, highlights the importance of systemic disease in C. difficile infection, and provides new insights into the mechanism of action for this therapeutic. Abbreviations: Acute kidney injury (AKI); Alanine Transaminase (ALT); Aspartate Aminotransferase (AST); C. difficile infection (CDI); chronic kidney disease (CKD); combined repetitive oligo-peptides (CROPS); cardiovascular disease (CVD); Double positive (DP); hematoxylin and eosin (H&E); immunohistochemical (IHC); multiple organ dysfunction syndrome (MODS); phosphate buffered saline (PBS); standard error of the mean (SEM); surface layer proteins (SLP); Single positive (SP); wild-type (WT).
Finite size effects on the collective oscillations of a trapped Bose gas

Sum rules are used to calculate the corrections to the hydrodynamic collective frequencies of a harmonically trapped Bose gas at T=0, due to finite size effects. We show that, with logarithmic accuracy, the relative corrections behave like $(a_{ho}/R)^4\log(R/a_{ho})$, where $R$ is the Thomas-Fermi radius of the condensate and $a_{ho}$ is the oscillator length. Results are given for both spherical and axi-symmetric trapping.
Motor and somatosensory symptoms determine cognitive error levels in functional neurological symptom disorder/conversion disorder.

INTRODUCTION The level of cognitive error in functional neurological symptom disorder (FNSD, conversion disorder) subtypes [psychogenic non-epileptic seizure (PNES), motor (M), PNES plus motor (PM), motor plus somatosensory (MS)] have not yet been investigated. AIM We aimed to qualify the level of cognitive error in FNSD subtypes. MATERIALS AND METHODS The disorder symptoms were assessed via the somatoform dissociation questionnaire (SDQ), the symptom check list-90-revised (SCL-90-R), and the global assessment scale (GAS). The cognitive distortions scale (CDS) was used to evaluate cognitive errors. RESULTS Mean ages of groups were 28.37±6.99 years (PNES, n=24), 27.90±6.22 years (M, n=21), 30.36±7.86 years (PM, n=19), 31.38±9.02 years (MS, n=21), and 30.87±7.17 years (control, n=48) (p=0.377). In terms of the global severity index of SCL-90-R, there were significant differences between PNES and PM (p=0.003); PNES and MS (p0.999); PM and MS (p=0.172). There was no significant difference between the CDS-PA scores of the patient groups (p>0.05). CONCLUSIONS Our study demonstrated that in FNSD, the somatosensory symptoms were more associated with cognitive errors related to interpersonal relationships than the motor symptoms and the motor symptoms were more than PNES.
The appendicular myology of Stegoceras validum (Ornithischia: Pachycephalosauridae) and implications for the head-butting hypothesis

In this study, we use an exceptional skeleton of the pachycephalosaur Stegoceras validum (UALVP 2) to inform a comprehensive appendicular muscle reconstruction of the animal, with the goal of better understanding the functional morphology of the pachycephalosaur postcranial skeleton. We find that S. validum possessed a conservative forelimb musculature, particularly in comparison to early saurischian bipeds. By contrast, the pelvic and hind limb musculature are more derived, reflecting peculiarities of the underlying skeletal anatomy. The iliotibialis, ischiocaudalis, and caudofemoralis muscles have enlarged attachment sites and the caudofemoralis has greater leverage owing to the distal displacement of the fourth trochanter along the femur. These larger muscles, in combination with the wide pelvis and stout hind limbs, produced a stronger, more stable pelvic structure that would have proved advantageous during hypothesized intraspecific head-butting contests. The pelvis may have been further stabilized by enlarged sacroiliac ligaments, which stemmed from the unique medial iliac flange of the pachycephalosaurs. Although the pubis of UALVP 2 is not preserved, the pubes of other pachycephalosaurs are highly reduced. The puboischiofemoralis musculature was likely also reduced accordingly, and compensated for by the aforementioned improved pelvic musculature.
Impact of a Multicomponent Educational Intervention on Community Pharmacy–Based Naloxone Services Implementation: A Pragmatic Randomized Controlled Trial

Background: Despite US naloxone access laws, community pharmacists lack training and confidence in providing naloxone. Objective: To assess the impact of the Empowering Community Pharmacists program on pharmacists’ knowledge, perceived barriers, attitudes, confidence, and intentions regarding naloxone services implementation, as well as naloxone prescriptions dispensed. Methods: A 3-month pragmatic randomized controlled trial was conducted from December 2018 to March 2019. Alabama community pharmacists were recruited by mail, email, phone, and fax and randomized to intervention (monthly resources/reminders + educational webinar) or control (monthly reminders only). Outcome measures were assessed via online surveys at baseline (T1), immediately post-intervention (T2), and 3 months post-intervention (T3), including naloxone knowledge (%correct); perceived barriers, attitudes, confidence, and intention regarding naloxone services implementation (7-point Likert-type scale; 1 = strongly disagree, 7 = strongly agree); and number of naloxone prescriptions dispensed. Mean differences between control and intervention from T1 to T3 were assessed using 2-way mixed analysis of variance and adjusted analyses were conducted using generalized estimating equations with negative binomial distribution to assess associations between variables. Results: Of 55 participants (n = 27 intervention, n = 28 control), most were female (80.3%), white (80.6%), in independently owned pharmacies (39.1%). Increases in mean [SD] confidence (5.52 [1.03]-6.16 [0.74], P < 0.0005) and intention (5.35 [1.51]-6.10 [0.96], P = 0.023) occurred from pre- to post-program within the intervention group and were statistically significant compared with control (confidence P = 0.016, intention P = 0.014). Confidence (exp(β) = 1.46, P = 0.031) and perceived barriers (exp(β) = 0.75, P = 0.022) were associated with number of naloxone prescriptions dispensed. Conclusion and Relevance: The Empowering Community Pharmacists program improved community pharmacists’ confidence and intention regarding naloxone services implementation. Other states can adapt program elements according to their laws. ClinicalTrials.gov Identifier: NCT05093309
Viscous flow past plates

I devise a numerical method of high order in space (FDMHS) to simulate flow past a finite plate and a semi-infinite plate. The method solves the incompressible Navier-Stokes equation in the stream function-vorticity formulation. The focus is to study a fundamental problem in fluid dynamics, namely, flow past sharp edges. Resolving this flow structure is difficult, in particular at early times. The difficulty is due to the fact that large velocity gradients and vorticity are present in a very thin boundary layer attached to the plate initially. FDMHS is a splitting method, implicit in time and uses compact fourth order finite differences. FDMHS has demonstrated satisfactory performance in our numerical simulations. For the finite plate case, three background flow are used: impulsively started, uniformly accelerated, and oscillating. Resolved computations show structure of the boundary layer separation and roll-up from very early times to relative large times. For the impulsively started, the details of vorticity structure at early times have been studied. We resolved the region of negative vorticity along the plate induced by and entrained into the leading vortex. A secondary entrainment of positive vorticity into the region of negative vorticity is also found. The maximum velocity decays as t−1/4 over a large initial time interval. For the uniformly accelerated, we show evolution in the appropriate non-dimensional variables, and find agreement with scaling laws observed in experiments. For the oscillating, we compared the viscous simulation using FDMHS with an inviscid vortex sheet method. Both are in excellent agreement at early times. There are difference at later times most likely caused by wall vorticity which is not accounted for by the vortex sheet model. The shed circulation is independent of viscosity initially for all three background flows. The effect of viscosity on the vorticity evolution and on quantities such as the shed circulation, core trajectory and vorticity, vortex size and