Miracle-dz/UniFAR-FTUs huggingface dataset:
Immune escaping of the novel genotypes of human respiratory syncytial virus based on gene sequence variation

Purpose Immune escaping from host herd immunity has been related to changes in viral genomic sequences. The study aimed to understand the diverse immune responses to different subtypes or genotypes of human respiratory syncytial virus (RSV) in pediatric patients. Methods The genomic sequences of different subtypes or RSV genotypes, isolated from Beijing patients, were sequenced and systematically analyzed. Specifically, the antiviral effects of Palivizumab and the cross-reactivity of human sera from RSV-positive patients to different subtypes or genotypes of RSV were determined. Then, the level of 38 cytokines and chemokines in respiratory and serum samples from RSV-positive patients was evaluated. Results The highest nucleotide and amino acid variations and the secondary and tertiary structure diversities among different subtypes or genotypes of RSV were found in G, especially for genotype ON1 with a 72bp-insertion compared to NA1 in subtype A, while more mutations of F protein were found in the NH-2 terminal, including the antigenic site II, the target of Palivizumab, containing one change N276S. Palivizumab inhibited subtype A with higher efficiency than subtype B and had stronger inhibitory effects on the reference strains than on isolated strains. However, RSV-positive sera had stronger inhibitory effects on the strains in the same subtypes or genotypes of RSV. The level of IFN-α2, IL-1α, and IL-1β in respiratory specimens from patients with NA1 was lower than those with ON1, while there were higher TNFα, IFNγ, IL-1α, and IL-1β in the first serum samples from patients with ON1 compared to those with BA9 of subtype B. Conclusions Diverse host immune responses were correlated with differential subtypes and genotypes of RSV in pediatric patients, demonstrating the impact of viral genetics on host immunity.
The interplay between prolactin and cardiovascular disease

Hyperprolactinemia can be caused by several conditions and its effects on the hypothalamic-pituitary-gonadal axis are understood in more detail. Nevertheless, in recent decades, other metabolic effects have been studied and data pointed to a potential increased cardiovascular disease (CVD) risk. A recent study showed a decrease in total and LDL- cholesterol only in men with prolactinoma treated with dopamine agonists (DA) supporting the previous results of a population study with increased CVD risk in men harboring prolactinoma. However, other population studies did not find a correlation between prolactin (PRL) levels and CVD risk or mortality. There is also data pointing to an increase in high-density lipoprotein levels, and decreases in triglycerides, carotid-intima-media thickness, C-reactive protein, and homocysteine levels in patients with prolactinoma on DA treatment. PRL was also implicated in endothelial dysfunction in pre and postmenopausal women. Withdrawal of DA resulted in negative changes in vascular parameters and an increase in plasma fibrinogen. It has been shown that PRL levels were positively correlated with blood pressure and inversely correlated with dilatation of the brachial artery and insulin sensitivity, increased homocysteine levels, and elevated D-dimer levels. Regarding possible mechanisms for the association between hyperprolactinemia and CVD risk, they include a possible direct effect of PRL, hypogonadism, and even effects of DA treatment, independently of changes in PRL levels. In conclusion, hyperprolactinemia seems to be associated with impaired endothelial function and DA treatment could improve CVD risk. More studies evaluating CVD risk in hyperprolactinemic patients are important to define a potential indication of treatment beyond hypogonadism.
Determination of the Smagorinsky–Lilly constant CS

The Smagorinsky–Lilly (SL) SGS model νt=(CSΔ)2S yields a constant CS=0.20–0.22 which is a factor of 2 larger than what is needed in LES calculations; in addition, Deardorff and Hunt et al. suggested empirical corrections to the SL model to account for the effects of stratification and shear. In this paper, we propose an SGS model that naturally includes stratification and shear (recovering the two previous models) and that gives rise to a value of CS∼0.11. The three basic assumptions underlying the SL model are (1) Fickian approximation, b=−2νtS, where b is the Reynolds stress tensor and S is the strain rate tensor, (2) SGS satisfy Kolmogorov law, and (3) local equilibrium, P=e, where P and e are the rates of production and dissipation. We avoid (1) by using the most general b=b(S,R) relationship, where R is the vorticity, and (3) by letting the ratio P/e vary. The most critical ingredient is (2). We derive the energy spectrum E(k) in the presence of buoyancy N and shear S and show that the SGS scales are.
Novel immune-related prognostic model and nomogram for breast cancer based on ssGSEA

This study aimed to construct an immune-related prognostic model and a nomogram to predict the 1-, 3-, and 5-year overall survival (OS) of breast cancer patients. We applied single-sample gene set enrichment analysis to classify 1,053 breast cancer samples from The Cancer Genome Atlas (TCGA) database into high and low immune cell infiltration clusters. In cluster construction and validation, the R packages “GSVA,” “hclust,” “ESTIMATE,” and “CIBERSORT” and GSEA software were utilized. ImmPort, univariate Cox regression analysis, and Venn analysis were then used to identify 42 prognostic immune-related genes. Eventually, the genes TAPBPL, RAC2, IL27RA, ULBP2, PSMB8, SOCS3, NFKBIE, IGLV6-57, CXCL1, IGHD, AIMP1, and CXCL13 were chosen for model construction utilizing least absolute shrinkage and selection operator regression analysis. The Kaplan–Meier curves of both the training and validation sets indicated that the overall survival of patients in the low-risk group was superior to that of patients in the high-risk group (p < .05). The areas under curves (AUCs) of the model at 1, 3, and 5 years were, respectively, . 697, . 710, and . 675 for the training set and . 930, . 688, and . 712 for the validation set. Regarding clinicopathologic characteristics, breast cancer-related genes, and tumor mutational burden, effective differentiation was achieved between high-risk and low-risk groups. A nomogram integrating the risk model and clinicopathologic factors was constructed using the “rms” R software package. The nomogram’s 1-, 3-, and 5-year AUCs were . 828, . 783, and . 751, respectively. Overall, our study developed an immune-related model and a nomogram that could reliably predict OS for breast cancer patients, and offered insights into tumor immune and pathological mechanisms.
CD4+ T lymphocyte recovery in the modern antiretroviral therapy era: Toward a new threshold for defining immunological non-responders

Introduction Despite the high level of efficacy of modern antiretroviral therapy (ART) in reducing HIV viremia and the control of viral replication, some people living with HIV (PLWH) do not recover their CD4+ T cell count. Methods To evaluate the frequency and predictive factors of discordant immune responses, we performed a retrospective cohort study of 324 antiretroviral-naïve PLWH who initiated first-line ART between 2008 and 2018 and maintained HIV RNA < 50 copies/ml during 36 months of follow-up. PLWH were defined as immunological non-responders (INRs) when CD4+ T cell count was < 20% compared with baseline (INR20%), or < 500 cells/mm3 (INR500) or < 200 cells/mm3 (INR200) at 36 months. Results The prevalence of INR20%, INR500, and INR200 was 12.5%, 34.6%, and 1.5%, respectively. After adjustment for possible confounders, CD4 nadir showed a significant association with all INR definitions, with lower values predicting INR500 (aOR 0.98, 95% CI 0.98–0.99, p < 0.001) and INR200 (aOR 0.98, 95% CI 0.95–1.01, p = 0.096). Moreover, a higher baseline CD4/CD8 ratio was inversely related to the probability of being INR500 (OR 0.03, 95% CI 0.01–0.12, p < 0.001) and INR200 (OR 0.002, 95% CI 18–7–67.72, p = 0.255). By contrast, INR20% had a higher CD4 nadir and CD4/CD8 ratio than other INRs, suggesting the identification of an heterogenous population with such definition. Discussion The present study highlights how INR200 has become rare in the contemporary ART era, and about one-third of PLWH meet the criteria for INR500. Overcoming the threshold of 500 CD4/mm3 could be an appropriate definition of immune response, in contrast with the older definitions of INR200 and INR20%. Early diagnosis and rapid treatment initiation, before CD4 counts and the CD4/CD8 ratio begin to decline, are critical for achieving an optimal immune response.
Neck-to-height ratio is positively associated with diabetic kidney disease in Chinese patients with type 2 diabetes mellitus

Introduction The aim of this study was to investigate the associations of neck circumference (NC) and neck-to-height (NHR) with diabetic kidney disease (DKD) in Chinese patients with type 2 diabetes mellitus (T2DM). Materials and methods A total of 2,615 patients with prevalent T2DM were enrolled. NHR was calculated through NC (cm) divided by height (cm), and prevalent DKD was defined as the urinary albumin-to-creatinine ratio (UACR) ≥ 30 mg/g or the estimated glomerular filtration rate (eGFR) < 60 ml/min per 1.73 m2 in the absence of other primary kidney diseases. Results The levels of NC and NHR were higher in DKD patients compared with non-DKD patients (38.22 vs. 37.71, P = 0.003; 0.232 vs. 0.227, P < 0.001, respectively). After full adjustments, individuals at the highest tertile of NHR had higher odds of DKD than those at the lowest tertile (multivariate-adjusted OR = 1.63, 95% CI: 1.22, 2.18), but this association was not pronounced with NC (multivariate-adjusted OR = 1.24, 95% CI: 0.87, 1.76). Individuals at the highest tertile of NHR had lower eGFR (β = -4.64, 95% CI: -6.55, -2.74) and higher UACR levels (β = 0.27, 95% CI: 0.10, 0.45) than those at the lowest tertile. The adverse association between NHR and prevalent DKD remained statistically significant among most of the subgroups analyzed and no interaction effects were observed. Conclusion The increase in NHR was adversely and independently associated with DKD in this Chinese T2DM population.
Epidemiology and outcomes of hyponatremia in patients with COVID-19—A territory-wide study in Hong Kong

Background Hyponatremia is common in COVID-19, but its epidemiology and impact on clinical outcomes in relation to different variants, especially the Omicron variant, requires further clarification. Methods This was a territory-wide retrospective study to investigate the epidemiology and outcomes of COVID-19 patients with hyponatremia from January 1, 2020 to March 31, 2022 in Hong Kong. The primary outcome was 30-day mortality of patients with COVID-19 and hyponatremia at presentation. Secondary outcomes included rate of hospitalization, intensive care unit (ICU) hospitalization, overall duration of hospitalization, and duration of ICU hospitalization. Results A total of 53,415 COVID-19 patients were included for analysis, of which 14,545 (27.2%) had hyponatremia at presentation. 9813 (67.5%), 2821 (19.4%), and 1911 (13.1%) had mild (130 to <135 mmol/L), moderate (125 to <130 mmol/L), and severe hyponatremia (<125 mmol/L) at presentation respectively. Age, male sex, diabetes, active malignancy, white cell count, serum creatinine, hypoalbuminemia, C-reactive protein, and viral loads were independent predictors for hyponatremia in COVID-19 patients (P < 0.001, for all). Hyponatremic patients had increased 30-day mortality (9.7 vs. 5.7%, P < 0.001), prolonged hospitalization (11.9 ± 15.1 days vs. 11.5 ± 12.1 days, P < 0.001), and more ICU admissions (7.0% vs. 3.3%, P < 0.001). Patients diagnosed during the “fifth wave” Omicron BA.2 outbreak had 2.29-fold risk (95% CI 2.02–2.59, P < 0.001) of presenting with hyponatremia compared to other waves. Conclusion Hyponatremia is common among COVID-19 patients, and may serve as a prognostic indicator for unfavorable outcomes and increased healthcare utilization in the evolving COVID-19 outbreak.
Athlete level, sport-type, and gender influences on training, mental health, and sleep during the early COVID-19 lockdown in Malaysia

Purpose: We evaluated the extent of changes in training practices, recovery, mental health, and sleep patterns of athletes during the early COVID-19 lockdown in a single country-cohort. Methods: A total of 686 athletes (59% male, 41% female; 9% World Class, 28% International, 29% National, 26% State, 8% Recreational) from 50 sports (45% individual, 55% team) in Malaysia completed an online, survey-based questionnaire study. The questions were related to training practices (including recovery and injury), mental health, and sleep patterns. Results: Relative to pre-lockdown, training intensity (−34%), frequency (−20%, except World-Class), and duration (−24%–59%, especially International/World-Class) were compromised, by the mandated lockdown. During the lockdown, more space/access (69%) and equipment (69%) were available for cardiorespiratory training, than technical and strength; and these resources favoured World-Class athletes. Most athletes trained for general strength/health (88%) and muscular endurance (71%); and some used innovative/digital training tools (World-Class 48% vs. lower classification-levels ≤34%). More World-Class, International, and National athletes performed strength training, plyometrics, and sport-specific technical skills with proper equipment, than State/Recreational athletes. More females (42%) sourced training materials from social media than males (29%). Some athletes (38%) performed injury prevention exercises; 18% had mild injuries (knees 29%, ankles 26%), and 18% received a medical diagnosis (International 31%). Lower-level athletes (e.g., State 44%) disclosed that they were mentally more vulnerable; and felt more anxious (36% vs. higher-levels 14%–21%). Sleep quality and quantity were “normal” (49% for both), “improved” (35% and 27%), and only 16% and 14% (respectively) stated “worsened” sleep. Conclusion: Lockdown compromised training-related practices, especially in lower-level athletes. Athletes are in need of assistance with training, and tools to cope with anxiety that should be tailored to individual country requirements during lockdown situations. In particular, goal-driven (even if it is at home) fitness training, psychological, financial, and lifestyle support can be provided to reduce the difficulties associated with lockdowns. Policies and guidelines that facilitate athletes (of all levels) to train regularly during the lockdown should be developed.
Environmental protection tax and total factor productivity—Evidence from Chinese listed companies

By improving its total factor productivity, China may attain higher quality and more sustainable economic growth. As a key market-based incentive for environmental regulation, does environmental protection tax increase total factor productivity and provide a win-win situation for both economic and environmental performance? It is a debate-worthy topic. Based on data of Chinese listed companies, this paper uses the triple difference method to analyze China’s environmental protection tax reform as a natural experiment. The results show that the environmental protection tax can significantly boost the firm’s total factor productivity by encouraging technological innovation and enhancing resource allocation. Based on analysis of heterogeneity, it appears that state-owned enterprises, larger corporations, and regions with more strict environmental enforcement are more responsive to environmental protection tax policies. This report provides critical empirical evidence for upgrading China’s tax framework to protect the environment.
Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations

Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbial mats to test whether our understanding of Patescibacteria metabolism allows the extrapolation of their in situ activities. Although our results revealed a circadian cycle in Patescibacteria activities, a strong streamlined genetic expression characterized the Patescibacteria populations. This result has a major consequence for the extrapolation of their physiology and environmental function since most transcribed genes were uncharacterized, indicating that the ecophysiology of Patescibacteria cannot be yet reliably predicted from genomic data.
Modeling sepsis, with a special focus on large animal models of porcine peritonitis and bacteremia

Infectious diseases, which often result in deadly sepsis or septic shock, represent a major global health problem. For understanding the pathophysiology of sepsis and developing new treatment strategies, reliable and clinically relevant animal models of the disease are necessary. In this review, two large animal (porcine) models of sepsis induced by either peritonitis or bacteremia are introduced and their strong and weak points are discussed in the context of clinical relevance and other animal models of sepsis, with a special focus on cardiovascular and immune systems, experimental design, and monitoring. Especially for testing new therapeutic strategies, the large animal (porcine) models represent a more clinically relevant alternative to small animal models, and the findings obtained in small animal (transgenic) models should be verified in these clinically relevant large animal models before translation to the clinical level.
Soil fertility and drought interact to determine large variations in wood production for a hyperdominant Amazonian tree species

Introduction The productivity of the Amazon Rainforest is related to climate and soil fertility. However, the degrees to which these interactions influence multiannual to decadal variations in tree diameter growth are still poorly explored. Methods To fill this gap, we used radiocarbon measurements to evaluate the variation in tree growth rates over the past decades in an important hyperdominant species, Eschweilera coriacea (Lecythidaceae), from six sites in the Brazilian Amazon that span a range of soil properties and climate. Results Using linear mixed-effects models, we show that temporal variations in mean annual diameter increment evaluated over a specific time period reflect interactions between soil fertility and the drought index (SPEI-Standardized Precipitation and Evapotranspiration Index). Discussion Our results indicate that the growth response of trees to drought is strongly dependent on soil conditions, a facet of forest productivity that is still underexplored, and which has great potential for improving predictions of future tropical tree growth in the face of projected climate change.
Quality of life in dogs with idiopathic epilepsy and their owners with an emphasis on breed—A pilot study

Epilepsy in dogs is a common chronic and serious disorder and may have an impact on the quality of life of the owners as well as the dogs themselves. The aim of this pilot study was to investigate the QoL score of dogs suffering from idiopathic epilepsy and their owners and if possible, investigate whether a breed specific difference exists. Owners, either Dutch or Belgium, were asked to participate in a web based SurveyMonkey questionnaire. A total of 402 questionnaires representing 402 dogs with epilepsy were suitable for further analysis. Of the 402 dogs, 253 were males and 149 were females. Ninety-nine different breeds were represented. Fourteen breeds (177 dogs in total) were used to calculate breed specific scores; Australian Shepherd (n = 8), Beagle (n = 7), Belgian Tervuren dog (n = 9), Belgian Groenendaeler dog (n = 8), Border Collie (n = 38), Chihuahua (n = 9), Dachshund (n = 13), Drentsche Patrijshond (a Dutch partridge dog) (n = 14), French Bulldog (n = 12), Golden Retriever (n = 17), Labrador Retriever (n = 18), and Rottweiler (n = 12). For the Border Collie, there was a statistically significant correlation between “epilepsy related death,” the severity of the seizures (p < 0.001) and cluster seizures (p < 0.001). The quality of life of the Border Collie was scored lower compared to all other dogs (p = 0.02). There were three breeds that had a minimal decrease in the overall quality of life score compared to all other dogs: the Chihuahua (p = 0.03), Dachshund (p = 0.001), and Golden retriever (p = 0.01). The score for “caring for my epileptic dog decreases my own QoL” was high for the Border Collie, Boxer, French Bulldog, and Rottweiler, but was only found to be statistically significantly higher in the Border Collie (p = 0.01). Scores for the Golden Retriever (p = 0.04) and Labrador (p = 0.006) were lower. In conclusion, this study reports breed specific quality of life scores of dogs with epilepsy and their owners, and underlines that breed by itself, is also an important factor when managing epilepsy in dogs.
A study on the blended learning effects on students majoring in preschool education in the post-pandemic era: An example of a research-method course in a Chinese university

The world has gradually entered the post-pandemic era. Although the pandemic has been slowing down, it still has a strong impact on the education scene. Thus, how to provide students with an effective and flexible learning style is currently an important educational issue. This study focused on the implementation of effective teaching to improve the learning effects based on these special circumstances. To ensure a realistic teaching situation, an experiment of blended learning was conducted in a university in the Guangxi Zhuang Autonomous Region of China for a short-term study, based on the consideration of pandemic supervision and control. In this experiment, a single-group quasi-experimental design method, using the extended O-PIRTATD/S model, was adopted in a research-method course designed for students majoring in preschool education. This research-method course was an 8-week flipped course, where the first 4 weeks were online teaching and the last 4 weeks were taught offline, thus combining as a blended learning course. A total of 115 active participants were recruited for this study. Based on the theoretical framework of the belief-action-outcome (BAO) model, five research hypotheses were proposed with the aim of constructing a learning behavior pattern based on cognitive beliefs which could be verified by structural equation modeling. The results of the study were concluded as follows: 1. Academic self-efficacy had a positive impact on learning engagement, but had a negative impact on cognitive load; 2. Cognitive load did not have a significant impact on learning engagement; 3. Learning engagement had a positive impact on the enhancement of academic self-confidence; and 4. Cognitive load had a negative impact on the enhancement of academic self-confidence.
Bending of Membranes by Anchored Polymers

Polymers which are attached to a fluid membrane by a single anchor exhibit a dilute mushroom regime and a semi-dilute brush regime. Scaling arguments and explicit calculations for ideal polymers show that the membrane is bent by the anchored polymer: For smooth bends, an anchored mushroom with linear size Rpo induces a spontaneous curvature of order T/κRpo, where T and κ are the temperature and the bending rigidity, respectively; for sharp cone-like bends, it induces a bending angle T/2πκ. A brush with mean anchor separation ξan leads to a curvature of order (Rpo/ξan)2/ν T/κξan.