Miracle-dz/UniFAR-FTUs huggingface dataset:
Wenfei Buqi Tongluo Formula Against Bleomycin-Induced Pulmonary Fibrosis by Inhibiting TGF-β/Smad3 Pathway

Pulmonary fibrosis (PF) is the end stage of various chronic and progressive interstitial lung diseases. TGF-β, a profibrotic cytokine, can promote epithelial–mesenchymal transition (EMT), extracellular matrix (ECM) accumulation, and fibroblast proliferation, which contribute to progressive lung remodeling in PF. The Wenfei Buqi Tongluo (WBT) formula has been certified to be effective in the prevention and treatment of PF in clinical practice and has inhibitory effects on EMT, inflammation, and profibrotic factors. However, the pharmacological mechanisms of WBT against PF need to be further explored. In this study, we first analyzed the chemical components of the WBT formula using the UHPLC/Q-TOF-MS analysis. The potential targets of the identified compounds from WBT were predicted by the network pharmacology, which was confirmed by in vivo and in vitro study. After screening by the PubChem database, we first identified the 36 compounds of WBT and predicted the TGF-β signaling pathway, with ECM degradation as potential mechanism of WBT against PF by the network pharmacology. Furthermore, WBT treatment inhibited the levels of TGF-β and Smad3 phosphorylation and subsequently alleviated EMT and ECM accumulation in the bleomycin-induced mouse model and TGF-β1–induced cell model. These findings indicate that WBT can block the progressive process of PF by inhibiting EMT and promoting ECM degradation via the TGF-β/Smad3 pathway. This study may provide new insights into the molecular mechanism of WBT for the prevention and treatment of PF in the clinical application.
Chromosome-Scale Genome of Masked Palm Civet (Paguma larvata) Shows Genomic Signatures of Its Biological Characteristics and Evolution

The masked palm civet (Paguma larvata) is a small carnivore with distinct biological characteristics, that likes an omnivorous diet and also serves as a vector of pathogens. Although this species is not an endangered animal, its population is reportedly declining. Since the severe acute respiratory syndrome (SARS) epidemic in 2003, the public has been particularly concerned about this species. Here, we present the first genome of the P. larvata, comprising 22 chromosomes assembled using single-tube long fragment read (stLFR) and Hi-C technologies. The genome length is 2.41 Gb with a scaffold N50 of 105.6 Mb. We identified the 107.13 Mb X chromosome and one 1.34 Mb Y-linked scaffold and validated them by resequencing 45 P. larvata individuals. We predicted 18,340 protein-coding genes, among which 18,333 genes were functionally annotated. Interestingly, several biological pathways related to immune defenses were found to be significantly expanded. Also, more than 40% of the enriched pathways on the positively selected genes (PSGs) were identified to be closely related to immunity and survival. These enriched gene families were inferred to be essential for the P. larvata for defense against the pathogens. However, we did not find a direct genomic basis for its adaptation to omnivorous diet despite multiple attempts of comparative genomic analysis. In addition, we evaluated the susceptibility of the P. larvata to the SARS-CoV-2 by screening the RNA expression of the ACE2 and TMPRSS2/TMPRSS4 genes in 16 organs. Finally, we explored the genome-wide heterozygosity and compared it with other animals to evaluate the population status of this species. Taken together, this chromosome-scale genome of the P. larvata provides a necessary resource and insights for understanding the genetic basis of its biological characteristics, evolution, and disease transmission control.
Wall-resolved and wall-modelled large-eddy simulation of plane Couette flow

Abstract We describe wall-resolved and wall-modelled large-eddy simulation (LES) of plane Couette (PC) flow. Subgrid-scale (SGS) motion is represented using the stretched-spiral vortex SGS model and the virtual wall model is employed for wall-modelled LES. Cases studied include direct numerical simulation (DNS) at friction Reynolds numbers $Re_\tau = 220$, wall-resolved LES at $Re_\tau \sim 500\text {--}3600$ and wall-modelled LES at $Re_\tau \sim 3600\text {--}2.8\times 10^{5}$. All LES performed show the presence of approximately spanwise periodic sets of streamwise rolls. Averaged (including spanwise) wall-normal profiles of the mean streamwise velocity show a consistent log region across all Reynolds numbers. Two distinct measures of turbulent intensity are explored, one of which recognizes the roll structure and one that does not. The spanwise variation of turbulence flow metrics is investigated. Mean streamwise velocity profiles show substantial spanwise variation but collapse well when normalized by local skin-friction velocities. Similar collapse is found for streamwise turbulent intensities. For all present LES, the mean skin-friction variation with the plate Reynolds number is found to match a simple analytical form (Pirozzoli et al., J. Fluid Mech., vol. 758, 2014, pp. 327–343) while the scaled centre-plane, mean-velocity gradient exhibits an inverse ProductLog dependence. Both the mean-flow roll energy and circulation, scaled with outer variables, decrease monotonically for $Re_\tau \gtrsim 500$. At lower $Re_\tau$, the mean streamwise zero-velocity line follows a wavy form in the spanwise direction, while at our larger $Re_\tau$, a mushroom shape emerges which could potentially enhance local momentum transport in the spanwise direction and be responsible for the weakening of the spanwise rolls.
Effect of habitual reading direction on saccadic eye movements: A pilot study

Cognitive processes can influence the characteristics of saccadic eye movements. Reading habits, including habitual reading direction, also affects cognitive and visuospatial processes, favouring attention to the side where reading begins. Few studies have investigated the effect of habitual reading direction on saccade directionality of low-cognitive-demand stimuli (such as dots). The current study examined horizontal prosaccade, antisaccade and self-paced saccade in subjects with two primary habitual reading directions. We hypothesised that saccades responding to the target in subject’s habitual reading direction would show a longer prosaccade latency and lower antisaccade error rate (errors being a reflexive glance to a sudden-appearing target, rather than a saccade away from it). Sixteen young Chinese participants with primary habitual reading direction from left to right and sixteen young Arabic and Persian participants with primary habitual reading direction from right to left were recruited. Subjects needed to look towards a 5°/ 10°target in the prosaccade task or look towards the mirror image location of the target in the antisaccade task and look between two 10-degree targets in the self-paced saccade task. Only Arabic and Persian participants showed a shorter and directional prosaccade latency towards 5°target against their habitual reading direction. No significant effect of primary reading direction on antisaccade latency towards the correct directions was found. However, we found that Chinese readers generated significantly shorter prosaccade latencies and higher antisaccade directional errors compared with Arabic and Persian readers. The present study provides an insight into the effect of reading habits on saccadic eye movements in response to low-cognitive-demand stimuli and offers a platform for future studies to investigate the relationship between reading habits and neural mechanisms of eye movement behaviours.
Relationship Between the Lipid Accumulation Product Index and Arterial Stiffness in the Chinese Population With Hypertension: A Report From the China H-Type Hypertension Registry Study

Background Lipid accumulation product (LAP) index, as a new index to predict cardiovascular disease (CVD), has attracted the attention of many researchers. The relation of the LAP index with brachial-ankle pulse wave velocity (baPWV) has been evaluated in several previous studies and yielded inconsistent results. This study aimed to investigate the association between the LAP index and arterial stiffness in the Chinese population with hypertension. Methods We conducted a cross-sectional analysis in 4,926 Chinese population with hypertension (aged 64.42 ± 9.44 years). The LAP index was developed from population-based frequency plots of adult waist circumferences and circulating triglyceride concentrations according to men and women. Arterial stiffness was determined by measuring baPWV. Results The multivariate linear regression analyses showed that the LAP index was independently and positively associated with baPWV [beta coefficients (β), 24.10 cm/s; 95% CI: 5.72, 42.49 cm/s]. Consistently, the multivariate logistic regression analyses showed a positive association between the LAP index risk of elevated baPWV (>75th percentile) [odds ratio (OR), 1.19; 95% CI 1.01, 1.41]. A restricted cubic spline showed that a significant linear association existed between the LAP index and baPWV. In different subgroups of diastolic blood pressure (DBP), there is interaction between the LAP index and baPWV (DBP <90, 90–99, ≥100 mm Hg; p-interaction = 0.006). Conclusion LAP is significantly positively associated with baPWV and elevated baPWV in Chinese hypertensive adults and especially among participants with DBP ≤ 99 mm Hg.
Velvet Antler Peptides Reduce Scarring via Inhibiting the TGF-β Signaling Pathway During Wound Healing

Aim Scar formation generally occurs in cutaneous wound healing in mammals, mainly caused by myofibroblast aggregations, and currently with few effective treatment options. However, the pedicle wound (about 10 cm in diameter) of the deer can initiate regenerative healing, which has been found to be achieved via paracrine factors from the internal tissues of antlers. Methods Enzymatically digested velvet antler peptides (EVAP) were prepared along with other types of antler extracts as the controls. The effects of EVAP on healing of full-thickness skin wounds were evaluated using rats in vivo, and on myofibroblast transdifferentiation tested using transforming growth factor-β1 (TGF-β1)-induced human dermal fibroblasts in vitro. Results EVAP significantly accelerated the wound healing rate, reduced scar formation, and improved the healing quality, including promoted angiogenesis, increased number of skin appendages (hair follicles and sebaceous glands) and improved the distribution pattern of collagen fibers (basket-wave like) in the healed tissue. Moreover, EVAP significantly down-regulated the expression levels of genes pro- scar formation (Col1a2 and TGF-β1), and up-regulated the expression levels of genes anti-scar formation (Col3a1 and TGF-β3), and suppressed the excessive transdifferentiation of myofibroblasts and the formation of collagen I in vivo and in vitro. Furthermore, we found these effects were highly likely achieved by inhibiting the TGF-β signaling pathway, evidenced by decreased expression levels of the related genes, including TGF-β1, Smad2, p-Smad2, α-SMA, and collagen I. Conclusions EVAP may be a promising candidate to be developed as a clinic drug for regenerative wound healing.
Effects of Different Intensities and Durations of Aerobic Exercise on Vascular Endothelial Function in Middle-Aged and Elderly People: A Meta-analysis

Background Previous studies have found that aerobic exercise was more effective in improving vascular endothelial function than resistance training, high-intensity interval training (HIIT), and other types of exercise, while the effects between different intensities and durations of aerobic exercise were unclear. Therefore, we performed this meta-analysis to investigate the effects of different intensities and durations of aerobic exercise on the vascular endothelial function of middle-aged and elderly people. Methods: Databases were searched up to April 2021 for studies evaluating the influences of different intensities and durations of aerobic exercise on endothelial function assessed by flow-mediated dilation (FMD) among healthy middle-aged and elderly people. Data were pooled using random-effects models to obtain the weighted mean difference (WMD) and 95% confidence intervals (CIs). Results A total of 9 studies involving 221 participants fulfilled the inclusion criteria. Aerobic exercise improved the overall FMD of healthy middle-aged and elderly people [WMD, 1.33 (95% CI, 0.37–2.28), P < 0.05]. Specifically, vigorous-intensity exercise increased FMD significantly in healthy middle-aged and elderly people [WMD, 1.10 (95% CI, 0.27–1.93), P < 0.05], while moderate-intensity exercise had no significant association with FMD [WMD, 1.49 (95% CI, −0.62 to 3.60), P = 0.17]. In addition, long-term (8 weeks or above) aerobic exercise increased the FMD in healthy middle-aged and elderly people [WMD, 1.63 (95% CI, 0.61–2.66), P < 0.05], while one-time acute aerobic exercise had no significant association with FMD of healthy middle-aged and elderly people [WMD, 0.89 (95% CI, −1.47 to 3.24), P = 0.46]. Specifically, 8 weeks or above of vigorous-intensity exercise increased FMD significantly in healthy middle-aged and elderly people [WMD, 1.48 (95% CI, 1.06–1.90), P < 0.01], while 8 weeks or above of moderate aerobic exercise had no significant association with FMD [WMD, 1.49 (95% CI, −0.62 to 3.60), P = 0.17]. Conclusion Aerobic exercise, especially 8 weeks or above of vigorous-intensity aerobic exercise, improved the endothelial function in healthy middle-aged and elderly people.
α9-Containing Nicotinic Receptors in Cancer

Neuronal nicotinic acetylcholine receptors containing the α9 or the α9 and α10 subunits are expressed in various extra-neuronal tissues. Moreover, most cancer cells and tissues highly express α9-containing receptors, and a number of studies have shown that they are powerful regulators of responses that stimulate cancer processes such as proliferation, inhibition of apoptosis, and metastasis. It has also emerged that their modulation is a promising target for drug development. The aim of this review is to summarize recent data showing the involvement of these receptors in controlling the downstream signaling cascades involved in the promotion of cancer.
Effects of Docosahexanoic Acid on Gut Microbiota and Fecal Metabolites in HIV-Infected Patients With Neurocognitive Impairment: A 6-Month Randomized, Double-Blind, Placebo-Controlled Trial

Neurocognitive impairment (NCI) and gut microbiota dysbiosis are prevalent in patients with HIV infection. Docosahexanoic acid (DHA) supplementation may alleviate multiple neurocognitive diseases symptoms and plays important role in regulating gut microbiota. However, it is not known whether DHA algae oil supplements can alleviate neurocognitive impairment (NCI) and regulate gut microbiota and fecal metabolites. A randomized, double-blind, placebo-controlled trial was performed on 68 HIV-infected patients with NCI. Participants were randomized to receive a 3.15 g daily DHA algae oil supplement or placebo for 6 months. We collected blood and fecal samples from these patients before and after the trial. Mini mental state examination (MMSE) and neuropsychological tests (NP tests) were administered to assess the cognitive status of participants. The influence of DHA algae oil on the gut microbiota, fecal metabolomics, plasma proinflammatory, and oxidative stress factors was also investigated. There were no significant changes in NCI according to global diagnosis score (GDS) and MMSE score within the two groups, while patients receiving DHA had improvement in several blood lipids, pro-inflammatory and oxidative stress factors. The DHA supplement increased α-diversity indexes, increased abundances of Blautia, Bifidobacterium, Dorea, Lactobacillus, Faecalibacterium, Fusobacterium, and Agathobacter, and decreased abundances of Bacteroides and Prevotella_9. Furthermore, DHA supplement was correlated with improved fecal lipid metabolites as indicated by ceramides, bile acids, glycerophospholipids. In addition, the DHA supplement was associated with altered cholesterol metabolism and purine metabolism pathways. A daily supplement of DHA algae oil for 6 months has been shown to promote favorable transformations in gut microbiota, profiles of fecal metabolomic, and factors responsible for proinflammatory and oxidative stress, which might be beneficial for the prognosis of HIV-infected patients with NCI in the long-term. Clinical Trial Registration https://clinicaltrials.gov/ct2/show/NCT04242004, identifier: NCT04242004.
Dual-Task nTMS Mapping to Visualize the Cortico-Subcortical Language Network and Capture Postoperative Outcome—A Patient Series in Neurosurgery

Background Perioperative assessment of language function in brain tumor patients commonly relies on administration of object naming during stimulation mapping. Ample research, however, points to the benefit of adding verb tasks to the testing paradigm in order to delineate and preserve postoperative language function more comprehensively. This research uses a case series approach to explore the feasibility and added value of a dual-task protocol that includes both a noun task (object naming) and a verb task (action naming) in perioperative delineation of language functions. Materials and Methods Seven neurosurgical cases underwent perioperative language assessment with both object and action naming. This entailed preoperative baseline testing, preoperative stimulation mapping with navigated Transcranial Magnetic Stimulation (nTMS) with subsequent white matter visualization, intraoperative mapping with Direct Electrical Stimulation (DES) in 4 cases, and postoperative imaging and examination of language change. Results We observed a divergent pattern of language organization and decline between cases who showed lesions close to the delineated language network and hence underwent DES mapping, and those that did not. The latter displayed no new impairment postoperatively consistent with an unharmed network for the neural circuits of both object and action naming. For the cases who underwent DES, on the other hand, a higher sensitivity was found for action naming over object naming. Firstly, action naming preferentially predicted the overall language state compared to aphasia batteries. Secondly, it more accurately predicted intraoperative positive language areas as revealed by DES. Thirdly, double dissociations between postoperatively unimpaired object naming and impaired action naming and vice versa indicate segregated skills and neural representation for noun versus verb processing, especially in the ventral stream. Overlaying postoperative imaging with object and action naming networks revealed that dual-task nTMS mapping can explain the drop in performance in those cases where the network appeared in proximity to the resection cavity. Conclusion Using a dual-task protocol for visualization of cortical and subcortical language areas through nTMS mapping proved to be able to capture network-to-deficit relations in our case series. Ultimately, adding action naming to clinical nTMS and DES mapping may help prevent postoperative deficits of this seemingly segregated skill.
Spatial Distribution of the Pepper Blight (Phytophthora capsici) Suppressive Microbiome in the Rhizosphere

The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.
Greater Acute Concussion Symptoms Are Associated With Longer Recovery Times in NCAA Division III Collegiate Athletes

We examined the association between the severity of acute concussion symptoms and time to return to school and to sports in National Collegiate Athletic Association (NCAA) Division III collegiate athletes. We hypothesized that students with the lowest burden of acute symptoms, measured in the first 72 h, would have the fastest return to school and sports and those with the highest burden of symptoms would have the slowest return to school and sports. This injury surveillance cohort included 808 athletes from 11 NCAA Division III colleges who sustained a concussion between 2014 and 2019. Athletic trainers documented time to return to school and to sports. Kruskal-Wallis tests with post-hoc planned comparison Mann-Whitney U tests were used to assess whether athletes took longer to return based on their acute symptom burden (Low, Medium, or High). Survival analysis (Kaplan Meier with log rank tests) was used to compare the recovery times based on acute symptom burden (censored at 28 days). Chi-square tests compared the proportion of those who had not yet returned to school or sports at various recovery benchmarks (i.e., 1 week, 10 days, 2 weeks, 3 weeks, 4 weeks) based on acute symptom burden. Women (median = 5 days) took slightly longer than men (median = 4 days) to return to school (p = 0.001; r = −0.11, small effect). Women and men did not differ on time to return to sports (p = 0.32, r = −0.04). A greater proportion with high acute symptoms remained out of school at 5 (odds ratio, OR = 4.53), 7 (OR = 4.98), and 10 (OR = 4.80) days compared to those with low acute symptoms. A greater proportion with high acute symptoms remained out of sports at 10 (OR = 4.11), 14 (OR = 3.46), and 21 (OR = 3.01) days compared to those with low acute symptoms. This study shows a strong association between having a high burden of acute post-concussion symptoms and having a slower return to school and sports in Division III collegiate athletes. Moreover, it also illustrates the converse: that those athletes with a low burden of acute symptoms have a faster return to school and sports.