Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Different Recovery Strategies After High-Intensity Functional Training: A Crossover Randomized Controlled Trial

We aimed to determine whether voluntary exercise or surface neuromuscular electrical stimulation (NMES) could enhance recovery after a high-intensity functional training (HIFT) session compared with total rest. The study followed a crossover design. Fifteen male recreational CrossFit athletes (29 ± 8 years) performed a HIFT session and were randomized to recover for 15 min with either low-intensity leg pedaling (“Exercise”), NMES to the lower limbs (“NMES”), or total rest (“Control”). Perceptual [rating of perceived exertion (RPE) and delayed-onset muscle soreness (DOMS) of the lower-limb muscles], physiological (heart rate, blood lactate and muscle oxygen saturation) and performance (jump ability) indicators of recovery were assessed at baseline and at different time points during recovery up to 24 h post-exercise. A significant interaction effect was found for RPE (p = 0.035), and although post hoc analyses revealed no significant differences across conditions, there was a quasi-significant (p = 0.061) trend toward a lower RPE with NMES compared with Control immediately after the 15-min recovery. No significant interaction effect was found for the remainder of outcomes (all p > 0.05). Except for a trend toward an improved perceived recovery with NMES compared with Control, low-intensity exercise, NMES, and total rest seem to promote a comparable recovery after a HIFT session.
Identification and Expression Analysis of WRKY Gene Family in Response to Abiotic Stress in Dendrobium catenatum

Dendrobium catenatum has become a rare and endangered medicinal plant due to habitat loss in China. As one of the most important and largest transcription factors, WRKY plays a critical role in response to abiotic stresses in plants. However, little is known regarding the functions of the WRKY family in D. catenatum. In this study, a total of 62 WRKY genes were identified from the D. catenatum genome. Phylogenetic analysis revealed that DcWRKY proteins could be divided into three groups, a division supported by the conserved motif compositions and intron/exon structures. DcWRKY gene expression and specific responses under drought, heat, cold and salt stresses were analyzed through RNA-seq data and RT-qPCR assay. The results showed that these genes had tissue-specificity and displayed different expression patterns in response to abiotic stresses. The expression levels of DcWRKY22, DcWRKY36 and DcWRKY45 were up-regulated by drought stress. Meanwhile, DcWRKY22 was highly induced by heat in roots, and DcWRKY45 was significantly induced by cold stress in leaves. Furthermore, DcWRKY27 in roots and DcWRKY58 in leaves were extremely induced under salt treatment. Finally, we found that all the five genes may function in ABA- and SA-dependent manners. This study identified candidate WRKY genes with possible roles in abiotic stress and these findings not only contribute to our understanding of WRKY family genes, but also provide valuable information for stress resistance development in D. catenatum.
Abcc6 Null Mice—a Model for Mineralization Disorder PXE Shows Vertebral Osteopenia Without Enhanced Intervertebral Disc Calcification With Aging

Chronic low back pain is a highly prevalent health condition intricately linked to intervertebral disc degeneration. One of the prominent features of disc degeneration that is commonly observed with aging is dystrophic calcification. ATP-binding cassette sub-family C member 6 (ABCC6), a presumed ATP efflux transporter, is a key regulator of systemic levels of the mineralization inhibitor pyrophosphate (PPi). Mutations in ABCC6 result in pseudoxanthoma elasticum (PXE), a progressive human metabolic disorder characterized by mineralization of the skin and elastic tissues. The implications of ABCC6 loss-of-function on pathological mineralization of structures in the spine, however, are unknown. Using the ABCC6-/- mouse model of PXE, we investigated age-dependent changes in the vertebral bone and intervertebral disc. ABCC6-/- mice exhibited diminished trabecular bone quality parameters at 7-months which remained significantly lower than the wild-type mice at 18 months-of-age. ABCC6-/- vertebrae showed increased TRAP staining along with decreased TNAP staining, suggesting an enhanced bone resorption as well as decreased bone formation. Surprisingly, however, loss of ABCC6 resulted only in a mild, aging disc phenotype without evidence of dystrophic mineralization. Finally, we tested the utility of oral K3Citrate to treat the vertebral phenotype since it is shown to regulate hydroxyapatite mechanical behavior. The treatment resulted in inhibition of osteoclastic response and an early improvement in mechanical properties of the bone underscoring the promise of potassium citrate as a therapeutic agent. Our data suggest that although ectopic mineralization is tightly regulated in the disc, loss of ABCC6 compromises vertebral bone quality and dysregulates osteoblast-osteoclast coupling. Author Summary Inherited mutations in the ABCC6 transporter gene results in mineralization, often in the form of hydroxyapatite, of connective tissues throughout the body, predominantly affecting the skin, eyes, and blood vessels. Functional loss of ABCC6 causes reduced levels of the potent mineralization inhibitor pyrophosphate (PPi) in blood resulting in these pathologies. Pathological mineralization is also a prominent feature of intervertebral disc degeneration, but the role of ABCC6 and systemic PPi levels and its correlation to disc mineralization and vertebral bone health has remained unexplored. In this study, we show for the first time that loss of ABCC6 in mice results in significant decline in vertebral bone quality and mild age-related disc degeneration without increased incidence of abnormal mineralization. Importantly, treatment of ABCC6 deficient mice with K3Citrate resulted in restoration of early cellular changes which drive bone loss and mechanical function of the vertebrae. In summary, our data reveal that ABCC6 is dispensable for mineralization prevention in the intervertebral disc. Unexpectedly, we found that vertebral bone quality and bone cell activities are linked to ABCC6 function.
Identification of Potential Blind-Side Hypermelanosis-Related lncRNA–miRNA–mRNA Regulatory Network in a Flatfish Species, Chinese Tongue Sole (Cynoglossus semilaevis)

Blind-side hypermelanosis has emerged as a major concern in commercial rearing environments of the flatfish aquaculture industry. To date, the underlying molecular mechanisms are not well understood. To fill this gap, in this study, whole transcriptomic sequencing and analyses were performed using normal skins and hypermelanic skins of the blind side of Chinese tongue sole (Cynoglossus semilaevis). Differentially expressed long non-coding RNAs (DElncRNAs), miRNAs (DEmiRNAs), and differentially expressed genes as well as their competing endogenous RNA (ceRNA) networks were identified. A total of 34 DElncRNAs, 226 DEmiRNAs, and 610 DEGs were identified. Finally, lncRNA–miRNA–mRNA regulatory networks (involving 29 DElncRNAs, 106 DEmiRNAs, and 162 DEGs) associated with blind-side hypermelanosis were constructed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of 162 DEGs in ceRNA networks identified DEGs (e.g., oca2, mc1r, and ihhb) in pigmentation-related biological processes and DEGs (e.g., ca4, glul, and fut9) in nitrogen metabolism, glycosphingolipid biosynthesis, and folate biosynthesis pathways, as well as their corresponding DElncRNAs and DEmiRNAs to potentially play key regulatory roles in blind-side hypermelanosis. In conclusion, this is the first study on the ceRNA regulatory network associated with blind-side hypermelanosis in flatfish. These new findings expand the spectrum of non-coding regulatory mechanisms underpinning blind-side hypermelanosis, which facilitates the further exploration of molecular regulatory mechanisms of malpigmentation in flatfish.
A Statistical Model to Determine Biomechanical Limits for Physically Safe Interactions With Collaborative Robots

Collaborative robots (cobots) provide a wide range of opportunities to improve the ergonomics and efficiency of manual work stations. ISO/TS 15066 defines power and force limiting (PFL) as one of four safeguarding modes for these robots. PFL specifies biomechanical limits for hazardous impacts and pinching contacts that a cobot must not exceed to protect humans from serious injuries. Most of the limits in ISO/TS 15066 are preliminary, since they are based on unverified data from a literature survey. This article presents a human-subject study that provides new and experimentally verified limits for biomechanically safe interactions between humans and cobots. The new limits are specifically tailored to impact and pinching transferred through blunt and semi-sharp surfaces as they can occur in the event of human error or technical failures. Altogether 112 subjects participated in the study and were subjected to tests with emulated impact and pinching loads at 28 different body locations. During the experiments, the contact force was gradually increased until the load evoked a slightly painful feeling on the subject’s body location under test. The results confirm that the pain thresholds of males and females are different in specific body regions. Therefore, when defining biomechanical limits, the gender difference must be taken into account. A regression model was utilized to incorporate the gender effect as a covariate into a conventional statistical distribution model that can be used to calculate individual limits, precisely fitted to a specific percentile of a mixed group of male and female workers which interacting with cobots.
Optimizing Barium Titanate Nanocomposite Bone Scaffolds for Biomineralization in Dynamic Compression Bioreactors Using Time-Lapsed Microstructural Imaging and Smart Thresholding

Bone scaffolds made of calcium phosphate polymer nanocomposites have limited osteoinductive properties. Piezoelectric materials have attracted considerable interest in bone tissue engineering due to their potential to promote osteogenesis through additional electrical stimulation. Time-lapsed micro-CT imaging is a time-effective tool for in vitro optimization of such scaffolds but is challenged by nanocomposites with a high attenuation coefficient, such as one containing high amounts of piezoelectric barium titanate. We used high-resolution end-point micro-CT scans combined with histology and Raman spectroscopy to screen polydopamine functionalized nanocomposites containing 3–27 vol% barium titanate for collagenous extracellular matrix formation and mineralization. All compositions showed well-connected extracellular matrix and birefringent matured collagen after seven weeks of static human mesenchymal stem cell cultures. Nevertheless, high-resolution micro-CT analysis combined with smart thresholding during image processing enabled us to observe modest differences in ECM mineralization between groups suggesting that a volume fraction of 9–21% barium titanate facilitated the formation of dense mineral clusters in the pores even in the absence of mechanical stimuli, further corroborated by Raman spectroscopy. The same image processing approach facilitated the analysis of time-lapsed micro-CT images of scaffold cultures in dynamic compression bioreactors where 9 vol% barium titanate was the best nanocomposite composition, resulting in a significant twofold increased maturation rate under dynamic conditions. On the other hand, barium titanate content of ≥15 vol% did not improve mineralization. At 27 vol%, the biomineralization of the collagenous extracellular matrix was even impeded in the nanocomposite scaffolds, as evidenced by histology stainings. Overall, our approach enables time-lapsed quantitative assessment of high X-ray absorbing nanocomposite scaffolds for biomineralization under dynamic compression, facilitating the optimization of such mechanically responsive scaffolds.
Nutritional Status and Dietary Intake of School-Age Children and Early Adolescents: Systematic Review in a Developing Country and Lessons for the Global Perspective

Background The prevalence of double burden of malnutrition (DBM) is high in low- and middle-income countries (LMICs). Data on malnutrition trends is present for children <5 years of age, however the data for school-going children and adolescents aged 5–15 years is scarce. Objective This systematic review presents the pooled prevalence of nutritional status and dietary intake among school-going children and adolescents (5–15 years of age) in an LMIC of Pakistan and the perspective for broader global nutrition in this age group. Methods An electronic search of databases was run on Pubmed and Medline (via Ovid) along with gray literature and archives of local scientific journals till 2nd January 2021. Studies meeting the eligibility criteria were included and relevant data were extracted, and a pooled proportional analysis was performed. Results A total of 51 studies including 62,148 children of 5–15 years met the inclusion criteria, of which 30 studies reported on anthropometric indices alone, eight on dietary intake patterns while 13 reported both. All of the included studies had a cross-sectional study design. There were 20 studies from the province of Punjab, 15 from Sindh, eight from Khyber Pakhtoonkhwa, two from Balochistan, and three from multiple cities across Pakistan. The pooled proportional analysis showed that the proportion of underweight children and adolescents was 25.1% (95% CI 17.3–33.7%); stunting 23% (95% CI 11.8–36.7%); wasting 24% (95% CI 15.2–34%); thinness 12.5% (95% CI 9.4–16.1%); overweight 11.4% (95% CI 7.2–16.3%); and obesity 6.9% (95% CI 3–12%). A relatively high intake of carbohydrates, soft drinks, and sweets/chocolates; and a low intake of protein-rich foods, fruits, and vegetables, compared to the recommended daily allowance (RDA), was reported. Conclusion The limited data suggests the presence of DBM amongst children aged 5–15 years and also identified that dietary intake patterns are not meeting the recommended allowance. This review highlights the gaps and the need for larger, well-designed studies for this age group with the representation of different contexts and the need for similar studies in various LMICs, so that appropriate actions be deliberated and appropriate programs should be designed focusing on this vital population.
A Signature of N6-methyladenosine Regulator-Related Genes Predicts Prognoses and Immune Responses for Head and Neck Squamous Cell Carcinoma

This study aimed to construct a signature of N6-methyladenosine (m6A) regulator-related genes that could be used for the prognosis of head and neck squamous cell carcinoma (HNSCC) and to clarify the molecular and immune characteristics and benefits of immune checkpoint inhibitor (ICI) therapy using the prognostic signature to define the subgroups of HNSCC. This study showed that eighteen m6A regulators were abnormally expressed in the Cancer Genome Atlas (TCGA) HNSCC tissues compared with those in normal tissues. We constructed a signature of 12 m6A regulator-related genes using the Cox risk model, combined with the least absolute shrinkage and selection operator (Lasso) variable screening algorithm. Based on the median of the signature risk score, the patients were divided into high- and low-risk groups. The Kaplan–Meier survival analyses showed that patients with high-risk scores demonstrated poorer overall survival (OS) than those with low-risk scores based on TCGA-HNSCC data (p <0.001). The OS of high-risk patients was significantly worse than that of low-risk patients in the GSE65858 (p <0.001) and International Cancer Genome Consortium (ICGC) oral cancer cohorts (p = 0.0089). Furthermore, immune infiltration analyses showed that 8 types of immune cell infiltration showed highly significant differences between the two risk groups (p <0.001). In the Imvigor210CoreBiologies dataset of patients who received ICIs, the objective response rate (ORR) of the low-risk group (32%) was significantly higher than that of the high-risk group (13%). Additionally, patients in the high-risk group presented with a more significant adverse OS than that of the low-risk group (p = 0.00032). GSE78220 also showed that the ORR of the low-risk group (64%) was higher than that of the high-risk group (43%) and the OS of low-risk patients was better than that of high-risk patients (p = 0.0064). The constructed prognostic signature, based on m6A regulator-related genes, could be used to effectively distinguish between prognoses for HNSCC patients. The prognostic signature was found to be related to the immune cell infiltration of HNSCC; it might help predict the responses and prognoses of ICIs during treatment.
Biological Approaches Integrating Algae and Bacteria for the Degradation of Wastewater Contaminants—A Review

The traditional approach for biodegradation of organic matter in sewage treatment used a consortium of bacterial spp. that produce untreated or partially treated inorganic contaminants resulting in large amounts of poor-quality sludge. The aeration process of activated sludge treatment requires high energy. So, a sustainable technique for sewage treatment that could produce less amount of sludge and less energy demanding is required for various developed and developing countries. This led to research into using microalgae for wastewater treatment as they reduce concentrations of nutrients like inorganic nitrates and phosphates from the sewage water, hence reducing the associated chemical oxygen demand (COD). The presence of microalgae removes nutrient concentration in water resulting in reduction of chemical oxygen demand (COD) and toxic heavy metals like Al, Ni, and Cu. Their growth also offers opportunity to produce biofuels and bioproducts from algal biomass. To optimize use of microalgae, technologies like high-rate algal ponds (HRAPs) have been developed, that typically use 22% of the electricity used in Sequencing Batch Reactors for activated sludge treatment with added economic and environmental benefits like reduced comparative operation cost per cubic meter, mitigate global warming, and eutrophication potentials. The addition of suitable bacterial species may further enhance the treatment potential in the wastewater medium as the inorganic nutrients are assimilated into the algal biomass, while the organic nutrients are utilized by bacteria. Further, the mutual exchange of CO2 and O2 between the algae and the bacteria helps in enhancing the photosynthetic activity of algae and oxidation by bacteria leading to a higher overall nutrient removal efficiency. Even negative interactions between algae and bacteria mediated by various secondary metabolites (phycotoxins) have proven beneficial as it controls the algal bloom in the eutrophic water bodies. Herein, we attempt to review various opportunities and limitations of using a combination of microalgae and bacteria in wastewater treatment method toward cost effective, eco-friendly, and sustainable method of sewage treatment.
Genome-Wide Identification and Expression Analysis of VviYABs Family Reveal Its Potential Functions in the Developmental Switch and Stresses Response During Grapevine Development

Plant-specific YABBY (YAB) transcription factors play multiple roles in plant growth and development process. However, no comprehensive study has been performed in grapevines, especially to determine their roles in berry development and abiotic stress response. A total of seven VviYABs allocated to six chromosomal positions in grapevines were identified and classified into five subfamilies based on phylogenetic and structural analysis. Promoter element analysis and tissue-specific transcriptional response of VviYABs suggested that VviYABs might play vital roles in plant growth and development. VviYAB1, 2, 3, and 5 showed significantly higher expression levels in vegetative/green organs than in mature/woody tissues, implying that VviYABs might be involved in the regulatory switch from immature to mature developmental phases. The expression of VviYAB1, 2, 3, and VviFAS were gradually downregulated during berry developmental and ripening, which can be considered as putative molecular biomarkers between vegetative/green and mature/woody samples, and were used to identify key developmental and metabolic processes in grapevines. Furthermore, VviYAB1 expression was not markedly increased by gibberellic acid (GA3) treatment alone, but displayed significant upregulation when GA3 in combination with N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU) were applied, suggesting an involvement of VviYAB1 in fruit expansion by mediating cytokinin signaling pathway. Additionally, microarray and RNA-seq data suggested that VviYABs showed transcriptional regulation in response to various abiotic and biotic stresses, including salt, drought, Bois Noir, Erysiphe necator, and GLRaV-3 infection. Overall, our results provide a better understanding of the classification and functions of VviYABs during berry development and in response to abiotic and biotic stresses in grapevines.
Single-Cell Sequencing Facilitates Elucidation of HIV Immunopathogenesis: A Review of Current Literature

Knowledge gaps remain in the understanding of HIV disease establishment and progression. Scientists continue to strive in their endeavor to elucidate the precise underlying immunopathogenic mechanisms of HIV-related disease, in order to identify possible preventive and therapeutic targets. A useful tool in the quest to reveal some of the enigmas related to HIV infection and disease is the single-cell sequencing (scRNA-seq) technique. With its proven capacity to elucidate critical processes in cell formation and differentiation, to decipher critical hematopoietic pathways, and to understand the regulatory gene networks that predict immune function, scRNA-seq is further considered to be a potentially useful tool to explore HIV immunopathogenesis. In this article, we provide an overview of single-cell sequencing platforms, before delving into research findings gleaned from the use of single cell sequencing in HIV research, as published in recent literature. Finally, we describe two important avenues of research that we believe should be further investigated using the single-cell sequencing technique.
Fecal Microbiota Transplantation Donor and Dietary Fiber Intervention Collectively Contribute to Gut Health in a Mouse Model

Transforming the gut microbiota has turned into the most intriguing target for interventions in multiple gastrointestinal and non-gastrointestinal disorders. Fecal microbiota transplantation (FMT) is a therapeutic tool that administers feces collected from healthy donors into patients to help replenish the gut microbial balance. Considering the random donor selection, to maintain the optimal microbial ecosystem, post-FMT is critical for therapy outcomes but challenging. Aiming to study the interventions of different diets on recipients’ gut microbiota post-FMT that originated from donors with different diets, we performed FMT from domestic vs. wild pigs that are living on low-fiber vs. high-fiber diets into the pseudo-GF mouse, followed with fiber-free (FF) or fiber-rich (FR) diets post-FMT. Different patterns of gut microbiota and metabolites were observed when mice FMT from different donors were paired with different dietary fiber contents. Enrichment of bacteria, including Akkermansia and Parabacteroides, together with alteration of metabolites, including palmitic acid, stearic acid, and nicotinic acid, was noted to improve crypt length and mucus layer in the gut in mice FMT from wild pigs fed an FR diet. The results provide novel insight into the different responses of reconstructed gut microbiota by FMT to dietary fiber. Our study highlighted the importance of post-FMT precise dietary interventions.