Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder.

Single-cell RNA sequencing (scRNA-seq) is a revolutionary breakthrough that determines the precise gene expressions on individual cells and deciphers cell heterogeneity and subpopulations. However, scRNA-seq data are much noisier than traditional high-throughput RNA-seq data because of technical limitations, leading to many scRNA-seq data studies about dimensionality reduction and visualization remaining at the basic data-stacking stage. In this study, we propose an improved variational autoencoder model (termed DREAM) for dimensionality reduction and a visual analysis of scRNA-seq data. Here, DREAM combines the variational autoencoder and Gaussian mixture model for cell type identification, meanwhile explicitly solving 'dropout' events by introducing the zero-inflated layer to obtain the low-dimensional representation that describes the changes in the original scRNA-seq dataset. Benchmarking comparisons across nine scRNA-seq datasets show that DREAM outperforms four state-of-the-art methods on average. Moreover, we prove that DREAM can accurately capture the expression dynamics of human preimplantation embryonic development. DREAM is implemented in Python, freely available via the GitHub website, https://github.com/Crystal-JJ/DREAM.

Therapeutic effects of Reiki on interventions for anxiety: a meta-analysis.

PURPOSE: This study aimed to assess the therapeutic efficacy of Reiki therapy in alleviating anxiety. METHODS: In adherence to academic standards, a thorough search was conducted across esteemed databases such as PubMed, Web of Science, Science Direct, and the Cochrane Library. The primary objective of this search was to pinpoint peer-reviewed articles published in English that satisfied specific criteria: (1) employing an experimental or quasi-experimental study design, (2) incorporating Reiki therapy as the independent variable, (3) encompassing diverse patient populations along with healthy individuals, and (4) assessing anxiety as the measured outcome. RESULTS: The study involved 824 participants, all of whom were aged 18 years or older. Reiki therapy was found to have a significant effect on anxiety intervention(SMD=-0.82, 95CI -1.29∼-0.36, P = 0.001). Subgroup analysis indicated that the types of subjects (chronically ill individuals and the general adult population) and the dosage/frequency of the intervention (≤ 3 sessions and 6-8 sessions) were significant factors influencing the variability in anxiety reduction. CONCLUSION: Short-term Reiki therapy interventions of ≤ 3 sessions and 6-8 sessions have demonstrated effectiveness in reducing health and procedural anxiety in patients with chronic conditions such as gastrointestinal endoscopy inflammation, fibromyalgia, and depression, as well as in the general population. It is important to note that the efficacy of Reiki therapy in decreasing preoperative anxiety and death-related anxiety in preoperative patients and cancer patients is somewhat less consistent. These discrepancies may be attributed to individual pathophysiological states, psychological conditions, and treatment expectations.

High Fat Diet Alters Gut Microbiota and the Expression of Paneth Cell-Antimicrobial Peptides Preceding Changes of Circulating Inflammatory Cytokines.

Obesity is an established risk factor for many diseases including intestinal cancer. One of the responsible mechanisms is the chronic inflammation driven by obesity. However, it remains to be defined whether diet-induced obesity exacerbates the intestinal inflammatory status by cytokines produced in adipose tissue or the high fat diet first alters the gut microbiota and then drives intestinal inflammation. To address this question, we fed C57BL/6 mice with a high fat diet (HF, 60%) and sacrificed them sequentially after 8, 12, and 16 weeks, and then compositions of gut microbiota and expressions of antimicrobial peptides were determined. The compositions of gut microbiota were altered at 8 wk HF feeding, followed with reduced Paneth antimicrobial peptides lysozyme and Reg IIIγ after 12 and 16 wk HF feeding (p < 0.05), whereas elevations of circulating inflammatory cytokines IFNγ and TNF-α were observed until feeding a HF diet for 16 weeks (p < 0.05). These results indicated that high fat diet may stimulate intestinal inflammation via altering gut microbiota, and it occurs prior to the potential influence by circulating inflammatory cytokines. These findings emphasized the importance of microbiota, in addition to adipose tissue per se, in driving intestinal inflammation, which may thereafter promote intestinal tumorigenesis.

Cortical Changes of Dual Cognitive-Task Balance Training in Patients with Chronic Ankle Instability: A Randomized Trial.

CONTEXT: Researchers have shown that patients with chronic ankle instability (CAI) have deficits in memory and attention allocation. This functional deficit affects the lower extremity performance. Motor-cognitive dual-task training may improve lower limb dysfunction caused by central nervous system injury. Whether dual-task training is more favorable than single-task training for neuromuscular control in patients with single-task training still needs to be further proven. OBJECTIVE: To determine whether balance-cognitive dual-task training can influence cortical activity and has more effective treatment effects than balance single-task training. DESIGN: Randomized controlled clinical trial (Clinical Trials: XXX). SETTING: Rehabilitation training room. PATIENTS OR OTHER PARTICIPANTS: After recruitment, twenty-four patients with CAI (age=22.33±2.43 years, height=175.62±7.7 cm, mass=70.63±14.59 kg) were block randomized into two groups. INTERVENTION(S): Protocols were performed three times per week for six weeks. The single-task group underwent one-leg static balance training with and without vision and hopping balance training. The dual-task group underwent balance and cognitive training (backward counting task). MAIN OUTCOME MEASURE(S): The follow variables were assessed before and after the interventions: cortical activity, proprioception, muscle onset time, and dynamic balance. We performed MANOVAs to compare changes of main effects and interactions across groups and time. A post-hoc Bonferroni test was performed for pairwise comparisons when there were significant interactions with the MANOVAs. RESULTS: Twenty-four participants successfully completed the six-week interventions. Proprioception, peroneus longus muscle onset time, and dynamic postural control improved significantly after the interventions in both groups (P<0.05). Dual-task training was superior to single-task training in improving JPS plantarflexion, shortening peroneus longus muscle onset time, and altering cortical activity(P<0.05). CONCLUSIONS: A six-week balance training program or balance combined with cognitive training could improve the functional deficits associated with CAI. Meanwhile, the dual-task training could improve cortical activity and lower extremity function.

Exploring the mechanism of Pueraria lobata (Willd.) Ohwi in the regulation of obesity.

ETHNOPHARMACOLOGICAL RELEVANCE: Pueraria lobata (Willd.) Ohwi is a traditional medicinal and edible homologous plant rich in flavonoids, triterpenes, saponins, polysaccharides and other chemical components. At present, studies have shown that Pueraria lobata radix (PR) has the effect of lowering blood sugar, improving insulin sensitivity and inhibiting obesity. However, the specific mechanism of PR inhibits obesity is still unclear, and there are few researches on the anti-obesity effect of PR through the combination of network pharmacology and experiment. AIM OF THE STUDY: Pharmacology, molecular docking technology and experimental verification through the network, revealing the PR the material basis of obesity and the potential mechanism. METHODS AND RESULTS: The present study used network pharmacology techniques to investigate the therapeutic effect and mechanism of action of PR. Through relevant databases, a total of 6 main chemical components and 257 potential targets were screened. Protein interaction analysis shows that AKT1, AKR1B1, PPARG, MMP9, TNF, TP53, BAD, and BCL2 are core targets. Enrichment analysis shows that the pathway of PR in preventing obesity involves the cancer signaling pathway and the PI3K-Akt signaling pathway, which may be the main pathways of action. Further molecular docking verification indicates that its core target exhibits good binding activity with 4 compounds: formononectin, purerin, 7,8,4 '- trihydroxide and daidzein. Using the ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS) technology to detected and confirmed these main compounds. Cell experiment results revealed that puerarin inhibits cell proliferation and differentiation in a concentration dependent manner, significantly promoting cell apoptosis and affecting cell migration. Animal experiments have shown that puerarin reduces food intake and weight gain in mice. It was found that puerarin can upregulate HDL and downregulate TC, TG, and LDL blood biochemical indicators. Western blot results showed that puerarin significantly inhibited the expression of AKT1, AKR1B1, MMP9, TNF, TP53, BCL2, PPARG, and significantly increased the expression of BAD protein at both cellular and animal levels. CONCLUSION: The present study established a method for measuring PR content and predicted its active ingredients and their mechanisms of action in the treatment of obesity, providing a theoretical basis for further research.

Role of akirin in skeletal myogenesis.

Akirin is a recently discovered nuclear factor that plays an important role in innate immune responses. Beyond its role in innate immune responses, Akirin has recently been shown to play an important role in skeletal myogenesis. In this article, we will briefly review the structure and tissue distribution of Akirin and discuss recent advances in our understanding of its role and signal pathway in skeletal myogenesis.

Combination of Flos Sophorae and chili pepper as a nitrite alternative improves the antioxidant, microbial communities and quality traits in Chinese sausages.

The main issue remains finding a nitrite alternative able to provide its multiple functions. Flos Sophorae exerts antioxidant and prebiotic actions, chili pepper has potent coloring capacity, thus this study investigated whether combination of Flos Sophorae and chili pepper could address the multiple activities of nitrite in Chinese sausages. Dry-fermented sausages were prepared: control and four treatments added with 150 mg/kg sodium nitrite (Nit), 0.2% Flos Sophorae (FS), 1% chili pepper (CP), and combination of 0.2% Flos Sophorae and 1% chili pepper (FS + CP). Results indicated that FS, CP and FS + CP had higher moisture, antioxidant activity and numbers of beneficial Staphylococcus and yeasts Candida, and lower numbers of Escherichia coli and harmful fungi, while FS had lower redness and harder texture than control. Their combination inhibited the declines of capsanthin and antioxidant capacity with ripening time, further improved microbiological communities compared with CP, and resulted in higher redness, similar color score and bacterial community, less lipid oxidation and softer texture compared with Nit. These results suggested that Flos Sophorae in combination with chili pepper could replace the nitrite's contribution to red curing color and microbiological communities, and effectively hinder lipid oxidation in Chinese sausages.

Effects of Decabrominated Diphenyl Ether Exposure on Growth, Meat Characteristics and Blood Profiles in Broilers.

Decabrominated diphenyl ether (BDE-209) is widely used as a flame retardant and is detected at high levels in the environment. Its toxicities have been reported and have attracted attention. In the present study, broilers were used to determine the response in growth performance, carcass traits, meat quality, blood profiles and antioxidant system to BDE-209 exposure at doses of 0, 0.02, 0.4 and 4 mg/kg. The results showed that BDE-209 exposure at levels of 0.02 or 0.4 mg/kg increased feed intake and decreased feed efficiency. BDE-209 altered the blood profiles, such as reducing the numbers of white blood cells, lymphocytes and neutrophilic granulocytes. As compared with the control, BDE-209 exposure significantly increased abdominal fat percentages of broilers at 64.9-159.5% and adversely affected the selected biochemical indicators, including alkaline phosphatase (ALP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), creatine (CRE), which indicated its toxicity to liver and kidney functions. Moreover, BDE-209 exposure significantly increased plasma malondialdehyde (MDA) concentrations and decreased the activities of glutathione peroxidase (GSH-px) and superoxide dismutase (SOD), which implied aggravating oxidant stress and decline of antioxidant capacity in broilers. In conclusion, our data demonstrated that the environmental pollutant BDE-209 adversely influenced growth performance, increased the deposition of abdominal fat, impaired antioxidant capacity and the immune system and had potential toxicity to the liver and kidney of broilers.

Real-time PCR quantification of the predominant bacterial divisions in the distal gut of Meishan and Landrace pigs.

Firmicutes and Bacteroidetes are closely related to body fat in humans and mice, which are the two dominant bacterial divisions of gut microbiota in mammals. Here real-time PCR analysis indicated that Meishan pigs had a 34% reduction in percentage Bacteroidetes (P = 0.008) and a significantly lower proportion of Bacteroides (P = 0.013) than Landrace pigs. The percentage of Bacteroidetes or Bacteroides had a negative correlation with body fat (R2 was 0.63 for Bacteroidetes and 0.57 for Bacteroides, P < 0.05). There was a trend that the percentage of Firmicutes in Meishan pigs was higher in numerical value than in Landrace pigs, although this difference was not statistically significant (P = 0.290) between the two breeds. These suggested that body fat correlated with the percentage of Bacteroidetes division of the gut microbiota in the common pig breeds, and the differences of gut microbial ecology in obese versus lean animals may be analogous.

Rutin and Its Combination With Inulin Attenuate Gut Dysbiosis, the Inflammatory Status and Endoplasmic Reticulum Stress in Paneth Cells of Obese Mice Induced by High-Fat Diet.

Gut dysbiosis induced by high fat diet (HF) or obesity is a predisposing factor to develop diverse inflammatory diseases. Polyphenols and fibers, often eaten together, have been reported to have prebiotic actions, but their health promoting benefits still need to be further characterized and defined. This study attempted to understand how polyphenol rutin and polysaccharide inulin influence intestinal health in mouse model fed a HF (60 kcal%) diet. A total of 48 C57BL/6J mice were divided into four groups fed with a low fat (10% kcal%) control diet (LC), a high fat control diet (HC), a high-fat diet supplemented with rutin (HR), or a high-fat diet supplemented rutin and inulin (HRI) for 20 weeks. Rutin supplementation reduced the HF diet-induced increase of Firmicutes/Bacteroidetes (F/B) ratio, Deferribacteraceae population and plasma lipopolysaccharide (LPS) (p < 0.05); ameliorated inflammation as indicated by the decreased circulating inflammatory cytokines (p < 0.05) and the reduced expressions of intestinal inflammatory mediators (p < 0.05); and attenuated the endoplasmic reticulum (ER) stress in Paneth cells as indicated by the decreased expressions of the ER markers (p < 0.05). Compared to the rutin supplementation alone, the co-administration of rutin with inulin improved the utilization of rutin as indicated by its decreased excretion, suppressed a number of harmful bacteria including Deferribacteraceae and Desulfovibrionaceae (p < 0.05), and further reduced the expression of the key inflammatory cytokine TNF-α and increased the production of butyrate, despite the supplementation of inulin reversed the decrease of body weight induced by rutin supplementation due to an increased food intake. Taken together, our data demonstrated that rutin supplementation ameliorated the inflammatory status and ER stress in Paneth cells under a HF-induced obese state, and its co-administration with inulin further mitigated the inflammatory status, indicating the potential to combine polyphenol rutin and the polysaccharide inulin as a dietary strategy to ameliorate gut dysbiosis, to improve inflammatory status and thereby to reduce medical disorders associated with HF-induced obesity.

Effects of nutritional level on pork quality and gene expression of micro-calpain and calpastatin in muscle of finishing pigs.

The study was designed to investigate the effects of nutritional level (control diet (CD), 14.19% crude protein, 13.81MJ of DE/kg; low nutritional level diet (LND), 11.08% crude protein, 12.55MJ of DE/kg) on pork quality and gene expression of mu-calpain and calpastatin in muscle of finishing pigs. The LND treatment increased drip loss (P<0.05), had a trend to increase intramuscular fat (IMF) content (P=0.09), decreased Warner-Bratzler shear force (WBSF) of pork (P<0.05), improved mRNA level of mu-calpain (P<0.05) in skeletal muscle, but had no effect on gene expression of calpastatin, compared with the CD treatment. These data suggest that a moderately reduced energy and protein diet increased pork tenderness and intramuscular fat. The increase in tenderness by LND treatment may be partly due to increased gene expression of mu-calpain in muscle.