Search Results (7,298)

The human microbiome influences health and disease through diverse biochemical and functional outputs (e.g., enzymes, structural proteins, metabolites, and other cellular components) that affect nearly every aspect of human physiology. Metatranscriptomics (MT), an unbiased RNA sequencing approach, is a high-throughput and high-content method that quantifies both gut microbial taxonomy and active biochemical functions. Because microbial community composition and gene expression are dynamic, understanding temporal variation in the gut metatranscriptome across multiple time scales is essential. Here, we report the temporal dynamics of gut microbiome species and functions using a large cohort (n = 6157) with a clinically validated stool MT test. We quantified microbiome stability from hours to years and assessed taxonomic and functional resilience to major luminal perturbations, such as colonoscopy bowel preparation. Longitudinal analyses of samples collected within the same day, and across days, weeks, months, and years, revealed consistently high stability in both composition and gene expression within a single day and, importantly, across an approximate six-month period. Among individuals reporting stable diets and no antibiotic exposure, taxonomic and functional profiles remained stable for up to three years. Following colonoscopy preparation, our preliminary study of the microbiome demonstrated strong resilience, returning to its pre-procedure state within one week. Overall, these findings demonstrate that the gut microbiome is generally stable over a six-month time frame, with longer-term changes occurring gradually. These findings support the robustness of stool-based MT profiling for species-level and pathway-resolved functional analysis in longitudinal research and health applications. Full article

In Vietnamese primary mathematics education, geometry instruction often emphasizes rote calculation and formula memorization rather than meaningful contextualization, leaving students disconnected from abstract concepts and lacking opportunities to connect learning with cultural identity. This quasi-experimental study investigates how integrating generative AI tools (ChatGPT, DALL·E, Canva) with the culturally grounded Vietnamese folktale Bánh Chưng—Bánh Giầy can support Grade 5 students’ understanding of circle geometry. Employing a mixed-methods design with 30 students divided into experimental (AI + storytelling) and control (traditional instruction) groups, the study measured cognitive and affective learning outcomes through pre/post-tests, a validated 25-item questionnaire, interviews, and classroom observations. Quantitative results revealed significant improvements in the experimental group across all measured dimensions, learning interest, attentional focus, conceptual understanding, mathematics passion, and cultural preservation awareness, with large effect sizes. Qualitative findings confirmed enhanced engagement, multimodal conceptual clarity, and cultural affective resonance. The study demonstrates that low-cost, teacher-mediated generative AI can effectively support learning in resource-constrained primary settings when anchored in local narratives. Implications for ethical AI integration and teacher professional development in Vietnamese contexts are discussed. Full article

The SHAGGY-like kinase (SK) gene family regulates diverse developmental and abiotic stress response processes in plants. Although genome-wide analyses of SKs have been conducted in model plants such as Arabidopsis thaliana and rice, their characterization in the economically important crop Brassica rapa remains limited. In this study, we conducted a systematic genome-wide analysis of SK genes in three Brassica species. A total of 18, 16, and 18 SK members were identified in B. rapa, B. nigra, and B. oleracea, respectively, and phylogenetic analysis classified them into four distinct clades. Expression profiling revealed that BrSKβ-1 and BrSKβ-2 were specifically expressed in fertile floral buds, suggesting their critical roles in pollen development. Furthermore, co-expression analysis indicated that both genes were co-expressed with key regulators involved in pollen development, pollen sperm cell differentiation and pollen tube growth. Loss of BrSKβ-2 via CRISPR/Cas9 resulted in 25–65% pollen abnormality and reduced the germination rate of normal-appearing pollen to only 10%, confirming its essential role in male fertility. Together, these findings provide a comprehensive characterization of the SK gene family in Brassica and position BrSKβ-2 as a promising candidate for gene editing-based male sterility systems in B. rapa and related crops. Full article

In the post-antibiotic era, the Bacillus-based direct-fed beneficial microorganisms are emerging as a cornerstone for sustainable animal farming. This study aimed to screen and evaluate Bacillus strains with probiotic potential for use as feed additives. A total of 394 Bacillus strains were initially screened based on their extracellular enzyme production (cellulase, protease, and amylase) and antibacterial activities against Escherichia coli, Staphylococcus aureus, and Salmonella enterica. Two strains, Bacillus velezensis FJAT-10508 and FJAT-13563, were selected and subsequently subjected to in vitro probiotic characterization, safety assessment, and whole-genome analysis. The results demonstrated that both strains exhibited α-hemolysis, acceptable antibiotic susceptibility profiles, absence of invasion and cytotoxicity effect on the Caco-2 cells, and no mobile virulence or antibiotic resistance genes, indicating their safety as probiotic candidates. High endospore-forming efficiencies (72.4–90.8%), strong auto-aggregation (74–85%) and co-aggregation abilities (52–82%) were observed. In addition, both strains showed considerable tolerance to simulated gastrointestinal conditions, with vegetative cell and endospore survival rates of 28.33–38.33% and 85–89.67% at pH 2.0, and 38.33–43.33% and 90.33–96.33% in 0.3% bile salts, respectively. Overall, B. velezensis FJAT-10508 and FJAT-13563 demonstrated robust in vitro probiotic properties, supporting their potential application as reliable Bacillus-based feed additives. Full article

Background: ChatGPT is a large language model (LLM) online chatbot developed by OpenAI and launched in November 2022. Early adoption studies have shown high readiness to use this technology for health-related questions and self-diagnosis. However, the quality and clinical adequacy of health-related responses remain incompletely characterized. This study aimed to explore responses generated by ChatGPT-3.5 and ChatGPT-4.0 to common patient questions regarding scoliosis. Methods: Ten scoliosis-related frequently asked questions (FAQs) were selected from a larger pool of over 250 patient-facing questions compiled from 17 publicly available FAQ webpages and informed by a Google Trends analysis. Questions were harmonized, grouped by theme, and then reduced by rule-based expert review to a final set intended to represent common patient concerns. Results: The median ratings of ChatGPT-3.5 and ChatGPT-4.0 responses ranged from satisfactory, requiring minimal (2) to moderate clarification (3). Across the ten matched questions, no statistically detectable difference was found between models in this study setting (W = 8.0, p = 0.59; Cliff’s δ = −0.12 [95% CI −0.58, 0.40]); however, given the small question set, unblinded rating process, and poor inter-rater reliability, this should not be interpreted as evidence of equivalence, non-inferiority, or comparable model performance. The results apply only to the 10–15 April 2024, online snapshots of ChatGPT-3.5 and ChatGPT-4.0 and should not be generalized to later model iterations. Conclusions: This study should be interpreted as a clinically oriented observational report, intended to inform physician awareness and patient-physician communication rather than validate chatbot accuracy or safety. In this 10–15 April 2024, sample, both model outputs frequently required clinician clarification. Given the small FAQ set, low inter-rater reliability, unblinded design, and single-sample outputs, the findings do not establish equivalence or superiority and apply only to the specific 10–15 April 2024, model snapshots and evaluated questions. Full article

A structured optimization approach was applied to ultrasonic surface rolling process (USRP) parameters, aiming to enhance the material surface characteristics of TC4 titanium alloy. To overcome the premature convergence and limited exploration capability of the standard Whale Optimization Algorithm (WOA), three enhancement strategies were introduced, including population initialization based on an optimal point set, a sinusoidal nonlinear convergence factor, and an adaptive inertia-based position update strategy. By optimizing the structural parameters of the RBF neural network with the improved WOA, an IWOA–RBF predictive model for surface performance evaluation was developed and rigorously validated in terms of prediction accuracy. Using the developed IWOA–RBF model, a multi-criteria decision-making framework integrating the CRITIC weighting method and the TOPSIS ranking approach was constructed to evaluate surface quality. This framework was further combined with a multi-objective Grey Wolf Optimization (MOGWO) algorithm to perform Pareto-based optimization and determine the optimal USRP parameter set. Experimental validation showed that the optimized parameters resulted in a significant reduction in surface roughness, while enhancing both surface hardness and residual compressive stress. The results confirm the robustness and effectiveness of the proposed IWOA–RBF and MOGWO optimization framework, providing a reliable strategy for high-precision parameter optimization and coordinated enhancement of surface properties in the TC4 titanium alloy USRP. Full article

Large-scale pavement maintenance generates substantial amounts of reclaimed base course material (RBM), whose high-value reuse presents a critical challenge. Although cement is commonly used for stabilization, its high carbon footprint and shrinkage issues limit sustainability. This study proposes a 100% solid waste-based cementitious material (SWC) as an alternative stabilizer for pavement base layers containing high proportions of RBM. A comparative investigation was conducted between SWC-stabilized RBM (SSRBM) and ordinary Portland cement-stabilized RBM (CSRBM) regarding key road performance indicators. The results indicate that with 100% RBM, the 7-day compressive strength of SSRBM containing 4% SWC reaches 1.88 MPa, meeting the Chinese specification JTG/T 5521-2019. By incorporating 15% natural coarse aggregate, this strength can be increased by 35.4%. Furthermore, SSRBM demonstrates superior freeze–thaw resistance, with a freeze–thaw-retained unconfined compressive strength ratio of 93.9%, compared to 89.6% for CSRBM, and exhibits a lower drying shrinkage coefficient. Carbon emission analysis shows that the emissions per cubic meter of SSRBM are approximately 73% lower than those of CSRBM, presenting a viable and environmentally advantageous alternative for sustainable pavement construction. Full article

Particle swarm optimization (PSO) improves classification performance and reduces computational complexity in feature selection. However, it frequently experiences from premature convergence and insufficient exploration. To address these constraints, this paper suggests an adaptive binary PSO (ABPSO) algorithm specifically designed for feature selection. First, an adaptive transfer function and two adaptive learning coefficients are introduced to achieve a better balance between exploration and exploitation during the search process. Second, a hybrid learning mechanism that integrates personal best, global best, and elite solutions is utilized to enhance population diversity. Finally, a simulated annealing (SA)–based local search strategy is employed to further refine candidate solutions and improve convergence behavior. Experimental results demonstrate that ABPSO outperforms binary PSO (BPSO), harris hawks optimization (HHO), whale optimization algorithm (WOA), and ant colony optimization (ACO) in classification accuracy. In particular, ABPSO achieves the lowest classification error rates on the Dermatology (0.0106), Ionosphere (0.0705), Lung (0.1521), Sonar (0.0996), Spambase (0.0758), Statlog (0.1446), and Wine (0.0280) datasets. Full article

Background: Chlorophyll degradation is a characteristic sign of fruit ripening. However, the chlorophyll degradation pathway during pitaya fruit development remains unexplored. Methods and Results: Here, chlorophyll contents showed a downward trend across the five developmental stages of ‘Jindu No.1’ pitaya peels. Based on the pitaya genome data, twenty chlorophyll degradation genes were identified, including two NYCs, three CLHs, five SGRs, six PAOs, and four RCCRs, spread across eight pitaya chromosomes. In addition, their phylogenetic relationships, conserved motifs, and domains were analyzed using homologous genes from beet and Arabidopsis species. Transcriptomic data and RT-qPCR analyses of these genes suggested that three HuSGRs demonstrated a significant upward trend during pitaya peel maturation. Indeed, the HuSGR1 has the complete gene structure, including the chloroplast transit peptide, SGR domain, and variable C-terminal region. However, HuSGR2 and HuSGR3 contained the N- and C-terminal sequences, respectively, of HuSGR1. They were separated by a 690 bp distance on chromosome 8, forming a gene cluster. Overexpressed HuSGR2 or HuSGR3 alone resulted in a significant decrease in chlorophyll contents in tobacco leaves. Notably, a more obvious reduction of chlorophyll contents was observed when overexpressing them together. Conclusions: Our results show that HuSGR2 and HuSGR3 were involved in accelerating the chlorophyll degradation process, providing new insights into the molecular basis of color formation in pitaya peels. Full article

Background/Objectives: Thymic stromal lymphopoietin (TSLP) is central to the pathogenesis of atopic dermatitis (AD) and a promising therapeutic target. However, developing small-molecule TSLP inhibitors is challenging due to the difficulty in disrupting the TSLP-TSLPR interface. This study aimed to explore naturally sourced blockers of the TSLP-TSLPR interaction and identify novel candidate compounds for AD treatment. Methods: HuT78 cells were stimulated with PMA, ionomycin, and TSLP to establish an AD model. Inflammatory cytokines were measured by qRT-PCR and ELISA. JAK/STAT signaling was analyzed by Western blot. In female BALB/c mice, DNCB-induced AD-like skin lesions were topically treated with test compounds, followed by histopathological and immunohistochemical assessment. Results: Eight compounds were screened, and their key structural features were elucidated via structure–activity relationship (SAR) analysis. Among them, kaempferol-7-O-glucoside (K-7-G) emerged as the most potent candidate. It interfered with the TSLP-TSLPR interaction, selectively inhibited TSLP-mediated JAK2/STAT5 phosphorylation, and significantly downregulated IL-4 (p < 0.0001) and IL-13 (p < 0.001) levels. Topical application of 1% K-7-G significantly alleviated AD-like symptoms in a mouse model, decreasing dorsal skin thickness, dermatitis score, and scratching frequency while restoring the expression of filaggrin, loricrin, and occludin (p < 0.0001). Meanwhile, it significantly reduced key inflammatory mediators in a concentration-dependent manner, including TSLP, IL-4, IL-13, TNF-α, IFN-γ, and IgE. Conclusions: This study demonstrates that K-7-G is a novel natural TSLP inhibitor capable of blocking the TSLP-TSLPR signaling pathway and effectively improving AD symptoms. Further research may explore its therapeutic potential in other inflammatory diseases. Full article

Background: PYR/PYL/RCAR proteins are core abscisic acid (ABA) receptors that play essential roles in ABA signal transduction, plant growth and development, and abiotic stress responses. However, the PYL gene family in watermelon (Citrullus lanatus) has not been systematically characterized, limiting our understanding of ABA-mediated stress adaptation in this economically important crop. Methods: A genome-wide analysis was performed to identify ClPYL genes in watermelon using a hidden Markov model search. Phylogenetic relationships were reconstructed using the maximum likelihood method. Segmental duplication events were analyzed using synteny analysis. Conserved motifs, gene structures, and promoter cis-acting elements were characterized using MEME and PlantCARE. Expression profiles under drought, salt, and cold stresses were examined by quantitative real-time PCR (qRT-PCR) with three biological replicates. Results: In this study, 15 ClPYL genes were identified in watermelon through genome-wide analysis. Phylogenetic reconstruction classified these genes into four subfamilies, with subfamily II being exclusively present in cucurbits—a lineage-specific feature not observed in Arabidopsis. Synteny analysis revealed eight segmental duplication events involving members of subfamilies I, III, and IV, while subfamily II members were not associated with these duplications. Members within the same subfamily share similar exon-intron structures and conserved motifs. Promoter analysis revealed that ClPYL genes are enriched with various cis-acting elements associated with hormone signaling and abiotic stress responses. Expression profiling demonstrated that ClPYL genes exhibit diverse and dynamic expression patterns under drought, high-salinity, and cold stresses. Notably, genes such as ClPYL5 under drought, ClPYL02 under salt, and ClPYL15 under cold stress displayed persistent stress-responsive expression. Conclusions: These findings reveal the evolutionary conservation and diversification of the PYL family in watermelon and provide a set of candidate genes for functional studies aimed at dissecting ABA-mediated stress adaptation. This work establishes a genomic framework for developing stress-resilient watermelon varieties through molecular breeding. Full article

Diagnosis of atypical parkinsonian syndromes (APS), including progressive supranuclear palsy (PSP) and multiple system atrophy (MSA), rely on clinical criteria that often result in misclassification or delayed confirmation. Cerebrospinal fluid (CSF) metabolomics offers the potential to identify disease-specific biochemical “fingerprints”. The aim of the study is to identify CSF metabolomic biomarkers that distinguish PSP and MSA from each other and from non-neurodegenerative controls. Targeted mass spectrometry-based metabolomics was performed on CSF samples from 30 patients with MSA, 41 with PSP, and 30 age- and sex-matched non-neurodegenerative controls. Global metabolomic profiles showed no clear group separation. Both PSP and MSA showed elevated gut-derived metabolites p-cresyl sulfate and deoxycholic acid versus controls. In PSP, decreased cortisone and increased hexosylceramide d18:1/24:1 were observed, whereas in MSA, dihydroxyphenylalanine was elevated alongside homoarginine and creatinine. In the direct comparison of APS, levels of α-aminoadipic acid were increased in PSP compared to MSA. Pathway analysis highlighted disrupted glycerophospholipid metabolism in both APS disorders. Distinct metabolite panels mainly combining membrane-associated lipids, gut-derived and neurotransmitter-related metabolites demonstrated high diagnostic accuracy for distinguishing PSP and MSA from control groups (AUC = 0.95 for PSP and AUC = 0.98 for MSA), while a separate panel showed moderate performance in differentiating PSP from MSA (AUC = 0.85). Distinct but partially overlapping CSF metabolomic profiles characterize PSP and MSA. These metabolomic fingerprints highlight gut–brain axis involvement, alterations in cell membrane-related lipid metabolism, and disease-specific changes in neurotransmitter-related metabolites. Further, a panel of these metabolites showed strong potential as diagnostic biomarkers. Full article

Current smart packaging systems exhibit uneven release of active ingredients (rapid in the early stage and slow in the later stage), resulting in insufficient antibacterial and antioxidant properties. This study developed a pH-autonomous controlled-release sensor using Eudragit L100 and citrate as the matrix, with eugenol as the active component, and constructed a sandwich structure via electrospinning. The sensor can automatically release eugenol as needed in response to pH changes during shrimp storage, while simultaneously enabling visual monitoring of spoilage status. This innovation effectively extends the shelf life of fresh shrimp and provides a novel solution for the on-demand release of active ingredients in food preservation. Full article

Codon usage bias (CUB) is a universal feature in both mitochondrial and ribosomal genes, shaped by the combined forces of mutation and selection, and serves as a valuable indicator of evolutionary processes and phylogenetic signals. However, comprehensive analysis of CUB is lacking in the Leuciscinae family. We sequenced and annotated the complete mitochondrial genome of Abramis brama orientalis and examined codon usage patterns in all Leuciscinae species, subsequently finding the dominant evolutionary forces and phylogenetic relationships. We performed a PR2 bias plot, neutrality plot, effective number of codons (ENC) vs. GC3, relative synonymous codon use (RSCU) clustering and Ka/Ks calculations for 22 Leuciscinae species. We constructed the phylogenetic trees of Leuciscinae using Bayesian inference and maximum likelihood on concatenated mitochondrial sequences. The complete mitochondrial genome of Abramis brama orientalis was 16,607 bp, with typical vertebrate structure and high A + T bias. The codons of protein-coding genes in Leuciscinae have a preference for ending in A/C. All protein-coding genes were under strong purifying selection (Ka/Ks < 1). RSCU patterns and phylogenetic analyses showed two lines of Leuciscinae in the RSCU, with A. brama orientalis being a monophyletic group with A. brama. The results demonstrate the strong role for selection in shaping mitochondrial codon usage in Leuciscinae, despite mutational biases. The study clarified the taxonomic status of A. brama orientalis and provided a framework for understanding molecular evolution in this ecologically important freshwater fish family. Full article

Background: While Toxoplasma gondii infection poses a significant health threat, its impact on the localized intestinal lipid metabolism remains unclear. Methods: Thus, this study established an acute infection model in BALB/cJ mice and analyzed the colonic contents collected 10 days post-infection via untargeted lipidomics. The lipid profiles of the two groups diverged substantially, with a clear separation evident between infection and control conditions. Results: We identified 65 upregulated and 87 downregulated differential lipids, primarily falling into the glycerophospholipids and sphingolipids categories. Pathway enrichment analysis revealed that the choline metabolism in cancer and glycerophospholipid metabolism pathways was pinpointed as being among the most perturbed following infection. Correlation and network analyses further suggested that key molecules, such as LPC (20:4) and LPA (18:0), may mediate these metabolic pathway abnormalities by regulating related enzymatic activities. Conclusions: This systematic characterization of the intestinal lipid metabolic landscape in mice during acute T. gondii infection revealed the host intestinal lipid metabolic reprogramming induced by T. gondii infection. The findings offer a novel metabolic perspective for understanding T. gondii pathogenesis and host–parasite interactions. Full article