Search Results (2,354)

Coffee consumption has been associated with metabolic and cardiovascular health, but the molecular mechanisms underlying these associations remain unclear. This study investigated the association between coffee intake and circulating proteomic profiles across metabolic conditions using a pooled-serum, exploratory design. Participants were classified into four groups: normal weight (NW), normal weight with coffee intake (NWC), obese with hypertension (OBHT), and obese with hypertension with coffee intake (OBHTC). Differentially expressed proteins (DEPs) were identified using volcano plot criteria (|log₂FC| ≥ 1, FDR < 0.05), followed by Reactome pathway enrichment, Gene Ontology (GO) molecular function, and Enrichr-derived protein–protein interaction (PPI) analyses. Results: In NW vs. NWC, coffee intake was associated with proteins enriched in receptor-mediated signaling and phosphoinositide pathways. In OBHT vs. OBHTC, DEPs were linked to mitochondrial respiration and oxidoreductase activity. The NW vs. OBHT comparison showed downregulation of metabolic and signaling proteins with enrichment of mitochondrial and stress-response functions. In NWC vs. OBHTC, proteins related to cytokine signaling and vascular function were reduced, while redox-associated regulators were increased. PPI networks highlighted interconnected hubs integrating signaling, metabolism, and immune responses. Conclusion: These findings suggest context-dependent proteomic patterns associated with coffee intake. Given the pooled design and small sample size, results are hypothesis-generating and require validation. Full article

Cabbage (Brassica oleracea var. capitata), a member of the Brassicaceae family, is an important vegetable crop grown worldwide. Self-incompatibility (SI) in cabbage is a key trait that prevents self-fertilization and inbreeding, thereby maintaining genetic diversity within populations. Although several genes related to SI have been reported, its genetic control remains unclear. In this study, we developed an F₂ population from the highly self-compatible (SC) cabbage line 87-534 and the highly self-incompatible (SI) line 01-20, both of which exhibit the S5 haplotype. The segregation analysis of the F₂ population revealed the possible control of SI by a major gene with additional modifying genetic factors. Bulk segregant analysis sequencing (BSA-Seq) and RNA sequencing (RNA-Seq) were performed on SI and SC samples selected from the F₂ population. BSA-Seq revealed a candidate region on chromosome 7 (C07: 7.45 Mb to 8.93 Mb), including 32 differentially expressed genes (DEGs). RNA-Seq identified a total of 2400 DEGs between the two pools, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested that plant hormone biosynthesis and signaling, plant immune response were significantly enriched and may be involved in SI. The combined analysis of BSA-Seq and RNA-Seq identified six candidate genes associated with SI, and their expression was confirmed using quantitative real-time PCR (qRT-PCR). Among them, Bol023956 encodes fructokinase, Bol023986 is involved in plant defense response, Bol024018 is related to pollen development, Bol024012 encodes a transport protein for phytohormones, Bol023943 encodes chorismate mutase 3, and Bol012515 is an important regulatory gene for chloroplast synthesis. These six genes, potentially linked to SI, should be targets for further validation. These findings provide insights into the molecular mechanisms of SI in cabbage and the selection of superior cabbage varieties. Full article

Hypoxia is a prevalent pathophysiological condition. Prolonged exposure to hypobaric hypoxia can lead to maladaptation, increasing the risk of chronic hypoxic diseases such as high-altitude polycythemia (HAPC). Dauricine, an alkaloid derived from the root of Menispermum dauricum DC, has been demonstrated to possess anti-hypoxic properties; however, its underlying molecular mechanisms remain elusive. In this study, a potential multi-target anti-hypoxic mechanism of dauricine was proposed and computationally evaluated using an integrated approach combining network pharmacology, molecular docking, and molecular dynamics simulations. Common targets between dauricine and hypoxia-related genes were identified through network pharmacology screening. A protein–protein interaction (PPI) network was constructed to identify core targets, followed by Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Molecular docking was subsequently employed to evaluate the binding affinities between dauricine and the candidate core targets, while molecular dynamics simulations were performed to assess the dynamic stability of the resulting complexes. Additionally, the drug-likeness and safety profiles of dauricine were assessed. The results suggest that dauricine may exert its anti-hypoxic effects by modulating candidate core targets, including ESR1, PIK3CA, and MTOR, and by acting on key signaling pathways such as PI3K-Akt, MAPK, and mTOR. This study provides a theoretical foundation for the further investigation of dauricine as a multi-target candidate for intervention in hypoxia and establishes a bioinformatics basis for subsequent experimental validation. Full article

Digital transformation in higher education has increasingly shifted from a technology-centered agenda toward a multidimensional institutional process involving governance, quality assurance, process redesign, and data-driven decision-making. This study proposes and operationalizes an analytical framework for examining digital transformation in universities through an interactive Human–Machine Interface developed in Python. The framework is structured around three complementary methodological cores: ontology-based modeling, statistical reliability analysis, and multiobjective optimization. The ontology module organizes the semantic structure of digital transformation dimensions, revealing their relational hierarchy and structural relevance. The statistical module evaluates internal consistency and distributional behavior through Cronbach’s alpha, corrected item–total correlation, and density-based inspection. The optimization module formulates intervention selection as a constrained multiobjective problem, allowing the identification of efficient portfolios under cost, readiness gain, equity, and feasibility criteria. The analytical environment also incorporates interactive dashboards, VOSviewer-style relational exploration, and exportable high-resolution figures. Results show that digital transformation readiness is heterogeneous across groups, that governance-oriented dimensions occupy a central semantic role, and that institutional intervention planning benefits from Pareto-efficient decision support rather than single-criterion ranking. The study contributes a coherent bridge between conceptual models of digital transformation and an operational analytical environment capable of supporting institutional diagnosis, evidence-based prioritization, and strategic planning in regulated higher education settings. Full article

This article analyzes how twentieth- and twenty-first-century Afro-Colombian women poets from the Pacific region challenge and reframe the feminization of the land and the naturalization of the Black female body within colonial and Eurocentric epistemologies. Drawing on a framework that conceptualizes body, territory, spirituality, and community as an interdependent continuum, the article conducts close textual analysis to demonstrate how these poets construct territory and the Black female body as sentient sites. These sites are simultaneously shaped by historical violence, forced displacement, extractive economies, and racialized gender constructs, while preserving ancestral knowledge and collective memory. The findings show that Valencia Córdoba develops the body–territory through metaphor and anaphora as a generative space; Grueso Romero deploys orality and the sea as transatlantic archives of ancestry and identity; and Truque articulates urban displacement as an ontological rupture that affects memory and Black subjectivity. Ultimately, the article advances the concept of body–territory as a decolonial aesthetic and analytical tool through which Afro-Colombian women’s poetry articulates environmental justice, gendered racialization, and forms of resistance within the Afrodiasporic diaspora. Full article

This paper presents a process-centric ontology for the semantic representation of cyber–physical systems (CPSs) within knowledge-based production planning (KPP). The approach integrates physical systems (PSs), cyber systems (CSs), and CPSs into a unified semantic model based on a three-layer classification. The ontology was implemented using OWL and integrated into a Neo4j-based graph architecture to support semantic querying and process modeling. The evaluation was conducted using prototypical manufacturing scenarios, including semiconductor and mechanical engineering domains. Validation included (i) consistency checking using the HermiT reasoner, (ii) execution of SPARQL queries for retrieving CPS-related process information, and (iii) integration into a three-stage planning model. The results show that the ontology enables consistent semantic representation and cross-domain querying of CPS-based production processes. The work provides a validated proof-of-concept and establishes a foundation for future research on ontology-based production systems. Full article

Ongoing processes appear to be both open-ended and, in an important sense, complete. In the context of the Growing Block Theory of time, this combination generates a tension: if a process is genuinely ongoing, it seems incomplete; yet if it is complete, it appears closed and no longer directed at a non-existent future. This paper argues that this tension is only apparent. Building on Stout’s conception of occurrent continuants and on the distinction between temporal existence and temporal location central to Growing Block accounts, I examine two hybrid views according to which a process, considered as ongoing, and processes, considered as having gone on, fall under different categories of persistence. I argue that both versions of the hybrid view ultimately fail to account for the relation between dynamic existence and temporal location in a growing universe. As an alternative, I propose understanding ongoing processes as temporally expanding wholes with open boundaries. In this view, an ongoing process is always complete, though not completed, because its boundary at the edge of becoming is dynamically open rather than a genuine temporal part. This account preserves the motivations behind hybrid views while avoiding their ontological costs. Full article

Background: Ovarian cancer (OVCA) remains the most lethal gynecologic malignancy, with poor prognosis largely due to late-stage diagnosis and therapy resistance. Pyroptosis, a pro-inflammatory form of programmed cell death, has recently emerged as a regulator of tumor progression and immune regulation. This study aimed to systematically profile pyroptosis-related genes and identify robust biomarkers for OVCA. Methods: Microarray data from the GSE54388 dataset were analyzed to characterize pyroptosis-related gene expression. Immune cell infiltration was assessed using xCell, and pathway enrichment was performed via Gene Set Enrichment Analysis (GSEA). Weighted Gene Co-expression Network Analysis (WGCNA) identified hub genes, followed by Gene Ontology (GO) and Reactome enrichment. Machine learning algorithms (Support Vector Machine, XGBoost, and Generalized Linear Model) were employed for feature selection and biomarker identification. Validation was conducted across independent bulk and scRNA-seq datasets, with GEPIA2 used to compare OVCA and normal samples and KMplot for survival analysis. Results: OVCA samples showed significantly reduced infiltration of CD4⁺ and CD8⁺ T cells, mast cells, monocytes, neutrophils, and immature dendritic cells compared to normal samples. GSEA revealed enrichment of cell cycle-related pathways, implicating pyroptosis-related genes as key regulators of mitotic progression. From 1097 differentially expressed genes, 22 pyroptosis-related DEGs (PYRDEGs) were identified, with nine hub genes (CASP1, CEP55, CHMP4C, HTRA1, IL18, MELK, PKM, PTX3, TNFSF13B) strongly associated with OVCA. Functional enrichment linked these genes to cytokinesis, inflammasome activity, and immune signaling. Machine learning consistently identified CEP55 as the core biomarker, demonstrating high diagnostic accuracy (AUC up to 0.972) and significant upregulation in OVCA samples. Correlation analysis linked CEP55 expression to altered immune cell populations, including positive associations with Th1 and class-switched memory B-cells and negative associations with iDCs, Tregs, and M2 macrophages. CEP55 was highly expressed across bulk and scRNA-seq datasets (cancer epithelial and CD8+ TEMRA cells) and negatively correlated with overall survival (OS) and progression-free survival (PFS). Conclusions: Pyroptosis-related genes play pivotal roles in OVCA pathogenesis. CEP55 emerges as a promising biomarker for early detection and a potential therapeutic target, bridging cell cycle regulation with immune modulation. Full article

Background/Objectives: Lens development is an essential component of visual-system development during fish embryogenesis, yet its transcriptional timing remains poorly characterized in European seabass (Dicentrarchus labrax). This study aimed to provide a stage-resolved transcriptomic characterization of lens-associated gene expression in D. labrax embryos and to relate these patterns to classical embryological stages. Methods: Publicly available RNA-seq data from embryos at the mid-gastrula, late somitogenesis, and hatching stages were analyzed. A targeted lens-associated gene set was defined using Gene Ontology annotations, with emphasis on genes assigned to the structural constituent of the eye lens category. Expression patterns were examined using normalized counts, variance-stabilized data, principal component analysis, and pairwise differential expression analysis. Results: Lens-associated genes displayed clear stage-dependent expression dynamics. Principal component analysis separated samples primarily by developmental stage, with the first two components explaining 89.3% of the total variance. The strongest biological shift occurred between mid-gastrula and late somitogenesis, when transcripts encoding β-crystallins and lens-fiber architecture components increased markedly. Among the most pronounced changes were the induction of crybb1l3 and cryba4, along with increased expression of membrane and cytoskeletal genes, such as the lim2 paralogs and bfsp1. By hatching, this structural-gene expression pattern was partly maintained, while specific crystallin-related loci, including crybg1a, showed further stage-associated increases. Conclusions: These findings define stage-specific patterns of lens-associated gene expression in D. labrax embryos and indicate that lens-associated structural gene expression is most pronounced during late somitogenesis among the stages analyzed. This work provides a useful reference for future studies of visual development in European seabass and for aquaculture-oriented investigations of early sensory ontogeny. Full article

Soybean (Glycine max (L.) Merr.) is a globally crucial food crop and a model plant for studying symbiotic nitrogen fixation in legumes. Triacontanol (TRIA) is a natural plant growth regulator that enhances photosynthetic efficiency, stress tolerance, antioxidant enzyme activities and yield in crops. However, its regulatory role in nodulation and nitrogen fixation in legumes remains unclear. In this study, soybean seedlings inoculated with Bradyrhizobium japonicum strain USDA110 were treated with different concentrations of TRIA (0, 0.33, 0.5, 1 and 2 μg/mL). Then, oxidative stress indicators and comparative transcriptomic analysis were performed to check the oxidative status and screen the candidate genes under TRIA treatment. Our results showed that the 0.5 μg/mL TRIA treatment produced the greatest nodule number. TRIA treatment significantly induced antioxidant responses in soybean roots. Comparative transcriptome identified 867 differentially expressed genes (DEGs), Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of DEGs revealed that a large number of genes were enriched in pathways related to oxidative activity. Combined with the expression pattern, we identified a Glutathione S-Transferase family gene, GmHSP26 (Glyma.07G139700), whose expression was induced by both TRIA and rhizobial infection, with its promoter activity was activated throughout the entire process of nodule development. Further function study using overexpression and gene editing proved that GmHSP26 was a positive regulator of soybean nodulation. Collectively, this study identifies the optimal TRIA concentration for promoting soybean nodulation, reveals the function and mechanism of GmHSP26 in response to TRIA-regulated nodulation, and provides a theoretical basis and genetic resource for enhancing nodulation and nitrogen fixation in leguminous crops through exogenous growth regulators. Full article

This article advances a transdisciplinary framework for planetary health education grounded in multispecies responsibility and Indigenous relational ontologies. Addressing the limitations of anthropocentric environmental paradigms, the paper proposes an expanded Stratified Relational Responsibility Model integrating ethical, ecological, and neurobiological dimensions of human–more-than-human relations. The framework bridges insights from environmental ethics, anthropology, and affective neuroscience to examine how relational awareness, emotional regulation, and embodied cognition shape pro-environmental behavior. Four pedagogical pillars are introduced to support behavioral transformation, emphasizing relational perception, affective attunement, ethical reflexivity, and collective responsibility. The article further discusses implementation challenges within Western educational contexts and highlights the need for culturally responsive adaptation. By situating human agency within multispecies networks, the model contributes to ongoing debates in planetary health and sustainability education, offering a theoretically robust and practically oriented approach to fostering ecological responsibility. Full article

The analysis of dynamic causal mechanisms underlying shipboard fires and explosions is often restricted by the unstructured and fragmented nature of accident investigation reports. This study proposes a framework integrating ontology-driven information extraction with Dynamic Bayesian Networks (DBNs) to model temporal accident evolution. An ontology comprising 41 nodes was constructed through a structured expert elicitation process to formalize the domain knowledge. To process 198 bilingual accident reports, an extraction pipeline was deployed, incorporating XLM-RoBERTa, BiLSTM-CRF, and an entity-marker relation classifier. Large language model (LLM)-directed weak supervision, constrained by token-level information entropy filtering, was employed to expand the training corpus, necessitating only 2.5% manual verification. The extracted semantic dependencies were utilized to initialize a three-slice DBN (precursor, initial fire, and escalation/explosion). The network structure was jointly optimized through ontology constraints (112 forbidden and 4 mandatory edges), the Hill-Climbing algorithm, and BDeu scoring. The proposed DBN achieved an AUC of 0.759 ± 0.086 and a Brier Score of 0.192 ± 0.021 (1000 bootstrap iterations), demonstrating superior predictive performance over traditional interpretable models (Static BN, HMM, ETA) with large effect sizes (Cohen’s d > 1.0), while maintaining competitive accuracy and enhanced causal interpretability relative to XGBoost. This framework offers a scalable, data-driven methodology for dynamic probabilistic risk assessment in maritime safety. Full article

Inflammation plays a key role in the pathogenesis of many diseases, including cardiovascular disease and ischemic stroke. However, despite the existence of known inflammatory genes, the question of estimating their total number and the possibility of discovering new ones remains open. This study sought and analyzed genes involved in inflammation among genes related to cardiovascular disease and ischemic stroke. Human genes associated with ischemic stroke (N = 1177) and cardiovascular disease (N = 1756) were retrieved from the DisGeNET platform. Inflammatory and immune response genes were obtained from the Gene Ontology, NCBI, and Reactome databases. An additional list of 140 inflammatory genes was compiled based on our previously obtained data on the differential gene expression in a rat brain under transient middle cerebral artery occlusion. Genes that occurred simultaneously in both the inflammatory gene lists and gene lists of diseases were selected and considered. The resulting combined gene list included 1285 inflammatory genes. The NFKB1 and RELA genes demonstrated the highest frequencies across the various inflammatory gene selection resources we examined. Using a combination of experimental and bioinformatics approaches, a representative list of inflammatory genes important for the pathogenesis of ischemic stroke was compiled. The identified genes may be crucial for the development of anti-inflammatory therapeutic strategies for this disease. Full article

This essay offers a relational reinterpretation of the doctrine of the Trinity through perichoresis, understood as the mutual indwelling communion of Father, Son and Holy Spirit in which distinction is preserved without separation and unity without domination. More than a technical term of patristic theology, perichoresis names the dynamic communion that constitutes the life of the triune God. Drawing on biblical intuition and patristic formulation and engaging modern Trinitarian theologians in sustained dialogue, this essay develops a historical, contextual and practical approach that incorporates Korean cultural metaphors and Clinical Pastoral Education (CPE). It argues that perichoresis functions not merely as a doctrinal safeguard but as a theological grammar that reorients ontology toward relationality and frames Christian life as participatory communion. Rather than remaining a conceptual proposal, this essay ultimately envisions a perichoretic paradigm in which life itself is understood as participation in the living communion of the Trinity. Full article

This article develops theoretically an integrative analytical construct (InMeDiT Capital, acronym for informational, media, digital and technological capital) derived from Pierre Bourdieu’s social field theory framework to expand its conceptual capacity to interpret and explain specific relational dynamics within a hyper-digitised social context that directly affects families. Based on Bourdieu’s social field theory, different types of classic capital and other more novel types (informational, media, digital, or technological) have been defined. The characteristics of 21st-century society require that the latter be addressed from an integrative perspective. Methodologically, the work is based on a critical and systematic review of the literature. Based on this analysis, a process of conceptual abstraction and theoretical modelling was carried out that can be described as phenomenological in its attempt to capture the depth of the concepts. This consisted of (1) defining the ontological and relational assumptions of the original framework, (2) isolating the analytical mechanisms relevant to the phenomenon under study, and (3) reorganising these elements into a coherent conceptual structure. The result is an updated conceptual framework (InMeDiT Capital) that maintains epistemological consistency with social field theory, but introduces a novel conceptual articulation through its hybridisation, the dimensions that comprise it, and an operational framework for diagnosing and mobilising capital in the family context. Full article