Search Results (4,827)

Whether the calyx tube of the Korla fragrant pear falls off seriously affects the fruit quality. ‘Xinnonglinxiang’ is a mutant variety of the Korla fragrant pear, which has a high calyx removal rate under natural conditions, and calyx tube fall seriously affects the fruit quality. The mechanism behind the high calyx removal rate of ‘Xinnonglinxiang’ remains unclear; thus, Korla fragrant pear (PT) and ‘Xinnonglinxiang’ (YB) with different degrees of calyx abscission were used as examples and the abscission areas of calyx tubes were collected in the early (21 April), middle (23 April), and late (25 April) shedding stages to explore the regulatory mechanism behind the abscission. The combination of the results of physiological, cytological, and transcriptomic methods indicated the highest number of differentially expressed genes (DEGs) in the middle of shedding. GO (Gene Ontology) enrichment analysis showed that the expression levels of genes related to the CEL (cellulase) and PG (polygalacturonase) activity functional pathways differed significantly in the two varieties during the three periods, whereas Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were significantly concentrated in the plant hormone signal transduction pathway in all three periods. The expression levels of genes related to the plant hormone signal transduction pathway differed significantly for the two varieties during calyx shedding. Five gene modules were obtained using Weighted Gene Co-Expression Network Analysis (WGCNA), and transcriptome data were correlated with five physiological index values. Two key modules that highly correlated with the Eth (ethylene) response were then screened, and 20 core genes were identified, with IRX10, IRX9, and OXI1 likely the hub genes that are involved in the regulation of calyx shedding in the YB variety. The obtained results provide reliable data for the screening of candidate genes for calyx shedding and analysis of the regulatory mechanism behind a high calyx shedding rate, providing a theoretical basis upon which the calyx shedding rate of fruits can be improved through genetic improvement. Full article

Pimpled eggs have defective shells, which severely impacts hatching rates and transportation safety. In this study, we constructed single-cell resolution transcriptomic and chromatin accessibility maps from uterine tissues of chickens using single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq). We identified 11 major cell types and characterized their marker genes, along with specific transcription factors (TFs) that determine cell fate. CellChat analysis showed that fibroblasts had the most extensive intercellular communication network and that the chickens laying pimpled eggs had amplified immune-related signaling pathways. Differential expression and enrichment analyses indicated that inflammation in pimpled egg-laying chickens may lead to disruptions in their circadian rhythm and changes in the expression of ion transport-related genes, which negatively impacts eggshell quality. We then integrated TF analysis to construct a regulatory network involving TF–target gene–Gene Ontology associations related to pimpled eggs. We found that the transcription factors ATF3, ATF4, JUN, and FOS regulate uterine activities upstream, while the downregulation of ion pumps and genes associated with metal ion binding directly promotes the formation of pimpled eggs. Finally, by integrating the results of scRNA-seq and scATAC-seq, we identified a rare cell type—ionocytes. Our study constructed single-cell resolution transcriptomic and chromatin accessibility maps of chicken uterine tissue and explored the molecular regulatory mechanisms underlying pimpled egg formation. Our findings provide deeper insights into the structure and function of the chicken uterus, as well as the molecular mechanisms of eggshell formation. Full article

This paper proposes a robust methodology for integrating process-specific data and domain expert knowledge into linked knowledge graphs. These graphs utilize an ontology that provides a standardized vocabulary for material science and facilitates the creation of semantic models for various processes along the digital process chain. A generic template for structuring processes is proposed, simplifying subsequent data retrieval. The templates of specific processes are designed collaboratively by domain and ontology experts, aided by a proposed interview template that bridges the knowledge gap. Following the digitalization of material data through semantic modeling, machine-readable data with contextual metadata is stored in a graph database, which can be efficiently queried using the SPARQL language, enabling seamless integration into data pipelines. To demonstrate this approach, a knowledge graph is developed to represent the process chain of AlSi10Mg objects manufactured via permanent mold casting, capturing their complete history from the initial manufacturing step to final non-destructive testing and mechanical characterization. This methodology enhances data interoperability and accessibility while providing context-rich data for training AI models, potentially accelerating new knowledge discovery in material science. Full article

Objectives: This present study focuses on analyzing the adaptive behaviors of individuals on the autism spectrum as perceived by parents and teachers of these individuals. Methods: This study was conducted in Poland with the use of the ABAS-3 (Adaptive Behavior Assessment System). The ABAS-3 tool involves both parents (or primary caregivers) and teachers in the diagnostic process and monitoring of adaptive development. The study included 99 individuals (29 girls, 70 boys) aged between 5 and 21 years. Results: The analysis of the results showed statistically significant discrepancies in the perception of adaptive skills diagnosed as assessed by parents and teachers. Furthermore, differences were found in the predictors of the General Adaptive Composite and adaptive domains. Conclusions: The results indicate the complexity of the assessment of adaptive skills by a parent of a child with autism spectrum disorder, as well as a teacher, and the need to include different perspectives in the process of diagnosing and supporting individuals with ASD. Full article

Emphasizing their evolutionarily conserved role in stress adaptation mechanisms, ribosomal protein genes (RPGs) are observed to be downregulated in various stressors and across phyla. However, this evolutionarily conserved stress response is not well explored in mouse models of neurobiological stress. This study investigates the dysregulation patterns of RPGs in various murine preclinical stress paradigms across different brain regions using available transcriptomic data and identifies the non-canonical ribosomal functions using synaptic gene-ontology terms. Without a discernible structure across different brain areas, we observed heterogeneous dysregulation, encompassing either up or downregulation in both cytoplasmic and mitochondrial RPGs. However, downregulation was more prominent than upregulation, and the overall dysregulation seems more prevalent in the chronic stress paradigm compared to stress paradigms involving acute and early-life stress. Enrichment analysis significantly associates dysregulated RPGs with post-synaptic gene ontology terms, emphasizing their involvement in synaptic modulation. Overall, the study demonstrates ribosomal dysregulation as an evolutionarily conserved stress response mechanism during different mouse stress paradigms. We discuss the possibility that the variability in the directionality of dysregulation may emerge as a potential marker of neuronal activity in response to diverse stress paradigms and the involvement of paradigm-specific RPG dysregulation either in the process of global downscaling of ribosome biogenesis or in the process of ribosomal heterogeneity, each leading to a different effect. Full article

The design of complex aerospace systems requires a broad multidisciplinary knowledge base and an iterative approach to accommodate changes effectively. Engineering knowledge is commonly represented through engineering analyses and descriptive models with underlying semantics. While guidelines from systems engineering methodologies exist to guide the development of system models, creating a system model from scratch with every new application/system requires research into more adaptable and reusable modeling frameworks. In this context, this research demonstrates how a physics-based multidisciplinary analysis and optimization tool, SUAVE, can be leveraged to develop a system model. By leveraging the existing physics-based knowledge captured within SUAVE, the process benefits from the expertise embedded in the tool. To facilitate the systematic creation of the system model, an ontological metamodel is created in SysML. This metamodel is designed to capture the inner workings of the SUAVE tool, representing its concepts, relationships, and behaviors. By using this ontological metamodel as a modeling template, the process of creating the system model becomes more structured and organized. Overall, this research aims to streamline the process of building system models from scratch by leveraging existing knowledge and utilizing an ontological metamodel as a modeling template. This approach enhances formal knowledge representation and its consistency, and promotes reusability in multidisciplinary design problems. Full article

Cultural diversity often complicates the understanding of sustainability, sometimes making its concepts seem vague. This issue is particularly evident in food systems, which rely on both renewable and nonrenewable resources and drive significant environmental changes. The widespread impacts of climate change, aggravated by the overuse of natural resources, have highlighted the urgency of balancing food production with environmental preservation. Society faces a pivotal challenge: ensuring that food systems produce ample, accessible, and nutritious food while also reducing their carbon footprint and protecting ecosystems. Agriculture 5.0, an innovative approach, combines digital advancements with sustainability principles. This study reviews current knowledge on digital agriculture, analyzing scientific data through an undirected bipartite network that links journals and author keywords from articles retrieved from Clarivate Web of Science. The main goal is to outline a framework that integrates various sustainability concepts, emphasizing both well-studied (economic) and underexplored (socioenvironmental) aspects of Agriculture 5.0. This framework categorizes sustainability concepts into material (tangible) and immaterial (intangible) values based on their supporting or influencing roles within the agriculture domain, as documented in the scientific literature. Full article

Corn leaf blight and stem rot caused by Colletotrichum graminicola are significant diseases that severely affect corn crops. Glycosyltransferases (GTs) catalyze the transfer of sugar residues to diverse receptor molecules, participating in numerous biological processes and facilitating functions ranging from structural support to signal transduction. This study identified 101 GT genes through functional annotation of the C. graminicola TZ–3 genome. Subsequent analyses revealed differences among the C. graminicola GT (CgGT) genes. Investigation into subcellular localization indicated diverse locations of CgGTs within subcellular structures, while the presence of multiple domains in CgGTs suggests their involvement in diverse fungal biological processes through versatile functions. The promoter regions of CgGT genes are enriched with diverse cis-acting regulatory elements linked to responses to biotic and abiotic stresses, suggesting a key involvement of CgGT genes in the organism’s multi-faceted stress responses. Expression pattern analysis reveals that most CgGT genes were differentially expressed during the interaction between C. graminicola and corn. Integrating gene ontology functional analysis revealed that CgGTs play important roles in the interaction between C. graminicola and corn. Our research contributes to understanding the functions of CgGT genes and investigating their involvement in fungal pathogenesis. At the same time, our research has laid a solid foundation for the development of sustainable agriculture and the utilization of GT genes to develop stress-resistant and high-yield crop varieties. Full article

Broad-spectrum crop protection technologies, such as abamectin and bifenthrin, are globally relied upon to curb the existential threats from economic crop pests such as the generalist herbivore Tetranychus urticae Koch (TSSM). However, the rising cost of discovering and registering new acaricides, particularly for specialty crops, along with the increasing risk of pesticide resistance development, underscores the urgent need to preserve the efficacy of currently registered acaricides. This study examined the overall genetic mechanism underlying adaptation to abamectin and bifenthrin in T. urticae populations from commercial hop fields in the Pacific Northwestern region of the USA. A transcriptomic study was conducted using four populations (susceptible, abamectin-resistant, and two bifenthrin-resistant populations). Differential gene expression analysis revealed a notable disparity, with significantly more downregulated genes than upregulated genes in both resistant populations. Gene ontology enrichment analysis revealed a striking consistency among all three resistant populations, with downregulated genes predominately associated with chitin metabolism. In contrast, upregulated genes in the resistant populations were linked to biological processes, such as peptidase activity and oxidoreductase activity. Proteolytic activity by peptidase enzymes in abamectin- and bifenthrin-resistant TSSM populations may suggest their involvement in acaricide metabolism. These findings provide valuable insights into the molecular mechanisms underlying acaricide resistance in the TSSM. This knowledge can be utilized to develop innovative pesticides and molecular diagnostic tools for effectively monitoring and managing resistant TSSM populations. Full article

The representation and utilization of environmental information by service robots has become increasingly challenging. In order to solve the problems that the service robot platform has, such as high timeliness requirements for indoor environment recognition tasks and the small scale of indoor scene data, a method and model for rapid classification of household environment domain knowledge is proposed, which can achieve high recognition accuracy by using a small-scale indoor scene and tool dataset. This paper uses a knowledge graph to associate data for home service robots. The application requirements of knowledge graphs for home service robots are analyzed to establish a rule base for the system. A domain ontology of the home environment is constructed for use in the knowledge graph system, and the interior functional areas and functional tools are classified. This designed knowledge graph contributes to the state of the art by improving the accuracy and efficiency of service decision making. The lightweight network MobileNetV3 is used to pre-train the model, and a lightweight convolution method with good feature extraction performance is selected. This proposal adopts a combination of MobileNetV3 and transfer learning, integrating large-scale pre-training with fine-tuning for the home environment to address the challenge of limited data for home robots. The results show that the proposed model achieves higher recognition accuracy and recognition speed than other common methods, meeting the work requirements of service robots. With the Scene15 dataset, the proposed scheme has the highest recognition accuracy of 0.8815 and the fastest recognition speed of 63.11 microseconds per sheet. Full article

It is established that BCG vaccination results in the development of both a specific immune response to mycobacterial infections and a nonspecific (heterologous) immune response, designated as trained immunity (TRIM), to other pathogens. We hypothesized that local BCG immunization may induce an early immune response in bone marrow and spleen innate immunity cells. The early transcriptomic response of various populations of innate immune cells, including monocytes, neutrophils, and natural killer (NK) cells, to BCG vaccination was examined. To this end, C57Bl/6J mice were subcutaneously immunized with 10⁶ CFU of BCG. Three days following BCG administration, the three cell populations were collected from the control and BCG-vaccinated groups using FACS. All cell populations obtained were utilized for the preparation and sequencing of RNA-seq libraries. The analysis of FACS data revealed an increase in the proportion of splenic NK cells and monocytes 3 days post-vaccination. Transcriptomic analysis revealed the deregulation of genes associated with the regulation of immune response (according to Gene Ontology terms) in NK cells, monocytes, and unsorted bone marrow cells. Two NK cell-specific immune ligands (Tnfsf14 and S100a8) and two bone marrow-specific immune receptors (C5ar1 and Csf2rb) were identified among differentially expressed genes. No alterations were identified in neutrophils in either their percentage or at the transcriptomic level. Thus, in this study, we demonstrated that BCG vaccination provides an early increase in the proportion of murine bone marrow and spleen immune cell populations, as well as transcriptomic alterations in monocytes, NK cells, and non-sorted bone marrow cells. This early innate immune response may be beneficial for enhancing TRIM. Full article

The Internet of Things (IoT) is gaining increasing attention in healthcare due to its potential to enable continuous monitoring of patients, both at home and in controlled medical environments. In this paper, we explore the integration of IoT with human-robotics in the context of motor rehabilitation for groups of patients performing moderate physical routines, focused on balance, stretching, and posture. Specifically, we propose the I-TROPHYTS framework, which introduces a step-change in motor rehabilitation by advancing towards more sustainable medical services and personalized diagnostics. Our framework leverages wearable sensors to monitor patients’ vital signs and edge computing to detect and estimate motor routines. In addition, it incorporates a humanoid robot that mimics the actions of a physiotherapist, adapting motor routines in real-time based on the patient’s condition. All data from physiotherapy sessions are modeled using an ontology, enabling automatic reasoning and planning of robot actions. In this paper, we present the architecture of the proposed framework, which spans four layers, and discuss its enabling components. Furthermore, we detail the current deployment of the IoT system for patient monitoring and automatic identification of motor routines via Machine Learning techniques. Our experimental results, collected from a group of volunteers performing balance and stretching exercises, demonstrate that we can achieve nearly 100% accuracy in distinguishing between shoulder abduction and shoulder flexion, using Inertial Measurement Unit data from wearable IoT devices placed on the wrist and elbow of the test subjects. Full article

Background: Rheumatoid arthritis (RA) is a common systemic autoimmune inflammatory disease that can cause joint damage. We have recently reported that oral magnesium supplementation significantly reduces disease severity and joint damage in models of RA. Methods: In the present study, we analyzed the transcriptome of spleens and synovial tissues obtained from mice with KRN serum-induced arthritis (KSIA) consuming either a high Mg supplemented diet (Mg2800; n = 7) or a normal diet (Mg500; n = 7). Tissues were collected at the end of a 15-day KSIA experiment. RNA was extracted and used for sequencing and analyses. Results: There was an enrichment of differentially expressed genes (DEGs) belonging to Reactome and Gene Ontology (GO) pathways implicated in RA pathogenesis such as RHO GTPases, the RUNX1 pathway, oxidative stress-induced senescence, and the senescence-associated secretory phenotype. Actc1 and Nr4a3 were among the genes with the highest expression, while Krt79 and Ffar2 were among the genes with the lowest expression in synovial tissues of the Mg2800 group compared with the Mg500 group. Spleens had an enrichment for the metabolism of folate and pterines and the HSP90 chaperone cycle for the steroid hormone receptor. Conclusions: We describe the tissue transcriptomic consequences of arthritis-protecting Mg supplementation in KSIA mice. These results show that oral Mg supplementation may interfere with the response to oxidative stress and senescence and other processes known to participate in RA pathogenesis. We provide new evidence supporting the disease-suppressing effect of increased Mg intake in arthritis and its potential to become a new addition to the therapeutic options for RA and other autoimmune and inflammatory diseases. Full article

To elucidate the unidentified roles of a selective peroxisome proliferator-activated receptor α (PPARα) agonist, pemafibrate (Pema), on the pathogenesis of retinal ischemic diseases (RID)s, the pharmacological effects of Pema on the retinal pigment epithelium (RPE), which is involved in the pathogenesis of RID, were compared with the pharmacological effects of the non-fibrate PPARα agonist GW7647 (GW). For this purpose, the human RPE cell line ARPE19 that was untreated (NT) or treated with Pema or GW was subjected to Seahorse cellular metabolic analysis and RNA sequencing analysis. Real-time cellular metabolic function analysis revealed that pharmacological effects of the PPARα agonist actions on essential metabolic functions in RPE cells were substantially different between Pema-treated cells and GW-treated cells. RNA sequencing analysis revealed the following differentially expressed genes (DEGs): (1) NT vs. Pema-treated cells, 37 substantially upregulated and 72 substantially downregulated DEGs; (2) NT vs. GW-treated cells, 32 substantially upregulated and 54 substantially downregulated DEGs; and (3) Pema vs. GW, 67 substantially upregulated and 51 markedly downregulated DEGs. Gene ontology (GO) analysis and ingenuity pathway analysis (IPA) showed several overlaps or differences in biological functions and pathways estimated by the DEGs between NT and Pema-treated cells and between NT and GW-treated cells, presumably due to common PPARα agonist actions or unspecific off-target effects to each. For further estimation, overlaps of DEGs among different pairs of comparisons (NT vs. Pema, NT vs. GW, and Pema vs. GW) were listed up. Angiopoietin-like 4 (ANGPTL4), which has been shown to cause deterioration of RID, was the only DEG identified as a common significantly upregulated DEG in all three pairs of comparisons, suggesting that ANGPTL4 was upregulated by the PPARα agonist action but that its levels were substantially lower in Pema-treated cells than in GW-treated cells. In qPCR analysis, such lower efficacy for upregulation of the mRNA expression of ANGPTL4 by Pema than by GW was confirmed, in addition to substantial upregulation of the mRNA expression of HIF1α by both agonists. However, different Pema and GW-induced effects on mRNA expression of HIF1α (Pema, no change; GW, significantly downregulated) and mRNA expression of ANGPTL4 (Pema, significantly upregulated; GW, significantly downregulated) were observed in HepG2 cells, a human hepatocyte cell line. The results of this study suggest that actions of the PPARα agonists Pema and GW are significantly organ-specific and that lower upregulation of mRNA expression of the DR-worsening factor ANGPTL4 by Pema than by GW in ARPE19 cells may minimize the risk for development of RID. Full article

Background/Objectives: Climate change-induced temperature elevations pose significant challenges to livestock reproduction, particularly affecting testicular function in small ruminants. This study investigates the acute heat-stress response in goat Sertoli cells (SCs), aiming to elucidate the molecular mechanisms underlying heat-induced damage to male reproductive tissues. Methods: SCs were isolated from testes of 4-month-old black goats and exposed to heat stress (44 °C for 2.5 h). We employed transcriptome sequencing, CCK-8 assay, electron microscopy, ROS measurement, autophagy detection, Western blot analysis, and lactate concentration measurement. Bioinformatics analyses including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein–protein interaction network analyses were performed on the transcriptome data. Results: Heat stress significantly reduced SC viability, induced oxidative stress and autophagy, and altered gene expression profiles. We identified 1231 significantly differentially expressed genes, with significant enrichment in membrane-related processes and metabolic pathways. Metabolism-related genes, including PKLR, ACOT11, and LPCT12, were significantly downregulated. Protein–protein interaction network analysis revealed ten hub genes potentially crucial in the heat-stress response: HSP90AA1, HSPA5, BAG3, IGF1, HSPH1, IL1A, CCL2, CXCL10, ALB, and CALML4. Conclusions: This study provides comprehensive insights into the molecular mechanisms underlying goat SC response to heat stress. The identified genes and pathways, particularly those related to metabolism and stress response, offer potential targets for developing strategies to mitigate heat-stress effects on livestock reproduction. These findings contribute to our understanding of climate change impacts on animal husbandry and may inform the development of heat-stress resistant livestock lines. Full article