Search Results (4,623)

Gastrodin, a highly potent compound found in the traditional Chinese medicine Gastrodia elata Blume, exhibits significant antihypertensive properties. However, its role and the mechanism behind its protective effects on hypertensive cardiac conditions are not well understood. This study aims to investigate the cardiac protective effects and underlying mechanisms of gastrodin in angiotensin II (Ang II)-induced hypertensive models, both in vivo and in vitro. Treatment with gastrodin significantly decreased blood pressure and the heart weight/tibial length (HW/TL) ratio and attenuated cardiac dysfunction and pathological damage in Ang II-infused C57BL/6 mice. RNA sequencing analysis (RNA-seq) revealed 697 up-regulated and 714 down-regulated transcripts, along with 1105 signaling pathways, in Ang II-infused C57BL/6 mice following gastrodin treatment, compared to Ang II-induced hypertensive mice. Furthermore, the analyses of the top 30 Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway indicated significant enrichment in apoptosis and the peroxiredoxin 2 (PRDX2)/p53 pathway. Consistently, gastrodin treatment significantly reduced myocardial apoptosis in both the cardiac tissues of Ang II-induced hypertensive mice and Ang II-stimulated H9c2 cells. Additionally, gastrodin treatment significantly decreased the protein levels of PRDX2, p53, cleaved caspase-3, cleaved caspase-9, and Bax/Bcl-2 ratio in the cardiac tissues of Ang II-infused mice and H9c2 cells stimulated with Ang II. In conclusion, gastrodin treatment can mitigate hypertension-induced myocardial apoptosis in hypertensive mice by inhibiting the PRDX2/p53 pathway. Full article

Soil salinity is a major limiting factor in soybean (Glycine max (L.) Merr.) yield in Xinjiang, China. Therefore, breeding soybean to tolerate highly saline soils is crucial to improve its yield. To explore the molecular mechanisms underlying the response of soybean to salt stress, we performed a comparative transcriptome analysis of root and leaf samples collected from two local soybean cultivars. The salt-tolerant cultivar ‘Xin No. 9’ (X9) showed higher photosynthetic activity than the salt-sensitive cultivar ‘Xinzhen No. 9’ (Z9) under salt stress. In total, we identified 13,180 and 13,758 differential expression genes (DEGs) in X9 and Z9, respectively, of which the number of DEGs identified in roots was much higher than that in leaves. We constructed the co-expression gene modules and conducted Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The results suggested there were distinct differences in the mechanisms of response to salt stress between the two soybean cultivars; i.e., the salt-tolerant cultivar X9 exhibited alterations in fundamental metabolism, whereas the salt-sensitive cultivar Z9 responded to salt stress mainly through the cell cycle. The possible crosstalk among phytohormone signaling, MAPK signaling, phenylpropanoid biosynthesis, starch and sucrose metabolism, and ribosome metabolism may play crucial roles in the response to salt stress in soybean. Our results offered a comprehensive understanding of the genes and pathways involved in the response to salt stress in soybean and provided valuable molecular resources for future functional studies and the breeding of soybean varieties with enhanced tolerance to salinity. Full article

Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and serve crucial regulatory functions in both animals and plants. Nevertheless, there is limited understanding of lncRNAs and their patterns of expression and roles in sharks. In the current study, we systematically identified and characterized lncRNAs in the blue shark (Prionace glauca) from four tissues (liver, spleen, muscle, and kidney) using high-throughput sequencing and bioinformatics tools. A total of 21,932 high-confidence lncRNAs were identified, with 8984 and 3067 stably and tissue-specific expressed lncRNAs, respectively. In addition, a total of 45,007 differentially expressed (DE) lncRNAs were obtained among tissues, with kidney versus muscle having the largest numbers across tissues. DE lncRNAs trans target protein-coding genes were predicted, and functional gene ontology enrichment of these genes showed GO terms such as muscle system processes, cellular/metabolic processes, and stress and immune responses, all of which correspond with the specific biological functions of each tissue analyzed. These results advance our knowledge of lncRNAs in sharks and present novel data on tissue-specific lncRNAs, providing key information to support future functional shark investigations. Full article

Flooding stress caused by climate change is a serious threat to crop productivity. To enhance our understanding of flooding stress in soybean, we analyzed the transcriptome of the roots of soybean plants after waterlogging treatment for 10 days at the V2 growth stage. Through RNA sequencing analysis, 870 upregulated and 1129 downregulated differentially expressed genes (DEGs) were identified and characterized using Gene Ontology (GO) and MapMan software (version 3.6.0RC1). In the functional classification analysis, “alcohol biosynthetic process” was the most significantly enriched GO term in downregulated DEGs, and phytohormone-related genes such as ABA, cytokinin, and gibberellin were upregulated. Among the transcription factors (TFs) in DEGs, AP2/ERFs were the most abundant. Furthermore, our DEGs encompassed eight soybean orthologs from Arabidopsis and rice, such as 1-aminocyclopropane-1-carboxylate oxidase. Along with a co-functional network consisting of the TF and orthologs, the expression changes of those genes were tested in a waterlogging-resistant cultivar, PI567343. These findings contribute to the identification of candidate genes for waterlogging tolerance in soybean, which can enhance our understanding of waterlogging tolerance. Full article

Oyster mushroom spherical virus (OMSV) is a mycovirus that inhibits mycelial growth, induces malformation symptoms, and decreases the yield of fruiting bodies in Pleurotus ostreatus. However, the pathogenic mechanism of OMSV infection in P. ostreatus is poorly understood. In this study, RNA sequencing (RNA-seq) was conducted, identifying 354 differentially expressed genes (DEGs) in the mycelium of P. ostreatus during OMSV infection. Verifying the RNA-seq data through quantitative real-time polymerase chain reaction on 15 DEGs confirmed the consistency of gene expression trends. Both Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses highlighted the pivotal role of primary metabolic pathways in OMSV infection. Additionally, significant changes were noted in the gene expression levels of carbohydrate-active enzymes (CAZymes), which are crucial for providing the carbohydrates needed for fungal growth, development, and reproduction by degrading renewable lignocellulose. The activities of carboxymethyl cellulase, laccase, and amylase decreased, whereas chitinase activity increased, suggesting a potential mechanism by which OMSV influenced mycelial growth through modulating CAZyme activities. Therefore, this study provided insights into the pathogenic mechanisms triggered by OMSV in P. ostreatus. Full article

In light of current risks and environmental impacts, HBIM (historic building information modeling) offers a highly efficient and interactive method for managing historical data and representing the current states of ancient clay structures. In this study, traditional geodetic techniques were employed to digitally locate a structure without compromising its topographic information to create an accurate model. Tools such as total stations, GNSS receivers, and UAVs were utilized to generate detailed topography of the study site and its surroundings. An ontology-based data management structure was also developed to store historical data and site intervention projects, adhering to the ISO 12006-2 standard. This was achieved through automated scripts in Dynamo softwarev.2.18.1. A comparison between the point cloud (279 images) and total station data (600 points) revealed a georeferencing accuracy difference of +/−0.003 m. Consequently, the developed methods can effectively represent similar structures digitally. The proposed ontological structure facilitates automated storage of internal and external information. Full article

This paper presents a method for creating the system architecture of existing industrial objects based on Model-Based Systems Engineering (MBSE) principles. The method aims to form a digital representation of physical objects, which is crucial in the digital transformation of industrial enterprises. It allows for the accurate reflection of all components, processes, functions, and interrelationships within an object. The methodology includes stages of data collection, structuring, development of ontological models, and the integration of a comprehensive system architecture into the digital space. This method was tested using a small hydroelectric power plant, revealing its key advantages and disadvantages and identifying areas for further improvement. The main findings indicate a significant improvement in understanding the system architecture for scenario modeling and digital operation of the objects. Despite challenges such as the need for multiple iterations and high data requirements, the methodology demonstrates the potential for applying MBSE in the digital transformation of existing industrial objects. Full article

Emerging distributed intelligence paradigms for the Internet of Things (IoT) call for flexible and dynamic reconfiguration of elementary services, resources and devices. In order to achieve such capability, this paper faces complex interoperability and autonomous decision problems by proposing a thorough framework based on the integration of the Semantic Web of Things (SWoT) and Social Internet of Things (SIoT) paradigms. SWoT enables low-power knowledge representation and autonomous reasoning at the edge of the network through carefully optimized inference services and engines. This layer provides service/resource management and discovery primitives for a decentralized collaborative social protocol in the IoT, based on the Linked Data Notifications(LDN) over Linked Data Platform on Constrained Application Protocol (LDP-CoAP). The creation and evolution of friend and follower relationships between pairs of devices is regulated by means of novel dynamic models assessing trust as a usefulness reputation score. The close SWoT-SIoT integration overcomes the functional limitations of existing proposals, which focus on either social device or semantic resource management only. A smart mobility case study on Plug-in Electric Vehicles (PEVs) illustrates the benefits of the proposal in pervasive collaborative scenarios, while experiments show the computational sustainability of the dynamic relationship management approach. Full article

Growth differentiation among farmed sea urchins (Strongylocentrotus intermedius) poses a significant challenge to aquaculture, with there being a limited understanding of the underlying molecular mechanisms. In this study, sea urchins with varying growth rates, reared under identical conditions, were analyzed for feeding behavior, gut microbiota, and transcriptomes. Large-sized sea urchins demonstrated significantly higher feeding ability and longer duration than smaller ones. The dominant phyla across all size groups were Campylobacterota, Proteobacteria, and Firmicutes, with Campylobacterota showing the highest abundance in small-sized sea urchins (82.6%). However, the families Lachnospiraceae and Pseudomonadaceae were significantly less prevalent in small-sized sea urchins. Transcriptome analysis identified 214, 544, and 732 differentially expressed genes (DEGs) in the large vs. medium, large vs. small, and medium vs. small comparisons, respectively. Gene Ontology and KEGG pathway analyses associated DEGs with key processes such as steroid biosynthesis, protein processing within the endoplasmic reticulum, and nucleotide sugar metabolism. Variations in phagosomes and signaling pathways indicated that size differences are linked to disparities in energy expenditure and stress responses. These findings provide a foundation for future investigations into the regulatory mechanisms underlying growth differences in S. intermedius and provide clues for the screening of molecular markers useful to improve sea urchin production. Full article

The combustion of fuel with high sulfur concentrations produces a large number of sulfur oxides (SO_x), which have a range of negative effects on human health and life. The preparation of catalysts with excellent performance in the oxidative desulfurization (ODS) process is highly effective for reducing SO_x production. In this paper, cross-linked polyvinylimidazole (VE) was successfully created using a simple ontology aggregation method, after which a catalyst of polyvinylimidazolyl heteropolyacid clusters (VE-HPA) was prepared by adding heteropolyacid clusters. Polyvinylimidazolyl-phosphotungstic acid (VE-HPW) showed an outstanding desulfurization performance, and the desulfurization efficiency reached 99.68% in 60 min at 50 °C with H₂O₂ as an oxidant. Additionally, the catalyst exhibited recyclability nine consecutive times and remained stable, with a removal rate of 98.60%. The reaction mechanism was eventually proposed with the assistance of the free radical capture experiment and GC-MS analysis. Full article

The scientific literature has revealed that there is often a discrepancy between urban planning initiatives and the actual development of cities. Urban development is a complex process strongly affected by the self-organisation of citizens and entrepreneurs, who produce services and events, create new public places, and shape urban regeneration through everyday practices. However, the actors of self-organised urban development are rarely met in participatory urban planning practices. The gap raises the research problem of how to recognise and facilitate civic engagement in urban development. The authors of this article have been investigating the ontology and methodology of urban planning and development over the past two decades, culminating in the framework of expanded urban planning. The article aims to present multiple approaches to civic engagement in urban planning and development, based on an updated longitudinal study conducted in a Helsinki neighbourhood. The authors argue that urban planning should be updated with expanded urban planning (EP), which extends the focus of civic engagement from public participation to self-organisation and everyday life practices. Full article

The vast corpus of heterogeneous biomedical data stored in databases, ontologies, and terminologies presents a unique opportunity for drug design. Integrating and fusing these sources is essential to develop data representations that can be analyzed using artificial intelligence methods to generate novel drug candidates or hypotheses. Here, we propose Non-Negative Matrix Tri-Factorization as an invaluable tool for integrating and fusing data, as well as for representation learning. Additionally, we demonstrate how representations learned by Non-Negative Matrix Tri-Factorization can effectively be utilized by traditional artificial intelligence methods. While this approach is domain-agnostic and applicable to any field with vast amounts of structured and semi-structured data, we apply it specifically to computational pharmacology and drug repurposing. This field is poised to benefit significantly from artificial intelligence, particularly in personalized medicine. We conducted extensive experiments to evaluate the performance of the proposed method, yielding exciting results, particularly compared to traditional methods. Novel drug–target predictions have also been validated in the literature, further confirming their validity. Additionally, we tested our method to predict drug synergism, where constructing a classical matrix dataset is challenging. The method demonstrated great flexibility, suggesting its applicability to a wide range of tasks in drug design and discovery. Full article

The whole train design of an Electric Multiple Unit (EMU) involves multiple domains and scenarios, thus requiring comprehensive consideration of various factors during the design process. Traditional design methods often utilize text-based approaches to model systems; however, such documentation-based designs often suffer from semantic heterogeneity, inconsistent data sources, and also struggle to provide a more intuitive overview of the overall design process. To address these issues, this paper proposes a method based on ontology–knowledge collaborative drive to achieve integration of the overall EMU design. Firstly, we employ the System Modeling Language (SysML) to construct the Model-Based Systems Engineering (MBSE) model of the EMU, establishing functional and physical architecture element models, with the EMU MBSE model serving as input. Subsequently, in the requirement model, architecture model, and traceability model, we utilize top-level ontology to construct the EMU ontology framework in a top-down manner. Lastly, leveraging the Neo4j database, we employ a knowledge graph (KG) approach to fill domain knowledge into each model in a bottom-up manner, thereby realizing the ontology–knowledge collaborative drive for the overall EMU design construction. The effectiveness of the proposed method is validated using the EMU Passenger Information System (PIS) and Traction transformer System (TS) as examples. Full article

This paper explores the application of The World Avatar (TWA) dynamic knowledge graph to connect isolated data and assess the impact of rising sea levels in Singapore. Current sea level rise vulnerability assessment tools are often regional, narrow in scope (e.g., economic or cultural aspects only), and are inadequate in representing complex non-geospatial data consistently. We apply TWA to conduct a multi-perspective impact assessment of sea level rise in Singapore, evaluating vulnerable buildings, road networks, land plots, cultural sites, and populations. We introduce OntoSeaLevel, an ontology to describe sea level rise scenarios, and its impact on broader elements defined in other ontologies such as buildings (OntoBuiltEnv ontology), road networks (OpenStreetMap ontology), and land plots (Ontoplot and Ontozoning ontology). We deploy computational agents to synthesise data from government, industry, and other publicly accessible sources, enriching buildings with metadata such as property usage, estimated construction cost, number of floors, and gross floor area. An agent is applied to identify and instantiate the impacted sites using OntoSeaLevel. These sites include vulnerable buildings, land plots, cultural sites, and populations at risk. We showcase these sea level rise vulnerable elements in a unified visualisation, demonstrating TWA’s potential as a planning tool against sea level rise through vulnerability assessment, resource allocation, and integrated spatial planning. Full article

Since its inception, the intricate mathematical formalism of quantum mechanics has empowered physicists to describe and predict specific physical events known as quantum processes. However, this success in probabilistic predictions has been accompanied by a profound challenge in the ontological interpretation of the theory. This interpretative complexity stems from two key aspects. Firstly, quantum mechanics is a fundamental theory that, so far, is not derivable from any more basic scientific theory. Secondly, it delves into a realm of invisible phenomena that often contradicts our intuitive and commonsensical notions of matter and causality. Despite its notorious difficulties of interpretation, the most widely accepted set of views of quantum phenomena has been known as the Copenhagen interpretation since the beginning of quantum mechanics. According to these views, the correct ontological interpretation of quantum mechanics is incompatible with ontological realism in general and with philosophical materialism in particular. Anti-realist and anti-materialist interpretations of quantum matter have survived until today. This paper discusses these perspectives, arguing that materialistic interpretations of quantum mechanics are compatible with its mathematical formalism, while anti-realist and anti-materialist views are based on wrong philosophical assumptions. However, although physicalism provides a better explanation for quantum phenomena than idealism, its downward reductionism prevents it from accounting for more complex forms of matter, such as biological or sociocultural systems. Thus, the paper argues that neither physicalism nor idealism can explain the universe. I propose then a non-reductionistic form of materialism called inclusive materialism. The conclusion is that the acknowledgment of the qualitative irreducibility of ontological emergent levels above the purely physical one does not deny philosophical materialism but enriches it. Full article