Search Results (4,510)

The advent of the digital era has put forward an urgent need for the digitization of metrology, and the digitization of metrology vocabularies is one of the fundamental and critical steps to achieve the digital transformation of metrology. Metrology vocabulary ontology can facilitate the exchange and sharing of data and is an important way to achieve the digitization of metrology vocabulary. Time metrology vocabulary is a special and important part of the whole metrology vocabulary, and constructing its ontology can reduce the problems caused by semantic confusion, help to smooth the progress of metrological work, and promote the digital transformation of metrology. Currently, the existing ontology for metrology vocabulary is primarily the MetrOnto ontology, but it lacks a systematic description of the vocabulary of time metrology. To address this issue, improve the metrology vocabulary ontology, and lay the groundwork for realizing the digital transformation of metrology, this paper takes time metrology vocabulary as the research object; proposes a classification principle that meets the inherent requirements of time transfer in the digital world; adopts the seven-step method of ontology construction to construct an ontology specialized in time metrology vocabulary, OTMV (Ontology of Time Metrology Vocabulary); and conducts an ontology consistency check, a machine-readable validation, a machine-understandable primary validation, and information retrieval validation on it. The validation results show that OTMV has correct syntactic and logical consistency and is capable of realizing machine-readable, machine-understandable, and information retrieval. The construction of this ontology provides a systematic description of the time measurement vocabulary that can address the problem of word expression of time metrology vocabulary in the digital world and lay the foundation for the digitization of our metrology vocabulary, as well as its readability, understandability, and sharing. Full article

Foreign body response (FBR) is a universal reaction to implanted biomaterial that can affect the function and longevity of the implant. A few studies have attempted to identify targets for treating FBR through the use of single-cell RNA sequencing (scRNA-seq), though the generalizability of these findings from an individual study may be limited. In our study, we perform a meta-analysis of scRNA-seq data from all available FBR mouse studies and integrate these data to identify gene signatures specific to FBR across different models and anatomic locations. We identify subclusters of fibroblasts and macrophages that emerge in response to foreign bodies and characterize their signaling pathways, gene ontology terms, and downstream mediators. The fibroblast subpopulations enriched in the setting of FBR demonstrated significant signaling interactions in the transforming growth factor-beta (TGF-β) signaling pathway, with known pro-fibrotic mediators identified as top expressed genes in these FBR-derived fibroblasts. In contrast, FBR-enriched macrophage subclusters highly expressed pro-fibrotic and pro-inflammatory mediators downstream of tumor necrosis factor (TNF) signaling. Cell–cell interactions were additionally interrogated using CellChat, with identification of key signaling interactions enriched between fibroblasts and macrophages in FBR. By combining multiple FBR datasets, our meta-analysis study identifies common cell-specific gene signatures enriched in foreign body reactions, providing potential therapeutic targets for patients requiring medical implants across a myriad of devices and indications. Full article

Currently, there is a growing amount of evidence for the involvement of dopamine receptors and the functionally related trace amine-associated receptor, TAAR1, in upper intestinal function. In the present study, we analyzed their expression in the duodenum using publicly accessible transcriptomic data. We revealed the expression of DRD1, DRD2, DRD4, DRD5, and TAAR1 genes in different available datasets. The results of the gene ontology (GO) enrichment analysis for DRD2 and especially TAAR1 co-expressed genes were consistent with the previously described localization of D2 and TAAR1 in enteric neurons and secretory cells, respectively. Considering that co-expressed genes are more likely to be involved in the same biological processes, we analyzed genes that are co-expressed with TAAR1, DRD2, DRD4, and DRD5 genes in healthy mucosa and duodenal samples from patients with functional dyspepsia (FD) or diabetes-associated gastrointestinal symptoms. Both pathological conditions showed a deregulation of co-expression patterns, with a high discrepancy between DRDs and TAAR1 co-expressed gene sets in normal tissues and patients’ samples and a loss of these genes’ functional similarity. Meanwhile, we discovered specific changes in co-expression patterns that may suggest the involvement of TAAR1 and D5 receptors in pathologic or compensatory processes in FD or diabetes accordingly. Despite our findings suggesting the possible role of TAAR1 and dopamine receptors in functional diseases of the upper intestine, underlying mechanisms need experimental exploration and validation. Full article

The grey tree frog, Dryophytes versicolor, survives whole-body freezing for weeks during cold winter months. Survival in a state devoid of available food, water, or oxygen forces a reliance on metabolic rate depression (MRD) and the reprioritization of bodily functions. This study utilizes next-generation sequencing (NGS) and bioinformatic analyses to characterize changes in the microRNAome of D. versicolor. When comparing control to frozen groups, five microRNAs (miRNA) were found to be differentially regulated (miR-143-3p, miR-30e-3p, miR-10a-5p, miR-140-3p, and miR-148a-3p), suggesting that they play key roles in freeze survival. The KEGG and GO analyses of these changes predicted a significant negative enrichment of terms associated with cell proliferation and active metabolism while simultaneously predicting the upregulation of cell signalling terms. These results suggest a fast-acting regulatory role for miRNA in contributing to the reorganization of gene expression and the limitation of energy-expensive processes during MRD in the hind leg skeletal muscle of the frog. Full article

Lion transformation, among San-Bushmen, is arguably the most dramatic and spectacular instance of animal transformation. Transformation is a central component of San curing and initiation ritual and of certain San hunting practices. Moreover, it is a recurrent theme in San mythology, art and cosmology, all of them domains of San expressive and symbolic culture that are pervaded by ontological mutability (manifested most strikingly in the therianthropes of San myth and art). Lion transformation is a phenomenon that has received much mention in the ethnographic literature on Khoisan ritual and belief, through information that is based not on first-hand but second- or third-hand ethnographic and ethno-historical information. In the paper, I describe my own eye-witness account of what San people deemed a lion transformation by a trance dancer, which I observed in my early field work among Ghanzi (Botswana) Naro and = Au//eisi San in the 1970s. This is followed by my own musings on the actuality or reality of lion transformation, from both my own perspective and from what I understand to be the indigenous perspective. In terms of the latter, lion transformation—and animal transformation in general—is a plausible proposition. Indigenous doubt and scepticism, deriving from a rarely if ever fully conclusive witnessing of such transformations, are assuaged in a number of epistemological, cosmological and phenomenological ways. These are not available to a Western cultural outsider with a Cartesian mindset, nor to a Westernized—and perhaps also Christianized—insider, whose cosmos has become “disenchanted” through historical–colonial and contemporary–acculturational influences. Full article

The sugar content in watermelon significantly influences its flavor. To understand the sugar accumulation pattern in small-fruited watermelon and identify candidate genes involved in sugar synthesis and conversion, we measured the sugar content (sucrose, fructose, and glucose) at five developmental stages: 10d, 16d, 22d, 28d, and 34d post-pollination. Two watermelon varieties with the largest sugar content difference at 28d post-pollination (high-sugar G38-28 and low-sugar 482276-28) were selected for transcriptome sequencing. Differentially expressed genes (DEGs) were validated using RT-qPCR. Additionally, the sugar contents of three commercial varieties (‘Su Meng NO.5’, ‘Su Meng NO.6’, ‘Su Meng NO.7’) and their parents were compared at five stages. Results showed glucose and fructose levels peaked between 22d and 28d, followed by a decrease, while sucrose content continuously increased. F1 hybrids exhibited glucose and sucrose trends similar to their paternal parent and fructose trends similar to their maternal parent. Transcriptome sequencing identified 9337 DEGs (5072 upregulated and 4265 downregulated). Gene Ontology analysis highlighted overrepresentation in categories such as pectinase and oxidoreductase activity. KEGG analysis identified 12 DEGs involved in sugar synthesis and conversion pathways, including phenylpropanoid biosynthesis and pentose and glucuronate interconversions. RT-qPCR validation corroborated the transcriptome data. These findings explain the distinct sugar accumulation patterns in G38-28 and 482276-28 at the transcriptional level, offering insights for genetic breeding and regulation of key sugar-related genes in watermelon. Full article

Nowadays, ubiquitous technology makes life easier, especially devices that use the internet (IoT). IoT devices have been used to generate data in various domains, including healthcare, industry, and education. However, there are often problems with this generated data such as missing values, duplication, and data errors, which can significantly affect data analysis results and lead to inaccurate decision making. Enhancing the quality of real-time data streams has become a challenging task as it is crucial for better decisions. In this paper, we propose a framework to improve the quality of a real-time data stream by considering different aspects, including context-awareness. The proposed framework tackles several issues in the data stream, including duplicated data, missing values, and outliers to improve data quality. The proposed framework also provides recommendations on appropriate data cleaning techniques to the user to help improve data quality in real time. Also, the data quality assessment is included in the proposed framework to provide insight to the user about the data stream quality for better decisions. We present a prototype to examine the concept of the proposed framework. We use a dataset that is collected in healthcare and process these data using a case study. The effectiveness of the proposed framework is verified by the ability to detect and repair stream data quality issues in selected context and to provide a recommended context and data cleaning techniques to the expert for better decision making in providing healthcare advice to the patient. We evaluate our proposed framework by comparing the proposed framework against previous works. Full article

Background: Diabetic retinopathy (DR) is a leading cause of vision loss, with complex mechanisms. The study aimed to comprehensively explore vitreous humor of diabetic and non-diabetic individuals, paving the way for identifying the potential molecular mechanisms underlying DR. Methods: Vitreous samples from type 2 diabetic and non-diabetic subjects, collected post-mortem, were analyzed using liquid chromatography–mass spectrometry. Pathway enrichment and gene ontology analyses were conducted to identify dysregulated pathways and characterize protein functions. Results: Pathway analysis revealed dysregulation in multiple metabolic and signaling pathways associated with diabetes, including glycerolipid metabolism, histidine metabolism, and Wnt signaling. Gene ontology analysis identified proteins involved in inflammation, immune response dysregulation, and calcium signaling. Notably, proteins such as Inositol 1,4,5-trisphosphate receptor type 2 (ITPR2), Calcium homeostasis endoplasmic reticulum protein (CHERP), and Coronin-1A (CORO1A) were markedly upregulated in diabetic vitreous, implicating aberrant calcium signaling, inflammatory responses, and cytoskeletal reorganization in DR. Conclusions: Our study provides valuable insights into the intricate mechanisms underlying DR and highlights the significance of inflammation, immune dysregulation, and metabolic disturbances in disease progression. Identification of specific proteins as potential biomarkers underscores the multifactorial nature of DR. Future research in this area is vital for advancing therapeutic interventions and translating findings into clinical practice. Full article

Online Mendelian Inheritance in Animals (OMIA is a freely available information resource, which includes information for Equus inherited traits/diseases (collectively called phenes). The database focuses on Mendelian traits and their likely causal variants (mutations). Some of these Mendelian traits are favored by humans, e.g., coat color, while others are diseases. Additions to OMIA are based on publications of peer-reviewed research. Maintaining up-to-date information in OMIA is a challenge, owing to the multiplicity of species, the increase in the number of relevant publications, and as reference genomes and methods of citation continue to evolve. This challenge has been successfully aided by contributions from scientists from around the world. In some cases, those scientists are faculty members who charge their students with curation as an educational activity. Recently, OMIA has introduced computerized lists of standardized names and synonyms (called ontologies) for breeds of Equus and other animals and for phene categories. These ontologies facilitate increased connectivity between OMIA and other online resources. OMIA is and will continue to be a major reference resource for Mendelian phenes in the genus Equus. Full article

We propose several hierarchical graphs that represent the semantic relations between physical theories, their fundamental constants and units of measurement. We begin with an alternative representation of Zel’manov’s cube of fundamental constants as a concept lattice. We then propose the inclusion of a new fundamental constant, Milgrom’s critical acceleration, and discuss the implications of such analysis. We then look for the same fundamental constants in a graph that relates magnitudes and units of measurement in the International System of Units. This exercise shows the potential of visualizing hierarchical networks as a tool to better comprehend the symmetries, interrelations and dependencies of physical magnitudes, units and theories. New regimes of application may be deduced, as well as an interesting reflection on our ontologies and corresponding theoretical objects. Full article

Phosphorus (P) and iron (Fe) deficiency are major limiting factors for plant productivity worldwide. White lupin (Lupinus albus L.) has become a model plant for understanding plant adaptations to P and Fe deficiency, because of its ability to form cluster roots, bottle-brush-like root structures play an important role in the uptake of P and Fe from soil. However, little is known about the signaling pathways involved in sensing and responding to P and Fe deficiency. Sucrose, sent in increased concentrations from the shoot to the root, has been identified as a long-distance signal of both P and Fe deficiency. To unravel the responses to sucrose as a signal, we performed Oxford Nanopore cDNA sequencing of white lupin roots treated with sucrose for 10, 15, or 20 min compared to untreated controls. We identified a set of 17 genes, including 2 bHLH transcription factors, that were up-regulated at all three time points of sucrose treatment. GO (gene ontology) analysis revealed enrichment of auxin and gibberellin responses as early as 10 min after sucrose addition, as well as the emerging of ethylene responses at 20 min of sucrose treatment, indicating a sequential involvement of these hormones in plant responses to sucrose. Full article

The museum system is exposed to a high risk of seismic hazards. However, it is difficult to carry out seismic hazard prevention to protect cultural relics in collections due to the lack of real data and diverse types of seismic hazards. To address this problem, we developed a deep-learning-based multi-source feature-fusion method to assess the data on seismic damage caused by collected cultural relics. Firstly, a multi-source data-processing strategy was developed according to the needs of seismic impact analysis of the cultural relics in the collection, and a seismic event-ontology model of cultural relics was constructed. Additionally, a seismic damage data-classification acquisition method and empirical calculation model were designed. Secondly, we proposed a deep learning-based multi-source feature-fusion matching method for cultural relics. By constructing a damage state assessment model of cultural relics using superpixel map convolutional fusion and an automatic data-matching model, the quality and processing efficiency of seismic damage data of the cultural relics in the collection were improved. Finally, we formed a dataset oriented to the seismic damage risk analysis of the cultural relics in the collection. The experimental results show that the accuracy of this method reaches 93.6%, and the accuracy of cultural relics label matching is as high as 82.6% compared with many kinds of earthquake damage state assessment models. This method can provide more accurate and efficient data support, along with a scientific basis for subsequent research on the impact analysis of seismic damage to cultural relics in collections. Full article

The aim of this study was to investigate the antioxidant and anti-inflammatory effects of skimmianine on cerebral ischemia–reperfusion (IR) injury. Twenty-four female Wistar albino rats were randomly divided into three groups: Sham, Ischemia–Reperfusion (IR), and IR + Skimmianine (40 mg/kg Skimmianine). Cerebral ischemia was induced using a monofilament nylon suture to occlude the middle cerebral artery for 60 min. Following 23 h of reperfusion, the animals were sacrificed 14 days later. The effects of skimmianine on brain tissue post-IR injury were examined through biochemical and immunochemical analyses. In silico analysis using the Enrichr platform explored skimmianine’s potential biological processes involving IBA-1, IL-6, and NF-κB proteins. In the IR group, MDA levels increased, while SOD and CAT antioxidant enzyme activities decreased. In the IR + Skimmianine group, skimmianine treatment resulted in decreased MDA levels and increased SOD and CAT activities. Significant increases in IBA-1 expression were observed in the IR group, which skimmianine treatment significantly reduced, modulating microglial activation. High levels of IL-6 expression were noted in pyramidal neurons, vascular structures, and neuroglial cells in the IR group; skimmianine treatment reduced IL-6 expression, demonstrating anti-inflammatory effects. Increased NF-κB expression was observed in neurons and blood vessels in the gray and white matter in the IR group; skimmianine treatment reduced NF-κB expression. Gene Ontology results suggest skimmianine impacts immune and inflammatory responses via IBA-1 and IL-6, with potential effects on estrogen mechanisms mediated by NF-κB. Skimmianine may be a potential therapeutic strategy due to its antioxidant and anti-inflammatory effects on cerebral IR injury. Full article

Despite huge efforts, tuberculosis (TB) is still a major public health threat worldwide, with approximately 23% of the human population harboring a latent TB infection (LTBI). LTBI can reactivate and progress to active and transmissible TB disease, contributing to its spread within the population. The challenges in diagnosing and treating LTBI patients have been major factors contributing to this phenomenon. Exosomes offer a novel avenue for investigating the process of TB infection. In this study, we conducted small RNA sequencing to investigate the small RNA profiles of plasma exosomes derived from individuals with LTBI and healthy controls. Our findings revealed distinct miRNA profiles in the exosomes between the two groups. We identified 12 differentially expressed miRNAs through this analysis, which were further validated via qRT-PCR using the same exosomes. Notably, six miRNAs (hsa-miR-7850-5p, hsa-miR-1306-5p, hsa-miR-363-5p, hsa-miR-374a-5p, hsa-miR-4654, has-miR-6529-5p, and hsa-miR-140-5p) exhibited specifically elevated expression in individuals with LTBI. Gene ontology and KEGG pathway analyses revealed that the targets of these miRNAs were enriched in functions associated with ferroptosis and fatty acid metabolism, underscoring the critical role of these miRNAs in regulating the intracellular survival of Mycobacterium tuberculosis (Mtb). Furthermore, our results indicated that the overexpression of miR-7850-5p downregulated the expression of the SLC11A1 protein in both Mtb-infected and Mtb-uninfected THP1 cells. Additionally, we observed that miR-7850-5p promoted the intracellular survival of Mtb by suppressing the expression of the SLC11A1 protein. Overall, our findings provide valuable insights into the role of miRNAs and repetitive region-derived small RNAs in exosomes during the infectious process of Mtb and contribute to the identification of potential molecular targets for the detection and diagnosis of latent tuberculosis. Full article

A transcriptome-wide association study (TWAS) was conducted on genome-wide association study (GWAS) summary statistics of malignant melanoma of skin (UK Biobank dataset) and The Cancer Genome Atlas-Skin Cutaneous Melanoma (TCGA-SKCM) gene expression weights to identify melanoma susceptibility genes. The GWAS included 2465 cases and 449,799 controls, while the gene expression testing was conducted on 103 cases. Afterward, a gene enrichment analysis was applied to identify significant TWAS associations. The melanoma’s gene–microRNA (miRNA) regulatory network was constructed from the TWAS genes and their corresponding miRNAs. At last, a disease enrichment analysis was conducted on the corresponding miRNAs. The TWAS detected 27 genes associated with melanoma with p-values less than 0.05 (the top three genes are LOC389458 (RBAK), C16orf73 (MEIOB), and EIF3CL). After the joint/conditional test, one gene (AMIGO1) was dropped, resulting in 26 significant genes. The Gene Ontology (GO) biological process associated the extended gene set (76 genes) with protein K11-linked ubiquitination and regulation of cell cycle phase transition. K11-linked ubiquitin chains regulate cell division. Interestingly, the extended gene set was related to different skin cancer subtypes. Moreover, the enriched pathways were nsp1 from SARS-CoV-2 that inhibit translation initiation in the host cell, cell cycle, translation factors, and DNA repair pathways full network. The gene-miRNA regulatory network identified 10 hotspot genes with the top three: TP53, BRCA1, and MDM2; and four hotspot miRNAs: mir-16, mir-15a, mir-125b, and mir-146a. Melanoma was among the top ten diseases associated with the corresponding (106) miRNAs. Our results shed light on melanoma pathogenesis and biologically significant molecular interactions. Full article