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At least 19 recordsLinked to original sources
PubMed2025

Identification and classification of ion-channels across the tree of life provide functional insights into understudied CALHM channels.

The ion channel (IC) genes encoded in the human genome play fundamental roles in cellular functions and disease and are one of the largest classes of druggable proteins. However, limited knowledge of the diverse molecular and cellular functions carried out by ICs presents a major bottleneck in developing selective chemical probes for modulating their functions in disease states. The wealth of sequence data available on ICs from diverse organisms provides a valuable source of untapped information for illuminating the unique modes of channel regulation and functional specialization. However, the extensive diversification of IC sequences and the lack of a unified resource present a challenge in effectively using existing data for IC research. Here, we perform integrative mining of available sequence, structure, and functional data on 419 human ICs across disparate sources, including extensive literature mining by leveraging advances in large language models to annotate and curate the full complement of the "channelome". We employ a well-established orthology inference approach to identify and extend the IC orthologs across diverse organisms to above 48,000. We show that the depth of conservation and taxonomic representation of IC sequences can further be translated to functional similarities by clustering them into functionally relevant groups, which can be used for downstream functional prediction on understudied members. We demonstrate this by delineating co-conserved patterns characteristic of the understudied family of the Calcium Homeostasis Modulator (CALHM) family of ICs. Through mutational analysis of co-conserved residues altered in human diseases and electrophysiological studies, we show that these evolutionarily-constrained residues play an important role in channel gating functions. Thus, by providing new tools and resources for performing large comparative analyses on ICs, this study addresses the unique needs of the IC community and provides the groundwork for accelerating the functional characterization of dark channels for therapeutic intervention.

CALHM1↗
PubMed2025

ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation.

MOTIVATION: Hypothesis generation is a fundamental problem in biomedical text mining that aims to generate ideas that are new, interesting, and plausible by discovering unexplored links between biomedical concepts. Despite significant advances made by existing approaches, they do not fully leverage the evolutionary properties of biomedical concepts. This is limiting because scientific knowledge continually evolves over time, with new facts being added and old ones becoming obsolete. Thus, it is crucial to capture the evolutionary properties of biomedical concepts from multiple perspectives (e.g. spatial, temporal, and semantic) to generate hypotheses that reflect the up-to-date information landscape of the biomedical domain. RESULTS: We introduce a novel framework, ConceptDrift, that models the hypothesis generation task as a sequence of temporal graphlets and simultaneously encodes spatial, temporal, and semantic change. Unlike existing approaches that treat these dimensions independently, ConceptDrift is the first to provide a holistic understanding of concept evolution by integrating them into a unified framework. Grounded in the theories of the Distributional Hypothesis and Conceptual Change, our method adapts these principles to the unique challenges of large-scale biomedical literature. We conduct extensive experiments across multiple datasets and demonstrate that ConceptDrift consistently outperforms state-of-the-art baselines in generating accurate and meaningful hypotheses. Our framework shows immediate practical benefits for web-based literature mining tools in life sciences and biomedicine, offering more robust and predictive feature representations. AVAILABILITY AND IMPLEMENTATION: https://github.com/amir-hassan25/ConceptDrift (DOI: 10.6084/m9.figshare.29975476).

Semantics↗
PubMed2026

[Effects and mechanisms of ethanol extract of Salvia miltiorrhiza on liver fibrosis in mice].

To identify clinically advantageous TCMs for anti-hepatic fibrosis and to elucidate the effects and molecular mechanisms of Salvia miltiorrhiza ethanol extract in the intervention of liver fibrosis, this study screened high-frequency anti-hepatic fibrosis TCMs through a review of clinical literature. The S. miltiorrhiza active components, potential targets, and liver fibrosis-related disease targets were obtained using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), the GeneCards database, and other databases. Gene Ontology(GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analyses were performed on the shared targets between drugs and diseases. Molecular docking was conducted to evaluate the binding affinities between key components and core targets. In animal experiments, male Kunming mice were used to establish a liver fibrosis model induced by carbon tetrachloride(CCl_4). The mice were administered low, medium, and high doses of S. miltiorrhiza ethanol extract by gavage. The liver index, as well as serum aspartate aminotransferase(AST) and alanine aminotransferase(ALT) levels, were measured. Histopathological changes in liver tissue were observed using hematoxylin-eosin(HE) staining and Masson's trichrome staining. Western blot analysis was used to detect the protein expression levels of α-smooth muscle actin(α-SMA), Collagen Ⅰ, and heat shock protein 90 alpha family class A member 1(HSP90AA1) in liver tissue. The results showed that S. miltiorrhiza was the most frequently used TCM in clinical anti-hepatic fibrosis. A total of 65 active components and 135 potential targets were identified, and 109 common targets were obtained by intersecting these with liver fibrosis-related targets. The core targets included tumor protein p53(TP53), serine/threonine protein kinase AKT1(AKT1), Jun proto-oncogene(JUN), signal transducer and activator of transcription 3(STAT3), and HSP90AA1, which were mainly enriched in pathways related to cancer, hepatitis B, and the PI3K-AKT signaling pathway. Molecular docking indicated that the main active components of S. miltiorrhiza bound stably to the core targets, with the strongest binding affinity observed for HSP90AA1. Animal experiments demonstrated that the liver index, serum ALT and AST levels, and the expression of α-SMA, Collagen Ⅰ, and HSP90AA1 in liver tissue were significantly increased in the model group, accompanied by obvious pathological manifestations of fibrosis. Compared with the model group, different dose groups of S. miltiorrhiza ethanol extract reduced the liver index and serum ALT and AST levels to varying degrees, alleviated pathological damage and collagen deposition in liver tissue, and downregulated the protein expression of α-SMA, Collagen Ⅰ, and HSP90AA1. In conclusion, S. miltiorrhiza ethanol extract exerts a significant protective effect on CCl_4-induced liver fibrosis in mice, and its mechanisms may be related to the inhibition of HSP90AA1 expression and the regulation of liver fibrosis-related signaling pathways.

Animals↗
PubMed1979

[Pseudotumoral rheumatoid coxitis (author's transl)].

Two cases of rheumatoid coxitis of the macrogeodic type are reported. In one case, there was a very large anfractuous cavity in the socket and head, complicated by a pathological fracture of the socket, which raised the suspicion of a malignant tumor. The authors review the characteristics of these macrogeodic forms of rheumatoid arthritis, about forty cases having been reported in the published literature.

Adult↗
PubMedDate not supplied

[Preliminary report concerning the histologica patterns of an anthracotic pneumoconiosis observed in the area of Londrina, Brasil (author's transl)].

The A. presents a preliminary report concerning on the histologic patterns of an anthracotic pneumoconiosis found in necropsies of the "Hospital Universitário da Universidade de Londrina", Paraná, Brazil, and in some cases from the Legal Institute of the same town. The lesions, on its histologic pattern are comparable to those observed in the lung of coal and iron mines workers as described in the consulted literature. The cases studied (plantations workers and dwellers at rural and suburban areas) are proceeding from an essencially agricultural region, without detectable polluition by industry or others known factors. This agricultural zone presents some geophysic peculiarities and dust from the errosive soil, is a constant factor in the local athmosphere. The soil is so called "Terra Roxa" (red soil) and in its physicochemical composition there is a great amount of iron oxides, silica (silt, agril laceous material), aluminium, manganese, organic compounds. In this preliminary report the A. suggests further research for a better knowledge of the composition of the respirable air and if dust exposures are or not responsible for the lung lesions.

Autopsy↗
PubMed1979

[Contribution to aetiology by the primary pulmonary sarcoma in comparison to the pulmonary carcinoma (author's transl)].

On 41 primary pulmonary sarcomas in the years 1957 till 1974 and on 192 pulmonary carcinomas in the year 1969 cancerogene noxes and endogene factors were analysed, compared and discussed with literature. Smoking of cigarettes, chronic bronchitis and radioactive radiation at underground mining are also significantly accumulated in our study and are recognized as cancerogenes. There is no correlation between pulmonary sarcomas and these exogene factors. The constant frequency in the last decades, the non-existing sex disposition, the ten till fifteen years lower sarcoma manifestation with a continuous increase already in the second decade of life and the protected position of the mesenchyme do not suggest a causal connexion between exogene cancerogene influence and pulmonary sarcoma formation. Rather make us suppose an endogene tumour disposition. Pulmonary sarcomas correlate as to localisation, sex relation and not provable exogene cancerogena with the adenocarcinoma of the lungs. The causal connexion between trauma and sarcoma formation in a thoracotomy cicatrice as well as the possibility of a sarcomatous degeneration are discussed.

Asbestosis↗
PubMed1979

[Current aspects of clinical bronchopulmonary and cardiovascular clinical pharmacology. Talampicillin in acute bronchopulmonary diseases in mine workers].

The results observed with talampicilline in our clinical study confirmed the observations made by others regarding the activity and the improved tolerance for this drug versus ampicilline. The use of a high daily dosage of 3 g per day was neither a cause of more frequent nor more severe side-effects than the usually smaller posology used in other studies published in the literature.

Adult↗
PubMed1991

Relation between somatic development and some environmental factors in the male population of vocational mining schools in the Lublin Coal Basin.

Somatic development of a child, although genetically determined, depends also on the influence of biogeographic and socio-economic factors of the environment. The effects of these factors popular in the literature are seen in the differences of somatic development of children brought up in urban and rural environments. In comparison with urban population, country children are characterized by lower growth and body mass, delayed manifestation of sexual maturity, greater amount of incorrect posture features, worse state of nutrition and lower index of mental development. The differences in somatic development of children were also found while comparing the size of agglomeration and socio-professional factors determining parents' level of education and financial situation of the family. One could also observe the improvement of somatic development of children living in regions of quick and intensive urbanization and industrialization.

Adolescent↗
PubMed2026

Artificial Intelligence for Natural Products Discovery and Development.

Natural products (NPs) remain a cornerstone of modern drug discovery, offering stereochemical complexity and diverse bioactivities that precisely modulate therapeutic targets, refined through billions of years of evolution. However, their research has long been hindered by inefficient, empirical workflows, high resource consumption, structural complexity, and the "multicomponent, multi-target" nature of their mechanisms. The exponential growth of genomic, metabolomic, and spectral data has overwhelmed conventional analytical methods, exposing critical bottlenecks in handling high-dimensional, heterogeneous datasets that exceed human interpretive capacity. Artificial intelligence (AI) is emerging as a transformative paradigm to address these challenges, integrating multi-omics and chemical data to shift NP research from fragmented empiricism toward mechanism-driven, precision-oriented development. By leveraging deep learning architectures- including graph neural networks, Transformers, and diffusion-based generative models-AI enables systematic decoding of NP biosynthesis, automated structure elucidation, rational target identification, knowledge extraction from vast unstructured scientific literature, and de novo molecular design. This review comprehensively surveys recent advances in AI applications across the full NP discovery and development pipeline, encompassing genome mining, structure-based and ligand-based virtual screening, multimodal structural characterization, lead optimization, and biosynthetic pathway engineering. We further examine the emerging roles of protein-centric, molecule- centric, and multimodal foundation models, as well as large language models, in bridging genotype-to-chemotype gaps and unlocking unstructured scientific knowledge. Finally, we discuss critical challenges including data scarcity, representational limitations for complex stereochemistry, physical plausibility in generative models, and the urgent need for experimental validation, while outlining future directions toward autonomous experimentation, closed-loop optimization, and human-AI collaborative discovery.

Artificial intelligence↗
PubMed2026

Acupoint Selection Patterns and Potential Mechanisms of Acupuncture in Knee Osteoarthritis: A Combined Data Mining and Network Pharmacology Study.

OBJECTIVE: To identify the core acupoint prescription and Kellgren-Lawrence (K-L) grade-dependent compatibility patterns of acupuncture for KOA through complex network analysis, and to predict the potential molecular mechanisms underlying the core prescription via network pharmacology. METHODS: Literature was retrieved from PubMed, EMbase, Cochrane Library, Web of Science, CNKI, Wanfang, VIP, and SinoMed (inception to September 3, 2025). Frequency, association rule, complex network, and K-L grade subgroup analyses were applied. Potential targets of the core prescription were identified via network pharmacology and intersected with disease targets from OMIM, Therapeutic Target, GeneCards, and DrugBank. A protein-protein interaction (PPI) network was constructed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the potential molecular mechanisms. RESULTS: We included 522 studies, yielding 582 prescriptions involving 123 acupoints. The core prescription comprised 24 acupoints, including Dubi (ST35), Neixiyan (EX-LE4), Liangqiu (ST34), Xuehai (SP10), Zusanli (ST36), Yanglingquan (GB34), Yinlingquan (SP9), among others. K-L subgroup analysis revealed ST35, GB34, SP9, and SP10 as universal core acupoints. The mild-to-moderate subgroup mainly used local acupoints, while the moderate-to-severe subgroup centered on ST35, with increased distal acupoint usage and higher degree values. Network pharmacology analysis identified 77 overlapping targets. Core targets included tumor necrosis factor (TNF), interleukin 6 (IL6), interleukin 1 beta (IL1B), tumor protein p53 (TP53), matrix metallopeptidase 9 (MMP9), signal transducer and activator of transcription 3 (STAT3), transforming growth factor beta 1 (TGFB1), caspase 3 (CASP3), and B-cell lymphoma 2 (BCL2), which were enriched in inflammation and immunity, cartilage metabolism, and tissue repair pathways. CONCLUSION: The core acupoint prescription for KOA features local acupoints combined with distal ones, exhibiting distinct patterns across K-L grades. Our computational findings suggest that core acupoints may potentially delay knee joint degeneration by synergistically regulating inflammation, cartilage metabolism, apoptosis, and tissue repair, although these predictions require experimental validation. These findings provide preliminary evidence and a theoretical basis for standardized clinical point selection and further mechanistic research.

KOA↗
PubMed1976

Effect of ascorbic acid on rate of heat acclimatization.

There is some indication in the literature that ascorbic acid (vitamin C) may reduce the physiological responses to heat stress. Consequently, the effect of ascorbic acid ingestion on heat-strain indicators has been studied on a group of 60 mining recruits undergoing climatic room acclimatization. Of the 60 men, 19 received a daily dose of 250 mg ascorbic acid; 21 a daily dose of 500 mg ascorbic acid; and 20 received a placebo daily. Measurements of rectal temperature, heart rate, and hourly sweat rate were made on all subjects during the 4 h of heat exposure per day for 10 days. The wet bulb temperature was 32.2 degrees C, the dry bulb 33.9 degrees C, the air movement 0.4 m/s, and the work rate 35 W. The results indicate that the rate and degree of acclimatization, as assessed by 4th-h rectal temperature, is enhanced by ascorbic acid supplementation and that no differences in response could be shown between daily dosages of 250 and 500 mg of vitamin C.

Acclimatization↗
PubMed2026

Systematic functional evaluation of CNGA1 missense variants associated with retinitis pigmentosa.

BACKGROUND: Missense variants are frequently classified as variants of uncertain significance (VUS) according to the guidelines of the American College of Medical Genetics and Genomics and the Association of Molecular Pathology (ACMG/AMP). Consequently, disease relevance remains elusive, impeding molecular genetic diagnostics, patients` and family genetic counseling, and identification of patients eligible for clinical trials. Functional studies are critical for resolving the clinical significance of VUS. CNGA1 encodes the main subunit of the rod cyclic nucleotide-gated (CNG) channel, a vital component of the phototransduction cascade. Variants in CNGA1 are a rare cause of autosomal recessive retinitis pigmentosa and a phase I/II gene augmentation trial (NCT06291935) is currently ongoing highlighting the necessity to differentiate benign from pathogenic variants. METHODS: CNGA1 missense variants compiled from retinal disease patient cohorts, public databases and literature were functionally investigated using a medium-throughput aequorin-based assay and in vitro minigene splice assays for predicted exonic spliceogenic variants. Functional data were correlated with the in silico prediction of five variant effect predictors (VEPs) and applied to support or revise variants' ACMG/AMP classification. RESULTS: Data mining revealed 86 missense CNGA1 variants - including three novel - most of them lacking functional data; 65.1% of the variants were initially classified as VUS. The aequorin-based assay showed that 72.1% of tested variants significantly impaired CNG channel function and were classified as functionally abnormal, while 23.3% were functionally normal and 5% remained functionally uncertain. Correlation of the functional data with in silico predictions identified AlphaMissense and CPT-1 to be the most suitable tools for assessing CNGA1 missense variants. Using in vitro minigene splice assays, two putative missense variants were shown to induce missplicing. Based on the functional findings, 62.1% of the variants initially classified as VUS were re-categorized as likely pathogenic or likely benign. Furthermore, 93.3% of the variants initially classified as likely pathogenic showed an effect on CNGA1 channel function, confirming their disease relevance and supporting their reclassification as pathogenic. CONCLUSION: This study represents the first comprehensive functional assessment of disease-associated CNGA1 missense variants, thus significantly advancing the understanding of their disease relevance and improving molecular genetic diagnostics in patients.

Humans↗
PubMed1979

[Dyspnea symptoms in coalminers].

One of the authors observed an excess of dyspnea complaints in coalminers without bronchitis, massive fibrosis or emphysema in different epidemiological surveys. An abnormally high prevalence of dyspnea complaints in coalminers has also been reported by other investigators in different countries. It seems therefore necessary to study whether the type of complaints observed in our country can be validated by appropriate functional investigations. A research on this problem is in progress in our laboratory. In this preliminary publication a review of the literature concerning the mechanisms of dyspnea is presented. Such a study was necessary in order to make an adequate choice of the functional measurements usable for our validation study.

Carbon Dioxide↗
PubMedDate not supplied

The mitochondrial activation of silicate and its role in silicosis, black lung disease and lung cancer.

Silicate substitutes for phosphate in the transitory uncoupling of rat liver mitochondria induced by hydrazine when beta-hydroxy-butyrate is the substrate. Uncoupling is blocked by rutamycin. Just as in the case when phosphate is combined with hydrazine, ATP, ADP, PPi, and Mg++ protect against hydrazine when silicate is combined with hydrazine. A high level of ADP in the absence of added phosphate, but in the presence of silicate, induces a pseudo state three of the mitochondria. Silicate, like sulfate and arsenate which have been reported previously, is activated by the enzymes which mediate oxidative phosphorylation. These results serve to explain a role for silicate in silicosis, black lung disease, and cancer. In addition, since there is suggestive evidence in the literature that lung tissue solubilizes asbestos fibers, these results not only expand the confluence between oxidative phosphorylation and chemical carcinogenesis but are correlated with the synergistic carcinogenicity of asbestos and smoking observed by epidemiologists.

Adenosine Diphosphate↗