Biomedical subjects

Yibo Wang

Publications and source records attributed to Yibo Wang.

10 recordsLinked to original sources

PubMed2026

OmniExtract: an automatic data extraction tool based on large language model and prompt engineering.

Extracting structured information from documents or scientific papers is crucial for data sharing and retrieval. Recent advances in large language models (LLMs) have demonstrated strong capabilities in language understanding, and a number of LLM-based tools have been developed for extraction-oriented tasks. However, it's still difficult to find a universal and user-friendly tool for various practical extraction tasks. To address this challenge, we propose OmniExtract, an automatic data extraction tool with user-friendly configuration files that can adapt to various data extraction tasks. OmniExtract employs a prompt optimization method to refine task-specific prompts and achieve high extraction performance. It also supports comprehensive data extraction from both documents and tables, making it applicable to a broad range of data sources. Evaluation results show that OmniExtract obtains a high accuracy ~90% for three datasets. Furthermore, two additional data extraction applications of OmniExtract in real-world scenarios have been presented, achieving an accuracy of 92.21% and ~90% precision and recall, respectively. Specifically, OmniExtract can handle tabular files of various sizes and formats, and achieve over 99% precision and recall on table information extraction tasks. The data reliability performance shows that OmniExtract is a valuable tool for database updating. An online testing service is available at https://ngdc.cncb.ac.cn/omniextract/. The service can be deployed locally with the code in https://github.com/wyb39/OmniExtract.

Large Language Models↗

PubMed2026

Complete genome sequence of the first alphahypovirus from the phytopathogenic fungus Curvularia americana on Poa pratensis in China.

In the present study, a novel positive-sense single-stranded RNA virus was identified from Curvularia americana strain 32 - 2, a phytopathogenic fungus infecting Poa pratensis in China, which was designated as "Curvularia americana hypovirus 1" (CaHV1). The complete genome of CaHV1 consists of 14,386 nucleotides (nt) with a single large open reading frame (ORF) (nt position 593 to 14035). The ORF encodes a putative polyprotein (4,480 amino acids) containing two potential conserved domains, which includes a Domain of Unknown Function 3525 (DUF3525) and Helicase. BLASTp analysis showed that amino acid sequence of the polyprotein of CaHV1 shared the highest amino acid sequence identity with that of Bipolaris oryzae hypovirus 1 (63.52%). Phylogenetic analysis based on amino acid sequence of the polyprotein indicated that CaHV1 clustered together with members of the genus Alphahypovirus within the family Hypoviridae. To the best of our knowledge, this is the first report of an alphahypovirus infecting C. americana.

Genome, Viral↗

PubMed2026

A single small molecule-based human embryo model reveals V-ATPase requirement in mammalian blastocyst cavitation.

Human naïve pluripotent stem cells (nPSCs) can be induced by various combinations of signaling factors to generate blastocyst-like structures, termed blastoids. Despite rapid progress in human blastoid models, their potential to uncover fundamental mechanisms of early human development remains limited, leaving key morphogenetic processes poorly understood. Here, we describe a simple and robust system in which dimethyl sulfoxide (DMSO) alone induces blastoid formation from human nPSCs. This model recapitulates key pre- and post-implantation features and exhibits enhanced polar trophectoderm (TE) organization, more efficient attachment within an implantation-relevant window, improved epiblast lumenogenesis associated with amniotic cavity formation, and more robust, sustained expansion of embryonic lineages following attachment. Using this system, we reveal a previously unrecognized mechanism underlying TE cavitation and identify lysosome-associated genes - particularly subunits of the proton pump V-ATPase - as essential regulators of blastoid cavitation. DMSO treatment upregulates key V-ATPase subunits (ATP6V0A4 and ATP6V1B1), which are also enriched in the TE of human embryos. Genetic or pharmacological inhibition of V-ATPase activity disrupts lysosomal acidification, blocks intracellular vacuole formation, and impairs blastoid cavitation, whereas overexpression of V-ATPase subunits rescues this phenotype. Furthermore, genetic and pharmacological perturbations of V-ATPase function significantly compromise cavitation in both mouse and human blastocysts. Finally, DMSO treatment induces membrane biomechanical changes characteristic of early embryonic development, suggesting a mode of action distinct from conventional small-molecule, signaling pathway-based induction strategies. This simple DMSO-based blastoid model recapitulates key aspects of human blastocyst development and reveals a conserved requirement for V-ATPase-mediated lysosomal acidification during early mammalian embryogenesis.

Humans↗

PubMed2025

CRISPR-Cas9-mediated knockout of OsKCS11 in rice reveals potential crosstalk between very-long-chain fatty acids and cytokinin.

Very-long-chain fatty acids (VLCFAs) play crucial roles in various physiological processes in plants. Through our investigation using a CRISPR-Cas9 knockout mutant library in rice, we identified a semi-dwarf rice mutant named CRISPR-Cas-based dwarf-1 (csd-1). This mutant displayed multiple developmental defects, such as decreased plant height, panicle length, seed size, and seed-setting rate. Whole-genome resequencing analysis revealed that a T-nucleotide insertion in β-ketoacyl-CoA synthase 11 (KCS11), responsible for the initial step in fatty acid elongation, was responsible for the observed defects in csd-1. The identity of csd-1 was confirmed through genetic complementation and CRISPR-Cas9-mediated knockout. Expression analysis indicated that OsKCS11 was present in various tissues, with differential abundance observed through RT-qPCR and promoter GUS staining, and strong localization at the node position by RNA in situ hybridization; furthermore, OsKCS11 protein was confirmed to be in the endoplasmic reticulum. Furthermore, csd-1 exhibited significantly reduced levels of linolenic acid (18:3), C24:0-OH, C28:0-alkanes, C29:0-alkanes, alpha-tocopherol, and C33:0-alkanes, while trans-nonadecenoic acid and behenic acid levels were increased. Cytokinin analysis revealed significant increases in isopentenyladenine (IPA) and cis-zeatin (cZ) levels in csd-1. Molecular investigations indicated upregulation of genes involved in cytokinin biosynthesis or signaling, suggesting a potential link between VLCFAs and cytokinin synthesis through acetyl-CoA. This study not only proposed an alternative gene mapping method based on whole-genome resequencing but also elucidated the mechanism by which VLCFAs influence cytokinin synthesis and signaling.

Oryza↗

PubMed2006

CardioSignal: a database of transcriptional regulation in cardiac development and hypertrophy.

BACKGROUND: Although extensive research has characterized intricate genetic programs in heart system, the information generated is highly fragmented. Here we have developed a new database called CardioSignal, which was designed for integration of regulatory information on the transcriptional regulation involved in heart development and cardiac hypertrophy. METHODS: Data about sequences, positions and functional annotation of transcription binding sites, cis-regulatory modules as well as promoters were collected from scientific literature. Genes involved in both processes were also manually gathered, particularly those preferentially expressed in the heart. Data was stored in MySQL database and Perl was used as the server-side programming language. RESULTS: Currently, CardioSignal contains 677 cardiac genes from twenty species. Among them are 128 cardiac transcription factors. Of the approximately 179 individual promoters from six species, the database also documented 247 experimentally verified binding sites and 64 cis-regulatory modules. CardioSignal may be searched for the promoter of a specific gene by specifying a gene name, Entrez geneID, swissProt accession number and so on. Downstream targets of transcriptional factors and cardiac regulatory modules can also be retrieved through a user-friendly web interface. Also available is experimental supporting evidence. Computational analysis tools were implemented for on-the-fly motif finding and comparative genomic analysis respectively. CONCLUSIONS: CardioSignal offers a unique resource as it contains simultaneously the promoter collected while correlating the information of transcription factor binding sites and cis-regulatory modules from heart system. We are hopeful that its implementation will contribute toward the elucidation of the complex processes in cardiac development and hypertrophy.

Animals↗

PubMed2006

Land-cover changes and its impacts on ecological variables in the headwaters area of the Yangtze River, China.

Land cover changes affect ecological landscape spatial pattern, and evolving landscape patterns inevitably cause an evolution in ecosystem functionality. Various ecological landscape variables, such as biological productivity (plant biomass and stock capacity), soil nutrients (organic matter and N content) and water source conservation capacity are identified as landscape function characteristics. A quantitative method and digital model for analyzing evolving landscape functionality in the headwaters areas of the Yangtze River, China were devised. In the period 1986-2000, patch transitions of the region's evolving landscapes have been predominantly characterized by alpine cold swamp meadow, with the highest coverage tending to be steppified meadow or steppe, and desertification landscape such as sand and bare rock land expansion. As the result of such changes, alpine swamp areas decreased by 3.08 x 10(3) km2 and the alpine cold sparse steppe and bare rock and soil land increased by 6.48 x 10(3) km2 and 5.82 x 10(3) km2, respectively. Consequently, the grass biomass production decreased by 2627.15 Gg, of which alpine cold swamp meadows accounted for 55.9% of this loss. The overall stock capacity of the headwaters area of the Yangtze River decreased by 920.64 thousand sheep units, of which 502.02 thousand sheep units decreased in ACS (Alpine cold swamp) meadow transition. Soil organic matter and N contents decreased significantly in most alpine cold meadow and swamp meadow landscape patches. From 1986 to 2000 the total losses of soil organic matter and total N in the entire headwaters region amounted to 150.2 Gkg and 7.67 Gkg. Meanwhile, the landscape soil water capacity declined by 935.9 Mm3, of which 83.9% occurred in the ACS meadow transition. In the headwater area of the Yangtze River, the complex transition of landscape resulted in sharp eco-environmental deterioration. The main indication for these changes involved the intensity of the climate in this region is becoming drier and warmer, resulting in a gradual degradation of the permafrost.

Agriculture↗

PubMed2006

VKORC1 haplotypes are associated with arterial vascular diseases (stroke, coronary heart disease, and aortic dissection).

BACKGROUND: The haplotypes in the gene vitamin K epoxide reductase complex subunit 1 (VKORC1) have been found to affect warfarin dose response through effects on the formation of reduced-form vitamin K, a cofactor for gamma-carboxylation of vitamin K-dependent proteins, which is involved in the coagulation cascade and has a potential impact on atherosclerosis. We hypothesized that VKORC1-dependent effects on the coagulation cascade and atherosclerosis would contribute to susceptibility for vascular diseases. METHODS AND RESULTS: To test the hypothesis, we studied the association of polymorphisms of VKORC1 with stroke (1811 patients), coronary heart disease (740 patients), and aortic dissection (253 patients) compared with matched controls (n=1811, 740, and 416, respectively). Five common noncoding single-nucleotide polymorphisms of VKORC1 were identified in a natural haplotype block with strong linkage disequilibrium (D'>0.9, r2>0.9), then single-nucleotide polymorphism (SNP) +2255 in the block was selected for the association study. We found that the presence of the C allele of the +2255 locus conferred almost twice the risk of vascular disease (odds ratio [OR] 1.95, 95% confidence interval [CI] .58 to 2.41, P<0.001 for stroke; OR 1.72, 95% CI 1.24 to 2.38, P<0.01 for coronary heart disease; and OR 1.90, 95% CI 1.04 to 3.48, P<0.05 for aortic dissection). We also observed that subjects with the CC and CT genotypes had lower levels of undercarboxylated osteocalcin (a regulator for the bone), probably vascular calcification, and lower levels of protein induced in vitamin K absence or antagonism II (PIVKA-II, a des-gamma-carboxy prothrombin) than those with TT genotypes. CONCLUSIONS: The haplotype of VKORC1 may serve as a novel genetic marker for the risk of stroke, coronary heart disease, and aortic dissection.

Aged↗

PubMed2005

NELIN, a new F-actin associated protein, stimulates HeLa cell migration and adhesion.

A new gene (GenBank Accession No. AF114264) was cloned from umbilical vein wall tissue by using RT-PCR. The gene shares high similarity to the gene encoding F-actin binding protein nexilin, so named as NELIN. A clone of 2737bp contains open reading frame of 1344bp extending from 412 to 1755. NELIN was expressed primarily in the heart and skeletal muscle among eight tested normal tissues. Immunofluorescence and immunoprecipitation demonstrated that NELIN product was associated with F-actin. Stable transfection of NELIN into HeLa cells increased the cell migration by 2.17-fold and the adhesion by 1.67-fold, respectively, compared to cells with the empty vector (P<0.05). The results support that NELIN product is an F-actin associated protein and mediates cell motility.

Actins↗

PubMed2005

Vitamin k epoxide reductase: a protein involved in angiogenesis.

Vitamin K epoxide reductase (VKOR) is a newly identified protein which has been reported to convert the epoxide of vitamin K back to vitamin K, a cofactor essential for the posttranslational gamma-carboxylation of several blood coagulation factors. We found that the gene is expressed ubiquitously including vascular endothelial cells, smooth muscle cells, fibroblasts and cardiomyocytes, and is overexpressed in 11 tumor tissues on microarray. Stable transfection of VKOR cDNA into tumor cell line A549 and H7402 did not promote the cell proliferation. These results promoted us to hypothesize that VKOR may also be involved in angiogenesis. To test this hypothesis, the expression of VKOR was studied in different vascular cells in developmental and pathologic heart tissues. The effects of overexpression and suppressing expression of VKOR on endothelial cell proliferation, migration, adhesion, and tubular network formation were explored. We found that VKOR expression in arteries was prominent in vascular endothelial cells and was high in the ventricular aneurysm tissue of human heart and human fetal heart. In vitro studies showed that overexpression of VKOR slightly but significantly stimulated human umbilical vein endothelial cell proliferation (by 120%), migration (by 118%), adhesion (by 117%), as well as tubular network formation. Antisense to VKOR gene inhibited the proliferation (by 67%), migration (by 64%), adhesion (by 50%), and tubular network formation. Our findings support the impact of VKOR in the process of angiogenesis; hence, the molecule may have a potential application in cardiovascular disease and cancer therapy.

Adenoviridae↗

PubMed2003

Elevated plasma homocysteine was associated with hemorrhagic and ischemic stroke, but methylenetetrahydrofolate reductase gene C677T polymorphism was a risk factor for thrombotic stroke: a Multicenter Case-Control Study in China.

BACKGROUND AND PURPOSE: It is still controversial whether elevated plasma homocysteine and the C677T polymorphism of methylenetetrahydrofolate reductase (MTHFR) gene are risk factors for stroke. The aim of the present study was to investigate the association between the 2 factors and stroke in Chinese in a large case-control study. METHODS: We recruited 1823 stroke patients (807 cerebral thrombosis, 513 lacunar infarction, 503 intracerebral hemorrhage) and 1832 controls. Total plasma homocysteine was determined by high-performance liquid chromatography. C677T polymorphism was genotyped by polymerase chain reaction and HinfI digestion. RESULTS: Total plasma homocysteine levels were significantly higher in cases than controls (median, 14.7 versus 12.8 micromol/L; P<0.001) and associated with an increased risk of 1.87-fold (95% confidence interval [CI], 1.58 to 2.22) for overall stroke, 1.72-fold (95% CI, 1.39 to 2.12) for cerebral thrombosis, 1.89-fold (95% CI, 1.50 to 2.40) for lacunar infarction, and 1.94-fold (95% CI, 1.48 to 2.55) for intracerebral hemorrhage. The C677T mutation of the MTHFR gene was positively correlated with plasma homocysteine levels in both controls (beta=0.250, P<0.001) and cases (beta=0.272, P<0.001) and more frequently in cases than in controls (47.0% versus 44.2%, P=0.017). The TT genotype was associated with an increased risk for overall stroke (odds ratio, 1.27; 95% CI, 1.04 to 1.56) and thrombotic stroke (odds ratio, 1.37; 95% CI, 1.06 to 1.78). CONCLUSIONS: The C677T polymorphism of the MTHFR gene was associated with increased risk of cerebral thrombotic stroke in Chinese. Total plasma homocysteine was correlated with both ischemic and hemorrhagic stroke, suggesting potential initiation of homocysteine-lowering therapy in this population.

Brain Ischemia↗