Biomedical subjects

Yi Peng

Publications and source records attributed to Yi Peng.

14 recordsLinked to original sources

PubMed2026

A Network Pharmacology and Molecular Docking Study of TongBi Formula for Osteoarthritis.

This study applied network pharmacology combined with molecular docking to predict the potential therapeutic targets and molecular mechanisms of TongBi Formula (TBF) in osteoarthritis (OA). Active components and corresponding targets of TBF were retrieved from the traditional Chinese medicine Systems Pharmacology Database and Analysis Platform, while OA-related targets were collected from Online Mendelian Inheritance in Man, GeneCards, DrugBank, and Therapeutic Target Database. A network visualization and analysis software was used to construct compound-target and protein-protein interaction (PPI) networks. Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using the Database for Annotation, Visualization and Integrated Discovery platform. Molecular docking analysis was conducted using a molecular docking software to evaluate the predicted binding affinity between key active compounds and core target proteins. A total of 47 overlapping targets between TBF and OA were identified. PPI network analysis highlighted JUN, RELA, IL6, MAPK1, and IL10 as potential hub targets. Enrichment analysis suggested that TBF may regulate inflammation, lipid metabolism, and multiple intracellular signaling pathways associated with OA progression. Molecular docking results demonstrated favorable predicted binding affinities between core active compounds and key OA-related protein targets. These findings provide a computational framework for understanding the potential mechanisms of TBF against OA and support further experimental validation.

Molecular Docking Simulation↗

PubMed2026

Multi-Omics Integration Identifies a Five-Gene Metabolic Signature With Experimental Validation in Clear Cell Renal Cell Carcinoma.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is hallmarked by profound metabolic reprogramming; however, its intricate crosstalk with the tumor immune microenvironment (TIME) and its clinical ramifications remain inadequately elucidated. This study aims to systematically decipher the metabolic-immune interplay in ccRCC through multi-omics integration, with the goal of identifying robust prognostic biomarkers and actionable therapeutic vulnerabilities. AIMS: This study aims to systematically decipher the metabolic-immune interplay in clear cell renal cell carcinoma (ccRCC) through multi‑omics integration, and to identify robust prognostic biomarkers and actionable therapeutic vulnerabilities that can inform precision risk stratification and individualized treatment strategies. METHODS: We integrated bulk transcriptomic, genomic, and clinical data from multiple ccRCC cohorts. Differential expression and functional enrichment analyses were performed to characterize metabolic pathway alterations. Mendelian randomization (MR) was employed to infer causal relationships between metabolic disorders and ccRCC risk. A machine learning-based prognostic framework, incorporating SHAP (SHapley Additive exPlanations) for feature interpretability, was constructed and rigorously validated. TIME heterogeneity was dissected using deconvolution algorithms, while drug sensitivity, tumor mutation burden (TMB), and TIDE scores were utilized to assess therapeutic responses and immune evasion. Candidate gene function was evaluated through in vitro gain- and loss-of-function assays, with expression validated via TCGA, HPA, western blot, and qRT-PCR. RESULTS: Enrichment analysis identified coordinated dysregulation in lipid metabolism, energy homeostasis, and hypoxia response pathways. MR analysis confirmed lipid metabolism disorders as a causal risk factor for ccRCC. Our machine-learning model, centered on five core SHAP-identified features (SUCLA2, ACAT1, PC, SUCLG1, and HMGCS2), demonstrated superior predictive accuracy over conventional clinical staging. Immune profiling unveiled dichotomous TIME states: the low-risk group retained active immune surveillance, whereas the high-risk group was enriched with immunosuppressive subsets. Drug sensitivity screening pinpointed LY2109761 and carmustine as high-risk-specific candidate agents. Furthermore, TMB and TIDE analyses stratified high-risk patients displaying genomic instability and immune evasion phenotypes. Functionally, SUCLA2 knockdown significantly enhanced ccRCC cell proliferation and invasion, while its overexpression suppressed these malignant phenotypes, corroborating its tumor-suppressive role. Expression patterns of the hub genes were consistently validated across multi-level datasets and experimental assays. CONCLUSION: This study establishes a precision oncology framework for ccRCC by functionally linking metabolic biomarkers, immunophenotypes, and stratified therapeutic strategies. Importantly, we identify SUCLA2 as a potential functional tumor suppressor and a promising target for further mechanistic and translational investigation.

Humans↗

PubMed2006

[The effect of micro-trauma technic with small incision on treating hallux valgus].

OBJECTIVE: To explore an effective micro-trauma technic with small incision for hallux valgus. METHODS: From August 2002 to June 2004, 136 cases (263 feet) with hallux valgus were treated with micro-trauma technic with small incision and postoperative external elastic fixation. Of all the cases, 7 were males and 129 were females. Their ages ranged from 19 to 84 years. According to Coughlin classification, there were 24 gentle cases, 63 medium cases, and 49 severe cases. All the feet were with some degree of pain and flatfoot. Symptom, sign and the results of X-ray were evaluated. RESULTS: Wound healed at stage I. All cases were followed up for 8 to 26 months, 19 months on average. Hallux valgus of the 263 feet were completely healed, feet pain disappeared, and no nonunion or osteonecrosis was observed. X-ray examination indicated that 105 feet's hallux valgus angle was less than 12 degrees, inter metatarsal angle less than 9 degrees, and remedy subluxation of the tibial sesamoid less than 50%. Evaluation on the result indicated that there were 84 cases of excellent result, 48 cases of good result, 3 cases of fair result, and 1 case of poor result. The rate of excellent and good was 97%. CONCLUSION: With less injury, less pain, complete restoration, and fewer possibility of relapse, micro-trauma technic with small incision is effective in treating hallux valgus.

Adult↗

PubMed2006

[The deletion of nucleotides of NS gene from 263 to 277 of H5N1 increases viral virulence in chicken].

Since 2000, more and more NS fragment of H5N1 subtype influenza A virus had a unique deletion of nuleotides from 263 to 277. In order to investigate the biological significance of the mutation, four recombinants, RWSN-848, RWSN-m848, RWSN-248 and RWSN-m248, were generated via eight-plasmid reverse genetic system. These reassortants had the same inner gene and outer gene derived from A/WSN/33(H1N1) and A/D/SD/04(H5N1), respectively. But their NS genes were different. RWSN-m248 and RWSN-848 were isogenic with RWSN-248 and RWSN-m848 respectively, except for the NS gene, the formers encoded a mutant NS with a deletion from 263 - 277 nucleotides. All of the four recombinants could grow well in embryonated chicken eggs and had the similar viral titer, EID50 and MDT. Infections were done with the same Multiplicity of infection (MOI, 0.001), and the viruses in supernatants from infected cells were titrated at 12, 24, 36, and 48 h post-infection by plaque assay in fresh MDCK. The results show that four viruses grown well and had the same viral title in Vero cell, a non-IFN-responsive cell system. But in MDCK and COS-1, the cell lines can produce IFN, RWSN-248 and RWSN-m848 had a higher viral titer (two fold) than RWSN-m248 and RWSN-848. It revealed that the deletion of nucleotides of NS from 263 - 277 of H5N1 influences decreases viral growth ability in IFN producing cell line. IVPI were done for the virulence test of reassorted H5N1 viruses. Ten six-week-old SPF White Leghorn chickens were inoculated intravenously with 0.2mL of a 1:10 dilution of allantoic fluid containing each of the four recombinant viruses. The chickens were daily monitored for disease signs and death for 10 days post-inoculation. Finally, IVPI was counted for each virus. RWSN-m248 caused 4 chickens died in 10 days and its index was 1.63. RWSN-248 only caused one chicken died and its index was 0.45. RWSN848 caused 3 chickens died in 10 days and its index was 0.81. RWSN-m848 caused one of the ten chickens died and its' index was only 0.175. The results revealed that the deletion of nucleotides of NS gene from 263 to 277 sites increases H5N1 pathogenesis in chicken.

Animals↗

PubMed2006

[Construction of a recombinant adenovirus vector for interferon-gamma-inducible protein 10 and the adenovirus preparation].

OBJECTIVE: To construct a recombinant adenovirus vector for expressing interferon-gamma-inducible protein 10 (IP-10) by homogenous bacterial recombination. METHODS: IP-10 gene was cloned into the shuttle plasmid pAdTrack-CMV that contained the coding sequence of enhanced green fluorescent protein (EGFP). The shuttle plasmid was then transformed into E. coli BJ5183 with pAdEasy-1 vector by chemical transformation. The recombinant adenovirus vector pAd/IP-10 was identified by enzyme digestion with Pac I and the linearized plasmid was transfected into HEK293 cells. RESULTS: The positive clones were identified with enzyme digestion and polymerase chain reaction (PCR) and were further verified by DNA sequencing. The recombinant adenovirus of high titration was obtained after transfection and packaging in HEK293 cells. CONCLUSION: A recombinant adenovirus vector for expression of IP-10 has been constructed successfully and high-titer active adenovirus is obtained for functional study of IP-10 protein.

Adenoviridae↗

PubMed2005

cAMP-mediated mechanisms for pain sensitization during opioid withdrawal.

Chronic opioid-induced drug dependence and withdrawal syndrome after opioid cessation remain a severe obstacle in clinical treatment of chronic pain and opioid drug addiction. One of the key symptoms during opioid withdrawal is a state of sensitized pain. The most significant molecular adaptation induced by chronic opioids in the brain is upregulation of the cAMP-signaling pathway. Although the cAMP system is known to have multiple effects on central neuron functions, how its upregulation mediates behavioral opioid dependence and withdrawal-induced pain in vivo remains unclear. In this study, we demonstrate that withdrawal from chronic morphine significantly upregulates the mRNA level of adenylyl cyclase (AC) VI and VIII isoforms and immunoreactivity of ACV/VI in the nucleus raphe magnus (NRM), a brainstem site critically involved in opioid modulation of pain. In cellular studies of NRM neurons containing mu-opioid receptors, we show that morphine withdrawal significantly increases glutamate synaptic transmission via a presynaptic mechanism mediated by an upregulated cAMP pathway. Morphine withdrawal also enhances the hyperpolarization-activated current in these neurons by increased intracellular cAMP. Both of the withdrawal-induced cAMP actions increase the excitability of these mu-receptor-containing neurons, which are thought to facilitate spinal pain transmission. Furthermore, in morphine-dependent rats in vivo, blocking the cAMP pathway significantly reduces withdrawal-induced pain sensitization. These results illustrate neurobiological mechanisms for the cAMP-mediated withdrawal pain and provide potential therapeutic targets for the treatment of opioid dependence and withdrawal-related problems.

2-Amino-5-phosphonovalerate↗

PubMed2005

[Construction and expression of green fluorescent protein fusion vector of p38 regulated/activated protein kinase].

OBJECTIVE: To construct the expression vector of p38 regulated/activated protein kinase (PRAK) fused to green fluorescent protein which is capable of expression in mammalian cells. METHODS: PRAK with His-tag in pET-14b expression vector was subcloned into the green fluorescent protein vector pEGFP-C2. The recombinant vector was then transfected into HeLa cells, followed by observation of the cells with fluorescent microscope. RESULTS: Identification by enzyme digestion, PCR and sequencing confirmed successful construction of the recombinant vector, which was highly expressed in HeLa cells. Green fluorescence of the fusion protein EGFP-PRAK was observed mainly in the cell nuclei. CONCLUSION: The expression vector of PRAK fused to green fluorescent protein is successfully constructed and expressed in mammalian cells, which may facilitate the study of intracellular localization and translocation of PRAK.

Gene Expression↗

PubMed2004

Auditing concept categorizations in the UMLS.

The Unified Medical Language System (UMLS) integrates about 880,000 concepts from 100 biomedical terminologies. Each concept is categorized to at least one semantic type of the Semantic Network. During the integration, it is unavoidable that some categorization errors and inconsistencies will be introduced. In this paper, we present an auditing technique to find such errors and inconsistencies. Our technique is based on an expert reviewing the pure intersections of meta-semantic types of a metaschema, a compact abstract view of the UMLS Semantic Network. We use a divide and conquer approach, handling differently small pure intersections and medium to large pure intersections. By using this approach, we limit the number of concepts reviewed, for which we expect a high percentage of errors. We reviewed all concepts in 657 pure intersections containing one to 10 concepts. Various kinds of errors are identified and the analysis of the results are presented in the paper. Also, we checked the pure intersections containing more than 10 concepts for their semantic soundness, where the semantically suspicious pure intersections are presented in the paper and their concepts are reviewed.

Abstracting and Indexing↗

PubMed2004

[Construction and expression of the fusion vector of His-tagged human ARPC2 gene].

OBJECTIVE: To construct the expression vector of His-ARPC2 fusion protein and obtain its expression and purification in E. coli. METHODS: ARPC2 cDNA codon region was amplified by PCR from human liver cDNA library and cloned into pET-14b vector following the routine procedures. After identification by enzyme digestion, PCR and sequencing, the positive clones were transformed into BL21 (DE3) competent cells, and the expression of His-ARPC2 fusion protein was induced with IPTG and further purified by Ni-NTA affinity chromatography. RESULTS: The constructed His-ARPC2 fusion protein vector was highly efficiently expressed in E. coli. With Ni-NTA affinity chromatography, a purified His fusion protein with relative molecular mass of approximately 36 000 was obtained. CONCLUSION: The expression vector of His-ARPC2 fusion protein is constructed, expressed and purified under non-denaturing conditions, which may significantly facilitate future study of the physiological functions of ARPC2 and characterization of its interaction proteins.

Actin-Related Protein 2↗

PubMed2003

Dimerization by domain hybridization bestows chaperone and isomerase activities.

Thioredoxin, DsbA, the N-terminal active-site domain a and the non-active-site domain b of protein-disulfide isomerase are all monomeric with a thioredoxin fold, and each exhibits low or no isomerase and chaperone activity. We have linked the N terminus of the above four monomers, individually, to the C terminus of the N-terminal domain of DsbC via the flexible linker helix of the latter to produce four domain hybrids, DsbCn-Trx, DsbCn-DsbA, DsbCn-PDIa, and DsbCn-PDIb. These four hybrid proteins form homodimers, and except for DsbCn-PDIb they exhibit new or greatly elevated isomerase as well as chaperone activity. Three-dimensional structure prediction indicates that all the four domain hybrids adopt DsbC-like V-shaped structure with a broad uncharged cleft between the two arms for binding of non-native protein folding intermediates. The results provide strong evidence that dimerization creates chaperone and isomerase activity for monomeric thiol-protein oxidases or reductases, and suggesting a pathway for proteins to acquire new functions and/or higher biological efficiency during evolution.

Binding Sites↗

PubMed2003

A simple parameter relating sequences with folding rates of small alpha helical proteins.

It is found that the helix parameter (HP), which favors clustering of non-polar residues, is linearly correlated with the logarithms of rate constants of folding of small two-state alpha-helical proteins. The definition is HP = N(H)(-1) sigma [f(i)+ (f(i-1)+f(i+1))/2], where f(i)=1 or -1, if the i'th residue is hydrophobic or hydrophilic, respectively, N(H) is the number of hydrophobic residues and the summation is taken over the hydrophobic residues.

Algorithms↗

PubMed2002

The cohesive metaschema: a higher-level abstraction of the UMLS Semantic Network.

The Unified Medical Language System (UMLS) joins together a group of established medical terminologies in a unified knowledge representation framework. Two major resources of the UMLS are its Metathesaurus, containing a large number of concepts, and the Semantic Network (SN), containing semantic types and forming an abstraction of the Metathesaurus. However, the SN itself is large and complex and may still be difficult to view and comprehend. Our structural partitioning technique partitions the SN into structurally uniform sets of semantic types based on the distribution of the relationships within the SN. An enhancement of the structural partition results in cohesive, singly rooted sets of semantic types. Each such set is named after its root which represents the common nature of the group. These sets of semantic types are represented by higher-level components called metasemantic types. A network, called a metaschema, which consists of the meta-semantic types connected by hierarchical and semantic relationships is obtained and provides an abstract view supporting orientation to the SN. The metaschema is utilized to audit the UMLS classifications. We present a set of graphical views of the SN based on the metaschema to help in user orientation to the SN. A study compares the cohesive metaschema to metaschemas derived semantically by UMLS experts.

Algorithms↗

PubMed2002

Using the metaschema to audit UMLS classification errors.

The Unified Medical Language System integrates about 800,000 concepts from 99 biomedical terminologies. Each concept is assigned to at least one semantic type of the Semantic Network. During the integration, it is unavoidable that some classification errors and inconsistencies will be introduced. In this paper, we present an auditing technique to find such errors and inconsistencies. Our technique is based on an expert reviewing the pure intersections of meta-semantic types of the metaschema, a compact abstract view of the Semantic Network. Results regarding the pure intersections are reported. The analysis results for pure intersections with 1 to 6 concepts are presented. Various kinds of errors are identified.

Semantics↗

PubMed2002

Auditing the UMLS for redundant classifications.

The UMLS's Semantic Network (SN) serves as a valuable abstraction for the underlying concept repository called the Metathesaurus (META). Specifically, the SN forms a classification layer for the META, with each of the META's constituent concepts assigned to one or more semantic types in the SN. The rule in the design of the SN is to have concepts explicitly assigned to the lowest possible semantic types in the SN's IS-A hierarchy. Implicit assignment to higher semantic types can be inferred via the IS-A relationships. However, in subsequent versions of the UMLS, unnecessary, simultaneous assignments to descendant and ancestor semantic types have been discovered (e.g., 8,622 in the UMLS 1998 version and 12,657 in the 2001 version). The assignment of concepts to such ancestor semantic types is called redundant classification. There is a need for an automated auditing tool that can identify all these redundant classifications. In this paper, an efficient algorithm for this auditing task is introduced. Details of its application to the current (2001) version of the UMLS are presented and the results are discussed.

Algorithms↗