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Search Results: 1 - 10 of 8838 matches for " Zuguang Gu "
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Gene regulation is governed by a core network in hepatocellular carcinoma
Zuguang Gu, Chenyu Zhang, Jin Wang
BMC Systems Biology , 2012, DOI: 10.1186/1752-0509-6-32
Abstract: In this study, we aimed to identify the most important gene regulations that are dysfunctional in HCC generation. Our method for constructing gene regulatory network is based on predicted target interactions, experimentally-supported interactions, and co-expression model. Regulators in the network included both transcription factors and microRNAs to provide a complete view of gene regulation. Analysis of gene regulatory network revealed that gene regulation in HCC is highly modular, in which different sets of regulators take charge of specific biological processes. We found that microRNAs mainly control biological functions related to mitochondria and oxidative reduction, while transcription factors control immune responses, extracellular activity and the cell cycle. On the higher level of gene regulation, there exists a core network that organizes regulations between different modules and maintains the robustness of the whole network. There is direct experimental evidence for most of the regulators in the core gene regulatory network relating to HCC. We infer it is the central controller of gene regulation. Finally, we explored the influence of the core gene regulatory network on biological pathways.Our analysis provides insights into the mechanism of transcriptional and post-transcriptional control in HCC. In particular, we highlight the importance of the core gene regulatory network; we propose that it is highly related to HCC and we believe further experimental validation is worthwhile.Hepatocellular carcinoma (HCC) is the major histological subtype of liver cancer, and is among the most lethal cancers worldwide. The high cancer rates are especially found in the East, South-East Asia and sub-Saharan Africa [1]. Infection with hepatitis B (HBV) or C (HCV) viruses was found to be the main cause of the development of HCC in developing countries [1,2]. However, the current knowledge regarding the mechanisms of molecule interactions that lead to the disease pathogene
Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes
Zuguang Gu, Jialin Liu, Kunming Cao, Junfeng Zhang, Jin Wang
BMC Systems Biology , 2012, DOI: 10.1186/1752-0509-6-56
Abstract: A systematic and extensible pathway enrichment method in which nodes are weighted by network centrality was proposed. We demonstrate how choice of pathway structure and centrality measurement, as well as the presence of key genes, affects pathway significance. We emphasize two improvements of our method over current methods. First, allowing for the diversity of genes’ characters and the difficulty of covering gene importance from all aspects, we set centrality as an optional parameter in the model. Second, nodes rather than genes form the basic unit of pathways, such that one node can be composed of several genes and one gene may reside in different nodes. By comparing our methodology to the original enrichment method using both simulation data and real-world data, we demonstrate the efficacy of our method in finding new pathways from biological perspective.Our method can benefit the systematic analysis of biological pathways and help to extract more meaningful information from gene expression data. The algorithm has been implemented as an R package CePa, and also a web-based version of CePa is provided.As omics and high throughput technology continues to develop, researchers can increasingly understand biological phenomena at the systems level; that is, can elucidate the complicated interactions between genes and molecules responsible for biological functions [1]. Microarray technology has been widely used to measure gene expression profiles and has produced huge amounts of data for biological analysis [2]. However, traditional single gene analysis tells us little about the cooperative roles of genes in real biological systems. New challenges for microarray data analysis are to find specific biological functions affected by a group of related genes. Biological pathways are sets of genes or molecules that act together by chemical reactions, molecule modifications or signalling transduction to carry out such functions [3]. Since pathways are essentially integrated ci
InterMitoBase: An annotated database and analysis platform of protein-protein interactions for human mitochondria
Zuguang Gu, Jie Li, Song Gao, Ming Gong, Junling Wang, Hua Xu, Chenyu Zhang, Jin Wang
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-335
Abstract: InterMitoBase provides a comprehensive interactome of human mitochondria. It contains the PPIs in biological pathways mediated by mitochondrial proteins, the PPIs between mitochondrial proteins and non-mitochondrial proteins as well as the PPIs between mitochondrial proteins. The current version of InterMitoBase covers 5,883 non-redundant PPIs of 2,813 proteins integrated from a wide range of resources including PubMed, KEGG, BioGRID, HPRD, DIP and IntAct. Comprehensive curations have been made on the interactions derived from PubMed. All the interactions in InterMitoBase are annotated according to the information collected from their original sources, GenBank and GO. Additionally, InterMitoBase features a user-friendly graphic visualization platform to present functional and topological analysis of PPI networks identified. This should aid researchers in the study of underlying biological properties.InterMitoBase is designed as an integrated PPI database which provides the most up-to-date PPI information for human mitochondria. It also works as a platform by integrating several on-line tools for the PPI analysis. As an analysis platform and as a PPI database, InterMitoBase will be an important database for the study of mitochondria biochemistry, and should be particularly helpful in comprehensive analyses of complex biological mechanisms underlying mitochondrial functions.The mitochondrion is an essential organelle in eukaryotic cells that plays important roles in a variety of important processes such as apoptosis, signal transduction and cell cycle [1]. Mitochondrial dysfunction is linked to many common diseases including heart disease, diabetes, Parkinson disease and dementia. To understand the mechanism underlying the biological functions and diseases associated with the mitochondria, it is important to determine protein-protein interactions (PPIs) that facilitate mitochondrial functions.The extensive use of experimental approaches including 2D gel electrophoresi
Generalized Dynamic Modeling of Iron-Gallium Alloy (Galfenol) for Transducers  [PDF]
Yimin Tan, Zuguang Zhang, Jean Zu
Journal of Applied Mathematics and Physics (JAMP) , 2015, DOI: 10.4236/jamp.2015.38120

In this research, using the energy approach, a generalized dynamic model is derived for Galfenol (Iron-Gallium Alloy) based on the mechanical strain theory and the Jiles-Atherton model. Experiments have been conducted to measure the relationship between the strain and the magnetic field. Using experimental data, unknown parameters in the model have been identified by a developed optimization algorithm. Results show that the novel dynamic model with identified parameters is capable of describing the performance of the Galfenol rod. Simulation and experiment dynamic responses of Galfenol rods are derived. The simulation and the experiment both agree that the magnitude of the strain output decreases with the increase of the excitation frequency.

Regulation of Traditional Chinese Medicine Drugs: Efficacy and Safety
Boletín Latinoamericano y del Caribe de Plantas Medicinales y Aromáticas , 2009,
Abstract: Los documentos reguladores requeridos para el registro de Medicinas Tradicionales Chinas (MTCs) se dividen en 4 niveles: Axtas. Reglamentación, Regulación y Guías. Con estas regulaciones, el registro de MTCs consiste en un proceso de dos fases (IND/NDA) y dos niveles (provincial y estatal). Los requerimientos para Investigación y Desarrollo y producción de MTCs se han normalizado siguiendo los internacionalmente reconocidos procedimientos GLP, GCP, GMP, etc. Para registrar un producto cuatro dossieres se deben presentar a la Administración Estatal China para Medicamentos y Alimentos (SFDA): Parte I: Descripción y revisión de la droga; Parte II: datos CMC; Parte III: farmacología y toxicología data; Parte IV: estudios clínicos data. En la Parte III, hay una lista de los ensayos y estudios clínicos y pre-clínicos toxicológicos necesarios para la comercialización de estos productos, que pueden diferir según sus categorías. Consideraciones adicionales para el uso seguro de MTCs safe use are se describen en detalles Finalmente los progresos en el seguimiento y monitorización post-marketing y la vigilancia de reacciones adversas de MTCs en China son brevemente discutidas.
MiRmat: Mature microRNA Sequence Prediction
Chenfeng He, Ying-Xin Li, Guangxin Zhang, Zuguang Gu, Rong Yang, Jie Li, Zhi John Lu, Zhi-Hua Zhou, Chenyu Zhang, Jin Wang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0051673
Abstract: Background MicroRNAs are known to be generated from primary transcripts mainly through the sequential cleavages by two enzymes, Drosha and Dicer. The sequence of a mature microRNA, especially the ‘seeding sequence’, largely determines its binding ability and specificity to target mRNAs. Therefore, methods that predict mature microRNA sequences with high accuracy will benefit the identification and characterization of novel microRNAs and their targets, and contribute to inferring the post-transcriptional regulation network at a genome scale. Methodology/Principal Findings We have developed a method, MiRmat, to predict the mature microRNA sequence. MiRmat is essentially composed of two parts: the prediction of Drosha processing site and the identification of Dicer processing site. Based on the analysis of microRNAs from 12 species, we found that the patterns of free energy profiles are conserved among vertebrate microRNA hairpins. Therefore, we introduced in our method the free energy distribution pattern of the downstream part of pri-microRNA secondary structure and Random Forest algorithm to predict the mature microRNA sequence. Based on the evaluation on an independent test dataset from 10 vertebrates, MiRmat was shown to identify 77.8% of the Drosha processing sites and 92.8% of the Dicer sites within a deviation of 2 nt. In a more stringent evaluation by excluding the microRNAs sharing the same family between the training set and test set, MiRmat kept a rather well performance of 71.9% and 87.2% of the identification rate on the Drosha and Dicer site respectively, which represents the ability to deal with the novel microRNA family. MiRmat outperforms other state-of-the-art methods and has a high degree of efficacy for the prediction of mature microRNA sequences of vertebrates. Conclusion MiRmat was developed for identifying microRNA mature sequence(s) by introducing the free energy distribution of RNA stem-loop structure and the Random Forest algorithm. We prove that MiRmat has better performance than the existing tools and is applicable among vertebrates. MiRmat is freely available at http://mcube.nju.edu.cn/jwang/lab/soft/M?iRmat/.
A Thought of Study on Toxicology of Chinese Medicines

Ye Zuguang,

世界科学技术-中医药现代化 , 2003,
Abstract: 因为中药具有与西药不同的一些特点,故中药毒理学研究的内容和方法学也有许多独特之处。中药多由多组分所组成,使得两药或多药联合用药的试验研究成为中药毒理学的重要组成部分,同时使得中药毒代动力学研究颇具难度;应加大对矿物性中药作用特点和安全性评价的研究,从而使之在临床上更加合理科学的使用;中药毒性作用不仅包括一般意义上的不良反应,还要包括在中药作用下机体所出现的“不良征候”。
Factor Analysis-Based Optimal Selection of Rock-Breaking Bit Applied in Deep Layer of Songliao Basin
Zuguang Li,Yinghu Zhai,Xu Zhang
Journal of Geography and Geology , 2009, DOI: 10.5539/jgg.v1n2p28
Abstract: Correctly choosing rock-breaking bit is critical in oil drilling. The optimal model of selecting a bit has been established based on the Factor Analysis Theory. Through selecting primitive variables, and using SPSS (Statistical Package for the Social Sciences) to get factor loading matrix, factor rotation and factor score, we have reasonably evaluated and optimized the selection of rock-breaking bits applied in deep layer drilling of Songliao Basin. The calculated results are consistent with the observation from actual applications. It indicates that the method studied here is reasonably reliable and valuable for broader applications.
The generalized self-similarity and scaling invariance in fluid motions
Shida Liu,Shikuo Liu,Mingshun Jiang,Zuguang Zheng
Chinese Science Bulletin , 1997, DOI: 10.1007/BF02882524
The generalized self-similarity and scaling in variance in fluid motions

Shida Liu,Shikuo Liu,Mingshun Jiang,Zuguang Zheng,

科学通报(英文版) , 1997,
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