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Articles by Y. Huang
Total Records ( 8 ) for Y. Huang
  J Meng , S. J Gao and Y. Huang

Motivation: Clustering is a popular data exploration technique widely used in microarray data analysis. When dealing with time-series data, most conventional clustering algorithms, however, either use one-way clustering methods, which fail to consider the heterogeneity of temporary domain, or use two-way clustering methods that do not take into account the time dependency between samples, thus producing less informative results. Furthermore, enrichment analysis is often performed independent of and after clustering and such practice, though capable of revealing biological significant clusters, cannot guide the clustering to produce biologically significant result.

Result:We present a new enrichment constrained framework (ECF) coupled with a time-dependent iterative signature algorithm (TDISA), which, by applying a sliding time window to incorporate the time dependency of samples and imposing an enrichment constraint to parameters of clustering, allows supervised identification of temporal transcription modules (TTMs) that are biologically meaningful. Rigorous mathematical definitions of TTM as well as the enrichment constraint framework are also provided that serve as objective functions for retrieving biologically significant modules. We applied the enrichment constrained time-dependent iterative signature algorithm (ECTDISA) to human gene expression time-series data of Kaposi's sarcoma-associated herpesvirus (KSHV) infection of human primary endothelial cells; the result not only confirms known biological facts, but also reveals new insight into the molecular mechanism of KSHV infection.

Availability: Data and Matlab code are available at


Supplementary information: Supplementary data are available at Bioinformatics online.

  W. T Wong , X. Y Tian , Y Chen , F. P Leung , L Liu , H. K Lee , C. F Ng , A Xu , X Yao , P. M Vanhoutte , G. L Tipoe and Y. Huang

Bone morphogenic protein (BMP)4 can stimulate superoxide production and exert proinflammatory effects on the endothelium. The underlying mechanisms of how BMP4 mediates endothelial dysfunction and hypertension remain elusive.


To elucidate the cellular pathways by which BMP4-induced endothelial dysfunction is mediated through oxidative stress–dependent upregulation of cyclooxygenase (COX)-2.

Methods and Results:

Impaired endothelium-dependent relaxations, exaggerated endothelium-dependent contractions, and reactive oxygen species (ROS) production were observed in BMP4-treated mouse aortae, which were prevented by the BMP4 antagonist noggin. Pharmacological inhibition with thromboxane prostanoid receptor antagonist or COX-2 but not COX-1 inhibitor prevented BMP4-induced endothelial dysfunction, which was further confirmed with the use of COX-1–/– or COX-2–/– mice. Noggin and knockdown of BMP receptor 1A abolished endothelium-dependent contractions and COX-2 upregulation in BMP4-treated aortae. Apocynin and tempol treatment were effective in restoring endothelium-dependent relaxations, preventing endothelium-dependent contractions and eliminating ROS overproduction and COX-2 overexpression in BMP4-treated aortae. BMP4 increased p38 mitogen-activated protein kinase (MAPK) activity through a ROS-sensitive mechanism and p38 MAPK inhibitor prevented BMP4-induced endothelial dysfunction. COX-2 inhibition blocked the effect of BMP4 without affecting BMP4-induced ROS overproduction and COX-2 upregulation. Importantly, renal arteries from hypertensive rats and humans showed higher levels of COX-2 and BMP4 accompanied by endothelial dysfunction.


We show for the first time that ROS serve as a pathological link between BMP4 stimulation and the downstream COX-2 upregulation in endothelial cells, leading to endothelial dysfunction through ROS-dependent p38 MAPK activation. This BMP4/ROS/COX-2 cascade is important in the maintenance of endothelial dysfunction in hypertension.

  L. Chen , Q. Li , Z. Yang , Z. Ye , Y. Huang , M. He , J. Wen , X. Wang , B. Lu , J. Hu , C. Liu , C. Ling , S. Qu and R. Hu
  Aim  To assess the relationship between serum total osteocalcin and measurements of adiposity, glucose tolerance, lipid profile, adipokine and chronic low-grade inflammation in middle-aged and elderly Chinese subjects.

Methods  We performed a cross-sectional community-based study in central Shanghai. Serum total osteocalcin was measured by radioimmunoassay in 783 men and 946 post-menopausal women. Their associations with measurements of adiposity, glucose tolerance, lipid profile and chronic low-grade inflammation were examined.

Results  Serum total osteocalcin levels revealed a sexual dimorphism, with post-menopausal women having significantly higher levels than men (< 0.001). Serum osteocalcin levels of participants with self-reported cardiovascular disease were significantly lower (= 0.044) than those without. In men, serum osteocalcin levels of participants with the metabolic syndrome were significantly lower than those without the metabolic syndrome (= 0.036). Serum osteocalcin correlated negatively with fasting serum insulin, homeostasis model assessment of insulin resistance, alanine aminotransferase, triglycerides and total cholesterol, and positively with homeostasis model assessment of β-cell function in both men and post-menopausal women (all < 0.05). In men, serum osteocalcin correlated negatively with BMI, diastolic blood pressure, fasting plasma glucose and 2-h oral glucose tolerance test glucose after adjustment for age (all < 0.05). In post-menopausal women, serum osteocalcin correlated negatively with waist-hip ratio, LDL cholesterol and C-reactive protein, and positively with adiponectin (all < 0.05). Serum osteocalcin was not associated with CXC chemokine ligand 5 level (> 0.05). Alanine aminotransferase was an independent predictor of serum osteocalcin in both men and post-menopausal women (both < 0.001). Adiponectin was an independent predictor of serum osteocalcin in post-menopausal women (= 0.011). Serum osteocalcin was an independent predictor of homeostasis model assessment of β-cell function in both genders (both < 0.05).


  W. Gu , Y. Huang , Y. Zhang , J. Hong , Y. Liu , W. Zhan , G. Ning and W. Wang


To compare the carotid intima-media thickness in patients with newly diagnosed Type 1 or Type 2 diabetes ranging from 14 to 30 years of age.


Demographic, anthropometric and laboratory data were obtained from 404 adolescents and young adults (103 subjects with Type 1 diabetes, 94 with Type 2 diabetes, 153 obese subjects and 54 normal control subjects). Carotid intima-media thickness was assessed based on Doppler ultrasound examination and compared among the four groups.


Our data showed significant increases in carotid intima-media thickness in subjects with Type 1 diabetes, Type 2 diabetes and obese subjects compared with the control subjects, with those in the group with Type 2 diabetes demonstrating the greatest change (P < 0.001). Age, BMI, percentage of fat, waist-hip ratio and total triglycerides were significantly correlated with both common and internal carotid intima-media thickness segments. From a stepwise multiple linear regression model, the independent determinants of common carotid intima-media thickness were age, BMI, HbA1c and HDL cholesterol (adjusted R2 = 0.152, P < 0.001). After adjustment for age, sex and HbA1c, the odds ratio for increased carotid intima-media thickness was 1.67 (95% CI 1.19-2.33, P = 0.003) for obese subjects, 2.38 (95% CI 1.59-9.47, P = 0.001) for subjects with Type 1 diabetes and 3.93 (95% CI 1.90-6.07, P = 0001) for subjects with Type 2 diabetes compared with the control subjects.


Compared with young control subjects, we found significant increases in carotid intima-media thickness in patients with newly diagnosed Type 1 diabetes and Type 2 diabetes, with patients with Type 2 diabetes showing greater carotid intima-media thickness. Traditional cardiovascular risk factors, such as obesity, dyslipidaemia, hypertension and hyperglycaemia, could cause vessel changes even in adolescents and young adults.

  Yuan Dong , Zhong Xie , Baoqing Hu , Y. Huang and S. Zhang
  Study and formulate the data classification system and data standard, forming the Beibu Bay resources a standardized and environmental data system. Develop data acquisition and processing, database building and sharing technology standard, realizes data acquisition, conversion, processing, inspection, analysis, display the process sequence and sharing. According to the technical regulation, standard and integrated arrangement of Beibu Bay based data, thematic data resources environment, social and economic data and other data and information and combined with the network information technology, integrated "Guangxi Beibu Bay Economic Zone Based on the major projects" the implementation process of the acquisition, the formation of scientific data, analysis results and literature data, to establish a network of federal database, data network based on the intersection of environment, realize the network data integration; functional requirements through the analysis from the distributed environment, heterogeneous data processing, data integration and management, uncertainty, automation and intelligent and pointed out that the spatial data seamless integration is a systems engineering, need to meet the demanding requirements of in many aspects, Presents the design principle of system resources and environment in Beibu Bay seamless data integration system. A detailed analysis of the Beibu Bay resources and Environmental data system of spatial data center architecture and the general pattern, put forward the feasibility of seamless integration framework of spatial data center based on model. Research and design of system architecture for seamless integration of Beibu Bay of space data, focusing on design key components of seamless integration framework, global directory system, a multi-layer intelligent middleware etc.
  Q. Huang , Y.L. Li , X. Xu , Y. Huang , Z.W. Cui , D.Y. Yu and W.F. Li
  The aim of this study is to investigate the effects of Bacillus subtilis BS02 on viability and immune responses of RAW 264.7 cells. RAW 264.7 cells were stimulated with and without B. subtilis spores for 12 h in the treatment group and the control group, respectively. Cytotoxic effect of B. subtilis BS02 on macrophages was measured by cell viability and LDH cytotoxicity assay. Immune responses of macrophage elicited by B. subtilis BS02 were analyzed by measuring the activities of Acid Phosphatase (ACP) and Lactate Dehydrogenase (LDH), the production of Nitric Oxide (NO) and inducible Nitric Oxide Synthase (iNOS) and the secretion of inflammatory cytokines. The results showed that after 12 h incubation, B. subtilis BS02 spores had no influence on viability of RAW 264.7 cells; ACP and LDH activities, the production of NO and iNOS, the levels of inflammatory cytokines [Tumor Necrosis Factor-alpha (TNF-α), Interferon-gamma (IFN-γ), Interleukin-1 beta (IL-1β), IL-6, IL-8, IL-10 and IL-12] were significantly higher than that in the control group (p<0.01). These results indicate that B. subtilis BS02 is not only safe for RAW 264.7 cells but also can activate macrophage immune function.
  S Yang , B Vanderbeld , J Wan and Y. Huang

Drought is the most important environmental stress affecting agriculture worldwide. Exploiting yield potential and maintaining yield stability of crops in water-limited environments are urgent tasks that must be undertaken in order to guarantee food supply for the increasing world population. Tremendous efforts have been devoted to identifying key regulators in plant drought response through genetic, molecular, and biochemical studies using, in most cases, the model species Arabidopsis thaliana. However, only a small portion of these regulators have been explored as potential candidate genes for their application in the improvement of drought tolerance in crops. Based on biological functions, these genes can be classified into the following three categories: (1) stress-responsive transcriptional regulation (e.g. DREB1, AREB, NF-YB); (2) post-transcriptional RNA or protein modifications such as phosphorylation/dephosphorylation (e.g. SnRK2, ABI1) and farnesylation (e.g. ERA1); and (3) osomoprotectant metabolism or molecular chaperones (e.g. CspB). While continuing down the path to discovery of new target genes, serious efforts are also focused on fine-tuning the expression of the known candidate genes for stress tolerance in specific temporal and spatial patterns to avoid negative effects in plant growth and development. These efforts are starting to bear fruit by showing yield improvements in several crops under a variety of water-deprivation conditions. As most such evaluations have been performed under controlled growth environments, a gap still remains between early success in the laboratory and the application of these techniques to the elite cultivars of staple crops in the field. Nevertheless, significant progress has been made in the identification of signaling pathways and master regulators for drought tolerance. The knowledge acquired will facilitate the genetic engineering of single or multiple targets and quantitative trait loci in key crops to create commercial-grade cultivars with high-yielding potential under both optimal and suboptimal conditions.

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