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Search Results: 1 - 10 of 18229 matches for " HAO Chi "
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A fast SCOP fold classification system using content-based E-Predict algorithm
Pin-Hao Chi, Chi-Ren Shyu, Dong Xu
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-362
Abstract: With a sufficient amount of ground truth data, our system is able to assign the known folds for newly-discovered proteins in the latest SCOP v1.69 release with 92.17% accuracy. Our system also recognizes the novel folds with 89.27% accuracy using 10 fold cross validation. The average response time for proteins with 500 and 1409 amino acids to complete the classification process is 4.1 and 17.4 seconds, respectively. By comparison with several structural alignment algorithms, our approach outperforms previous methods on both the classification accuracy and efficiency.In this paper, we build an advanced, non-parametric classifier to accelerate the manual classification processes of SCOP. With satisfactory ground truth data from the SCOP database, our approach identifies relevant domain knowledge and yields reasonably accurate classifications. Our system is publicly accessible at http://ProteinDBS.rnet.missouri.edu/E-Predict.php webcite.Protein structure classification is well-known to be an important research topic in computational and molecular biology. Through the use of structural classification, life science researchers and biologists are able to study evolutionary evidence from similar proteins that have been conserved in multiple species. In addition, similar 3-D conformations of enzyme active sites and binding sites may correlate with biochemical functions [1]. In recent years, structural genomics projects [2-5] have aimed to link protein sequences to possible functions via high-throughput techniques such as X-ray crystallography and nuclear magnetic resonance (NMR) that determine 3-D protein structures. With a large-scale set of newly-discovered structures, a system that classifies similar protein structures with high efficiency and accuracy becomes an indispensable requirement to the study of structure-to-function relationships.Several classification systems categorize proteins based on structural similarities. The Class, Architecture, Topology, Homologous Su
Sliding mode control on electro-mechanical systems
Vadim I. Utkin,Hao-Chi Chang
Mathematical Problems in Engineering , 2002, DOI: 10.1080/10241230306724
Abstract: The first sliding mode control application may be found in the papers back in the 1930s in Russia. With its versatile yet simple design procedure the methodology is proven to be one of the most powerful solutions for many practical control designs. For the sake of demonstration this paper is oriented towards application aspects of sliding mode control methodology. First the design approach based on the regularization is generalized for mechanical systems. It is shown that stability of zero dynamics should be taken into account when the regular form consists of blocks of second-order equations. Majority of applications in the paper are related to control and estimation methods of automotive industry. New theoretical methods are developed in the context of these studies: sliding made nonlinear observers, observers with binary measurements, parameter estimation in systems with sliding mode control.
Aging-Shifted Prostaglandin Profile in Endothelium as a Factor in Cardiovascular Disorders
Hao Qian,Na Luo,Yuling Chi
Journal of Aging Research , 2012, DOI: 10.1155/2012/121390
Abstract: Age-associated endothelium dysfunction is a major risk factor for the development of cardiovascular diseases. Endothelium-synthesized prostaglandins and thromboxane are local hormones, which mediate vasodilation and vasoconstriction and critically maintain vascular homeostasis. Accumulating evidence indicates that the age-related changes in endothelial eicosanoids contribute to decline in endothelium function and are associated with pathological dysfunction. In this review we summarize currently available information on aging-shifted prostaglandin profiles in endothelium and how these shifts are associated with cardiovascular disorders, providing one molecular mechanism of age-associated endothelium dysfunction and cardiovascular diseases. 1. Introduction Cardiovascular disorders, including atherosclerosis, coronary artery disease, heart failure, and hypertension, remain the leading cause of death worldwide [1]. These diseases are among several pathological conditions that are associated with aging [2–4], and age is a primary risk factor for their development [5, 6]. Endothelium is a thin layer of epithelial cells which line the interior of lymph and blood vessels and is a major component of the vascular wall. One important contributor to the development of cardiovascular diseases is a dysfunctional endothelium. Endothelial dysfunction is considered a fair predictor of cardiovascular diseases [4, 7–11]. Furchgott and Zawadzki unequivocally demonstrated that the endothelium is required for normal vessel relaxation [12]. Besides inducing relaxation, normal and healthy endothelium regulates vessel wall permeability, blood flow, vascular tone, and structure and exerts anticoagulant and fibrinolytic properties [13]. Aging adversely affects these normal functions of the endothelium, enhancing vasospasm and thrombosis, leading to eventual cardiovascular diseases [4, 14–16]. Age-impaired vascular relaxation has been shown in different human vascular beds including brachial artery, aorta, coronary artery, carotid, and mesenteric microvessels [14–21]. In line with these reports, additional evidence has been obtained in different vascular beds of animals including dogs [2, 22], rats [2, 23–32] and mice [33, 34]. This reduced relaxation is accompanied with increased blood pressure [35–39]. Elevated blood pressure is an important cardiovascular risk factor that can eventually lead to heart failure. Normal endothelial function is regulated by a controlled balance between endothelium-dependent relaxing factors and endothelium-dependent contracting factors. The main
Mixture Effective Permittivity Simulations Using Imlmqrf Method on Preconditioned EFIE
Hao-Gang Wang;Chi H. Chan
PIER , 2006, DOI: 10.2528/PIER05072603
Abstract: Effective permittivity of mixtures of lossy dielectric are important quantities to be studied in microwave remote sensing of soil moisture, sea ice, dry and wet snow, in geophysical probing of properties of porous rocks and in composite materials. In this paper, these quantities are studied with large-scale numerical solutions of Maxwell equations in the electroquasistatic limit using fast electromagnetic algorithms. The preconditioned EFIE method instead of scalar potential scattering method for the simulation of the relative permittivity of the mixture with conducting particles in quasi-static environment is introduced. Furthermore, Algorithm IMLMQRF, which is kernel independent for quasi-static problems with a complexity of ( log ), is implemented to accelerate the matrix-vector multiply when CG iteration is applying on this preconditioned EFIE system. Subsequently, numerical examples, viz., the permittivity extractions from two lattice structures and one random distribution structure with the unknowns from about 1,000 to 50,000 are efficiently simulated by our method in this paper. The numerical results demonstrate the efficiency of this hybrid method.
Sliding mode control on electro-mechanical systems
Utkin Vadim I.,Chang Hao-Chi
Mathematical Problems in Engineering , 2002,
Abstract: The first sliding mode control application may be found in the papers back in the 1930s in Russia. With its versatile yet simple design procedure the methodology is proven to be one of the most powerful solutions for many practical control designs. For the sake of demonstration this paper is oriented towards application aspects of sliding mode control methodology. First the design approach based on the regularization is generalized for mechanical systems. It is shown that stability of zero dynamics should be taken into account when the regular form consists of blocks of second-order equations. Majority of applications in the paper are related to control and estimation methods of automotive industry. New theoretical methods are developed in the context of these studies: sliding made nonlinear observers, observers with binary measurements, parameter estimation in systems with sliding mode control.
On the Characteristic of Orthogonality for Multi-Carrier-Based Systems  [PDF]
Hao Wei Huang, Joy Iong-Zong Chen, Chi-Tsung Huang
Engineering (ENG) , 2013, DOI: 10.4236/eng.2013.58077
Abstract:

The dominate factors caused by reasons of losing the orthogonality in fading channel including FBC (fading branch correlation), CFO (carrier frequency offset), and even the CPN (carrier phase noise) are novel discussion in this letter. The first one factor causes the ISI (inter-symbol interference), and, however, the latter two will lead to the phenomenon of CPE (common phase error) and ICI (inter-carrier interference). On the other hand, they will lead to the loss of orthogonality for the radio system with multi-carrier modulating schemes, i.e., both them mainly deteriorate a wireless communication system. Eventually, in this letter not only the analytical expressions are derived, but a three dimension numerical results from the analysis involve the three parameters also illustrated is.

Heavy Long-lived Mossbauer State of Niobium
Yao Cheng,Chi-Hao Lee
Physics , 2011,
Abstract: A heavy niobium state showing 1/3 residual resistance is discovered below the superconducting transition temperature. This niobium sample contains high-density long-lived Mossbauer excitation.
Investigation of Streptococcus pyogenes Carriage in Population Vulnerable to Scarlet Fever during 2015-2017 in Shanghai, China  [PDF]
Mingliang Chen, Chi Zhang, Dechuan Kong, Hao Pan, Xi Zhang, Min Chen
Journal of Biosciences and Medicines (JBM) , 2018, DOI: 10.4236/jbm.2018.611009
Abstract:
This study aimed to investigate the carriage of Streptococcus pyogenes in population vulnerable to scarlet fever and to compare their genotypic characterization between different age groups. Pharyngeal swabs were collected from 120 - 150 students in each of the three districts in Shanghai in May and December during 2015 to 2017, while emm typing and detection of 12 superantigen genes were performed to characterize the isolates. During 2015-2017, the average carriage rate in students was 5.7% (135/2,371), without significant difference between different years or districts. The carriage rate was significantly different between children from the three age groups, with 2.4% in 3 - 4 years, 5.4% in 5 - 9 years, and 9.1% in 10 - 14 years. Eight emm types were found, including emm 1, emm 4, emm 12, emm 22, emm 75, emm 89, emm 70 and emm 241, among which emm 12 accounted for 60%, and emm 1 27.5%. The predominance of emm 12 was found in each year, but the proportion of emm 12 was lower in 10 - 14 years (43.3%) than in 3 - 4 years (86.7%) and in 5 - 9 years (73.3%) (P = 0.002 and 0.003). Superantigen genes of speB, speC, speG, ssa and smeZ were found in almost all the isolates. The average carriage of S. pyogenes in population vulnerable to scarlet fever was 5.7% in Shanghai, highest in 10 - 14 years (9.1%), while emm 12 was the predominant type.
Effect of B-vitamin Supplementation on Stroke: a Meta-Analysis of Randomized Controlled Trials
Chi Zhang, Feng-Ling Chi, Tian-Hao Xie, Yu-Hao Zhou
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0081577
Abstract: Background B vitamins have been extensively used to reduce homocysteine levels; however, it remains uncertain whether B vitamins are associated with a reduced risk of stroke. Our aim was to evaluate the effects of B vitamins on stroke. Methodology and Principal findings We systematically searched PubMed, EmBase, and the Cochrane Central Register of Controlled Trials to identify studies for our analysis. Relative risk (RR) was used to measure the effect of B-vitamin supplementation on the risk of stroke. The analysis was further stratified based on factors that could affect the treatment effects. Of the 13,124 identified articles, we included 18 trials reporting data on 57,143 individuals and 2,555 stroke events. B-vitamin supplementation was not associated with a significant reduction in the risk of stroke (RR, 0.91, 95%CI: 0.82–1.01, P = 0.075; RD, -0.003, 95%CI: -0.007–0.001, P = 0.134). Subgroup analyses suggested that B-vitamin supplementation might reduce the risk of stroke if included trials had a man/woman ratio of more than 2 or subjects received dose of folic acid less than 1 mg. Furthermore, in a cumulative meta-analysis for stroke, the originally proposed nonsignificant B-vitamin effect was refuted by the evidence accumulated up to 2006. There is a small effect with borderline statistical significance based on data gathered since 2007. Conclusions/Significance Our study indicates that B-vitamin supplementation is not associated with a lower risk of stroke based on relative and absolute measures of association. Subgroup analyses suggested that B-vitamin supplementation can effectively reduce the risk of stroke if included trials had a man/woman ratio of more than 2 or subjects received dose of folic acid less than 1 mg.
Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins
Yunjia Chen, Shihong Qiu, Chi-Hao Luan, Ming Luo
BMC Biotechnology , 2007, DOI: 10.1186/1472-6750-7-45
Abstract: With bioinformatics tools, we developed a domain/domain boundary prediction (DDBP) method, which was trained by available experimental data. Combined with an improved cloning strategy, DDBP had been applied to 57 proteins from C. elegans. Expression and purification results showed there was a 10-fold increase in terms of obtaining purified proteins. Based on the DDBP method, the improved GATEWAY cloning strategy and a robotic platform, we constructed a high throughput (HTP) cloning pipeline, including PCR primer design, PCR, BP reaction, transformation, plating, colony picking and entry clones extraction, which have been successfully applied to 90 C. elegans genes, 88 Brucella genes, and 188 human genes. More than 97% of the targeted genes were obtained as entry clones. This pipeline has a modular design and can adopt different operations for a variety of cloning/expression strategies.The DDBP method and improved cloning strategy were satisfactory. The cloning pipeline, combined with our recombinant protein HTP expression pipeline and the crystal screening robots, constitutes a complete platform for structure genomics/proteomics. This platform will increase the success rate of purification and crystallization dramatically and promote the further advancement of structure genomics/proteomics.One of the results from genome sequencing projects, such as the human genome project, is to promote the development of structural genomics/proteomics endeavors which focus on the large-scale determination of protein structures and functions. The traditional cloning and expression approach is inadequate for such a daunting task, and high throughput (HTP) methods are clearly necessary [1,2]. An integrated robotic pipeline can streamline the complex experimental procedures and makes it possible to carry out gene cloning and protein expression for a large amount of targets in a timely and reproducible manner. Some groups have developed the HTP cloning method including the design of ne
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