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Wen-Bo Xu

Publications and source records attributed to Wen-Bo Xu.

6 recordsLinked to original sources
PubMed2005

Prediction by support vector machines and analysis by Z-score of poly-L-proline type II conformation based on local sequence.

In recent years, the poly-L-proline type II (PPII) conformation has gained more and more importance. This structure plays vital roles in many biological processes. But few studies have been made to predict PPII secondary structures computationally. The support vector machine (SVM) represents a new approach to supervised pattern classification and has been successfully applied to a wide range of pattern recognition problems. In this paper, we present a SVM prediction method of PPII conformation based on local sequence. The overall accuracy for both the independent testing set and estimate of jackknife testing reached approximately 70%. Matthew's correlation coefficient (MCC) could reach 0.4. By comparing the results of training and testing datasets with different sequence identities, we suggest that the performance of this method correlates with the sequence identity of dataset. The parameter of SVM kernel function was an important factor to the performance of this method. The propensities of residues located at different positions were also analyzed. By computing Z-scores, we found that P and G were the two most important residues to PPII structure conformation.

Computational Biology↗
PubMed2005

Elevated plasma tissue-type plasminogen activator (t-PA) and soluble thrombomodulin in patients suffering from severe acute respiratory syndrome (SARS) as a possible index for prognosis and treatment strategy.

OBJECTIVE: To detect the presence of endothelial injury in patients with severe acute respiratory syndrome (SARS) via enhanced levels of tissue-type plasminogen activator (t-PA) and soluble thrombomodulin (sTM). METHODS: Case patients were from Xuanwu Hospital (Capital University of Medical Sciences, Beijing, China), and all of them met clinical criteria for SARS. Healthy controls were some of the hospital employees. Endothelial injury bio-markers tPA and sTM were detected by commercial ELISA-methods. RESULTS: Classic plasma markers of endothelial injury, tPA and sTM significantly elevated in SARS patients in comparison to controls [t-PA: 1.48 +/- 0.16 nmol/L versus 0.25 +/- 0.03 nmol/L (P<0.0001), and sTM: 0.26 +/- 0.06 nmol/L versus 0.14 +/- 0.02 nmol/L (P<0.05)]. The only patient who died had extremely high levels of these endothelial injury markers (t-PA: 2.77 nmol/L and sTM: 1.01 nmol/L). The likelihood ratio analysis indicated the excellent discriminating power for SARS at the optimal cut-point of 0.49 nmol/L for tPA and 0.20 nmol/L for sTM, respectively. Significant numerical correlations were found among these endothelial injury markers in SARS patients. The numerical coefficient of correlation Pearson r between t-PA and sTM was 0.5867 (P<0.05). CONCLUSION: Increased plasma concentrations of tPA and sTM in patients with SARS suggest the possibility of endothelial injury. SARS patients might need anticoagulant therapy or fibrinolytic therapy in order to reverse intraalveolar coagulation, microthrombi formation, alveolar and interstitial fibrin deposition. It may not only provide a useful treatment and prognostic index but also allow a further understanding of the pathological condition of the disease.

Adult↗
PubMed2004

A novel method of analyzing proline synonymous codons in E. coli.

Proline is a special imino acid in protein and the isomerization of the prolyl peptide bond has notable biological significance and influences the final structure of protein greatly, so the correlation between proline synonymous codon usage and local amino acid, the correlation between proline synonymous codon usage and the isomerization of the prolyl peptide bond were both investigated in the Escherichia coli genome by using a novel method based on information theory. The results show that in peptide chain, the residue at the first position C-terminal influences the usage of proline synonymous codon greatly and proline synonymous codons contain some factors influencing the isomerization of the prolyl peptide bond.

Codon↗
PubMed2004

Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition.

In this paper, a novel approach has been introduced to predict the disulfide-bonding state of cysteines in proteins by means of a linear discriminator based on their dipeptide composition. The prediction is performed with a newly enlarged dataset with 8114 cysteine-containing segments extracted from 1856 non-homologous proteins of well-resolved three-dimensional structures. The oxidation of cysteines exhibits obvious cooperativity: almost all cysteines in disulfide-bond-containing proteins are in the oxidized form. This cooperativity can be well described by protein's dipeptide composition, based on which the prediction accuracy of the oxidation form of cysteines scores as high as 89.1% and 85.2%, when measured on cysteine and protein basis using the rigorous jack-knife procedure, respectively. The result demonstrates the applicability of this new relatively simple method and provides superior prediction performance compared with existing methods for the prediction of the oxidation states of cysteines in proteins.

Amino Acid Sequence↗
PubMed2003

Global distribution of rubella virus genotypes.

Phylogenetic analysis of a collection of 103 E1 gene sequences from rubella viruses isolated from 17 countries from 1961 to 2000 confirmed the existence of at least two genotypes. Rubella genotype I (RGI) isolates, predominant in Europe, Japan, and the Western Hemisphere, segregated into discrete subgenotypes; international subgenotypes present in the 1960s and 1970s were replaced by geographically restricted subgenotypes after approximately 1980. Recently, active subgenotypes include one in the United States and Latin America, one in China, and a third that apparently originated in Asia and spread to Europe and North America, starting in 1997, indicating the recent emergence of an international subgenotype. A virus that potentially arose as a recombinant between two RGI subgenotypes was discovered. Rubella genotype II (RGII) showed greater genetic diversity than did RGI and may actually consist of multiple genotypes. RGII viruses were limited to Asia and Europe; RGI viruses were also present in most of the countries where RGII viruses were isolated.

Base Sequence↗