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Articles by J Zeng
Total Records ( 2 ) for J Zeng
  S Zhu , J Zeng and H. Mamitsuka

Motivation: Clustering MEDLINE documents is usually conducted by the vector space model, which computes the content similarity between two documents by basically using the inner-product of their word vectors. Recently, the semantic information of MeSH (Medical Subject Headings) thesaurus is being applied to clustering MEDLINE documents by mapping documents into MeSH concept vectors to be clustered. However, current approaches of using MeSH thesaurus have two serious limitations: first, important semantic information may be lost when generating MeSH concept vectors, and second, the content information of the original text has been discarded.

Methods: Our new strategy includes three key points. First, we develop a sound method for measuring the semantic similarity between two documents over the MeSH thesaurus. Second, we combine both the semantic and content similarities to generate the integrated similarity matrix between documents. Third, we apply a spectral approach to clustering documents over the integrated similarity matrix.

Results: Using various 100 datasets of MEDLINE records, we conduct extensive experiments with changing alternative measures and parameters. Experimental results show that integrating the semantic and content similarities outperforms the case of using only one of the two similarities, being statistically significant. We further find the best parameter setting that is consistent over all experimental conditions conducted. We finally show a typical example of resultant clusters, confirming the effectiveness of our strategy in improving MEDLINE document clustering.

  Y Li , J Zeng and Z. G. He

Virulence in pathogenic bacteria is due in part to the action of two-component systems. However, in the human pathogen Mycobacterium tuberculosis, the molecular mechanisms underlying these systems are as yet unclear. In this study, MtrA was shown to contain a functional C-terminus and also to have Ca2+ as its preferred cofactor for DNA binding. Further mutation experiments demonstrated that the C-terminus of MtrA was responsible for specific interactions with the target DNA motif and also with its partner protein, MtrB. The physical interaction between MtrA and MtrB inhibited DNA binding by MtrA. These findings yield critical information about the unique regulatory mechanisms of the essential MtrAB two-component system in this pathogen.

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