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Articles by S Zhu
Total Records ( 4 ) for S Zhu
  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.

  X. J He , Y. F Hsu , S Zhu , H. L Liu , O Pontes , J Zhu , X Cui , C. S Wang and J. K. Zhu
 

RNA-directed DNA methylation (RdDM) is a conserved mechanism for epigenetic silencing of transposons and other repetitive elements. We report that the rdm4 (RNA-directed DNA Methylation4) mutation not only impairs RdDM, but also causes pleiotropic developmental defects in Arabidopsis. Both RNA polymerase II (Pol II)- and Pol V-dependent transcripts are affected in the rdm4 mutant. RDM4 encodes a novel protein that is conserved from yeast to humans and interacts with Pol II and Pol V in plants. Our results suggest that RDM4 functions in epigenetic regulation and plant development by serving as a transcriptional regulator for RNA Pol V and Pol II, respectively.

  T Fei , K Xia , Z Li , B Zhou , S Zhu , H Chen , J Zhang , Z Chen , H Xiao , J. D. J Han and Y. G. Chen
 

Embryonic stem (ES) cells are under precise control of both intrinsic self-renewal gene regulatory network and extrinsic growth factor-triggered signaling cascades. How external signaling pathways connect to core self-renewal transcriptional circuits is largely unknown. To probe this, we chose BMP signaling, which is previously recognized as a master control for both self-renewal and lineage commitment of murine ES cells. Here, we mapped target gene promoter occupancy of SMAD1/5 and SMAD4 on a genome-wide scale and found that they associate with a large group of developmental regulators that are enriched for H3K27 trimethylation and H3K4 trimethylation bivalent marks and are repressed in the self-renewing state, whereas they are rapidly induced upon differentiation. Smad knockdown experiments further indicate that SMAD-mediated BMP signaling is largely required for differentiation-related processes rather than directly influencing self-renewal. Among the SMAD-associated genes, we further identified Dpysl2 (previously known as Crmp2) and the H3K27 demethylase Kdm6b (previously known as Jmjd3) as BMP4-modulated early neural differentiation regulators. Combined with computational analysis, our results suggest that SMAD-mediated BMP signaling balances self-renewal versus differentiation by modulating a set of developmental regulators.

  S Zhu , W Pan , P Shi , H Gao , F Zhao , X Song , Y Liu , L Zhao , X Li , Y Shi and Y. Qian
 

Interleukin 17 (IL-17) plays critical roles in the pathogenesis of various autoimmune diseases, including experimental autoimmune encephalomyelitis (EAE). How the signals triggered by this powerful inflammatory cytokine are controlled to avoid abnormal inflammatory responses is not well understood. In this study, we report that TRAF3 is a receptor proximal negative regulator of IL-17 receptor (IL-17R) signaling. TRAF3 greatly suppressed IL-17–induced NF-B and mitogen-activated protein kinase activation and subsequent production of inflammatory cytokines and chemokines. Mechanistically, the binding of TRAF3 to IL-17R interfered with the formation of the receptor signaling activation complex IL-17R–Act1–TRAF6, resulting in suppression of downstream signaling. TRAF3 markedly inhibited IL-17–induced expression of inflammatory cytokine and chemokine genes in vivo and consequently delayed the onset and greatly reduced the incidence and severity of EAE. Thus, TRAF3 is a negative regulator of IL-17R proximal signaling.

 
 
 
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