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Phylogeographic analysis of human papillomavirus 58

Science china(Life Sciences) 2009年第12期52卷 1164-1172页

作者： LI YanYun1, LI ZuoFeng2, HE YiFeng1, KANG Yu1, ZHANG XiaoYan1, CHENG MingJun1, ZHONG Yang2, 3· & XU CongJian1· 1 Obstetrics and Gynecology Hospital of Fudan University, shanghai 200011, china 2 shanghai bioinformation Research center, shanghai 200235, china 3 School of Life Sciences, Fudan University, shanghai 200433, china Obstetrics and Gynecology Hospital of Fudan University Shanghai China shanghai Bio-information Research center Shanghai China School of Life Sciences Fudan University Shanghai China

Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV58 high-incidence nations and regions, like china's Mainland, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in china's Mainland, and 14 new HPV58-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, china, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV58 variant, while china's Mainland and Southeast Asia are "transit points" and the new sources of HPV58 after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer.

关键词： human papillomavirus 58 (HPV58) cervical cancer phylogeography molecular evolution

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Performance and mechanism study for low-temperature SCR of NO with propylene in excess oxygen over Pt/TiO_2 catalyst

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Journal of Environmental Sciences 2010年第9期22卷 1441-1446页

作者： Zhixiang Zhang,Mingxia Chen,Zhi Jiang,Wenfeng Shangguan Research center for Combustion and Environmental technology,shanghai Jiao Tong University,shanghai 200240,china. Research center for Combustion and Environmental technology Shanghai Jiao Tong University Shanghai 200240 China

A 0.5 wt.% Pt/TiO2 catalyst was prepared and used for the low-temperature selective catalytic reduction （SCR） of NO with C3H6 in the presence of excess oxygen. The effects of Pt loading and 02 concentration on Pt/TiO2 catalytic performance for low-temperature SCR were investigated. It was found that optimal Pt loading was 0.5 wt.% and excess 02 favored low-temperature SCR of NOx. The mechanism of low-temperature SCR of NO with C3H6 was investigated with respect to the behavior of adsorbed species over Pt/TiO2 at 150~C using in situ DRIFTS. The results indicated that surface nitrosyl species （Pt~＋-NO and Ti3＋-NO） and pt2＋-CO are main reaction intermediates during the interactions of NO, C3H6 and 02. A simplified NO decomposition mechanism for the low-temperature SCR of NO with C3H6 was proposed.

关键词： NO low-temperature SCR Pt/TiO2 in situ DRIFTS

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Photocatalytic energy storage ability of TiO_2-WO_3 composite prepared by wet-chemical technique

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Journal of Environmental Sciences 2010年第3期22卷 454-459页

作者： Linglin Cao, Jian Yuan, Mingxia Chen, Wenfeng Shangguan Research center for Combustion and Environment technology, shanghai Jiao Tong University, shanghai 200240, china. Research center for Combustion and Environment technology Shanghai Jiao Tong University Shanghai 200240 China

TiO2-WO3 hybrid photocatalysts were prepared using wet-chemical technique, and their energy storage performance was characterized by electrochemical galvanostatic method. TiO2 powder was coupled with WO3 powder, which was used as electron pool and the reductive energy could be stored in. As a result, the prepared TiO2-WO3 had good energy storage ability while pure TiO2 showed no capacity and pure WO3 showed quite low performance. The energy storage ability was affected by the crystal structure of WO3 and calcination temperature. The photocatalyst had better capacity when WO3 had low degree of crystallinity, since its loose structure made it easier for electrons and cations to pass through. The photocatalytic energy storage performance was also affected by the molar ratio of TiO2 to WO3. Energy storage capacity was significantly dependent on the composition, reaching the maximum value at TiO2/WO3 1：1 （mol/mol）.

关键词： photocatalyst TiO2-WO3 energy storage

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A measure of semantic similarity between gene ontology terms based on semantic pathway covering

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Progress in Natural Science:Materials International 2006年第7期16卷 721-726页

作者： LI Rong, CAO Shunliang, LI Yuanyuan, TAN Hao, ZHU Yangyong, ZHONG Yang and LI Yixue ( Department of Computing and Information technology, Fudan University, shanghai 200433, china shanghai center for Bioin-formation technology, shanghai 200235, china School of Life Sciences, Fudan University, shanghai 200433, china Bioinfor-rnation center of shanghai Institute for Biological Sciences, Chinese Academy of Sciences, shanghai 200031, china) shanghai Ctr Bioinformat Technol Shanghai 200235 Peoples R China Fudan Univ Dept Comp & Informat Technol Shanghai 200433 Peoples R China Fudan Univ Sch Life Sci Shanghai 200433 Peoples R China Chinese Acad Sci Shanghai Inst Biol Sci Bioinformat Ctr Shanghai 200031 Peoples R China

Semantic similarity between Gene Ontology (GO) terms is critical in resolving semantic heterogeneousness when integrating heterogeneous biological databases. Traditionally, distance based and information content based measures are two major methods. In this paper, a new method based on semantic pathway covering is proposed and an algorithm, COMBINE algorithm, is presented, which considers information contents of two given nodes and those of all nodes included in the two nodes' pathways. Experiments show that COMBINE algorithm obtains the highest correlation index compared with those distance based and information content based algorithms.

关键词： Gene Ontology semantic similarity measure information content.

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NUMERICAL SIMULATIONS OF WAVE-INDUCED SHIP MOTIONS IN TIME DOMAIN BY A RANKINE PANEL METHOD

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Journal of Hydrodynamics 2010年第3期22卷 373-380页

作者： CHEN Jing-pu ZHU De-xiang china Ship Scientific Research center Shanghai 214082 China shanghai Institute of Computing technology Shanghai 200040 China

A time domain prediction of wave-induced ship motions by a Rankine panel method is investigated. Linear boundary conditions on free surface and mean wetted body surface are adopted, while the numerical damping method is used for the radiation conditions. The motions of two ships in regular head waves are computed by the present method. The related numerical results are compared with the experiment data and those from linear strip theory. The comparison shows satisfactory agreements for pitch and heave transfer functions.

关键词： Rankine source panel method time domain ship motion forward speed

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Performance Degradation due to Cascaded Erbium Doped Fiber Amplifier Power Transients in Wavelength Routed Optical Networking

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Chinese Journal of Lasers 2000年第1期9卷 48-51页

作者： JIN Yaohui ZENG Qingji TANG Xiaodong HAN Yiping (center for Broadband Optical Networking technology, shanghai Jiao Tong University, shanghai 200030, china) 上海交通大学上海

1　Ｉｎｔｒｏｄｕｃｔｉｏｎ　　Ｗａｖｅｌｅｎｇｔｈｒｏｕｔｅｄｏｐｔｉｃａｌｎｅｔｗｏｒｋｉｎｇｃａｎａｃｈｉｅｖｅｔｒａｎｓｍｉｓｓｉｏｎｓ,ｒｏｕｔｉｎｇ,ｓｗｉｔｃｈｉｎｇ,ａｎｄｐｒｏｔｅｃｔｉｏｎｓｏｆｈｉｇ... 详细信息

1　Ｉｎｔｒｏｄｕｃｔｉｏｎ　　Ｗａｖｅｌｅｎｇｔｈｒｏｕｔｅｄｏｐｔｉｃａｌｎｅｔｗｏｒｋｉｎｇｃａｎａｃｈｉｅｖｅｔｒａｎｓｍｉｓｓｉｏｎｓ,ｒｏｕｔｉｎｇ,ｓｗｉｔｃｈｉｎｇ,ａｎｄｐｒｏｔｅｃｔｉｏｎｓｏｆｈｉｇｈｓｐｅｅｄｉｎｆｏｒｍａｔｉｏｎ...

关键词： optical networks EDFA WDM power transients BER

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Comparisons of Graph-structure Clustering Methods for Gene Expression Data

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Acta Biochimica et Biophysica Sinica 2006年第6期38卷 379-384页

作者： Zhuo FANG~1,Lei LIU~(2,4),Jiong YANG~3,Qing-Ming LUO~(1*),and Yi-Xue LI~(2*) ~1 Hubei Bioinformatics and Molecular Imaging Key Laboratory,College of Life Science and technology, Huazhong University of Science and technology,Wuhan 430074,china ~2 shanghai center for Bioinformatics technology,shanghai 200235,china ~3 Department of EECS,Case Western Reserve University,Cleveland 44106,USA ~4 W.M.Keck center for Comparative and Functional Genomics,University of Illinois at Urbana-Champaign,Urbana 61801,USA Hubei Bioinformatics and Molecular Imaging Key Laboratory College of Life Science and Technology Huazhong University of Science and TechnologyWuhan 430074 China shanghai center for Bioinformatics technologyshanghai 200235 China W.M. Keck center for Comparative and Functional Genomics University of Illinois at Urbana-ChampaignUrbana 61801 USA Department of EECS Case Western Reserve UniversityCleveland 44106 USA

Although many numerical clustering algorithms have been applied to gene expression dataanalysis,the essential step is still biological interpretation by manual *** correlation betweengenetic co-regulation and affiliation to a common biological process is what biologists ***,weintroduce some clustering algorithms that are based on graph structure constituted by biological *** applying a widely used dataset,we compared the result clusters of two of these algorithms in terms ofthe homogeneity of clusters and coherence of annotation and matching *** results show that theclusters of knowledge-guided analysis are the kernel parts of the clusters of Gene Ontology (GO)-Clustersoftware,which contains the genes that are most expression correlative and most consistent with ***,knowledge-guided analysis seems much more applicable than GO-Cluster in a largerdataset.

关键词： clustering expression pattern biological function

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Current progress in epigenetic research for hepato-carcinomagenesis

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Science china(Life Sciences) 2009年第1期52卷 31-42页

作者： HUANG Jian National Human Genome Research center at shanghai-Ministry of Science and technology to build a healthy and disease Ge-nomics Laboratory,shanghai 201203,china National Human Genome Research center at shanghai-Ministry of Science and technology to build a healthy and disease Genomics Laboratory Shanghai China

Hepatocellular carcinoma is the main type of primary liver cancer,and also one of the most malignant *** present,the pathogenesis mechanisms of liver cancer are not entirely *** has been shown that inactivation of tumor suppressor genes and activation of oncogenes play a significant role in carcinogenesis,caused by the genetic and epigenetic *** the past,people generally thought that genetic mutation is a key event of tumor pathogenesis,and somatic mutation of tumor suppressor genes is in particular closely associated with *** deeper understanding of tumors in recent years,increasing evidence has shown that epigenetic silencing of those genes,as a result of aberrant hypermethylation of CpG islands in promoters and histone modification,is essential to carcinogenesis and *** term epigenetics refers to heritable changes in gene expression caused by regulation mechanisms,other than changes in the underlying DNA *** epigenetic processes include DNA methylation,genome imprinting,chromotin remodeling,histone modification and microRNA *** paper reviews recent epigenetics research progress in the hepatocellular carcinoma study,and tries to depict the relationships between hepatocellular carcinomagenesis and DNA methylation as well as microRNA regulation.

关键词： tumor heaptocellular carcinoma epigenetics DNA methylation microRNA

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Effect of heat-treatment on the surface properties of gallium phosphide nanosolids by Raman spectroscopy

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Rare Metals 2006年第3期25卷 253-259页

作者： ZHANG Zhaochun YUE Longyi GUO Jingkang School of Materials Science and technology Shanghai University Shanghai 200072 China Bioinformatics Research center Shanghai University Shanghai 200072 China

Raman spectra of gallium phosphide （GAP） nanosolids （unheated and heat-treated at 598 and 723 K, respectively） were investigated. It was observed that both the longitudinal optical mode （LO） and the transverse optical mode （TO） displayed an asymmetry on the low-wavenumber side. The scattering bands were fitted to a sum of four Lorentzians which were assigned to the LO mode, surface phonon mode, TO mode, and a combination of Ga-O-P symmetric bending and sum band formed from the X-point TA ＋ LA phonons, respectively. Analysis of the characteristic of surface phonon mode revealed that the surface phonon peak of the GaP nanosolids could be confirmed. In the infrared spectrum of the GaP nanoparticles, we observed the bands on account of symmetric stretching and bending of PO2, as well as stretching of Ga-O The Raman scattering intensity arising from the Ga-O-P linkages increased as increasing the heat-treatment temperature.

关键词： semiconductor materials nanosolids Raman spectrum gallium phosphide

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Fusion Protein of Interleukin 4 and Diphtherial Toxin with High Cytotoxicity to Cancer Cells

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Acta Biochimica et Biophysica Sinica 2004年第6期36卷 437-442页

作者： Yu-Jian ZHANG, Xiao-BoHU, Su-Xia LI1, Li-Ping TIAN, Sheng-Li YANG, and Yi GONG* Research center of Biotechnology, shanghai Institutes for Biological Sciences,Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, shanghai 200233, china State Key Laboratory of Bioreactor Engineering, East china University of Science and technology, shanghai 200237, china Research center of Biotechnology Shanghai Institutes for Biological SciencesChinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200233 China State Key Laboratory of Bioreactor Engineering East China University of Science and TechnologyShanghai 200237 China

Receptor of human interleukin 4 (hIL4R) has been found to be present on many types of cancer, so it may be a good target for cancer therapy. Here, fusion toxin gene DT4H has been constructed by fusing DNA sequence encoding the first 389 amino acids of diphtherial toxin (DT), which can not bind its own receptor, to human interleukin 4 (hIL4) gene. In order to improve the affinity of fusion toxin for hIL4R, a circularly permuted form of hIL4 (cpIL4) was used. The fusion gene was expressed in Escherichia coli where the fusion toxin DT4H was highly expressed. Purified DT4H was very cytotoxic to cancer cell line U251 cells, and moderate cytotoxic to HepG2 and MCF-7 cells. SGC-7901 cells were insensitive to it. The cytotoxic action of DT4H was specific because it was blocked by excess hIL4. These results suggest that DT4H may be a useful agent in the treatment of certain malignancies.

关键词： fusion toxin diphtherial toxin cancer therapy interleukin 4 IL-4 receptor

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