Browsing by Author "Wu, Peng"

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    Accepted Tutorials at The Web Conference 2022
    Tommasini, Riccardo; Basu Roy, Senjuti; Wang, Xuan; Wang, Hongwei; Ji, Heng; Han, Jiawei; Nakov, Preslav; Da San Martino, Giovanni; Alam, Firoj; Schedl, Markus; Lex, Elisabeth; Bharadwaj, Akash; Cormode, Graham; Dojchinovski, Milan; Forberg, Jan; Frey, Johannes; Bonte, Pieter; Balduini, Marco; Belcao, Matteo; Della Valle, Emanuele; Yu, Junliang; Yin, Hongzhi; Chen, Tong; Liu, Haochen; Wang, Yiqi; Fan, Wenqi; Liu, Xiaorui; Dacon, Jamell; Lye, Lingjuan; Tang, Jiliang; Gionis, Aristides; Neumann, Stefan; Ordozgoiti, Bruno; Razniewski, Simon; Arnaout, Hiba; Ghosh, Shrestha; Suchanek, Fabian; Wu, Lingfei; Chen, Yu; Li, Yunyao; Liu, Bang; Ilievski, Filip; Garijo, Daniel; Chalupsky, Hans; Szekely, Pedro; Kanellos, Ilias; Sacharidis, Dimitris; Vergoulis, Thanasis; Choudhary, Nurendra; Rao, Nikhil; Subbian, Karthik; Sengamedu, Srinivasan; Reddy, Chandan; Victor, Friedhelm; Haslhofer, Bernhard; Katsogiannis- Meimarakis, George; Koutrika, Georgia; Jin, Shengmin; Koutra, Danai; Zafarani, Reza; Tsvetkov, Yulia; Balachandran, Vidhisha; Kumar, Sachin; Zhao, Xiangyu; Chen, Bo; Guo, Huifeng; Wang, Yejing; Tang, Ruiming; Zhang, Yang; Wang, Wenjie; Wu, Peng; Feng, Fuli; He, Xiangnan (ACM, 2022-04-25)
    This paper summarizes the content of the 20 tutorials that have been given at The Web Conference 2022: 85% of these tutorials are lecture style, and 15% of these are hands on.
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    Accuracy of epidemiological inferences based on publicly available information: retrospective comparative analysis of line lists of human cases infected with influenza A(H7N9) in China
    Lau, Eric H. Y.; Zheng, Jiandong; Tsang, Tim K.; Liao, Qiaohong; Lewis, Bryan L.; Brownstein, John S.; Sanders, Sharon; Wong, Jessica Y.; Mekaru, Sumiko R.; Rivers, Caitlin; Wu, Peng; Jiang, Hui; Li, Yu; Yu, Jianxing; Zhang, Qian; Chang, Zhaorui; Liu, Fengfeng; Peng, Zhibin; Leung, Gabriel M.; Feng, Luzhao; Cowling, Benjamin J.; Yu, Hongjie (2014-05-28)
    Background Appropriate public health responses to infectious disease threats should be based on best-available evidence, which requires timely reliable data for appropriate analysis. During the early stages of epidemics, analysis of ‘line lists’ with detailed information on laboratory-confirmed cases can provide important insights into the epidemiology of a specific disease. The objective of the present study was to investigate the extent to which reliable epidemiologic inferences could be made from publicly-available epidemiologic data of human infection with influenza A(H7N9) virus. Methods We collated and compared six different line lists of laboratory-confirmed human cases of influenza A(H7N9) virus infection in the 2013 outbreak in China, including the official line list constructed by the Chinese Center for Disease Control and Prevention plus five other line lists by HealthMap, Virginia Tech, Bloomberg News, the University of Hong Kong and FluTrackers, based on publicly-available information. We characterized clinical severity and transmissibility of the outbreak, using line lists available at specific dates to estimate epidemiologic parameters, to replicate real-time inferences on the hospitalization fatality risk, and the impact of live poultry market closure. Results Demographic information was mostly complete (less than 10% missing for all variables) in different line lists, but there were more missing data on dates of hospitalization, discharge and health status (more than 10% missing for each variable). The estimated onset to hospitalization distributions were similar (median ranged from 4.6 to 5.6 days) for all line lists. Hospital fatality risk was consistently around 20% in the early phase of the epidemic for all line lists and approached the final estimate of 35% afterwards for the official line list only. Most of the line lists estimated >90% reduction in incidence rates after live poultry market closures in Shanghai, Nanjing and Hangzhou. Conclusions We demonstrated that analysis of publicly-available data on H7N9 permitted reliable assessment of transmissibility and geographical dispersion, while assessment of clinical severity was less straightforward. Our results highlight the potential value in constructing a minimum dataset with standardized format and definition, and regular updates of patient status. Such an approach could be particularly useful for diseases that spread across multiple countries.
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    Crystal Structures of TbCatB and Rhodesain, Potential Chemotherapeutic Targets and Major Cysteine Proteases of Trypanosoma brucei
    Kerr, Iain D.; Wu, Peng; Marion-Tsukamaki, Rachel; Mackey, Zachary B.; Brinen, Linda S. (PLOS, 2010-06-01)
    Background: Trypanosoma brucei is the etiological agent of Human African Trypanosomiasis, an endemic parasitic disease of sub-Saharan Africa. TbCatB and rhodesain are the sole Clan CA papain-like cysteine proteases produced by the parasite during infection of the mammalian host and are implicated in the progression of disease. Of considerable interest is the exploration of these two enzymes as targets for cysteine protease inhibitors that are effective against T. brucei. Methods and Findings: We have determined, by X-ray crystallography, the first reported structure of TbCatB in complex with the cathepsin B selective inhibitor CA074. In addition we report the structure of rhodesain in complex with the vinylsulfone K11002. Conclusions: The mature domain of our TbCatNCA074 structure contains unique features for a cathepsin B-like enzyme including an elongated N-terminus extending 16 residues past the predicted maturation cleavage site. N-terminal Edman sequencing reveals an even longer extension than is observed amongst the ordered portions of the crystal structure. The TbCatNCA074 structure confirms that the occluding loop, which is an essential part of the substrate-binding site, creates a larger prime side pocket in the active site cleft than is found in mammalian cathepsin B-small molecule structures. Our data further highlight enhanced flexibility in the occluding loop main chain and structural deviations from mammalian cathepsin B enzymes that may affect activity and inhibitor design. Comparisons with the rhodesainNK11002 structure highlight key differences that may impact the design of cysteine protease inhibitors as anti-trypanosomal drugs.