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Browsing by Author "Tang, Yi"

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    Identification and Genomic Characterization of Two Novel Hepatoviruses in Shrews from Yunnan Province, China
    Tang, Yi; Zhao, Kai; Yin, Hong-Min; Yang, Li-Ping; Wu, Yue-Chun; Li, Feng-Yi; Yang, Ze; Lu, Hui-Xuan; Wang, Bo; Yang, Yin; Zhang, Yun-Zhi; Yang, Xing-Lou (MDPI, 2024-06-17)
    Hepatitis A virus (HAV), a member of the genus Hepatovirus (Picornaviridae HepV), remains a significant viral pathogen, frequently causing enterically transmitted hepatitis worldwide. In this study, we conducted an epidemiological survey of HepVs carried by small terrestrial mammals in the wild in Yunnan Province, China. Utilizing HepV-specific broad-spectrum RT-PCR, next-generation sequencing (NGS), and QNome nanopore sequencing (QNS) techniques, we identified and characterized two novel HepVs provisionally named EpMa-HAV and EpLe-HAV, discovered in the long-tailed mountain shrew (Episoriculus macrurus) and long-tailed brown-toothed shrew (Episoriculus leucops), respectively. Our sequence and phylogenetic analyses of EpMa-HAV and EpLe-HAV indicated that they belong to the species Hepatovirus I (HepV-I) clade II, also known as the Chinese shrew HepV clade. Notably, the codon usage bias pattern of novel shrew HepVs is consistent with that of previously identified Chinese shrew HepV. Furthermore, our structural analysis demonstrated that shrew HepVs differ from other mammalian HepVs in RNA secondary structure and exhibit variances in key protein sites. Overall, the discovery of two novel HepVs in shrews expands the host range of HepV and underscores the existence of genetically diverse animal homologs of human HAV within the genus HepV.
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    SUNSHINE: Integrate TOSSIM and P-Sim
    Tang, Yi (Virginia Tech, 2011-09-23)
    Simulators are important tools for wireless sensor network (sensornet) design and evaluation. However, existing simulators only support evaluations of protocols and software aspects of sensornet design. Thus they cannot accurately capture the significant impacts of various hardware designs on sensornet performance. To fill in the gap, we proposed SUNSHINE, a scalable hardware-software cross-domain simulator for sensornet applications. SUNSHINE is the first sensornet simulator that effectively supports joint evaluation and design of sensor hardware and software performance in a networked context. SUNSHINE captures the performance of network protocols, software and hardware through the integration of two modules: a network simulator TOSSIM [1] and hardware-software simulator P-Sim composed of an instruction-set simulator SimulAVR [2] and a hardware simulator GEZEL [3]. This thesis focuses on the integration of TOSSIM and P-Sim. It discusses the integration design considerations and explains how to address several integration challenges: time conversion, data conversion, and time synchronization. Some experiments are also given to demonstrate SUNSHINE's cross-domain simulation capability, showing SUNSHINE's strength by integrating simulators from different domains.