Browsing by Author "Liu, Jianhua"

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    The Assessment Agent System: Assessing Comprehensive Understanding Based on Concept Maps
    Liu, Jianhua (Virginia Tech, 2010-09-10)
    This dissertation explores the feasibility of employing software agent technology to support large-scale assessment. The research included the design, development, and evaluation of the Assessment Agent System for assessing comprehensive understanding based on concept maps. The system was designed by following an agent-oriented software design method. The Assessment Agent System is composed of five types of software agents: instructor agent, student agent, management agent, assessment agent, and reporting agent. Each of these agents was designed to possess different capabilities. Software agents in the system, through communication and cooperation, collectively provide the functionalities of user-system interaction, user management, task authoring and management, assessment delivery, task presentation, response collection, automatic assessing with feedback, and reporting. Through the process of design, development, and evaluation of the Assessment Agent System, this study demonstrates an approach that employs an agent-oriented software design method to produce sophisticated educational software applications. Furthermore, this study explored the concept map assessing method for the Assessment Agent System. When node terms and linking phrases are provided, assessing student concept maps can be automated by comparing student concept maps with assessment criteria, proposition by proposition. However, the usefulness of the proposition-comparing method depends heavily on the accuracy and thoroughness of the criterion propositions. Therefore, assessment criteria need to be continually refined and improved through examining student-created propositions.
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    The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei
    Ooi, Wen Fong; Ong, Catherine; Nandi, Tannistga; Kreisberg, Jason F.; Chua, Hui Hoon; Sun, Guangwen; Chen, Yahua; Mueller, Claudia; Conejero, Laura; Eshaghi, Majid; Ang, Roy Moh Lik; Liu, Jianhua; Sobral, Bruno; Korbsrisate, Sunee; Gen, Yunn Hwen; Titball, Richard W.; Bancroft, Gregory J.; Valade, Eric; Tan, Patrick (Public Library of Science, 2013-09-12)
    Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions. Our results provide direct experimental support for the strand-specific expression of 5,467 Sanger protein-coding genes, 1,041 operons, and 766 non-coding RNAs. A large proportion of these transcripts displayed condition-dependent expression, consistent with them playing functional roles. The two Bp chromosomes exhibited dramatically different transcriptional landscapes — Chr 1 genes were highly and constitutively expressed, while Chr 2 genes exhibited mosaic expression where distinct subsets were expressed in a strongly condition-dependent manner. We identified dozens of cis-regulatory motifs associated with specific condition-dependent expression programs, and used the condition compendium to elucidate key biological processes associated with two complex pathogen phenotypes — quorum sensing and in vivo infection. Our results demonstrate the utility of a Bp condition-compendium as a community resource for biological discovery. Moreover, the observation that significant portions of the Bp virulence machinery can be activated by specific in vitro cues provides insights into Bp's capacity as an “accidental pathogen”, where genetic pathways used by the bacterium to survive in environmental niches may have also facilitated its ability to colonize human hosts.