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Understanding the mechanisms that regulate gene expression is a major challenge in biology. One of the most important tasks in this challenge is to identify the transcription factors binding sites (TFBS) in DNA sequences. The common representation of these binding sites is called “motif” and the discovery of TFBS problem is also referred as motif finding problem in computer science. Despite extensive efforts in the past decade, none of the existing algorithms perform very well. This dissertation focuses on this difficult problem and proposes three new methods (MotifEnumerator, PosMotif, and Enrich) with excellent improvements. An improved pattern-driven algorithm, MotifEnumerator, is first proposed to detect the optimal motif with reduced time complexity compared to the traditional exact pattern-driven approaches. This strategy is further extended to allow arbitrary don’t care positions within a motif without much decrease in solvable values of motif length. The performance of this algorithm is comparable to the best existing motif finding algorithms on a large benchmark set of samples. Another algorithm with further post processing, PosMotif, is proposed to use a string representation that allows arbitrary ignored positions within the non-conserved portion of single motifs, and use Markov chains to model the background distributions of motifs of certain length while skipping these positions within each Markov chain. Two post processing steps considering redundancy information are applied in this algorithm. PosMotif demonstrates an improved performance compared to the best five existing motif finding algorithms on several large benchmark sets of samples. The third method, Enrich, is proposed to improve the performance of general motif finding algorithms by adding more sequences to the samples in the existing benchmark datasets. Five famous motif finding algorithms have been chosen to run on the original datasets and the enriched datasets, and the performance comparisons show a general great improvement on the enriched datasets.

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No description available.

This paper investigates how people return to information in a dynamic information environment. For example, a person might want to return to Web content via a link encountered earlier on a Web page, only to learn that the link has since been removed. Changes can benefit users by providing new information, but they hinder returning to previously viewed information. The observational study presented here analyzed instances, collected via a Web search, where people expressed difficulty re-finding information because of changes to the information or its environment. A number of interesting observations arose from this analysis, including that the path originally taken to get to the information target appeared important in its re-retrieval, whereas, surprisingly, the temporal aspects of when the information was seen before were not. While people expressed frustration when problems arose, an explanation of why the change had occurred was often sufficient to allay that frustration, even in the absence of a solution. The implications of these observations for systems that support re-finding in dynamic environments are discussed.

The aim of this thesis is to discuss about the behavior how the graduates make the decision of finding a job in Shanghai and the causes of the behavior in the micro and individual aspects. This thesis also discusses about the possible effect of labor market of Shanghai and Taiwan and the problems graduates may face when they find a job and work in Shanghai in the macro aspect. The degree of risk preference and certainty of information will affect work intention in Shanghai and the decision where the graduates find a job from deriving the model. This research has several findings. First, most graduates intend to find a job of Shanghai in Taiwan and then work in Shanghai through being assigned by Taiwan¡¦s companies. Only few graduates find a job in Shanghai without finding a job of Shanghai in Taiwan previously. Second, this thesis also find that expected income of graduates , with relatives and friends investing and working in Shanghai, having been to Shanghai and information provided by media have positive effect on work intention that graduates go to work in Shanghai. At last, according to the wage difference of local executives and Taiwan executives, graduates will face the crisis that the wage is deduced and the work position is replaced by local executives

The motivation for this research was an improvement of the quality of the Earth’s gravity solutions from the GRACE mission data through an instrument-level study. The objective was a better understanding of the characteristics and sources of the highfrequency noise in the range of (0.02 ~ 0.1 Hz) in the dual one-way ranging (DOWR) and its effect on the gravity solution. For this purpose, the mathematical model of the DOWR observation was derived and the Allan variance was computed to establish an upper bound on the level of frequency instability of the ultra-stable oscillators (USO) to determine their contribution to the high-frequency noise. Because they are dominated by the high-frequency noise, the postfit residuals of the time derivative of the DOWR ranges were also examined to evaluate the contributions of various other factors such as system noise from the microwave signal receiver, external influences, and internal influences. The results indicate that the system noise is the dominant source of the excessive highfrequency noise. As one method of mitigation, a tighter bandwidth filter was applied to the DOWR processing, resulting in modest improvements in gravity solutions. / text

This thesis explores the use of small diameter, round timber in the construction of lightweight gridshell structures. The project intention is to develop a simple and accessible construction method, based on locally available material that embraces a diverse range of technology. The design is developed using a material based approach, which first explores the behavior and limits of the material through testing at full scale. This information is used in a rapid prototyping process of scale modeling which focuses on material and construction sequence to develop a structural system. Using available materials as a design parameter, the work is an exploration of how the gridshell system can be adapted to the specific context of rural Nova Scotia. This design method is explored through the design of a craft school at the Ross Creek Centre for the Arts in Ross Creek, Nova Scotia, Canada.

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

This paper investigates how people return to information in a dynamic information environment. For example, a person might want to return to Web content via a link encountered earlier on a Web page, only to learn that the link has since been removed. Changes can benefit users by providing new information, but they hinder returning to previously viewed information. The observational study presented here analyzed instances, collected via a Web search, where people expressed difficulty re-finding information because of changes to the information or its environment. A number of interesting observations arose from this analysis, including that the path originally taken to get to the information target appeared important in its re-retrieval, whereas, surprisingly, the temporal aspects of when the information was seen before were not. While people expressed frustration when problems arose, an explanation of why the change had occurred was often sufficient to allay that frustration, even in the absence of a solution. The implications of these observations for systems that support re-finding in dynamic environments are discussed.