As ocean ecosystems continue to deteriorate in the face of human induced pressures, marine management professionals are increasingly being urged to predict the impacts of various activities on ocean ecosystems. Many ecosystem interactions are still not adequately understood, so managers often turn to scientists to provide data and analysis on impacts resulting from specific actions. One important physical ocean process in need of more empirical data is microscale turbulence. Because it is responsible for mixing across isopycnal surfaces in stratified waters, turbulence is important in many physical, chemical and biological processes in the ocean. An elementary description of turbulence and mixing is presented along with a summary of the role of turbulence in marine ecosystems. In order to be of use to scientists, turbulence must be measured over large areas of the ocean. This paper presents a discussion of techniques for measuring turbulence. Measurements of turbulence are specialized and costly. A new microstructure data acqusition system was developed to acquire microstructure data eight times faster than present methods allow. The design details of the high-speed microstructure data acquisition system called MicroSoar are presented along with some preliminary data obtained from its deployment on actual cruises. / Graduation date: 1998

In the context of forest products, a cutting order is a list of dimension parts along with demanded quantities. The cutting-order problem is to minimize the total cost of filling the cutting order from a given lumber grade (or grades). Lumber of a given grade is supplied to the production line in a random sequence, and each board is cut in a way that maximizes the total value of dimension parts produced, based on a value (or price) specified for each dimension part. Hence, the problem boils down to specifying suitable dimension-part prices for each board to be cut. The method we propose is adapted from Gilmore and Gomory's linear programming approach to the cutting stock problem. The main differences are the use of a random sample to construct the linear program and the use of prices rather than cutting patterns to specify a solution. The primary result of this thesis is that the expected cost of filling an order under the proposed method is approximately equal to the minimum possible expected cost, in the sense that the ratio (expected cost divided by the minimum expected cost) approaches one as the size of the order (e.g., in board feet) and the size of the random sample grow large. A secondary result is a lower bound on the minimum possible expected cost. The actual minimum is usually impractical to calculate, but the lower bound can be used in computer simulations to provide an absolute standard against which to compare costs. It applies only to independent sequences, whereas the convergence property above applies to a large class of dependent sequences, called alpha-mixing sequences. Experimental results (in the form of computer simulations) suggest that the proposed method is capable of attaining nearly minimal expected costs in moderately large orders. The main drawbacks are that the method is computationally expensive and of questionable value in smaller orders. / Graduation date: 2001

published_or_final_version / Computer Science / Master / Master of Philosophy

RNA-seq sequencing has revolutionized the landscape of whole transcriptome sequencing and analysis. With its capacity of sequencing in a high-throughput and low-cost way, it produced ever increasingly amount of RNA-seq reads that are mines of treasure in biological and therapeutic studies. However, due to the complex nature and relatively un-developed knowledge base of transcription process, many challenges exist in the modeling and investigation of RNA-seq read data. It is of high importance to develop efficient computational tools to satisfy these needs. The first part of this thesis concentrates on algorithms for both upstream and downstream analysis of RNA-seq data. For the upstream, we aim to tackle down the problems of RNA-seq reads alignment where the segmental alignment causes the major difficulty. By employing a strategy of rigid extensive tries on read segmentations indices, we implemented an accurate algorithm for returning two-segmental alignments based on bi-directional BWT. For the downstream analysis, we study two types of gene fusion events which play a critical role in the formation of cancers. Unlike previous down-scoping-search methods, we applied a search-validate approach to design the framework. By introducing key techniques such as masking, two-segmental alignment and retention of multiple maps, we developed an efficient and robust tool for detecting gene fusions with high accuracy that proved by extensive simulation and real data tests. Optical mapping is a cutting edge technique for the study of genomic structural variations which address the defect and limitation of paired-end sequencing. It was designed with great improvement in accuracy, resolution and throughput than current techniques. Also, it produces much longer molecules which enables us to explore genomic regions rich in repetitive sequences. Optical mapping has the potential to enable us to draw a complete picture of the genome structure polymorphism and it is important for us to design tools for analysis of the data. The second part of the thesis is dedicated to the algorithms for both upstream and downstream analysis of optical map data. For the upstream, we formulated a robust scoring function, which combines the effectiveness of heuristic functions and the accuracy of statistical functions. Based on it, we implemented the high performance OMDP algorithm. For the downstream, we developed BP-OMDP which makes use of both split-mapping and disparity of coverage depth to call inversions in NA12878 human genome sample. / published_or_final_version / Computer science / Doctoral / Doctor of Philosophy

Not available / text

published_or_final_version / Computer Science / Master / Master of Philosophy

published_or_final_version / Electrical and Electronic Engineering / Master / Master of Philosophy

The architecture profession, like many other design professions, is being revolutionized through the usage and development of computers. Both computer hardware and software are reaching levels of high development in the area of graphics. Even though graphic systems are becoming more sophisticated, there is no current linkage of textual information with graphics. Architectural projects consist of both text (specifications) and graphics (working drawings). Consequently, this creative project develops a computer software system (series of programs) for linking and unifying text information (specifications) with working drawings. / Department of Architecture

Thesis (Ph. D.)--University of Texas at Austin, 1999. / Vita. Includes bibliographical references (leaves 152-160). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1973. / Typescript. Vita. Description based on print version record. Includes bibliographical references (leaves 339-355).