A number of computational methods have suggested means by which gene transcription – the process through which RNA is created from DNA – is activated, but there are factors at work that no model has been able to fully explain. In eukaryotes, gene regulation is quite complex, so models have primarily focused on a relatively simple species, Saccharomyces cerevisiae (budding yeast). Because of the inherent complexity in higher species, and even in yeast, a method of identifying transcription factor (TF) binding motifs (specific, short DNA sequences) must be efficient and thorough in its analysis. This thesis shows that a method using the Fast Orthogonal Search (FOS) algorithm to uncover binding motifs as well as cooperatively binding groups of motifs can explain variations in gene expression profiles, which reflect the level at which DNA is transcribed into RNA for a number of genes. The algorithm is very fast, exploring a motif list and constructing a final model within seconds to a few minutes. It produces model terms that are consistent with known motifs, while also revealing new motifs and interactions, and it causes impressive reductions in variance with relatively few model terms over the cell-cycle. / Thesis (Master, Electrical & Computer Engineering) -- Queen's University, 2008-08-21 10:30:24.293

We propose a linear mean square error channel estimator that exploits the joint space-time-frequency (STF) correlations of the wireless fading channel for applications in multiple-antenna orthogonal frequency division multiplexing systems. Our work generalizes existing channel estimators to the full dimensions including transmit spatial, receive spatial, time, and frequency. This allows versatile applications of our STF channel estimator to any fading environment, ranging from spatially-uncorrelated slow-varying frequency-flat channels to spatially-correlated fast-varying frequency-selective channels. / The proposed STF channel estimator reduces to a time-frequency (TF) channel estimator when no spatial correlations exist. In another perspective, the lower-dimension TF channel estimator can be viewed as an STF channel estimator with spatial correlation mismatch for space-time-frequency selective channels. / Computer simulations were performed to study the mean-square-error (MSE) behavior with different pilot parameters. We then evaluate the suitability of our STF channel estimator on a space-frequency block coded OFDM system. Bit error rate (BER) performance degradation, with respect to perfect coherent detection, is limited to less than 2 dB at a BER of 10-5 in the modified 3GPP fast-fading suburban macro environment. Modifications to the 3GPP channel involves reducing the base station angle spread to imitate a high transmit spatial correlation scenario to emphasize the benefit of exploiting spatial correlation in our STF channel estimator.

Session ID: TH-A4-3 / Joint 4th International Conference on Soft Computing and Intelligent Systems and 9th International Symposium on advanced Intelligent Systems, September 17-21, 2008, Nagoya University, Nagoya, Japan

Balanced Incomplete Block Designs and Binary Linear Codes are two combinatorial designs. Due to the vast application of codes in communication the field of coding theory progressed more rapidly than many other fields of combinatorial designs. On the other hand, Block Designs are applicable in statistics and designing experiments in different fields, such as biology, medicine, and agriculture. Finding the relationship between instances of these two designs can be useful in constructing instances of one from the other. Applying the properties of codes to corresponding instances of Balanced Incomplete Block Designs has been used previously to show the non-existence of some designs. In this research the relationship between (16,6,3)-designs and (25,12) codes was determined.

A systematic sectoral empirical orthogonal function (EOF) analysis of Southern Hemisphere (SH) extratropical tropospheric zonal-mean geopotential height (GH) is conducted in order to determine how EOF shapes and shape ordering is affected by a decrease in the width of the sector. Previous work (Kushner and Lee 2007) using surface pressure found that the two lead EOFs exchange shape as the sector width decreases below seventy degrees. In the present work, the 500hPa GH field is found to exhibit a similar feature. By fitting a idealized kinematic model, in the form of a Gaussian error function, to daily 500 hPa GH for each sector, the kinematic features of the shape reordering observed in the lead EOFs is shown to arise from the covariance structure of the fluctuating model parameters. The correlations between model parameters which are shown to influence the EOF shapes are further shown to be strongly influenced by statistical properties of daily mass and angular momentum fluctuations. / Graduate

Thesis (Ph. D.)--University of Washington. / Includes bibliographies.

Thesis (Ph. D.)--University of Hong Kong, 2008. / Also available in print.

Thesis (M.Sc.). / Written for the School of Computer Science. Title from title page of PDF (viewed 2008/01/15). Includes bibliographical references.

Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2008. / Includes bibliographical references (leaves 90-97). Also available in electronic version.

Thesis (M.Phil.)--Hong Kong University of Science and Technology, 2008. / Includes bibliographical references (p. 51-53 ). Also available in electronic version.