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    • Thesis


    • Authors: Eastwood, Erin L. (2006)

    • Drug target identification is a time consuming stage of the drug discovery process. Chemical genomics offers a solution to this hurdle. In chemical genomics, a target specific chemical ligand is applied on a genomic scale. This technique was used to identify the molecular target of anti-proliferative agents using changes in mRNA transcript levels upon treatment. Whole-genome transcription profiling experiments employed the eukaryotic model organism Saccharomyces cerevisiae for small-molecule perturbation experiments in addition to traditional genetics. Chemical genomics was used to examine the molecular target of borrelidin, a macrolide with conflicting published biological activitie...

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    • Thesis


    • Authors: Fang, Liang (2006)

    • In viewing a 3D scene, object features are seen on 3D surfaces infused with lightness and color at correct depths. By only focusing on how left and right features are correctly matched, most 3D vision models have not explained how this happens. A 3D LAMINART model (Grossberg and Howe, 2003; Cao and Grossberg, 2005) proposed that laminar cortical mechanisms interact to create 3D surface percepts using interactions between boundary and surface representations. Previous work using this model explained perception of relatively simple objects, like bars and blocks, in relatively simple spatial configurations that did not contain any mutual occlusions. This thesis extends the 3D LAMINART mo...

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    • Thesis


    • Authors: Walker, Megon Jarmaine (2006)

    • Understanding molecular interactions is at the core of computational biology and includes problems such as characterizing protein-protein, protein-small molecule, protein-DNA, and Protein-RNA binding events. These interactions are often elucidated by expensive and time-consuming assays during which candidate binders are screened against a target. The main aim of this dissertation is to improve the speed, cost, and overall efficiency of screening assays in the context of drug design and molecular systems biology. Sequential screening is an iterative process of experimentation and model refinement. Target binding activity is determined for samples of putative binders, results are used ...

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    • Thesis


    • Authors: Favaretto, Paola (2006)

    • In viewing a 3D scene, object features are seen on 3D surfaces infused with lightness and color at correct depths. By only focusing on how left and right features are correctly matched, most 3D vision models have not explained how this happens. A 3D LAMINART model (Grossberg and Howe, 2003; Cao and Grossberg, 2005) proposed that laminar cortical mechanisms interact to create 3D surface percepts using interactions between boundary and surface representations. Previous work using this model explained perception of relatively simple objects, like bars and blocks, in relatively simple spatial configurations that did not contain any mutual occlusions. This thesis extends the 3D LAMINART mo...

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    • Thesis


    • Authors: O'Lone, Raegan Brie (2006)

    • Estrogen receptors (ERs) are cell-specific mediators of physiological changes. They act primarily as transcriptional regulators through binding DNA at specific target sequences, such as estrogen response elements (EREs), within gene regulatory regions. Few primary target genes of ERs have been identified, especially in nonreproductive tissues such as the vasculature, where estrogen responses impact both sexes. I initially utilized a bioinformatics approach to characterize known ER-regulated promoters, both with regards to primary estrogen response elements and to secondary transcription factor binding sites that may coregulate estrogen responses. Secondary promoter elements were ident...

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    • Thesis


    • Authors: Tarus, Bogdan (2006)

    • It has been proposed that the amyloid ,3-protein (A/3-protein) plays a crucial role in the development of Alzheimer's Disease (AD). This dissertation presents the results of computational studies of the initial stages of A3-protein association. The objective of this work was to determine the stability and role of the A/3-protein monomers and low-order oligomers as metastable intermediates on the pathway for formation of larger aggregates and fibrils. A protocol based on shape complementarity is used to generate an assortment of possible dimer structures of the A310_35-protein congener. The ensemble of dimer structures are evaluated using rapidly computed estimates of the desolvation a...

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    • Thesis


    • Authors: Michelman-Ribeiro, Ariel (2006)

    • This dissertation investigates the transport of ions and particles and dynamics in polymer systems. The first study is of structural changes in agarose gels as ions mi¬grate through them under applied electric fields (E-fields). The second is on the trans¬lational diffusion of probes in polymer solutions and gels, using poly(vinyl alcohol) (PVA) as a model system. Understanding the transport of particles and ionic migra¬tion is important for applications such as biomedical devices and gel electrophoresis. In the first study, I performed small-angle light scattering (SALS) on agarose gels in E-fields, and observed anisotropic SALS patterns, which developed more quickly at higher E-fie...

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    • Thesis


    • Authors: Agarwal, Sachin Kumar (2006)

    • The unifying theme of this work is to provide new scalable solutions comprising algorithms, protocols, and data-structures, for solving data synchronization and set difference estimation problems. These problems are are repeatedly encountered in distributed systems and solving them efficiently directly affects the scalability of the distributed system, i.e., how many network hosts can participate in the distributed system. Our new solutions, if deployed, can significantly reduce communication, computational overhead, and meta-data stored on hosts as compared to currently used approaches for data synchronization and set difference estimation. Modern distributed network applications of...

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    • Thesis


    • Authors: Keck Lesica, Tara (2006)

    • The hippocampus is vital for memory formation, which depends critically on short term (lasting minutes or less) and long term (lasting 30 min to weeks) synaptic plasticity. Here, we describe a novel form of short-term plasticity in which synaptic efficacy depends exclusively on postsynaptic rate and explore the consequences of this phenomenon for long-term plasticity. We also examine the effects of action potential (AP) timing on input efficacy. Patch clamp experiments were performed in CA1 pyramidal cells. We applied periodic current pulses to induce postsynaptic APs at a frequency (f) of 0.5 Hz - 10 Hz. Following each AP by a time delay At, we induced small (2-4 mV) EPSPs in the pr...

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    • Thesis


    • Authors: VanCourt, Thomas David (2006)

    • Field Programmable Gate Arrays (FPGAs) have begun to appear as accelerators for general computation. Their potential for massive parallelism, high on-chip memory bandwidth, and customizable interconnection networks all contribute to demonstrated 100-1000x increases in application performance relative to current PCs. FPGA coprocessors have been available in niche markets for years, and are now appearing in mainstream supercomputers from vendors including Cray and Silicon Graphics. Available development tools do not address developers of computing applications, however. Traditional FPGA design tools meet the gate-level needs of logic designers, but present a computing model that vanish...

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    • Thesis


    • Authors: Bach, Ted (2006)

    • Cellular automata (CA) are a class of fine-grained, massively-parallel computational paradigms for describing discrete, spatially distributed dynamical systems governed by a discrete, homogeneous, local dynamics. CA computing applications include discrete physical models and empirical studies in algorithmic self-assembly, computation, complexity, and the statistical mechanics of emergence. Despite a number of existing CA applications, programming environments, and special-purpose hardware and software techniques for implementing them, there exists no implementation-independent architecture for computing with CA that is analogous to those used in similar types of co-processing applica...

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    • Thesis


    • Authors: Lakhina, Anukool (2006)

    • To attack this problem we adopt the general strategy of seeking low-dimensional approximations that preserve important traffic properties. Our starting point, and the first contribution of this dissertation, is to demonstrate that accurate low-dimensional approximations of network traffic often exist. We show that network-wide traffic measurements that exhibit as many as hundreds of dimensions can be approximated well using a much smaller set of dimensions (for example, less than ten). This observation of low effective dimensionality is key, and provides leverage on a number of problems related to network operations. In particular, low effective dimensionality leads us to make use of...

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    • Thesis


    • Authors: Pasol, Vicentiu (2006)

    • In this thesis I study the relation between the (CM) Elliptic Construction and the Mod¬ular Construction of p-adic L-functions in two variables which interpolate special values of Hecke L-functions. The first construction, due to N. Katz, and then R. Yager, is very explicit in terms of elliptic units using Iwasawa theory on formal groups. However, this construction does not imply the construction of a modular symbol for which the attached L-function is exactly this p-adic L-function. The Modular construction, developed by R. Greenberg and G. Stevens, is more general. They attach to any Hida family of p-stabilized modular forms a p-adic modular symbol with values in the space of two ...

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    • Thesis


    • Authors: Wu, Jie (2006)

    • One of the defining challenges in the post-genomic era is to develop computational and experimental tools to elucidate the mechanisms of bio-molecular interactions within the cell and between the cell and environment. The recent availability of an increasing number of completely sequenced genomes from diverse species has opened new possibilities for systematically annotating large numbers of genes by comparative genomics and deciphering the web of molecular interactions that underlie most cellular systems. High-throughput algorithms that explore the genomic context of genes and capture evolutionary signatures are needed to effectively complement and extend experimental techniques to e...

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    • Authors: Guirguis, Mina (2006)

    • One important consideration in realizing dependable computing systems and networks is to uncover vulnerabilities in their designs to adversarial attacks. Currently, the designs of these systems employ different forms of adaptation mechanisms in order to optimize their performance by ensuring that desirable properties, such as stability, efficiency and fairness, are not compromised. This thesis discovers and studies a new type of adversarial attacks that target such adaptation mechanisms by exploiting their dynamics of operation - i.e., the characteristics of their transient behavior. We coin this new breed of adversarial attacks, Reduction of Quality (RoQ) attacks. The premise of RoQ ...

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    • Thesis


    • Authors: Silva, David A. (2006)

    • Adipocyte differentiation from fibroblasts into fat cells (adipogenesis) is regulated by two families of transcription factors: CCAAT/enhancer binding proteins (C/EBPs), members of the basic leucine zipper family, and peroxisome proliferator-activated receptors (PPARs), which belong to the nuclear hormone receptor family. Adipocytes contribute to energy homeostasis with their ability to undergo lipogenesis and lipolysis, insulin-stimulated glucose transport, and secretion of hormones such as leptin and adiponectin. Alterations in adipocyte function play an important role in pathophysiological states, including diabetes and cardiovascular disease. Drosophila wingless (wg) and mouse mam...

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    • Authors: Degoricija, Lovorka (2006)

    • Dendrimers are well defined, highly branched macromolecules that consist of a core, internal branching units and a multitude of peripheral groups. Dendrimers possess low viscosities, high solubilities, single molecular weights, and a globular shape in solution. As a result, the architecture and physiochemical properties of dendrimers offer specific advantages over linear polymers. Currently, millions of people in the Unites States seek treatment for the repair of corneal wounds. The standard of care for repairing these wounds involves using sutures, which do not actively participate in healing of the surgical procedure. Another common medical problem involves the degradation of car...

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    • Thesis


    • Authors: Lei, Xiaoguang (2006)

    • The first enantioselective total synthesis of the ubiquitin-activating enzyme inhibitor (+)-panepophenanthrin has been achieved employing tartrate-mediated asymmetric nucleophilic epoxidation and stereoselective Diels-Alder dimerization of an epoxyquinol dienol monomer. Modification of the epoxyquinol monomer leading to panepophenanthrin by substitution of a tertiary hydroxyl for a methyl group led to mechanistic insight for the critical [4+2] dimerization. A complex, stereochemically well-defined chemical library with distinct skeletal frameworks has been achieved via elaboration of angular epoxyquinol scaffolds. The key strategy involved highly stereocontrolled [4+2] Diels-Alder cy...

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    • Thesis


    • Authors: He, Zhihua (2006)

    • The design of an efficient image representation methods using small numbers of features can facilitate image processing tasks such as compression of images and content-based retrieval of images from databases. In this dissertation, three methods for capturing and concisely representing two distinguishing characteristics of images, namely texture and structure, are developed. Applications of these compact representations of image characteristics to image compression as well as retrieval of images and hand-sketches of images from databases are given and performance is compared with other compression and retrieval methods. The first method to be introduced is a directional, hidden-Marko...

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    • Authors: Lee, Hyunjoo Jean (2006)

    • Improper gonad differentiation can lead to conditions ranging from reduced fertility to sex reversal. In mammals, Sty (sex determining region, Y chromosome) initiates testis development by directing supporting cell precursors to differentiate into testicular Sertoli cells rather than ovarian granulosa cells. How ovary development is initiated is poorly understood, and we sought to gain a better understanding of fetal ovary development by identifying cell-type-specific genes that might be involved in ovarian somatic cell differentiation. Our lab previously developed Sty--EGFP transgenic mice that express enhanced green fluorescent protein uniquely in the supporting cell lineage of b...