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  • Thesis


  • Authors: Kopkalli, Yasemin;  Co-Author: 2006 (There is great interest in identifying and characterizing new surfactants with predictable solubilization and reconstitution characteristics for use in membrane research. Among them, Triton X-100 and octyl glucoside (OG) are the best-studied surfactants. However, no physical data is available characterizing the interactions of two non-ionic pyrrolidinone surfactants, N-(2-ethylhexyl)-2-pyrrolidinone (C2,6P) and N-octyl-2-pyrrolidinone (C8P), with lipid bilayers. In the present study, their physical effects on dimyristoylphosphatidylcholine small unilamellar vesicles (DMPC SUVs) above the lipid phase transition temperature are described using surface tension, fluorescence spectroscopy, and isothermal titration calorimetry (ITC) methodologies. Surface tension methods show significant deviations from ideal behavior (attractive interactions) for these surfactant/lipid mixtures. In addition, fluorescence intensity studies of DPH and TMA-DPH labeled SUVs suggest that C8P interacts more favorably with both the acyl chain and head group regions of the bilayer over the corresponding branched chain C2,6P analogue. This is further supported by fluoresecence emission anisotropy measurements (EA). Both surfactants affect the membrane lipid order within the acyl chain region, and the corresponding phospholipid ‘melt’ transition temperature (Tm) values, which decrease linearly with increasing surfactant concentrations. Using the van’t Hoff model, the lipid bilayer-water partition coefficients for these surfactants have been estimated from the depression of the lipid phase transition temperature. Values for the lipid partition coefficient for C8P [(1.22±0.08)× 104] versus C2,6P [(4.09±0.78)× 103] further supports a more favorable bilayer association for C8P. ITC data reveals an endothermic association for both C8P and C2,6P together with a somewhat higher binding affinity [(6.78±0.92)×10-4M] for C8P compared with C2,6P [(8.46±0.83)×10-4 M], as predicted from fluorescence studies. We propose that C8P interacts and affects the lipid packing of bilayer membranes to a greater extent than C2,6P. Interactions of C2,6P appears to be more localized within the head group region of the bilayer. We conclude that C8P has great potential for biological applications, particularly membrane solubilization and membrane formation from micellar mixtures. In contrast, C2,6P may have potential for solubilization of extrinsic surface associated membrane proteins.)

  • Thesis


  • Authors: Xie, Qing;  Co-Author: 2006 (Most of today s software users interact with the software through a graphical user interface (GUI), which constitutes as much as 45-60% of the total code. The correct¬ness of the GUI is necessary to ensure the correctness of the overall software. Although GUIs have become ubiquitous, testing GUIs for functional correctness has remained a ne¬glected research area. Existing GUI testing techniques are extremely resource intensive primarily because GUIs have very large input spaces and evolve frequently. This dis¬sertation overcomes the limitations of existing techniques by developing a process with supporting models, techniques, and tools for continuous integration testing of evolving GUI-based applications. The key idea of this process is to create three concentric testing loops, each with speci c GUI testing goals, resource usage, and targeted feedback. The innermost fully automatic loop called crash testing operates on each code change of the GUI software. The second semi-automated loop called smoke testing operates on each day s GUI build. The outermost loop called comprehensive GUI testing is executed after a major version of the GUI is available. The primary enablers of this process, also devel- oped in this dissertation, include an abstract model of the GUI and a set of model-based techniques for test-case generation, test oracle creation, and continuous GUI testing. The model and techniques were obtained by studying GUI faults, interactions between GUI events, and why certain event interactions lead to faults. The continuous testing process and associated techniques are shown to be useful, via several large experiments involving millions of test cases, on both in-house and open-source GUI applications.)

  • Thesis


  • Authors: Zhao, Zhihe;  Co-Author: 2006 (A key aspect of design and the maintenance of underwater pipelines is the assessment of local scour and its propagation. Scouring around objects placed on a sandy bottom is very complex because it involves two-phase turbulent flows and a myriad of sediment transport modes. This dissertation addresses two principal configurations of scour around pipelines in two parts. First, clear-water scour around a long fixed pipeline placed just above a non-cohesive sandy bed is numerically simulated. Second, live-bed scour around a fixed pipeline and scour below a sagging pipeline are investigated. These two simulations are conducted by using an Eulerian two-phase model that implements Euler-Euler coupled governing equations for fluid and solid phases and a modified k - e turbulence closure for the fluid phase, the modeling system being a part of software FLUENT. Both flow-particle and particle-particle interactions are considered in the model. During the simulations, the interface between sand and water is specified using a threshold volume fraction of sand, and the evolution of the bedforms is studied in detail. For clear-water scour around a fixed pipeline, the predictions of bedform evolution are in agreement with previous laboratory measurements. Investigations into the mechanisms of scour reveal that three sediment transport modes (bed-load, suspended-load and laminated-load) are associated with the scour development. While some previously proposed scour development formulae for cylindrical objects are in good agreement with the simulations, scour predictions based on some operational mine-burial models show disparities with present simulations. For investigations of live-bed scour and scour under a sagging pipeline, the flow and pipeline evolve in two steps: (1) the local live-bed scour around the pipeline developed around a fixed pipeline; and (2) the pipeline is lowered to the scour hole in controlled fashion until it reaches the bottom of the scour hole. Three sagging velocities are simulated, and predicted scour profiles agree well with the laboratory data. General characteristics of flow fields, including turbulence, suspension of particles and sediment transport, are described paying attention to their dependence on pipeline sagging. Scour profiles simulated are also in agreement with a LES-based numerical study reported earlier.)

  • Thesis


  • Authors: Lee, Chung-Sheng;  Co-Author: 2006 (To successfully use the fiber-reinforced-polymer (FRP) overlay technique for the seismic retrofit and the blast-hardening of RC columns, the mechanical behavior of the FRP-confined concrete needs to be understood and its response needs to be accurately predicted. Although a number of studies have been conducted to-date, it is still not clear how the main parameters affect the axial stress-strain response of a FRP-confined concrete cylinder. In particular, while it is understood that FRP jackets inhibit dilatancy, current models do not capture the physics that leads to ascending or strain-softening responses vs. the level of lateral confinement. In this dissertation, a dilatancy-based analytical model for FRP-jacketed circular concrete cylinders in axial compression was developed. The proposed theory is applicable to both the heavily confined case with ascending axial loaded vs. axial strain response, and the lightly confined specimen with strain-softening behavior. As an extension of the circular model, a new model for rectangular FRP-confined sections was then developed. In addition to jacket membrane strain, the jacket flexural strains caused by the cross-sectional shape were taken into account, and the rupture strain of the FRP jacket in the corner zone was predicted. The present model was validated via a large set of existing test results, and excellent agreement with experimental data was observed. As the application of the proposed concrete model, a load-displacement model and an associated computational algorithm were developed and validated for the response and failure conditions of RC columns subject to combined axial and seismic-type (lateral) loads. On the other hand, excluding the strain rate effects on material parameters from modeling, an analytical procedure was also developed to predict the resistance function of FRP-jacketed RC columns subject to combined axial and uniform lateral (simulated blast) loads. The model was validated via the results of the UCSD quasi-static tests on “blast columns”, and satisfactory correlation with the experimental load-displacement curves were observed. The present models and the analytical procedures proposed in this dissertation can serve as design/analysis tools for the FRP overlay technique as applied to the seismic retrofit as well as the blast-hardening of RC columns.)

  • Thesis


  • Authors: Reck, Gregory M.;  Co-Author: 2006 (While most proteins in biological systems are inherently stable as a prerequisite to performing their functions, a small number of normally well-behaved proteins can engage in a process of aggregation that eventually leads to the formation of an insoluble material identified as an amyloid. Details of the aggregation process are not fully known, but for some model proteins the process can be initiated with known destabilizing conditions. While no sequence or structural similarities have been observed among the proteins, structural instability associated with a characteristic motif in the protein could be a common thread. The proposed strategy to search for such a feature employs a knowledge-based tool that examines the sequence-structure relationship in a specific target protein based on similar relationships drawn from a large representative sample of proteins. The tool incorporates a computational structural analysis known as tessellation to identify small geometric elements each containing four neighboring amino acid residues, and builds a potential score for the protein based on a statistical analysis of the appearance of these quadruplets in the reference set. Components of the protein potential score can be associated with the residues in the primary sequence leading to a potential profile or vector that characterizes the local compatibility of the protein structure with its sequence. The aim of this effort was to demonstrate a relationship between tessellation-derived potentials and thermodynamic measurements of protein stability. A major part of the study was to improve the representation of the protein environment by computationally hydrating the proteins used in the analysis. Several strategies were investigated for including the surrounding hydration water in the statistical analysis of the reference proteins. The resulting model has been used to successfully correlate the stability of several model proteins and to discriminate native proteins from large groups of decoy structures. Machine learning tools were also employed to search for information content in the potential profile vectors and to seek an association between the potential profiles of mutants of transthyretin and their amyloidogenic behavior.)

  • Thesis


  • Authors: Xu, Ruifeng;  Co-Author: 2006 (Collocation is a lexical phenomenon in which two or more words are habitually combined together as some conventional way of saying things. Collocation information is essential to many natural language processing tasks such as word sense disambiguation, machine translation, and information extraction. Most of current works on collocation extraction are statistical based with limited precision and recall because they can not well distinguish word co-occurrences, which are statistically 'significant, from true collocations, which are of habitual use and are thus either syntactically or semantically significant. The objective of this study is to investigate methods to improve the performance of Chinese collocation extraction algorithms. Different types of collocations are identified. Collocation extraction algorithms are then designed to target on different types of collocations using different features and criteria associated with these different types. In addition to improve statistical based collocation extraction algorithms, additional syntactic and semantic information are also incorporated into the algorithm to further improve the performance of collocation extraction. On the study of the statistical based algorithms, a new algorithm based on bi-directional word bi-grams is designed to help identify collocations with low co-occurrence frequency and are of fixed use. A large scale Chinese collocation answer set is established so that collocation extraction algorithms can be evaluated and compared objectively by using the same training corpus and corresponding answer set. Collocations are then categorized into four types based on their compositionality, substitutability, modifiability and internal association. Based on the characteristics of each type of collocations, a multi-stage window-based collocation extraction is built where the n-gram collocations and different types of bi- gram collocations are separately extracted in different stages using different strategies and different discriminative features. A Chinese shallow treebank, referred to as the PolyU Treebank, is annotated manually to provide syntactic and semantic knowledge to further help collocation extraction. This treebank is also used to train a chunker based on lexicalized Hidden Markov Model (HMM). The chunker provides ways to process running text for collocation extraction. By using the support collocation patterns and reject collocation patterns extracted from the annotated Chinese treebank and parsed running text, syntactic features are employed to further improve the performance of the window-based collocation extraction system. Experimental results show that the use of syntactic patterns can significantly improve the performance of collocation extraction, especially for filtering pseudo collocations. The extracted collocations were applied in the post-processing of a handwritten Chinese character recognition system. Experiments indicate that collocation information can be used in real application to improve the performance of these natural language related applications.)

  • Thesis


  • Authors: White, Elizabeth A.;  Co-Author: 2006 (The human cytomegalovirus (HCMV) IE2 86 kDa protein is an essential viral regulatory factor that has been shown in transient transfection and in vitro assays to transactivate early viral promoters and to interact with many viral and celular proteins. To understand the functions provided by this protein in the HCMV-infected cel, we have constructed and characterized a family of recombinant viruses containing changes to the IE2 gene and other parts of the HCMV major immediate early (IE) region. The study of these HCMV mutants has alowed us to confirm that several of the predicted functions of IE2 86 are relevant in the virus-infected cel and has identified new functions for the protein. Introducing smal deletions into the C-terminus of IE2 86 resulted in viruses that do not support early gene expression, replicate, or repress the major IE promoter. Surprisingly, these constructs also mediated up-regulation of several delayed early and late viral genes, suggesting that IE2 functions are required for the proper regulation of late viral gene expression. By constructing several viruses that do not express the IE2 40 and IE2 60 kDa proteins, which are present in infected cels at late times post infection, we continued to investigate the regulation of late gene expression by IE2. Again, we found that the IE2 40 and IE2 60 proteins are required for proper late gene expression and for repression of the major IE promoter. Interactions between the virus and the host cel are also crucial for proper HCMV replication, and a recombinant virus with a deletion in exon 3 of the major IE region demonstrated that IE2 86 is important not only for transactivation of viral early promoters, but also for dysregulation of the host cel cycle. Cels infected with this recombinant virus fail to exhibit diffuse PML staining at early times post infection and express less cyclin E protein and produce less infectious virus than do wild-type virus-infected controls. The experiments described in this dissertation demonstrate that IE2 86 is a multifunctional protein that contributes many functions, several of which were not previously identified, to HCMV replication in infected cels.)

  • Thesis


  • Authors: Feldman, Anna;  Co-Author: 2006 (Morpho-syntactic tagging is the process of assigning part of speech (POS), case, number, gender, and other morphological information to each word in a corpus. Morpho-syntactic tagging is an important step in natural language processing. Corpora that have been morphologically tagged are very useful both for linguistic research, e.g. finding instances or frequencies of particular constructions in large corpora, and for further computational processing, such as syntactic parsing, speech recognition, stemming, and word-sense disambiguation, among others. Despite the importance of morphological tagging, there are many languages that lack annotated resources. This is almost inevitable because these resources are costly to create. But, as described in this thesis, it is possible to avoid this expense. This thesis describes a method for transferring annotation from a morphologically annotated corpus of a source language to a corpus of a related target language. Unlike unsupervised approaches that do not require annotated data at all and, as a consequence, lack precision, the approach proposed in this dissertation relies on linguistic knowledge, but avoids large-scale grammar engineering. The approach needs neither a parallel corpus nor a bilingual lexicon, and requires much less linguistic labor than the standard technology. This dissertation describes experiments with Russian, Czech, Polish, Spanish, Portuguese, and Catalan. However, the general method proposed can be applied to any fusional language.)