Thesis (M.S.) in Quaternary and Climate Studies--University of Maine, 2001. / Includes vita. Includes bibliographical references (leaves 159-171).

Thesis (B.S.)--University of Wisconsin -- La Crosse, 2009. / Also available online. Includes bibliographical references (leaves 31-33).

Chlorate and perchlorate pollutions have become a problem in the environment in the last decades. Studies have shown that some bacteria can degrade these substances into unharmful substances such as chloride and molecular oxygen. One of these chlorate degrading bacteria is Ideonella dechloratans that uses chlorate reductase and chlorite dismutase to process chlorate. In the promoter gene sequence of chlorite dismutase there might be regulator sequences such as fumarate and nitrate reductase regulator (FNR) and aerobic respiration control protein (ArcA) that might control the transcription of this enzyme. This promoter sequence was placed in a pBBR1MCS-4-LacZ reporter vector and the possible regulatory sequences were changed through site-directed mutagenesis and tested on activity through beta-galactosidase assays. The changes in the FNR binding sequence gave beta-galactosidase activity that was close to a negative control which might give conclusions that either FNR has an important role or an important part of the promoter was hit. The changes in the ArcA regulator binding sequence did not give such big differences and no certainty can be given if this made important changes to the promoter.

This research examines and compares the distributions of archaeological sites and materials in order to investigate native settlement patterns and resources use throughout 12,000 years of prehistory and protohistoric time within the Apalachicola/Lower Chattahoochee River valley of northwest Florida, southwest Georgia, and southeast Alabama. Geographic Information Systems (GIS) are used to map the distributions of sites from different time periods and to explore their relation to various environmental characteristics that are now available in digital format. I employ tools now available in GIS to examine several longstanding research questions and expand upon archaeological interpretations within this region, where the University of South Florida (USF) has an ongoing research program. The results of this work illustrate change through time and space as cultures begin to adapt to post-Pleistocene ecological change, develop food production and complex societies, and react to the appearance of European groups.

Facebook is the dominant SNS for American students in the United States, and Renren.com is heavily used by Chinese students in China. Chinese international students in the United States are likely to use both the host and home SNSs to keep in touch with their friends in the host and home countries. The purpose of the study is to explore the similarities and differences between host and home SNS use among Chinese international students in the U.S. This study compares their use of Facebook and Renren.com with respect to intensity and patterns of use. It explores how these student sojourners in the U.S. use the two SNSs to build up and maintain their social networks and social capital and how their levels of acculturation to American host culture and maintenance of Chinese home culture are associated with their SNS use. Quantitative data collected through a survey of 212 Chinese international students at the University of Texas at Austin was analyzed to address these research questions. The findings suggest that Chinese international students use Renren.com more intensively than Facebook and prefer Renren.com to Facebook for the purposes of communication and information seeking. They are more likely to use Renren.com than Facebook to interact with Chinese friends whether in the U.S., in China, or in other parts of the world. The intensity of Facebook and Renren.com use were found to be positively associated with bridging social capital, but neither of the two is associated with bonding social capital. Only the intensity of Renren.com use was found to have a positive relationship with maintained social capital. Furthermore, the levels of acculturation to host culture are associated with the intensity of Facebook use, while the levels of maintenance to home culture are associated with the intensity of Renren.com use. / text

Altering the substrate specificity of proteases is a powerful process with possible applications in many areas of therapeutics as well as proteomics. Although the field is still developing, several proteases have been successfully engineered to recognize novel substrates. Previously in our laboratory, eight highly active OmpT variants were engineered with novel catalytic sites. The present study examined the roles of several residues surrounding the active site of OmpT while attempting to use rational design to modulate fine specificity enough to create a novel protease that prefers phosphotyrosine containing substrates relative to sulfotyrosine or unmodified tyrosine residues. In particular, a previously engineered sulfotyrosine-specific OmpT variant (Varadarajan et al., 2008) was the starting point for rationally designing fifteen new OmpT variants in an attempt to create a highly active protease that would selectively cleave phosphotyrosine substrates. Our design approach was to mimic the most selective phosphoryl-specific enzymes and binding proteins by increasing positive charge around the active site. Sulfonyl esters have a net overall charge of -1 near neutral pH, while phosphate monoesters have a net overall charge of -2. Selected active site residues were mutated by site-directed mutagenesis to lysine, arginine, and histidine. The catalytic activities and substrate specificities of each variant were characterized. Although several variants displayed altered substrate specificity, none preferred phosphotyrosine over sulfotyrosine containing peptides. Taken together, our results have underscored the subtle nature of protease substrate specificity and how elusive it can be to engineer fine specificity. Apparently, phosphotyrosine specific variants were not possible within the context of our starting sulfotyrosine specific OmpT derivative mutated to have single amino acid changes chosen on the basis of differential charge interactions. / text

This dissertation details work aimed at better understanding topographic effects in earthquake ground motions. The experiment, conducted in Central-Eastern Utah, used frequent and predictable seismicity produced by underground longwall coal mining as a source of low-intensity ground motions. Locally-dense arrays of seismometers deployed over various topographic features were used to passively monitor seismic energy produced by mining-induced implosions and/or stress redistribution in the subsurface. The research consisted of two separate studies: an initial feasibility experiment (Phase I) followed by a larger-scale main study (Phase II). Over 50 distinct, small-magnitude (M[subscript 'L'] < 1.6) seismic events were identified in each phase. These events were analyzed for topographic effects in the time domain using the Peak Ground Velocity (PGV), and in the frequency domain using the Standard Spectral Ratio (SSR) method, the Median Reference Method (MRM), and the Horizontal-to-Vertical Spectral Ratio (HVSR) method. The polarities of the horizontal ground motions were also visualized using directional analyses. The various analysis methods were compared to assess their ability to estimate amplification factors and determine the topographic frequencies of interest for each feature instrumented. The MRM was found to provide the most consistent, and presumably accurate, estimates of the amplification factor and frequency range for topographic effects. Results from this study clearly indicated that topographic amplification of ground motions does in fact occur. These amplifications were very frequency dependent, and the frequency range was correctly estimated in many, but not all, cases using simplified, analytical methods based on the geotechnical and geometrical properties of the topography. Amplifications in this study were found to generally range from 2 to 3 times a reference/baseline site condition, with some complex 3D features experiencing amplifications as high as 10. Maximum amplifications occurred near the crest of topographic features with slope angles greater than approximately 15 degrees, and the amplifications were generally oriented in the direction of steepest topographic relief, with some dependency on wave propagation direction. / text

Mercury -contaminated sediments often act as a sink of mercury and produce methyl-mercury, an acute neurotoxin which readily bio accumulates, due to the presence of bacterial communities hosted by the sediment. One common remediation approach to manage methyl-mercury is to amend the sediment by capping or directly mixing with a sorbent. This thesis aims to assess the capabilities of some calcium-based sorbent to act in that capacity. Laboratory experiments were implemented to simulate mercury fate and behavior in geochemical conditions that capping would likely create. Well-mixed slurries showed that gypsum materials were disparate and their behavior was similar from sand to organocaly. Mercury sorption capacities of these gypsums were poor with a sorption coefficient approximately equal to 300 L/kg. Reduction of methylmercury was minimal and even increased in two of the three materials. Therefore, the three gypsums, which tend to be more cohesive when wetted, doesn’t constitute a viable material for sediment capping. / text

On Site Inspection is the final measure for verifying compliance of Member States with the Comprehensive Nuclear-Test-Ban Treaty. In order to enable the use of ³⁷Ar as a radiotracer for On Site Inspection, the sources of radioargon background must be characterized and quantified. A radiation transport model of the University of Texas at Austin Nuclear Engineering Teaching Laboratory (NETL) TRIGA reactor was developed to simulate the neutron flux in various regions of the reactor. An activation and depletion code was written to calculate production of ³⁷Ar in the facility based on the results of the radiation transport model. Results showed ³⁷Ar production rates of (6.567±0.31)×10² Bq·kWh⁻¹ in the re- actor pool and the air-filled irradiation facilities, and (5.811±0.40)×10⁴ Bq·kWh⁻¹ in the biological shield. Although ⁴⁰Ca activation in the biological shield was found to dominate the total radioargon inventory, the contribution to the effluent release rate would be diminished by the immobility of Ar generated in the concrete matrix and the long diffusion path of mobile radioargon. Diffusion of radioargon out of the reactor pool was found to limit the release rate but would not significantly affect the integrated release activity. The integrated ³⁷Ar release for an 8 hour operation at 950 kW was calculated to be (1.05±0.8)×10⁷ Bq, with pool emissions continuing for days and biological shield emissions continuing for tens of days following the operation. Sensitivity analyses showed that estimates for the time-dependent concentrations of ³⁷Ar in the NETL TRIGA could be made with the calculated buildup coefficients or through analytical solution of the activation equations for only (n,[gamma]) reactions in stable argon or (n,[alpha]) reactions in ⁴⁰Ca. Analyses also indicated that, for a generalized system, the integrated thermal flux can be used to calculate the buildup due to air activation and the integrated fast flux can be used to calculate the buildup due to calcium activation. Based on the results of the NETL TRIGA, an estimate of the global research reactor source term for ³⁷Ar and an estimate of ground-level ³⁷Ar concentrations near a facility were produced. / text

Numerical modeling techniques commonly used to compute the response of soil and rock media under earthquake shaking are evaluated by analyzing the observations provided by instrumented borehole arrays. The NIED Kik-Net database in Japan is selected as the main source of borehole array data for this study. The stiffness of the site and the availability of high intensity motions are the primary factors considered towards the selection of appropriate Kik-Net borehole arrays for investigation. Overall, 13 instrumented vertical arrays are investigated using over 750 recorded ground motions characterized by low (less than 0.05 g) to high (greater than 0.3 g) recorded peak ground accelerations at the downhole sensor. Based on data from the selected borehole arrays, site response predictions using 1-D linear elastic (LE) analysis, equivalent linear (EQL) analysis, equivalent linear analysis with frequency-dependent soil properties (EQL-FD), and fully nonlinear analysis (NL) are compared with the borehole observations. Initially, the low intensity motions are used to evaluate common assumptions regarding 1-D site response analysis. First, we identify the borehole wavefield best simulating the actual boundary condition at depth by comparing the theoretical linear-elastic (LE) and observed responses. Then, we identify the best-fit small-strain damping profiles that can incorporate the additional in-situ attenuation mechanisms. Finally, we assess the validity of the one-dimensional modeling assumption. Our analyses indicate that the appropriate boundary condition for analysis of a borehole array depends on the depth of the borehole sensor and that, for most of the considered vertical arrays, the one-dimensional assumption reasonably simulates the actual wave propagation pattern. In the second part of this study, we evaluate the accuracy of the EQL, EQL-FD and NL site response methods by quantifying the misfit (i.e., residual) between the simulations and observations at different levels of shaking. The evaluation of the performance of the theoretical models is made both on a site-by-site basis and in an aggregated manner. Thereafter, the variability in the predicted response from the three site response methods is assessed. Comparisons with the observed responses indicate that the misfit of simulations can be significant at short periods and large strains. Moreover, all models seem to be characterized by the same level of variability irrespectively of the level of shaking. Finally, several procedures that can be used to improve the accuracy of the one-dimensional EQL, EQL-FD and NL site response analyses, are investigated. First, an attempt to take into account the shear strength of the soil materials at large shear strains is made. Additionally, several modifications to the EQL-FD approach are proposed. The proposed modifications are evaluated against recordings from the borehole arrays. Our analyses indicate that the accuracy of the theoretical models can be, partly, increased by incorporating the proposed modifications. / text