Earthquake-induced landslides are a significant seismic hazard that can generate large economic losses. Predicting earthquake-induced landslides often involves an assessment of the expected sliding displacement induced by the ground shaking. A deterministic approach is commonly used for this purpose. This approach predicts sliding displacements using the expected ground shaking and the best-estimate slope properties (i.e., soil shear strengths, ground water conditions and thicknesses of sliding blocks), and does not consider the aleatory variability in predictions of ground shaking or sliding displacements or the epistemic uncertainties in the slope properties. In this dissertation, a probabilistic framework for predicting the sliding displacement of flexible sliding masses during earthquakes is developed. This framework computes a displacement hazard curve using: (1) a ground motion hazard curve from a probabilistic seismic hazard analysis, (2) a model for predicting the dynamic response of the sliding mass, (3) a model for predicting the sliding response of the sliding mass, and (4) a logic tree that incorporates the uncertainties in the various input parameters. The developed probabilistic framework for flexible sliding masses is applied to a slope at a site in California. The results of this analysis show that the displacements predicted by the probabilistic approach are larger than the deterministic approach due to the influence of the uncertainties in the slope properties. Reducing these uncertainties can reduce the predicted displacements. Regional maps of seismic landslide potential are used in land-use planning and to identify zones that require detailed, site-specific studies. Current seismic landslide hazard mapping efforts typically utilize deterministic approaches to estimate rigid sliding block displacements and identify potential slope failures. A probabilistic framework that uses displacement hazard curves and logic-tree analysis is developed for regional seismic landslide mapping efforts. A computationally efficient approach is developed that allows the logic-tree approach to be applied for regional analysis. Anchorage, Alaska is used as a study area to apply the developed approach. With aleatory variability and epistemic uncertainties considered, the probabilistic map shows that the area of high/very high hazard of seismic landslides increases by a factor of 3 compared with a deterministic map. / text

Many different approaches exist for engineering bacterial genomes. The most common current methods include transposons for random mutagenesis, recombineering for specific modifications in Escherichia coli, and targetrons for targeted knock-outs. Site-specific recombinases, which can catalyze a variety of large modifications at high efficiency, have been relatively underutilized in bacteria. Employing these technologies in combination could significantly expand and empower the toolkit available for modifying bacteria. Targetrons can be adapted to carry functional genetic elements to defined genomic loci. For instance, we re-engineered targetrons to deliver lox sites, the recognition target of the site-specific recombinase, Cre. We used this system on the E. coli genome to delete over 100 kilobases, invert over 1 megabase, insert a 12-kilobase polyketide-synthase operon, and translocate a 100 kilobase section to another site over 1 megabase away. We further used it to delete a 15-kilobase pathogenicity island from Staphylococcus aureus, catalyze an inversion of over 1 megabase in Bacillus subtilis, and simultaneously deliver nine lox sites to the genome of Shewanella oneidensis. This represents a powerful, versatile, and broad-host-range solution for bacterial genome engineering. We also placed lox sites on mariner transposons, which we leveraged to create libraries of millions of strains harboring rearranged genomes. The resulting data represents the most thorough search of the space of potential genomic rearrangements to date. While simple insertions were often most adaptive, the most successful modification found was an inversion that significantly improved fitness in minimal media. This approach could be pushed further to examine swapping or cutting and pasting regions of the genome, as well. As potential applications, we present work towards implementing and optimizing extracellular electron transfer in E. coli, as well as mathematical models of bacteria engineered to adhere to the principles of the economic concept of comparative advantage, which indicate that the approach is feasible, and furthermore indicate that economic cooperation is favored under more adverse conditions. Extracellular electron transfer has applications in bioenergy and biomechanical interfaces, while synthetic microbial economics has applications in designing consortia-based industrial bioprocesses. The genomic engineering methods presented above could be used to implement and optimize these systems. / text

Nonlinear site response analyses are generally preferred over equivalent linear analyses for soft soil sites subjected to high-intensity input ground motions. However, both nonlinear and equivalent linear analyses often result in large induced shear strains (3-10%) at soft sites, and these large strains may generate unusual characteristics in the predicted surface ground motions. One source of the overestimated shear strains may be attributed to unrealistically low shear strengths implied by commonly used modulus reduction curves. Therefore, modulus reduction and damping curves can be modified at shear strains greater than 0.1% to provide a more realistic soil model for site response. However, even after these modifications, nonlinear and equivalent linear site response analyses still may generate unusual surface acceleration time histories and Fourier amplitude spectra at soft soil sites when subjected to high-intensity input ground motions. As part of this work, equivalent linear and nonlinear 1D site response analyses for the well-known Treasure Island site demonstrate the challenges associated with accurately modeling large shear strains, and subsequent surface response, at soft soil sites. Accounting for the uncertainties associated with the shear wave velocity profile is an important part of a properly executed site response analyses. Surface wave data from Grenoble, France and Mirandola, Italy have been used to determine shear wave velocity (Vs) profiles from inversion of surface wave data. Furthermore, Vs profiles from inversion have been used to determine boundary, median and statistically-based randomly generated profiles. The theoretical dispersion curves from the inversion analyses as well as the boundary, median and randomly generated Vs profiles are compared with experimentally measured surface wave data. It is found that the median theoretical dispersion curve provides a satisfactory fit to the experimental data, but the boundary type theoretical dispersion curves do not. Randomly generated profiles result in some theoretical dispersion curves that fit the experimental data, and many that do not. Site response analyses revealed that the greater variability in the response spectra and amplification factors were determined from the randomly generated Vs profiles than the inversion or boundary Vs profiles.

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The spatial arrangements of artifacts and features within archaeological sites have often been used to isolate activity areas and draw inferences about site function. This approach assumes that objects found in close proximity were used for the same task, and that artifacts are usually discarded where they were used. However, the location of artifact abandonment often has more to do with patterns of discard and use/reuse of the site throughout time than with the function or location of activities. This dissertation uses a comparative framework to address how the observed spatial structure of Middle Paleolithic sites in France sites was formed through centrifugal dispersion of lithic artifacts, i.e. the displacement of artifacts between their creation and the final location of their abandonments. Seven Middle Paleolithic sites were included in this study. The sites were excavated over large areas, from 200 to more than 2000 m². They range from small single component occupation sites to lithic raw material workshops with assemblages of more than 15,000 artifacts. The movement of artifacts is tracked through an analysis of sets of refitted lithics and through comparisons of the distributions of multiple classes of artifact across areas of the sites with differing artifact densities. Studying the distribution of lithic technological classes and tracking their movement through refitting sets provides new perspectives on the ways Paleolithic archaeological assemblages and sites were formed. The temporality of site use had a much greater impact on site structure than did activities that took place at any one point during a site's occupation. These data enabled me to assess the relative lengths and numbers of occupations for the seven sites in this study. The approach taken in this study not only provides a clearer understanding of site formation and structure than do studies that strive to isolate "activity areas," but it also provides information about the sizes of past human groups and the ways they moved among different localities on the landscape. Such insights are integral to the study of land use, mobility and economic adaptations among Paleolithic hunter-gatherers.

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The Greater than Class C (GTCC) Environmental Impact Statement (EIS) evaluated the potential impacts from the construction and operation of a new facility or facilities, or use of an existing facility, employing various disposal methods (geologic repository, intermediate depth borehole, enhanced near surface trench, and above grade vault) at six federal sites and generic commercial locations. For three of the locations being considered as possible locations, consulting tribes were brought in to comment on their perceptions on how GTCC low level radioactive waste would affect Native American resources (land, water, air, plants, animals, archaeology, etc.) short and long term. The consulting tribes produced essays that were incorporated into the EIS and these essays are in turn included in this collection. This essay was produced by the Wanapum Tribe for the Hanford Site.

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Effective conservation requires efficient population monitoring, which can be challenging for rare species like the desert tortoise (Gopherus agassizii). We compared two alternative survey methods that can be used to monitor tortoise populations: distance sampling and site occupancy estimation. In 2005 and 2006 combined, we surveyed 120 1-km transects to estimate density and 40 3-ha plots with five presence-“absence” surveys to estimate occupancy of Sonoran desert tortoises in two mountain ranges in southern Arizona. We found that monitoring programs based on an occupancy framework were more efficient and had greater power to detect linear trends. We also found that habitat use by Sonoran desert tortoises was influenced most by slope and aspect, contrasting with patterns observed in the Mojave Desert. Given its efficiency, power, and ability to gauge changes in distribution while accounting for variation in detectability, occupancy offers a promising alternative for long-term monitoring of Sonoran desert tortoise populations.