Shallow embankment slopes are commonly used to support elements of transport infrastructure in seismic regions. In this thesis, the seismic performance of such slopes in non-liquefiable granular soils has been investigated and an extensive programme of centrifuge testing was conducted to quantify the improvements to seismic slope performance which can be achieved by installing a row of discretely spaced vertical precast concrete piles. This study focussed on permanent movement and dynamic response at different positions within the slope, especially at the crest, which would form key inputs into the aseismic design of supported infrastructure. In contrast to previous studies, the evolution of this behaviour under multiple sequential strong ground motions is studied through dynamic centrifuge modelling, analytical (sliding-block) and numerical (Finite Element) models. This thesis makes three major contributions. Firstly, an improved sliding-block (‘Newmark’) approach is developed for estimating permanent deformations of unreinforced slopes during preliminary design phases, in which the formulation of the yield acceleration is fully strain-dependent, incorporating the effects of both material hardening/softening and geometric hardening (re-grading). This is supported by the development of numerical (Finite Element) models which can additionally predict the settlement profile at the crest of the slope and also the dynamic ground motions at this point, for detailed seismic design were also developed. It is shown that these new models considerably outperform existing state-of-the art models which do not incorporate the geometric changes for the case of an earthquake on a virgin slope. It is further shown that only the improved models can correctly capture the behaviour under further earthquakes (e.g. strong aftershocks) and therefore can be used to determine the whole-life performance of a slope under a suite of representative ground motions that the slope may see during its design life, and allow improved estimates of the seismic performance of slopes beyond their design life. The finite element models can accurately replicate the settlement profile at the crest (important for highway or rail infrastructure) and quantify the dynamic motions which would be input to supported structures, though these were generally over-predicted. Secondly, the principles of physical modelling have been used to produce realistically damageable model piles using a new model reinforced concrete (both a designed section specifically detailed to carry the bending moments induced by the slipping soil mass and a nominally reinforced section with low moment capacity). This was used to investigate how piles can stabilise slopes under earthquake events and how the permanent deformation and the dynamic response of stabilised slope are strongly influenced by the pile spacing (S/B) especially at the minimum pile spacing (i.e. S/B=3.5). This is consistent with previous suggestions made for the optimal S/B ratio for encouraging soil arching between piles at maximum spacing both under monotonic conditions, and for numerical investigations of the seismic problem. These were supported by further centrifuge tests on conventional ‘elastic’ piles which were instrumented to measure seismic soil-pile interaction. The importance of reinforcement detailing was also highlighted, with the nominally reinforced section yielding early in the earthquake; the damaged piles subsequently only offer a small (though measureable) reduction in seismic slope performance compared to the unreinforced case. It was demonstrated that both permanent deformations at the slope crest (e.g. settlement) and dynamic ground motions at the crest can be significantly reduced as pile spacing reduced. Finally, a coupled P-y and elastic continuum approach for modelling soil-pile interaction has been used to develop a Newmark procedure applicable for pile-reinforced slopes. It was observed that the single pile resistance is mobilising at beginning of the earthquake’s time and it is strongly influenced by pile stiffness properties, pile spacing and the depth of the slip surface. It was observed also that the depth of the slip surface and pile spacing (S/B) play an important role in the determination of the permanent deformation of the slope. The results show great agreement to centrifuge test data in term of the permanent deformation (settlement at the crest of the slope) with slight differences between the measured (centrifuge) and calculated (this procedure) maximum bending moments.

The Leishmania spp. are kinetoplastid protozoan parasites that cause a spectrum of highly prevalent and neglected tropical diseases known as leishmaniasis. The parasites must undergo two life forms during their life cycle: the extracellular promastigote life stage within the sand fly vector, and the intracellular amastigote life stage after internalization of host phagocytic cells. In the extracellular life stage, Leishmania promastigotes reside and develop to their infectious metacyclic form solely in the gut lumen of the sand fly, a process known as metacyclogenesis. During this process, other organisms that co-inhabit the sand fly gut, collectively known as the microbiome, influence parasite development. Based on the hypothesis that vector gut microbiota influence the development of parasite virulence, we sequenced midgut microbiomes of the sand fly Lutzomyia longipalpis with or without L. infantum infection. Sucrose fed sand flies contained a highly diverse, stable midgut microbiome. Blood feeding caused a decrease in bacterial richness, which eventually recovered. However, bacterial richness progressively decreased in L. infantum-infected sand flies. Furthermore, parasites altered the relative abundance of several bacterial phylogenies, including Pseudomonas and Serratia. Importantly, antibiotic-mediated perturbation of the midgut microbiome rendered sand flies unable to support parasite growth and consequent development to infectious metacyclic forms, and revealing the level of microbial diversity may induce flies resistant to infection. Together, these data suggest the sand fly midgut microbiome is a critical factor for Leishmania growth and differentiation prior to disease transmission. During the intracellular amastigote life form, macrophages are the primary cell type to phagocytize parasites. The effect of secreted factors such as exosomes from Leishmania-infected human cells and their effect on the immune response has not been extensively investigated. In this thesis, we characterized the proteome of primary human donor monocyte-derived macrophage (MDM) exosomes during L. infantum infection compared to donor-matched uninfected controls, and determined their impact on naïve MDMs measured by cytokine gene expression and resistance to subsequent parasite infection. Proteomic comparisons of infected and uninfected MDM exosomes were made using stable isotopic dimethyl labeling LC-MS/MS technology. A total of 484 human proteins were identified between four donors. Proteins significantly less abundant in exosomes derived from infected MDMs were matrix metalloprotease 9, galectin-3 binding protein, and several Annexins and histone proteins. Proteins more abundant included galectin-1, galectin-9, and serotransferrin and transferrin receptor 1. Interestingly, class I and class II MHC protein chains were differentially abundant in our samples. Furthermore, we observed several Leishmania spp. proteins in exosomes from infected MDMs as well. Naïve MDMs pretreated with exosomes from infected or uninfected MDM for 4 hours were not more resistant to L. infantum infection nor displayed increased gene expression of the pro-inflammatory cytokines IL-1α, IL-1β, IL-6, IL-8 or TNF-α. To date, the work presented in this thesis is the first to comprehensively identify the proteome in primary human MDM exosomes during Leishmania spp. infection, and to determine the impact of these exosomes on the immune response of other naïve human MDMs.

The translocation of organisms is becoming a frequently used tool in conservation biology. There are, however, a disproportionate number of unsuccessful attempts translocating populations of herpetofauna. Logistical and temporal limits of monitoring, combined with ambiguous metrics concerning "success," have led to few advances regarding reptile translocations. Successfully established and persistent populations are those in which both the founding population and subsequent generations show consistent or positive levels of survival and reproduction. A small population of the threatened Florida Sand Skink (Plestiodon reynoldsi) was translocated in 2007. Data collected from 2007 to 2009 confirmed survival and reproduction among the founding individuals, but the sampling did not include a long enough period to allow for the evaluation of the survival and reproduction of individuals born on the site. In this study, individuals were collected during two separate sampling events, one during the third spring and one during the sixth spring after the translocation occurred. Survival estimates, reproduction, population size and generation structure were calculated by combining and analyzing data from all years post-translocation. The numbers of both total and new individuals captured in the sixth year exceeded captures from every prior sampling event since monitoring began in 2008. Founding individuals represented only 14% of the total individuals captured, while the number of individuals born on site continued to increase. The proportion of recruits and increased number of hatchlings despite the loss of founders shows that the filial generations are producing offspring. The methods utilized in assessing this translocation effort will further the understanding of the population dynamics of the Florida Sand Skink and allow for more informed decisions in future management studies of this threatened species.

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Doctor of Philosophy / Suction caissons have been used in the offshore industry in the last two decades as both temporary mooring anchorages and permanent foundation systems. Although there have been more than 500 suction caissons installed in various locations around the world,understanding of this concept is still limited. This thesis investigates the installation aspect of suction caissons, focusing on the installation in dense sand and layered soils, where sand is inter-bedded by silt and weakly cemented layers. The research was mainly experimental, at both normal gravity and elevated acceleration levels in a geotechnical centrifuge, with some numerical simulations to complement the experimental observations. This study firstly explored the suction caisson installation response in the laboratory at 1g. The influence and effect of different design parameters, which include caisson size and wall thickness, and operational parameters including pumping rate and the use of surcharge were investigated in dense silica sand. The sand heave inside the caisson formed during these installations was also recorded and compared between tests. The 1g study also investigated the possibility of installing suction caissons in layered sand-silt soil, where caissons were installed by both slow and rapid pumping. The heave formation in this case is also discussed. The mechanism of heave formation in dense sand and deformation of the silt layer was further investigated using a half-caisson model and the particle image velocimetry (PIV) technique. The installation response at prototype soil stress conditions was then investigated in a geotechnical centrifuge. The effects of caisson size, wall thickness, as well as surcharge were investigated in various types of sand, including silica sand, calcareous sand dredged from the North Rankin site in the North West Shelf (Australia), and mixed soil where silica sand was mixed with different contents of silica flour. Comparison with the 1g results was also made. The general trend for the suction pressure during installation in homogenous sand was identified. The installation in layered soil was also investigated in the centrifuge. The installation tests were performed in various sand-silt profiles, where the silt layers were on the surface and embedded within the sand. Comparison with the results in homogenous sand was made to explore the influence of the silt layer. Installations in calcareous sand with cemented layers were also conducted. The penetration mechanism through the cemented layer is discussed, and also compared with the penetration mechanism through the silt layer. Finite element modelling was performed to simulate key installation behaviour. In particular, it was applied to simulate the sand deformation observed in the PIV tests. The likely loosening range of the internal sand plug during suction installation in silica sand was estimated. By investigating the development of hydraulic gradient along the inner wall, the principle underlying the suction response for different combinations of selfweight and wall thickness was identified. FE modelling was also performed to explore the influence of the hydraulic blockage by the silt layer. This study found that the caissons could penetrate into all soils by suction installation. Among the key findings are the observations that the suction pressure increases with depth following a distinct pressure slope, corresponding to a critical hydraulic condition along the inner wall; and the installation was possible in both layered sand-silt and uncemented-cemented soils if sufficient pumping was available. While the caisson could penetrate the weakly cemented layers well with no notable adverse effects, problems were observed in the installation in layered sand-silt soil. These include piping failure in slow pumping rate installation at 1g, and the formation of extremely unstable soil heave during installation.

This thesis explores the design of flexible pipes, buried in shallow trenches with dry sand backfill. The thesis reports the comprehensive analysis of twenty-two full-scale load tests conducted between 1989 and 1991 on pipe installations, mainly within a laboratory facility, at the University of South Australia. The pipes were highly flexible, spirally-wound, uPVC pipes, ranging in diameter from 300 to 450 mm. Guidelines were required by industry for safe cover heights for these pipes when subjected to construction traffic. The tests were designed by, and conducted under the supervision of, the author, prior to the author undertaking this thesis. As current design approaches for pipes could not anticipate the large loading settlements and hence, soil plasticity, experienced in these tests, finite element analyses were attempted. Extensive investigations of the materials in the installations were undertaken to permit finite element modelling of the buried pipe installations. In particular, a series of large strain triaxial tests were conducted on the sand backfill in the buried pipe installations, to provide an understanding of the sand behaviour in terms of critical state theory. Subsequently a constitutive model for the soil was developed. The soil model was validated before implementation in an element of finite element program, AFENA (Carter and Balaam, 1995). Single element modelling of the triaxial tests proved invaluable in obtaining material constants for the soil model. The new element was applied successfully to the analysis of a side-constrained, plate loading test on the sand. The simulation of the buried pipe tests was shown to require three-dimensional finite element analysis to approach the observed pipe-soil behaviour. Non-compliant side boundary conditions were ultimately adjudged chiefly responsible for the difficulty in matching the experimental data. The value of numerical analyses performed in tandem with physical testing was apparent, albeit in hindsight. The research has identified the prediction of vertical soil pressure above the pipe due to external loading as being the major difficulty for designers. Based on the finite element analyses of the field tests, a preliminary simple expression was developed for estimation of these pressures, which could be used with currently available design approaches to reasonably predict pipe deflections.

No description available.

<p>Leishmaniasis is a disease affecting more than 12 million people worldwide. It is caused by the protozoan parasite Leishmania, which is transmitted to humans and dog hosts through bites of infected sand flies belonging to genus Phlebotomine. Several studies have shown Polymerase Chain Reaction (PCR) to be effective for the diagnosis of VL in clinical samples compared to the classical methods. The aims of this study were first to compare four different sample preparation methods for the PCR diagnosis of visceral leishmaniasis (VL) using peripheral blood samples and furthermore to find a method that is sensitive, rapid, cost benefit, simple and easy to perform. Two preparation methods were compared for the isolation of leukocytes (with Ficoll and Tris –EDTA buffer) and two DNA isolation methods (with Proteinase K and QIAgen kit). From the methods that were compared, lysis of erythrocytes with TE and the QIAgen kit seems to be the most suitable to use.</p>

Microtextures recorded on quartz sand grain surfaces provide evidence of past environment. Environmental processes, such as transport by glacial ice, create unique microtextures on sand grain surfaces that can be observed under high magnification with a scanning electron microscope. These microtextures and their proportions tend to be unique to environment type, allowing investigators to infer the environmental conditions to which sediments have been exposed, for example to distinguish sediments from fluvial versus mass-wasted environments. Microtextural evidence also allows inferences about the history of sediments of unknown origin. This thesis determines the qualitative and quantitative microtextural fingerprint of glacigenic quartz sand grains deposited by small tropical alpine glaciers in Costa Rica, and compares that fingerprint to the fingerprints of highland Dominican Republic sediments of uncertain genesis, to gauge whether those, individually or grouped, resemble the Costa Rican glacigenic samples. I selected 18 samples (9 each from Costa Rica and the Dominican Republic) and analyzed a minimum of 100 quartz sand grains per sample using a scanning electron microscope. My sample sizes were dictated by the scale of empirical 99% confidence intervals that would allow meaningful comparison of samples. Analysis using literature-recommended numbers of quartz sand grains would entail such large confidence intervals that practically any results would have been indistinguishable. I recorded the presence or absence of 25 microtextures on each grain, and calculated the percentage of each microtexture’s occurrence in the sample. The percentages constituted the sample’s microtextural fingerprint. As a whole, the Costa Rican fingerprints were very similar to each other, and so were the Dominican Republic fingerprints. Further comparison led me to conclude that the Dominican Republic samples are statistically indistinguishable from the Costa Rican glacierized samples. This thesis is part of a larger project establishing protocols for distinguishing glacigenic from non-glacigenic sediments, and testing for glacigenicity of sediments in Costa Rica, the Dominican Republic, and elsewhere. My results can be applied in other studies distinguishing tropical highland glacigenic and non-glacial samples. My contribution will hopefully contribute toward completion of the project’s goals, specifically determining the presence or absence of past glaciers in the Dominican Republic.

Thesis (Ph. D.)--Flinders University, 2006. / Title from PDF t.p. (viewed on Mar. 11, 2007). Includes bibliographical references.