Open Access Theses
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Item type: Item , Access status: Open Access , Structural Analysis and Exhalite Studies in the Peelwood - Cordillera Area, NSWSlater, Raymond M.Field mapping in the Peelwood-Cordillera area reveals the complex spatial relationships exhibited by widely variable lithofacies, which reflect cyclical periods of deposition associated with an unstable, submarine volcanic environment. Rapid lateral and vertical facies changes, and the lack of useful marker horizons preclude the definition of major structural features, although it is probable that the area responded to deformation in a similar fashion to adjoining areas. Widely developed kink folding is interpreted as the result of a later phase of deformation, and is developed on all scal.es. The waning stages of active volcanic cycles are marked locally by the formation of sub-economic deposits of stratabound, pyritic base metal mineralization. Massive sulphides are general.ly enclosed by, and partial.ly laterally equivalent to, high silica cherty rocks believed also to be the result of volcanic exhalations. Geochemical analyses of the cherts show low and irregular abundances of all elements except silica, and the correlations they displayed indicate that most elements were probably supplied to these rocks from a detrital fraction. Petrographic evidence suggests at least partial derivation by silicification of pre-existing volcanic or volcaniclastic rocks, and the occurrence of radiolarian remains further supports a composite origin for these rocks, involving volcanic and elastic components in addition to chemical preci pitation.Item type: Item , Access status: Open Access , On the Nature and Normativity of Imagination(2018) Barner, Alma KarinAs a child, I often imagined that I was a space astronaut. Today I imagined what I could have for lunch and what I could wear for a concert. Pilots imagine performing water landings in an emergency. We might imagine full grown trees, while planting tree seeds. We use imagination to plan daily activities, prepare for important events, evaluate past choices and actions, predict other people’s mental states, and many more cognitive tasks. We imagine trees, while planting tree seeds, because we want to plant in a way that will leave enough space between the trees. We imagine what we could wear for a concert on our way home from work so that we know whether to do laundry first. The topic of this dissertation is the nature and normativity of imagination. While imagination plays a plethora of cognitive roles in reasoning, its nature and function is not very well understood. Moreover, it has received far less systematic attention from philosophers of mind than other mental states, such as beliefs, desires or perceptions. The dissertation aims to diminish this research gap. It has two parts, each of which contain two chapters. Part I focuses on the normativity of imagination, while Part II concerns the contents and phenomenology of imagination. It is a popular assumption in philosophy that imagination puts us in touch with the possible. The epistemic thesis that imagination is a guide to possibility has received a fair amount of attention in recent years. The normative thesis that imagination aims at the possible, like belief aims at truth, has only been discussed in passing. In Chapter 1 I give in-depth arguments against the normative thesis. Yet imaginings can only play cognitive roles, if they are normatively constrained in some way. In chapter 2 I present my own account of the normativity of imagination. On this view, imagination is not subject to intrinsic attitude-specific norms, but hypothetical norms, such as norms on intentions, and norms of instrumental rationality. I further argue that imagination shares semantic and normative properties with scientific models. Various prominent definitions of the nature of imagination appeal to perception. In Chapter 3 I critically evaluate the appeal to perception in defining the nature of imagination. I argue that common definitions of imagination cannot do justice to the nature of the contents and phenomenology of imagination, as the analogy to perception is taken too far. In the final chapter 4 I bring together the findings of the previous chapters and apply them to the case of imagining perceptual experiences. Here I argue that imagining perceptual experiences requires conceptual stipulations. This is designed to further illustrate and corroborate the views advanced. This dissertation highlights the uniqueness of imagination in many ways: Unlike beliefs, desires and perceptions, imagination is not subject to attitude-specific normativity (chapters 1 and 2). Imagination is akin to scientific model construction (chapter 2). Imagination is not always phenomenally similar to sense perception in important ways (chapter 3). Moreover, imagination contents involve conceptual stipulations, which further distinguishes them from perceptual states (chapters 3 and 4).Item type: Item , Access status: Open Access , Evolution of dosage compensation and x chromosome inactivation in therian mammals(2015-03) Rodriguez Delgado, Claudia,The sex chromosomes in therian mammals (eutherian mammals and marsupials) evolved from an identical autosomal pair. One of the two chromosomes in the original pair degraded in males due to suppression of recombination, resulting in monosomy of the X chromosome in males. It has been accepted for years that the differences in gene dosage that resulted from monosomy of the X chromosome in males were restored in a two-step way, firstly by upregulating the single X chromosome in males, then by transcriptionally silencing one X chromosome in females, in a process known as X chromosome inactivation (XCI). Though XCI has been extensively studied at the mechanistic and evolutionary level, upregulation of the X chromosome (which presumably preceded XCI) was assumed as a fact for decades, and has only been recently investigated and questioned. To gain insights into how the dosage compensation system evolved upon emergence of the sex chromosomes in therians, I tested upregulation of the X in marsupials and eutherian mammals distantly related to human and mouse. I observed that global upregulation of the X occurred in the marsupial lineage but not in the eutherian lineage. The eutherian X chromosome was augmented by the addition of an autosomal region (XAR), and I show that, similar to the marsupial X, this region has been upregulated in eutherians. Underlying differences in the XCI system between marsupials and eutherians have been previously described. I confirmed that paternally imprinted XCI is common to somatic tissues in the marsupial clade, in contrast to the conserved random XCI observed in eutherian embryonic tissues. I observed that as opposed to eutherians, escapee genes are not confined to the recent evolutionary strata on the X. A similarity with the eutherian clade is that the proportion of genes that escape XCI differs between species of the same clade; I observed that a greater proportion of genes (̃30%) escape XCI in tammar wallaby, in contrast to the 14% escape reported for opossum. I proposed a model for evolution of dosage compensation, where upregulation of the X chromosome started for a few dosage sensitive genes in the therian ancestor, and evolved into a global system in marsupials but not in eutherians. In addition, I discuss the relationship between upregulation of the X chromosome and evolution of XCI.Item type: Item , Access status: Open Access , Gamma-ray bursts : cosmological probes and their connection to supernovae(2014-08) Rapoport, SharonObserved from the nearest galaxies to the beginning of times, Gamma-ray bursts (GRBs) remain the most energetic event in the Universe known to date. As their cone of light travels through the cosmos, the imprint of everything in its path is embedded in the spectra and light curves we observe, providing us with the three dimensional map of matter. This thesis studies the statistical properties of strong MgII absorbers found along the line of sight to GRBs. Firstly, the possibility that the over abundance of these systems could be due to strong gravitational lensing bias is tested. While it is probable that the detection of GRBs and their counterparts in two independent bands ($\gamma$-rays and optical) leads to some lensing bias, it is found that it can not fully resolve the discrepancy in the statistics for these over-common absorbers. After ruling lensing as a potential explanation, a test for the statement that strong MgII are over abundant towards GRBs is conducted, finding that this observation is likely to suffer from low number statistics and can be made insignificant when considering dust obscuration towards the test sample of quasars. Beyond their capability to serve as cosmological probes, GRBs are a fascinating physical phenomenon. Focusing on long GRBs, which are believed to be associated with core-collapse supernovae (CC SNe), the following simulations are developed: evolving a pre- main sequence star using artificial mass loss recipe until before its core collapses --> parameterising the central engine with a piston driven explosion and following the hydrodynamics until the ejecta reaches homologous expansion --> solving for the post-explosion abundances using a post processing nuclear network --> using a radiative transfer (RT) code to calculate the observable properties of the SNe. Since the RT has never been previously used for CC SNe, a comparison of this code to what has been previously used for these SNe is made. The superiority of the code used in this thesis is proven by its ability to not only reproduce the main spectral features found in previous results, but to change the expectation of luminosity from the different viewing angles which could be done due to this coherent time dependent code. An observer located off the GRB axis is actually found to observe a brighter SN than the observe who detected the GRB itself. Once the proficiency of the RT code was proven, a grid of model spanning different explosion parameters and progenitor properties is created. An array of degeneracies between the model parameters is found, proving that using the Arnett relation for estimating the explosion energy and ejected progenitor mass suffers from large uncertainties."Item type: Item , Access status: Open Access , Chemoenzymatic syntheses of allocedrane and prezizaane-type sesquiterpenes(2015-01) Sharma, Mukesh KantVarious genetically modified microorganisms that over-express dioxygenase-type enzymes can be used for the whole-cell biotransformation of a wide range of arenes into the corresponding cis-1,2-dihydrocatechol (c-DHC). These metabolites, which are obtained in essentially enantiopure form, can serve as valuable starting materials in chemical synthesis. This thesis describes the application of certain c-DHCs to the synthesis of biologically active and or synthetically challenging natural products. In particular, it details the use of Type 1 intramolecular Diels-Alder (IMDA) adducts derived from c-DHCs in the synthesis of the tashironins and related compounds belonging to the allocedrane class of natural product. The tashironins possesses complex structures and display interesting biological properties including neurotropic activity. As such they are considered to be useful leads in developing new therapies for treating neurodegenerative afflictions such as Alzheimer's and Parkinson's diseases. In the process of the campaign towards tashironins, several highly oxygenated tri- and tetra-cyclic compounds were prepared. These are described in Chapter Two and Three and are expected to possess similar biological properties to the natural products. Chapter Four of the thesis describes the synthesis of members of prezizaane group of compounds that are biogenetically related to allocedranes, sesquiterpenoids that are highly prized in the flavour and fragrance industry. During the course of preparing the prezizaanes, a novel Wagner-Meerwein rearrangement of the allocedrane system was discovered that afforded a pleasantly smelling compound that is enantiomerically related to the natural product isopipitzol.Item type: Item , Access status: Open Access , Accelerating Computational Chemistry Algorithms: towards Accurate Binding Free Energies(2026) Yu, FionaAdvances in high performance computing (HPC) are pivotal for accelerating drug discovery by offering the capacity for large scale high accuracy virtual screening. There has been considerable interest in the large scale application of the Quantum Mechanical / Poisson-Boltzmann Surface Area (QM/PBSA) end point method towards predicting binding affinities of protein-ligand systems. However, its application is severely limited by the high computational costs of traditional QM methods as well as the slow performance of existing PBE solvers for PBSA calculations. This thesis presents methods and algorithms to overcome such bottlenecks. The first half of this thesis is dedicated to accelerating QM calculations. An automated accurate molecular fragmentation scheme is presented that divides large systems into smaller, computationally feasible partitions, whilst enhancing algorithmic parallelisability. Its applicability on protein and lipoglycans/glycolipids is demonstrated. On the other hand, improved initial guess methods for self-consistent field (SCF) calculations are presented (basis set projection and fragmentation) and their performance is systematically analysed against the traditional superposition of atomic density (SAD) scheme. Results consistently indicate the improved performance of SCF calculations with non-SAD schemes. To address the lack of fast PBE solvers to model solvation, a high-performance GPU-accelerated solver is presented. The algorithm exploits the sparsity pattern exposed in its application on molecular systems to accelerate matrix-vector contractions prevalent in conjugate gradient solvers, outperforming existing multi-core CPU and GPU-based PBE solvers. These tools are integrated into a QM/PBSA workflow and applied to large biologically relevant protein-ligand complexes to predict binding affinities. The influence of various factors---fragmentation level, protonation states, and solvation methods---on the performance of the proposed QM/PBSA workflow is systematically analysed and compared to other computational approaches including alchemical free energy and scoring function methods. This thesis seeks to improve upon the accuracy, computational efficiency and feasibility of large scale QM/PBSA workflows by leveraging chemical concepts and HPC optimisations. Beyond drug discovery, the methodologies presented have broad applicability to molecular molecular systems beyond proteins, supporting research in materials science, chemistry and energy applications. Such advancements become increasingly important as HPC systems continue to evolve, offering the potential to study molecular systems at even larger scales and and higher accuracy.Item type: Item , Access status: Open Access , Nonstandard estimation for the von Mises Fisher distribution(2017-07) Ghodsi, MaryamThe main focus of this thesis is to provide a theoretical analysis of certain statistical models incorporating constraints of various kinds. The models are motivated with data examples using spherical distributions fitted to asset allocation data related to financial portfolios. We fit models consisting of several von Mises Fisher distributions of di↵erent dimensions to a sample of such financial data. Our analysis of the properties of the corresponding hypothesis test statistics under this model combines Silvey’s approach towards constraints on the parameter space with Cherno↵’s innovations to find the asymptotic distributions of the likelihood ratio (deviance) statistics. Silvapulle and Sen detail situations when some constraints are imposed on either the parameter space or on the underlying distribution, where the information matrix is positive definite. But, in some examples, the expectation of the second derivative need not be a positive definite matrix. In such cases, methodology developed by Maller and others can be applied as it does not require the information matrix to be positive definite. Consequently, we apply this methodology to hypothesis tests for the equality of concentration parameters in the spherical subcomponent model. Properties of the tests are examined by simulations and a real data application is given.Item type: Item , Access status: Open Access , Walking at Weereewa(2015-11) Flemons, Lynne MareeIn Australia, over the past thirty years or so, there has been a change in the way non-Indigenous visual artists have interpreted the nation’s landscape. During this period a cultural shift has occurred, from one where the term ‘landscape’ refers to a view from a fixed point in time, as in the European landscape tradition, to a broader awareness where the landscape is interpreted in terms of its memory, history, mythology, as well as its physical features. This change in perception has its origins in a deeper understanding of the Australian landscape; one that has been promoted both through the works of Indigenous artists and by a broader desire amongst their non-Indigenous colleagues to experience this unique environment as a composite of all its elements rather than just a visual scene to be captured by the artist’s brush. To help me understand and articulate these changes I have drawn upon both phenomenology and cross-cultural mapping. Phenomenology is a philosophical concept describing our interactions with, and our reactions to, the phenomena that comprise everyday life. In my research I walked extensively on the lake bed of Weereewa (Lake George) at different times of the year, experiencing the whole environment, from the sky above to the tiniest crack in the mud, using all my physical senses while being constantly aware of the Aboriginal history on this lake bed that preceded me, and any other European presence, by thousands of years. I became embedded within the whole landscape; truly able to experience its many facets through my senses. This is the essence of phenomenology. Cross-cultural mapping, on the other hand, describes the way people of different cultures record their memories of a place. It asks the question, how have they mapped the land around them and for what purposes? In my research I looked at how both Indigenous and non-Indigenous artists have gone about the process of mapping the land, and it is from these findings, in combination with my own experiences on the lake that much of my studio work has developed. My studio work consists of cut-outs and drawings that reflect the physical and temporal phenomena of the Weeweera landscape: its clouds, shadows, changing colours, remnant water, cultural relics, land-use practices and the impacts of both weather and time on its human and geological histories. My experiences of the lake are represented as a series of ‘fragments’ that engage with its different histories: the Aboriginal, the settler and the geological. In developing these fragments into wall installations and watercolour works on paper, using a process I called an ecology of drawing, I have been able to bring together all the influences on my work, enabling me to express my experiences of the lake in a new visual language.Item type: Item , Access status: Open Access , Microbiome dynamics during rust fungal infections(2026) Graetz, AbigailPlants don't exist naturally in isolation. They are surrounded by, colonised by, and interact with, microorganisms. Plant microbiomes have many reported benefits to their hosts, from directly suppressing pathogen infection to improving nutrient availability. While leveraging these benefits for agricultural benefit is of great research interest, we lack fundamental understanding of the composition and diversity of plant microbiomes in non-model systems. Environmental DNA (eDNA) sequencing has opened new doors for profiling microbial communities, enabling molecular delineation of species with morphological similarities, or for which pure in vitro culture is not possible. Metabarcoding, using the 16S region for bacteria, or the internal transcribed spacer (ITS) region for fungi, can increase sample throughput, and identify many organisms simultaneously from a single sample. Using long-read sequencing to encompass entire metabarcode sequences can give insight at the species level, but this technology has not been thoroughly benchmarked for applications in microbial metabarcoding. In this thesis, I benchmark and optimise a wet lab and bioinformatics workflow for using Oxford Nanopore Technologies long-read sequencing to profile microbial communities with metabarcodes. I present a novel multiplexing strategy to improve cost-effectiveness, and use an in silico mock community to demonstrate robust, species-level identification of fungi using long-read ITS sequences. I have then applied my knowledge from this benchmarking work to two leaf microbiome datasets: a sample set of rust fungus-infected wild grasses, and a sample set encompassing three spore stages of the wheat stripe rust fungus (Puccinia striiformis f. sp. tritici) across the sexual and asexual phases of its life cycle. I compare fungal and bacterial community composition and abundance across levels of infection status and host plant, to better understand how rust fungal infection influences microbiome community dynamics in the phyllosphere.Item type: Item , Access status: Open Access , Exploring cortical information processing using optogenetics(2014-12) Rudinski, Stephen AlexanderOptogenetics provides a powerful new tool for studying the way neurons integrate the inputs they receive, and how this shapes information processing in the brain. In this thesis we apply this new tool to investigate the mechanisms governing information processing in the somatosensory cortex of the mouse. The first aspect of this study characterised the expression and activation of channelrhodopsin-2 (ChR2) in somatosensory barrel cortex of a widely used transgenic mouse line where ChR2 expression is driven by the Thy-1 promoter. Within somatosensory barrel cortex ChR2 expression was found in 96% of layer V and 72% of layer II/III pyramidal neurons. Expression of ChR2 was also found in the majority of fast-spiking interneurons in both layer II/III and V (78% and 86% respectively). This study shows that ChR2 expression is not limited to layer V pyramidal neurons in this mouse model as is commonly assumed. The second aspect of this study developed a spatiotemporally precise method for optogenetic stimulation based on a projector-based optical interface. As proof-of-principle, three studies were conducted to assess the application of this method. Firstly, subcellular dendritic photo-stimulation was used to investigate the somatic impact of distal dendritic inputs in cortical pyramidal neurons. Secondly, this method was applied to mapping the spatial distribution of synaptic inputs to neurons in layer II/III and IV within somatosensory barrel cortex. We demonstrate that layer II/III pyramidal cells receive the majority of their excitatory synaptic input from layer IV and II/III, with fewer and weaker inputs arising from layer V within the same barrel. Interneurons in layer II/III also received extensive excitatory synaptic input from layer IV in addition to surrounding layer II/III cells. The vertical profile of excitatory input to layer IV neurons indicated stronger input from layer IV and layer V than from layer II/III within the same barrel. Similar intra-columnar input profiles were also seen in interneurons residing in layer IV, where inputs were more numerous and stronger from layer IV than from layer II/III or layer V. Thirdly, using a thalamocortical slice we show that thalamocortical inputs arising from the thalamus have significantly higher connection probability and input strength in layer IV compared layer II/III and V. The final aspect of this study investigated how inhibition targeted to somatic versus dendritic compartments shapes the firing output of layer V pyramidal neurons, and how the location of excitatory input influences this process. The findings presented illustrate that when excitatory drive is close to the soma both somatic and dendritic GABAA-mediated inhibition has a purely subtractive effect on input-output relationships, whereas subtractive and divisive effects are observed during dendritic excitatory input. Somatic inhibition produces significantly more subtractive effects when excitation is driven somatically, whereas more divisive effects are observed during dendritic excitatory input. Together these findings suggest that both somatic and dendritic inhibition can generate divisive gain control provided excitatory drive is concentrated in dendritic compartments.Item type: Item , Access status: Open Access , The scope of global gene expression in peripheral blood for anti-doping testing(2016-09) Hausner, Sarah ClaudiaThis study aimed to determine, whether measures of gene expression can detect the effects of autologous blood transfusion, which is used illicitly by athletes to enhance performance. Gene expression data from blood samples collected longitudinally from subjects participating in two autologous blood transfusion Trials were analysed. Four participants in both Trials were transfused with 3U blood. Four additional subjects were transfused with 1U blood in the second Trial. In the first Trial samples were collected at baseline, 21 days post phlebotomy, and at 7, 14 and 28 days post re-infusion. During the second Trial samples were collected at baseline and 14-days post re-infusion. Chapter 2 describes transfusion-induced signatures of differentially expressed genes. Generalized linear modelling with subsequent Bayes moderation and FDR adjustment for multiple testing was used to identify characteristic transfusion-induced signatures of differentially expressed genes for follow-up testing at 7, 14, 21 and 28 days post re-infusion. We detected transfusion effects with 100% accuracy in samples collected 14 days post-transfusion in Trial 1 and reproduced these findings in Trial 2. The transfusion-response signatures were enriched for genes linked to the physiological response to autologous transfusion, including inhibition of erythropoiesis, impairment of cortical cytoskeleton and cell cortex formation and suppression of heme biosynthesis. These responses to transfusion remained detectable for at least 28 days after transfusion. Chapter 3 describes the results of the Weighted Gene Co-Expression Network Analysis, which results in a range of quantitative network descriptors with diagnostic potential (i.e., eigengene score, intra-modular connectivity score, extra-modular connectivity score). We identified conserved patterns of gene-expression network organisation through assignment of genes to distinct modules based on their co-expression similarity across all available sample data. We assessed the impact of transfusion on gene-expression networks by comparing intra- vs. extra- modular connectivities at different stages of the interventions. We also compared the characteristics of the modules with blood markers obtained from the participants. We investigated the functional enrichment of modules and of the most interconnected genes within each module (hubgenes). Finally, we quantified module-module interconnectedness and rated connection strength to assess the effect of transfusion on the transcriptome’s organisational structure. We were able to detect transfusion at 14 days post blood re-infusion with 100% accuracy in Trial 1 and reproduce these findings in Trial 2. The peripheral blood transcriptome is organised into distinct modules with characteristic transfusion-induced changes that reflect relevant physiological processes, such as suppression of erythropoiesis and metabolic response to alterations in blood composition. Peripheral blood transcriptome has great potential as a diagnostic tool for autologous blood transfusion, which remains hard to detect by other methods. It can also potentially detect physiologicaL responses to a wide range interventions. ‘Hubgene’ analysis, in particular, which allows assessment of intrinsic network properties through both quantitative (hubgene connectivities) and qualitative (hubgene function) measures, may be of great value in testing for responses to a wide range of substances and procedures, and in testing for yet unknown doping agents.Item type: Item , Access status: Open Access , Application of contrast techniques in X-ray microtomography to characterisation of rocks and hydrocarbon recovery(2017-08) Cheng, QianhaoX-ray microtomography (micro-CT) is the principal imaging tool for digital analysis of rock samples and provides the basis for simulation of rock properties and transport processes within the pore space. The accuracy of flow simulation predictions can be improved by extracting more input information from rock tomograms and by direct imaging of flowexperiments at their end states or during their course. These advances require development of techniques to selectively enhance the X-ray attenuation contrast of the features of interest, which may be rock surfaces or fluids in their pores. The ability to spatially register the 3D tomograms before and after an experiment then allows the subtle changes highlighted by contrast enhancement to be isolated and analysed. This thesis deals with three such contrast enhancement strategies and their applications to characterization of flow properties relevant to hydrocarbon recovery from reservoir rock. The first part of the thesis is directed at furthering understanding of the pore-scale mechanisms by which waterflooding using low salinity brine can improve oil recovery. A clay-containing outcrop sandstone was prepared in a mixed-wet state and micro-CT scanned after spontaneous imbibition of high salinity brine followed by low salinity brine. In this case the contrast between residual crude oil and brine in the pore space was achieved by moderately doping the brine by ion exchange of chloride for iodide. Oil saturation decreased by 10% due to imbibition of low salinity brine, and image analysis of the sequence of three registered tomograms (in the dry state and after the two imbibition steps) was used to characterize the pore-scale changes. All image metrics, including pore oil saturation, oil connectivity, oil-rock and oil-brine interfacial areas and oil-brine meniscus curvature confirmed that the additional recovery on exposure to low salinity brine was driven by a change in wettability state towards more water-wetting. Two techniques were then used to identify the minerals most responsible for this wettability change. One approach attempted to segment mineral classes within the rock phase guided by comparison of attenuation to registered mineral maps from SEM-EDS. However, this lacked the sensitivity to make statistically reliable conclusions. The second approach imaged the drained state with the irreducible brine strongly highlighted by sodium iodide to map the microporosity and thus the clays hosting it. This approach gave sufficient surface sensitivity to reveal that oil preferentially released from surfaces of clays rather than grains in the low salinity brine. The second part of the thesis focuses on improving the ability of micro-CT to extract finescale information from rock pores. The current resolution limit of micro-CT is around 1 pm, however many pores (micropores) in reservoir rocks lie below this size. It is well understood that registration of the tomograms of a rock before and after saturation with an X-ray dense liquid provides on subtraction a 3D map of porosity within sub-resolution pores. The aim of the second part of the thesis was to complement this pore volume map with a corresponding map of sub-resolution pore surface area. In this case iodine adsorption was used as the X-ray contrast technique, such that subtraction of the registered tomograms before and after adsorption isolated this local surface area contribution. A set of 10 rocks was prepared and analysed in this way using micro-CT supported by spectrophotometry. It was shown that the adsorbed iodine layer was so thin (below 1 nm) that only rocks of high internal surface area, such as from tight gas reservoirs, were well suited to this method. One complication was that carbonate rocks adsorbed less iodine than sandstones, although pre-treatment of carbonates by adsorption of asphaltenes from crude oil could partly reduce this difference. Application of the iodine adsorption method to a shale sample exposed the further difficulty of decoupling the adsorption contribution to internal surface area from bulk uptake of iodine within the solid organic matter in shales. The third part of the thesis targets further development and utilisation of contrast enhancement techniques tailored to the unique challenges of shales. Upscaling of simulated matrix transport properties from resolved nano-pore networks in tiny FIBSEM cubes to representative elementary volumes and core plugs requires accurate micro-CT images of pore space - hosted by minerals and by organic matter - over scales from microns to centimetres. 3D porosity mapping by differencing of registered tomograms before and after saturation was adapted to this purpose by using a very dense liquid, diiodomethane, to provide sufficient contrast in these very tight, low porosity rocks and to wet organic matter. A second tomogram difference was generated after selective staining of the organic matter by iodine, to provide a 3D map of local organic content and thus distinguish its internal porosity from that hosted by minerals. Further, bottom-up approaches to transport simulation within pores can be tested against top-down direct imaging of laboratory-prepared states during or after transport processes. In particular, diffusion is thought to be a key transport mechanism for recovering gas from the matrix of fractured shale reservoirs. To this end, the diiodomethanesaturated shale was used as the initial state for dynamic micro-CT imaging of diffusion of a miscible, X-ray transparent second liquid into the sample. Alternatively, the end state after drainage of diiodomethane in air by centrifugation was scanned to quantify wetting-phase saturation versus capillary pressure at each point in the sample, yielding a 3D map of pore throat diameter. Workflows for integration of these tomographic maps with high-resolution SEM images and SEM-EDS mineral maps of sections and FIBSEM cubes were applied to shales from three formations.Item type: Item , Access status: Open Access , IAEA safeguards : coping with uncertainty in international verification(2015-06-30) Robertson, Kalman AlecThis thesis examines the process by which the International Atomic Energy Agency (IAEA) verifies the compliance of non-nuclear-weapon states with the Nuclear Non-Proliferation Treaty and comprehensive safeguards agreements. The verification process consists of two interlocking phases: (1) planning verification activities and allocating verification resources, and (2) analysing collected data and drawing conclusions. Approaches to the two phases of verification are of central relevance to current policy debates on the development of the IAEA’s ‘state level concept’ for safeguards and for the resolution of compliance issues in several countries, particularly Iran and Syria. The continued absence of a substantive definition of non-compliance, or even a well defined procedure for exposing non-compliance, coupled with the IAEA’s increasing differentiation between states in order to meet verification objectives with limited resources, leave the IAEA and its safeguards regime vulnerable to claims of being ineffective, inefficient, irrelevant or discriminatory. Safeguards experts acknowledge that the identification and clarification of principles for determining safeguards priorities and for deriving safeguards conclusions will be a crucial step in strengthening the non-proliferation regime. In addition to assisting the development of these missing principles, the results of this thesis have broader consequences for the structure and development of international verification organisations. The approach taken by the IAEA is constrained by uncertainties inherent in the nature of the information sources available, the nuclear choices of states, and international responses to alleged violations, as well as ambiguities in the choice of verification standard. This thesis argues that efforts to reform the structure and procedures of the IAEA should use these fundamental uncertainties as the logical starting point for critical analysis of the IAEA’s safeguards. From the standpoint of achieving the objectives of verification, these uncertainties can be effectively managed by applying the concept of risk governance. The result of application of risk governance is a procedure that acknowledges both the technical and the political components of verification, while simultaneously enhancing the transparency of the IAEA’s operation, the credibility of the verification assurance, and the timeliness of identification of violations. The concept assists with distinguishing the roles of the IAEA’s Secretariat (risk identification and risk analysis) and the international community of states (risk evaluation and risk treatment) in each of the phases of verification. The Secretariat should focus on the structured provision of technical information to states. This thesis proposes refinements to the state level concept and new ‘Automatic Notice’ procedure to transform the existing, potentially political bases for the allocation of safeguards resources into transparent and objective criteria. Once the Secretariat has reported the existence of unresolved anomalies in the implementation of a safeguards agreement, a declaration of non-compliance and any subsequent international enforcement action are political decisions and must be left in the hands of states. The Automatic Notice procedure clarifies the operation of the Secretariat when compliance issues arise. It also provides states, whether acting through the IAEA’s Board of Governors or otherwise, with opportunities to craft effective solutions to potential proliferation crises.Item type: Item , Access status: Open Access , Photoluminescence-Based Characterization of Silicon Materials for Solar Cells(2026) Li, KingsleyThe ongoing global transition from fossil fuels to clean renewable energies relies heavily on the developments in crystalline silicon photovoltaics technology, which dominates the solar cell market. In modern high-efficiency crystalline silicon solar cells, such as Tunnel Oxide Passivated Contact and Silicon Heterojunction cells, the effective passivation of defect states has a critical impact on the device performance. During the passivation process, hydrogen is the key agent for both surface and bulk passivation, yet its fundamental transport kinetics within the silicon lattice remains under debate, as shown by significant discrepancies in the reported effective hydrogen diffusivity values. This thesis employs photoluminescence-based techniques to investigate carrier recombination and hydrogen diffusion in silicon materials. The work is divided into two complementary parts. First, time-resolved photoluminescence is used to measure the carrier lifetimes in heavily-doped silicon wafers under different conditions, in thin intrinsic silicon films, and thin doped polycrystalline silicon films. This experiment reveals the dominance of Auger recombination in heavily-doped silicon wafers and the impact of hydrogenation on different thin silicon films. The second part of the thesis develops a novel, steady-state spectrally-resolved photoluminescence methodology to quantify the effective hydrogen diffusivity in crystalline silicon. It is emphasized that this measurement specifically probes the effective diffusivity, which reflects the net result of all hydrogen interactions within the silicon lattice. Under thermal equilibrium, this technique reveals a strong doping dependence: while diffusivity in moderately-doped n-type and undoped silicon aligns with literature, it is significantly reduced in heavily-doped n-type and all p-type silicon. Supporting simulations suggest this reduction in effective diffusivity arises from complex interactions, including those between hydrogen charge states and the formation of hydrogen dimers or other metastable interactions. Furthermore, this research demonstrates the active control of hydrogen diffusion under non-equilibrium conditions. Strong laser illumination is shown to increase the effective hydrogen diffusivity significantly in heavily-doped n-type and moderately-doped p-type silicon. This light-enhanced diffusion is explained by an illumination-induced shift in the dominant hydrogen charge state, which mitigates the metastable interactions within the silicon lattice. In contrast, the illumination has a negligible effect where the metastable interactions remain dominant (heavily-doped p-type) or where the effective diffusivity is already high (moderately-doped n-type silicon). In summary, this thesis makes two principal contributions to the understanding of defect passivation in silicon photovoltaics. First, it employs time-resolved photoluminescence to quantify the carrier lifetimes and hydrogenation effects in key materials for high-efficiency solar cells. Second, this work develops a novel spectrally-resolved photoluminescence methodology to directly measure the effective hydrogen diffusivity, revealing its complex doping and illumination dependence. These findings provide critical, separate insights: the first into the Auger recombination limits, and the second into the hydrogen diffusion mechanisms. The established methods provide powerful tools for fundamental studies of defect kinetics in silicon photovoltaics.Item type: Item , Access status: Open Access , Money, markets and meaning - An exploration of meaning-based objections to commodification(2026) Lis-Clarke, NedIn contemporary capitalist economies, many goods are distributed through markets or valued primarily for the price they could obtain on a market. These kinds of goods are commodified. While markets are powerful tools to allocate scarce resources, many people object to commodifying certain goods. One common class of objection in philosophical debates about the moral limits of markets can be called meaning-based objections. These are claims that certain goods should not be commodified because to do so would violate their meaning. In this thesis, I first develop a taxonomy of meaning-based objections that systematises and distinguishes between a range of objections that have been advanced in the philosophical literature. I then defend this taxonomy and its component parts against criticisms that cast doubt on whether the meaning of a good can serve as a sound basis for ethical deliberations about commodification. I finally apply the meaning-based objections to a range of case studies: the sports betting industry; housing policy in Australia; music and the concept of 'selling out'; and the public sector consulting market. By exploring these case studies, I show that an analysis that gives primacy to the meaning of goods can be illuminating in commodification debates. I argue for a context-sensitive approach to ethical deliberations about commodification, one that is attentive to the heterogeneous character of markets and the shortcomings of other, non-market, methods of distribution and modes of valuation. I argue that the soundness of meaning-based objections cannot be decided in advance of applying them to the particular facts of different cases. In these ways, I aim to build on existing accounts that either treat markets as monolithic entities, fail to adequately consider alternative allocative methods, or seek to demonstrate the validity or invalidity of meaning-based objections without being attentive to important contextual factors.Item type: Item , Access status: Open Access , English, Nationalism, and The Politics of Language Use: Language Ideologies in Media Criticism of Yoon Suk Yeol’s Speech(2025) Cann, RoseWithin a speech community, language practices are informed by multiple, sometimes competing, ideological frameworks. In South Korea, language practices are shaped by long-standing linguistic nationalist sentiments surrounding the Korean language, alongside neoliberal orientations that position English as valuable global linguistic capital. Against this backdrop, former President Yoon Suk Yeol (2022–2025) was repeatedly criticised within the media for his apparent penchant for incorporating English-origin words into his Korean-language speech. Situated within these broader ideological tensions regarding language, national identity and pride, and the place of English within Korea, this thesis examines why the media criticised Yoon’s linguistic behaviour. Following a language ideological approach, this study analyses discourse within media texts that explicitly criticised Yoon’s use of English- origin words into his speech, with particular attention paid to metalinguistic commentary and evaluative framing. Treating such discourse as a site where language use is rendered socially and politically meaningful, these texts are analysed to identify how Yoon’s linguistic behaviour was discursively constructed within media’s criticism, which language ideologies underpinned these constructions, and how such ideologies shaped the discourse itself. The findings of this study show that the media’s criticism was structured predominantly through a linguistic nationalist framework, within which English was conceptualised as symbolically opposed to the Korean language itself and its associated values as the national language. While this framing enabled sustained critique of Yoon’s use of English-words at this symbolic level, it simultaneously constrained the focus of the media’s criticism to that level, leaving other ideologies of English that contribute to the reproduction of social and class inequalities in South Korea unchallenged. By demonstrating how linguistic nationalism both motivated and limited media criticism of language use in political discourse, this thesis contributes to research on language ideology, language use within political discourse, and the sociolinguistic context of English within South Korea.Item type: Item , Access status: Open Access , Te Waa of future mobilities: A model for Adaptation in Kiribati.Rimon, AkkaClimate change presents profound and escalating risks for low-lying states, with Kiribati experiencing these pressures in particularly acute and profound ways. As sea level rise, coastal erosion, and saltwater intrusion intensify, the biophysical limits of in-situ adaptation are becoming increasingly evident, raising critical questions about the long-term viability of place-based resilience strategies. This context underscores the need for integrated, inclusive, innovative and transboundary approaches that extend beyond the scope of national adaptation planning. Among the emerging responses, labour mobility initiatives, most notably the Pacific Australia Labour Mobility (PALM) scheme, are gaining prominence as potential mechanisms for enhancing climate resilience, diversifying livelihood options, and expanding adaptive capacity for highly vulnerable populations. In the absence of robust international legal frameworks or dedicated climate protection mechanisms for communities facing displacement from sea level rise, this research examines how labour migration to Australia can function as a consequential form of climate adaptation for Kiribati. Although labour mobility is increasingly recognised for its adaptive potential, substantial knowledge gaps remain in understanding how such pathways operate within, and contribute to, the adaptive capacities of climate-exposed small island economies. This study addresses this gap by analysing labour migration not merely as an economic opportunity, but as a strategic, anticipatory adaptation mechanism embedded within broader socio-ecological resilience processes. This thesis investigates the multi-faceted relationship between labour migration and climate adaptation, examining how both temporary and permanent forms of mobility, collectively referred to in this study as labour migration, can function as anticipatory, forward-looking responses to escalating climate threats. Central to this inquiry are questions about how labour migration can strengthen adaptive capacity and foster long-term resilience for communities on the front lines of the climate crisis. Employing Te Waa, the canoe, as a guiding metaphor for both research and migration, the study centres the lived experiences and voices of those most exposed to climate risks. It examines I-Kiribati perspectives on the value of labour migration as a climate adaptation strategy. Through this metaphorical vessel, the research co-creates knowledge that re-stories and re-journeys migration in an increasingly uncertain world. By foregrounding community agency and self-determined adaptation, the study offers nuanced insights into how labour mobility is increasingly perceived as a facilitator of both in-situ and ex-situ adaptation. It expands the understanding of labour migration's potential to alleviate pressure on frontline communities, reduce exposure to environmental stressors, and foster long-term resilience across social, economic, and cultural dimensions, grounded in the lived realities of I-Kiribati communities. Motivated by Kiribati's Migration with Dignity policy and the imperative to challenge climate apathy and climate coloniality, this research embraces the philosophy that migration, when approached strategically and voluntarily, is not a failure of adaptation nor a sign of weakness. Rather, it is a powerful act of resilience, an intentional and dignified choice that enables individuals and communities to navigate climate challenges with agency and foresight. Ultimately, this thesis contributes a spiritual and cultural lens to the evolving discourse on climate mobility, resilience, and climate justice. It affirms that migration is not merely a reactive measure, but a proactive, personal, and economic choice, one that empowers communities to confront the challenges of climate change with hope, dignity, autonomy.Item type: Item , Access status: Open Access , What makes a chengyu? Native speaker intuitions for categorising Chinese idiomatic expressionsGanon-Davey, Janet'Chengyu' are distinctive formulaic expressions central to Chinese language and culture. While many chengyu originate in classic literary texts, these expressions are widely used in contemporary communication, featuring in everything from Chinese literature and political discourse to advertisements and everyday conversation. Thousands of chengyu are listed in authoritative dictionaries and explicitly taught in the Chinese school curriculum, serving as markers of Chinese proficiency and cultural literacy. Yet despite their cultural prominence, extensive documentation, and formal transmission, we know little about ordinary Chinese speakers' understanding of chengyu. This thesis investigates how native Chinese speakers conceptualise 'chengyu'. It adopts a mixed-methods approach with three sequential research components: linguistic analysis, a chengyu rating study, and an experimental acceptability task. Analysis of acceptability judgements, native speaker ratings, and questionnaire responses from over 250 participants reveals that Chinese speakers do not share a common understanding of what constitutes a chengyu. Chengyu are better characterised as a culturally salient prototype category with intuitively recognised yet variable boundaries. Semantic compositionality, structural patterns, and individual backgrounds all influence which conventionalised four-character expressions are considered chengyu, challenging both broad dictionary classifications and narrow scholarly perspectives. Notably, speakers with tertiary qualifications and strong Chinese knowledge develop an increasingly conservative concept of chengyu, favouring expressions with idiosyncratic structures, opaque meanings, and cultural content. This research advances theoretical understanding of multiword expressions (MWEs) and linguistic categorisation, and offers practical insights for psycholinguistic research and language pedagogy. Chengyu exhibit a counterintuitive pattern whereby expression characteristics that facilitate learning -- semantic compositionality and structural symmetry (Liu & Cheung, 2014) -- undermine perceived authenticity. This inverse relationship between learnability and authenticity challenges MWE frameworks developed for incidentally acquired formulaic language, demonstrating how formal acquisition and cultural salience create distinct processing dynamics. For psycholinguistic research, these results underscore the importance of validating stimuli with study participants rather than relying on authoritative classifications. For language pedagogy, the findings motivate teaching approaches that distinguish culturally valued formulaic expressions from merely comprehensible ones. By documenting the shared expectations and individual variation that allow chengyu to remain salient across generations, this research provides an empirical foundation for studying how culture-specific linguistic categories are mentally represented, culturally transmitted, and effectively taught. Liu, L., & Cheung, H. T. (2014). Acquisition of Chinese quadra-syllabic idiomatic expressions: Effects of semantic opacity and structural symmetry. First Language, 34(4), 336-353. https://doi.org/10.1177/0142723714544409Item type: Item , Access status: Open Access , Care, Career, and Kinship: Essays in Labour and Family Economics(2026) Pritadrajati, DyahThis thesis comprises three empirical essays in labour and family economics that examine how childcare access, income support, and fertility shape labour-market behaviour and household welfare in low- and middle-income settings. Across the essays, I use quasi-experimental variation and large-scale microdata to study how households allocate labour and adjust to policy and demographic change under binding constraints. The first essay examines how access to part-day kindergarten affects maternal labour supply and intra-household time allocation in Indonesia, where female labour force participation remains low and childcare is predominantly informal. Using an instrumental-variable strategy based on statutory age-eligibility rules, the analysis shows that kindergarten enrolment increases mothers' employment and working hours, with larger responses among less-educated, rural, and lower-income women. These gains are not accompanied by displacement of informal care provided by co-resident adults. Adjustment instead occurs along intergenerational margins within households, with increased school participation and reduced labour force participation among older siblings, particularly girls. Additional work is concentrated in informal and flexible jobs, reflecting the short duration of kindergarten provision. The second essay studies how the design of unconditional cash transfer programmes shapes labour-market behaviour in Indonesia. Exploiting variation across programme phases implemented during periods of economic stress, the analysis compares transfers based on relatively static welfare indicators with later programmes that incorporated contemporaneous employment information into targeting. Using nationally representative panel data and difference-in-differences and event-study designs, the results show modest labour-market responses that vary with programme design. Programmes that incorporate employment-related information are associated with small reductions in employment and larger declines in formal-sector participation, reflecting behavioural adjustment along margins tied to observable employment characteristics, even when transfers are temporary and modest in size. The third essay studies how family size affects women's safety within households in Samoa, a high-fertility setting with limited reproductive autonomy. Using nationally representative survey data and an instrumental-variable approach based on same-sex sibling composition, the analysis shows that an additional dependent child increases the likelihood of intimate partner violence, with effects concentrated in physical and sexual abuse. The evidence points to heightened economic pressure, weaker bargaining positions, and constrained agency as important correlates of these outcomes. The findings highlight family size as a consequential, but often overlooked, dimension of intra-household power and welfare in high-fertility contexts.Item type: Item , Access status: Open Access , Applied Epidemiology of Infectious Diseases in the Western Pacific: Studies from Fiji, Tonga and Australia(2026) Jian, HollyThis volume presents four projects and additional public health experiences, which satisfy the competencies of the Master of Philosophy in Applied Epidemiology (MAE) program. Between February 2024 and December 2025, I undertook an MAE field placement at The University of Queensland's Operational Research and Decision Support for Prevention, Control and Elimination of Infectious Diseases (ODeSI) team. In Chapter 1, I present an analysis of COVID-19 mortality in Fiji in 2020-22, where I conducted descriptive, statistical and spatial scan analyses of COVID-19 deaths. My statistical analyses showed that older Fijians and indigenous Fijians (iTaukei) were more likely to die of COVID-19, as well as more likely to die at home. My spatial scan analysis also found evidence of significant spatiotemporal clustering of COVID-19 deaths, again with marked differences between ethnic groups in the location and size of clusters over time. Chapter 2 presents an investigation of an outbreak of Pseudomonas aeruginosa infections at a health facility, conducted with the Gold Coast Public Health Unit in Queensland, Australia. During this investigation, I was part of a multidisciplinary outbreak control team, which conducted environmental and epidemiological investigations to identify the cause of infection and prevent further cases. I determined that the likely cause of infection was the introduction of P. aeruginosa into cases' joints during intraarticular injection of contrast, which had been contaminated due to unhygienic handling and storage practices. In Chapter 3, I present a systematic review of global lymphatic filariasis (LF) post-validation surveillance (PVS) activities in 2025, which was conducted to inform my design of a PVS system for LF in Tonga. The review found considerable heterogeneity in the implementation of PVS. Financing and resource constraints underpinned many challenges to PVS implementation, while institutional commitment is a critical enabler of sustained surveillance. In Chapter 4, I present my design of a PVS system for LF in Tonga. I conducted a qualitative study where I interviewed key informants in the Tonga Ministry of Health to identify challenges and opportunities for establishing PVS, and synthesised my findings into recommendations for the development of a PVS strategy for Tonga. To be feasible, LF PVS must be designed for Tonga's unique systemic, organisational and operational environment; my proposed strategy consists of determining local risk level and context, and using this assessment to select from both active and passive surveillance methods. This thesis also describes other public health experiences that have contributed to my training in field epidemiology. This includes six weeks of fieldwork in Tonga, where I assisted with a serosurvey investigating resurgence of LF following its elimination seven years prior. I also investigated a Salmonella Typhimurium cluster with Queensland Health's OzFoodNet team. Lastly, I contributed to other publications within the ODeSI team. The work presented in this thesis demonstrates the role of applied epidemiology in public health decision-making in diverse settings across the Western Pacific region, from the Gold Coast to the Pacific Island Countries of Fiji and Tonga.