Open Access Theses

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Open Access
Investigating Lipid Modulation of Ion Channels Using Molecular Dynamics Simulations
(2024) Lin, YC
Ion channels are the molecular gatekeepers of our cells, activating in response to diverse stimuli to facilitate the movement of ions and solutes across biological membranes. As membrane proteins, the trafficking, localisation and function of ion channels are regulated by lipids through either direct binding interactions or by modulation of general membrane properties. Molecular dynamics (MD) simulations have emerged as a powerful tool to study lipid-protein interactions in atomistic detail. In my PhD, I used multiscale MD simulations to explore the regulatory interactions between membrane lipids and mechanically gated ion channels belonging to the Piezo and OSCA/TMEM63 families as well as voltage gated sodium ion channels. Piezo2 is a mammalian mechanosensitive ion channel involved in sensing touch, pain and proprioception. Piezo channels are regulated by their local membrane environment, particularly by cholesterol and phosphoinositides. MD simulations of Piezo2 in a complex mammalian membrane showed that the channel alters its local membrane composition such that it becomes enriched with specific lipids, including phosphoinositides, and forms specific, long-term interactions with a variety of lipids at functionally relevant sites. Another class of mechanically gated ion channels, the OSCA/TMEM63 family, are involved in osmoregulation in plants and play diverse physiological roles in humans. Their structural homology to the TMEM16 scramblases and the presence of a lipid-lined pore in the open state suggests that the channels may play a dual role in facilitating both ion permeation and lipid translocation. In MD simulations, we show that this is the case, and identify key bottleneck residues that control lipid and ion movement, uncovering the molecular mechanism behind how these channels can function as both ion channels and scramblases. Voltage-gated sodium channels (Nav) are crucial for the action potential, allowing the influx of sodium ions into excitable cells. The phosphoinositide PI(4,5)P2 diminishes Nav 1.4 activity by slowing channel opening, hastening fast inactivation, and slowing recovery. Through MD simulations, we demonstrate stable binding of PI(4,5)P2 to inactivated Nav at a conserved site within the DIV S4-S5 linker, linking the voltage sensing domain (VSD) to the pore. This suggests a competitive binding hypothesis with the Nav C-terminal domain during recovery, prolonging inactivation. In the resting state, phosphoinositides bind to VSD gating charges, hindering activation. These findings elucidate how phosphoinositides modify activation voltage dependence and inactivation recovery rates, holding promise for innovative therapies targeting Nav-related diseases.
Open Access
An Organic Approach for the Delineation of Foreign Product Avoidance
(2024) Seyrl, Christopher
Introduction Internationalisation represents a key means for firms to attain growth, whether it be recognition, market share, or profitability (Agndal & Elbe, 2007). However, a key barrier is foreign product avoidance (consumer ethnocentrism) (Keane & Morschett, 2016, pg. 228). Notwithstanding the augmentation of globalisation in recent decades, political and economic fragmentation have come to the forefront, presenting foreign product avoidance as a contemporary phenomenon. The intersection of globalisation and rising nationalism in reaction to neoliberalism indicates a potential resurgence in empirical observations of foreign product avoidance. Epistemologically, extant assumptions and explanations in the realm of consumer ethnocentrism are no more aligned with, and do not fully reflect the dynamic and multidisciplinary nature of ethnocentrism, advances across other disciplines, and changes in geo-economics and politics. Hence, a revisit and reconceptualisation of foreign product avoidance, namely, the factors which metamorphosise ethnocentric tendency to shape purchase behaviour, is timely and of utmost importance theoretically, methodologically and for international companies and firms. The purpose of the thesis is to investigate changes in consumer behaviour as globalisation shows signs of diminishing significance in the face of the fall of neoliberalism with the simultaneous rise of nationalism. As such, the main objectives were to identify the factors that shape consumer ethnocentric purchase behaviour, propose a methodology to delineate the phenomenon as it is experienced in relation to different products within a particular cultural context, and extrapolate insights which shape internationalisation strategies. Research Question(s) The following primary research question (and related sub-questions) guided the scope, structure, methodology, and overall direction of the thesis: "How can internationalising firms overcome the challenge of consumer ethnocentrism and generate appeal within a foreign target market, in light of rising nationalism and its concomitant resistance to globalisation?" a. What are the factors which influence consumer ethnocentric tendency to form purchase behaviour? b. How can the factors of consumer ethnocentrism be integrated to improve the informativeness of the CETSCALE? Methodology The thesis adopted a mixed methods approach. An exploratory instrument development methodology, consisting of a single qualitative study was followed by three correlational and descriptive quantitative studies. Thus, study one sought to identify potential products which exemplify each factor which was theoretically derived from the review of academic literature (country of origin, product category, luxuriousness, and linkage with the target market's culture). Study two reduced the list of examples. Study three tested the reliability of the CETSCALE, and study four applied the CETSCALE in combination with conjoint analysis (utilising the product profiles generated at the conclusion of the second study). All studies (except study one) were conducted in the Russian Federation. Findings Synthesised results and findings across the four studies indicate that Russian respondents indeed utilise heuristic processing when judging foreign products. Each factor carries a different level of importance. Based on the conjoint analysis, Russians prefer products to be German rather than Vietnamese (origin factor), luxurious rather than basic (luxuriousness factor), without a linkage to Russian culture, and to be non-ingestible (product category factor). Based on such insights, internationalising firms can generate appeal through a more well-informed marketing mix. For example, to relocate manufacturing to a sought-after country, or utilise advertising campaigns that emphasise luxuriousness. Subsequent benefits related to growth in market presence and profitability would abound in turn.
Open Access
A Critical Analysis of Human Ecology
(2005) Dyball, Robert Adam
This thesis proposes that a dynamical systems approach is a valuable means of understanding complex situations of human and ecological interrelationships. Such an approach forms a useful addition to the conceptual framework of human ecology because it enables understanding the dynamics of change in humanecological situations in ways that are simple and yet powerful. The thesis undertakes a historical review of the both the Australian National University’s Human Ecology program and the institutional context in which it developed. It finds in that review explanations for why the conceptual foundations of the program have not been articulated in this way, despite finding that much of the teaching and research practice of the Human Ecology program has been conducted in a manner conducive to such an approach. The thesis reviews some of the basic principles that the ANU Human Ecology program adopts and then, after detailing a particular approach to understanding systems dynamics, shows how this can extend the existing conceptual framework to provide a powerful explanation of change processes in humanecological situations. The value of this extended approach is demonstrated through application to a range of different situations found in the Snowy Mountains of New South Wales, Australia.
Open Access
Fast lifetime measurements as a probe of nuclear shapes in 188Pt and 190Pt
(2024) Alshammari, Hanaa
This thesis presents research on the application of fast-timing techniques with LaBr$_3$ detectors for gamma-ray detection to measure state lifetimes and probe nuclear shapes in $^{188}$Pt and $^{190}$Pt. These nuclides lie at the boundary between the stable platinum isotopes that may have triaxial or $\gamma$-soft shapes, and the lighter isotopes that show evidence of shape coexistence. This study presents the measured lifetimes of the first 2$^+$, 5$^-$, 7$^-$ and 12$^+$ states in $^{188}$Pt and $^{190}$Pt, populated through $^{176}$Yb($^{16}$O,$4n$) and $^{176}$Yb($^{18}$O,$4n$) reactions, respectively. The Generalised Centroid Difference method was employed to determine the $2^+$ and $5^-$ state lifetimes. This required knowledge of the Prompt Response Difference (PRD), which was deduced using a novel 3D fitting method that enables deduction of the PRD without the requirement generally used in the literature of manually adjusting data points to have a common decay energy reference. The $12^+$ and $7^-$ state lifetimes were determined by fitting time-difference spectra with a decaying exponential convolved with a Gaussian prompt response. While the evaluated $2_{1}^+$ lifetime for $^{190}$Pt is confirmed, a revision of the $2_{1}^+$ lifetime for $^{188}$Pt is suggested. These new results align with other observations of the evolving nuclear behaviour with increasing mass number. However, an evaluation of the $B(E2; 2{_{1}^+}\rightarrow 0{_{1}^+})$ strength across the mass chain suggests that remeasurements of $2_{1}^+$ lifetimes in lighter platinum nuclei are required. Interpretation of the structural and shape changes in these nuclei is further investigated through General-Collective-Model calculations for $^{186,188,190}$Pt. The results for high-spin states in $^{188}$Pt and $^{190}$Pt highlight significant discrepancies with previous literature, particularly for the lifetimes of the $12^+$ and $7^-$ states. Updated values show closer alignment with more recent measurements for $^{190}$Pt, but differ for $^{188}$Pt. Additionally, new measurements of decay branching ratios, derived from high-quality $\gamma$-$\gamma$ coincidence data, yield updated transition strengths that can be used in the future to challenge existing interpretations of the nuclear structure.
Open Access
Decolonising streams: a confluence of Indigenous and western sciences
(2024) Harriden, Kate
Storm water is not a hydrological process. It is a concept developed in a specific place/space, according to specific ways of being and valuing water. We know this because other ways of perceiving water exist absent of a similar construct. Water science is an integral element required for successful human collaborative living, including art, music, governance and economic systems, the sacred, housing and food. During the ongoing colonial age (~1600 - current), the water science and management practices and associated ways of being and valuing of what this dissertation calls western science, have increasingly dominated the global waterscape. One consequence of the human-centred exploitive values cocooned in western science is the global colonisation of urban streams. The prevalence of physically obdurate storm water systems and associated relational obduracy of the storm water concept and predictably resultant urban stream syndrome starkly outlines an example of stream colonisation. The problem is that storm water systems significantly modify hydrological systems and the systems dependent on them while generating what is regarded as waste water. Efforts over decades to develop solutions within the western science framework have not significantly ameliorated storm water impacts on urban streams, or its being perceived as waste water. The transformational capacity of using Indigenous water science and frameworks and methods in urban water management and subsequent decolonisation of urban streams is examined through a storm water focus. This dissertation argues each science's ontological and axiological underpinnings allowed one worldview to construct 'storm water' while discouraging the other from any such notion. This research demonstrates employing Indigenous scientific frameworks and methods; that is those water sciences developed with the stream and hydrological conditions in which they were used, could transform contemporary urban water management including stream rehabilitation the imported scientific worldview appears unable to achieve. This research found that using even high-level Indigenous sciences frameworks and methods (i.e., not at the detail of an individual Indigenous science) strongly influenced the nature of the water research questions asked and how they were addressed, field work options and overall research approach. An influence primarily due to the inclusion of Indigenous ways of being and valuing that gird the associated scientific frameworks and methods. Consequently, this research contributes to a small but growing body of academic material examining the (re)application of Indigenous sciences to urban streams, and urban water management broadly. Urban streams could flourish with Indigenous water sciences custodianship, improving more than stream health and water quality outcomes. The confluence of Indigenous and western water sciences', this research represents contributes to urban streams decolonisation efforts.
Open Access
A Piecewise Model for Gravitational Waves from Young Neutron Stars
(2024) Grace, Benjamin
To date over 90 gravitational wave detections have been made. These events have all originated from the coalescence of a binary system of compact objects, the majority of which have been binary black hole systems. Some of these detections have been from systems where one object was a neutron star and the other a black hole. Only two detections have been made where both objects in the binary system were neutron stars. The gravitational wave event GW170817 originated from the coalescence of a binary neutron star system. It was significant in that it was the first event of this origin, and was paired with an electromagnetic counterpart. Observations of GW170817 have led to new insights into previously unknown physics, such as the neutron star equation of state, formation of heavy elements and the origins of gamma ray bursts. Despite the significance of this event, little is known about the remnant object left after the collision. One possible object which may have formed after a coalescence event is a rapidly spinning neutron star. This neutron star may be long lived or have a finite lifespan before collapsing into a black hole. Continuous wave search techniques are designed to target spinning neutron stars as one of their primary sources. These techniques use a matched filtering process with a Taylor expansion signal model. Newly born neutron stars from a coalescence event are expected to be spinning down rapidly over a short time period. For such rapid spin downs, and for a long-transient time scale, Taylor expansions are not suitable signal models. In this thesis I present a new piecewise model which can accurately follow the frequency evolution of a young neutron star. The parameter space of this model is composed of the frequency, and derivatives in time of frequency, of a neutron star at specific points in time. This model has the flexibility to model spin downs which are outside the scope of Taylor expansions, by being able to model changing braking indices and other neutron star properties. We use the piecewise model to carry out two $\mathcal{F}$-statistic searches over the 1800~s of data from the LIGO and Virgo gravitational wave observatories following the coalescences of GW170817 and GW190425. No signal was found. We perform sensitivity studies for both searches. Peak sensitivities are achieved for both searches at a starting frequency of 1700~Hz of $1.64 \times 10^{-22}~\text{Hz}^{-1/2}$ for GW170817 and $10^{-22}~\text{Hz}^{-1/2}$ for GW190425.
Open Access
From Boots to Babies and Back Again: The Lived Experience of Pregnancy, Birth and Motherhood in the Australian Army
(2024) Montalban, Maureen
This research explores through a gender lens, what it means to serve in the Australian Army as a woman during specific life stages of their service; that is, during pregnancy, birth and motherhood. It explores the nature of maternal healthcare provided to servicewomen in the Australian Army. It also investigates the demands faced by servicewomen who are mothers, and how they internally make sense of that with respect to their own identity and the various roles they do or are expected to undertake. It also seeks to uncover how Australian Army servicewomen who are mothers attempt to manage the dilemma of serving two greedy institutions, when both expect and demand so much and whether this is, in fact, an impossible dilemma. This research is a multi-subject qualitative study using semi-structured interviews and was conducted with three cohorts: Australian Army servicewomen, Australian Army commanders and managers, and Defence medical officers. Results from this research found that there was a consistent narrative surrounding choice or lack thereof, from participants. They spoke about their inability to choose a preferred healthcare provider, which resulted in the medicalisation of childbirth more often than not. Another finding was the expressions of guilt in having to choose between their identity as an ideal solider and a good mother, and the perceived requirement they had to live up to these socially constructed ideals. Participants also articulated the tension in having to grapple with the demands between two greedy institutions and feeling they had to choose between service and motherhood. This research shows that mothers in the military face choices that position them as outsiders and overtly show them to be different. The military has always valued conformity, uniformity and sameness, and yet being a woman in the Army is not about conformity, uniformity or sameness. Women's bodies during pregnancy visibly highlight otherness. Women's changing bodies also disrupt operational requirements as their bodies are no longer available to be an empty vessel to fight war, which is how the Army has traditionally viewed its fundamental capability. This study makes a number of significant contributions. At a philosophical level, this research asks the question, 'Who is a soldier?' and the focus on the experience of servicewomen contributes to the disruption of the combat masculine warrior narrative. At a scholarly level, this research is interdisciplinary in nature. It contributes to the current literature on military sociology, military studies, gender culture, organisational culture, women's health and psychology. From a practical perspective, being an emic or insider researcher has provided me a platform to influence the organisation from the inside, in helping shape opinions, perceptions and policies. This research uncovers the contradictions and paradoxes servicewomen in the Australian Army experience, both knowingly and unknowingly, as a result of the tensions they face in having to choose between their identities, between the institutions they serve, and in the lack of choice they have regarding agency of their bodies and their healthcare. Ultimately what this thesis demonstrates is that people's everyday lived experiences are the centre of the Australian Army and the institution of motherhood, and that both institutions must evolve to reimagine and redefine what an ideal soldier and good mother looks like in order to support our service people be the very best version of themselves.
Open Access
Antimicrobial resistance and sexually transmissible infections: the hunt for evidence to inform national policy
(2024) Chew, Alison
This thesis consists of work undertaken for the Master of Philosophy (Applied Epidemiology) (MAE) while completing a placement within the Communicable Disease, Epidemiology and Surveillance Section of the Australian Government Department of Health and Aged Care. It describes four projects undertaken to meet MAE competencies and additional work I undertook as part of the placement. I present the first analysis of gonococcal antimicrobial sensitivity data collected on the National Notifiable Diseases Surveillance System in Australia. It describes gonorrhoea resistance to seven antimicrobials and determines risk factors for resistance to first line antibiotics for the treatment of gonorrhoea in Australia. My epidemiological project consists of a mixed methods study investigating the reasons for inadequate treatment of syphilis in pregnancy in Australia. Presented are a descriptive analysis, case control study and a qualitative review of documents describing the clinical and public health management of congenital syphilis cases. Equitable access to antenatal care was found to be vitally important if elimination of congenital syphilis is to become a reality in Australia. Using the United States Centre for Disease Control and Prevention's Guidelines for Evaluating Public Health Surveillance Systems I conducted an evaluation of CARAlert, the national alert system for critical antimicrobial resistances. I found the system was simple, stable and flexible; however, there were concerns related to overall utility due to timeliness, data depth, sensitivity and representativeness. I recommended the purpose of CARAlert be reviewed and then made recommendations to improve timeliness, data depth, sensitivity and representativeness based on its intended aims and objectives. In November 2022, there was an outbreak of acute gastrointestinal illness associated with a single caterer who supplied food to several events in the Canberra region over three days. The outbreak was confirmed to be caused by foodborne norovirus. I undertook retrospective cohort studies on two days to identify risk factors for illness and found that foods associated with illness and foods prepared by an asymptomatic food handler with a recently ill child were similar. As part of the placement, I was also involved in the Mpox outbreak that commenced in May 2022 in Australia. I contributed to the drafting of the Series of National Guidelines (SoNG) for Mpox and was the technical writer for the permanent listing of Mpox on the National Notifiable Diseases List. I present this material as an additional thesis chapter. Finally, I describe and reflect on two teaching activities undertaken to meet course requirements.
Open Access
The metabolic role of the ferredoxin redox system in apicomplexan parasites
(2024) Henkel, Stephanie
Apicomplexan parasites, including Plasmodium sp. (the causative agent of malaria) and Toxoplasma gondii (causing toxoplasmosis), are a large phylum of unicellular, obligate intracellular organisms. They harbor an essential plastid-like organelle, named the apicoplast. As the apicoplast was derived via secondary endosymbiosis of a red algae, it possesses several metabolic pathways that differ from the human host, and since perturbing its function results in parasite death, the organelle is an attractive target for drugs. Within the apicoplast, an electron transfer system is required for several enzymatic reactions; this is provided by the ferredoxin redox system. It consists of the plant-type ferredoxin-NADP+ reductase (ptFNR) and its redox partner plant-type ferredoxin (ptFd). Via protein-protein interactions, ptFd provides electrons to several enzymes of the isoprenoid pathway and to the lipoic acid synthase (LipA), which is involved in the fatty acid synthesis. Thus, the plant-type ferredoxin redox system in apicomplexan parasites is a promising drug target due to its potential involvement in several essential metabolic processes. Recently published work demonstrated that ptFd in T. gondii (TgFd) is an essential protein. A tetracycline-inducible knock-down (ikd) approach was used to replace the endogenous single copy of TgFd with a myc-tagged copy (TgFdmyc) by double cross-over homologous recombination, and severe growth inhibition of parasites was observed upon Fd depletion. Metabolomic analyses show a 30% decrease in C14:0 fatty acids and a significantly lower gliding motility (20%) in the TgFd ikd strain compared to the TgFd ikd complemented (TgFd cikd) strain. In this thesis, targeted metabolomic analysis of the isoprenoid biosynthesis metabolites demonstrates that T. gondii Fd has an essential physiological function as an electron donor for the last two enzymes of the pathway. Furthermore, results of this work show that inhibition of the host isoprenoid biosynthesis contributes to the slow onset of death in TgFd knockdown parasites, indicating that the lack of isoprenoid precursors after induced Fd knockdown can to some extent be compensated by host-derived isoprenoids. Fd has been implicated in artemisinin resistance in P. falciparum; a single point mutation in P. falciparum ptFd (PfFd; D97Y) has been found in genome-wide association studies to be associated with artemisinin (ART) resistant Kelch13 mutant strains. In this thesis an ART resistant P. falciparum line containing the PfFd mutation iv was genetically reverted to PfFd wildtype using CRISPR/Cas9 and characterised in a ring stage survival assay, in order to evaluate the role of Fd in resistance to artemisinin. While preliminary results of this study have shown a decrease in proliferation of the transgenic ART-resistant P. falciparum line, meanwhile it has been demonstrated elsewhere that the Fd D97Y mutation does not contribute directly to ART resistance. A reverse two-hybrid system (RTHS) for TgFd and its interacting proteins TgFNR and TgLipA was established previously in E. coli, with the aim to use it with the split intein circular ligation of peptides and proteins (SICLOPPS) methodology for screening a large library of genetically encoded small cyclic peptides for their ability to interrupt protein-protein interactions of Fd. In this thesis, cyclic peptide libraries of different sizes were generated, which can now be used for further research to screen for peptides that interrupt the interactions between TgFd and TgFNR and TgLipA. Together, the findings of this study contribute to a better understanding of the metabolic role of Fd in T. gondii and P. falciparum, supporting its importance for the parasite’s metabolism and underlining its potential as a drug target in apicomplexan parasites.
Open Access
Engaging local communities in parent-based programs: lessons learnt from an Intimate Partner Violence and substance misuse intervention in Sri Lankan pre-schools.
(2024) Wallace, Polly
I undertook this doctoral research, based in Sri Lanka, to work with local communities to develop and implement a community-based intervention, and to document learnings along the way. The intervention was a community-based advocacy program that aimed to be affordable, adaptable, effective, sustainable, and community driven. It addressed complex issues of intimate partner violence (IPV) and substance misuse in a complex social setting (vulnerable communities of poor families/parents with children attending government preschools in two urban locations). My research focus was the process and insights gained from the community engagement undertaken during this intervention study, rather than the intervention study itself. My research aims were: to work with community to design and implement a community led training program that addresses a complex issue (IPV and substance misuse); and to review the process of engaging community in designing and implementing the program to understand how to maximise its effectiveness in the target population. This thesis documents the processes and lessons learnt. The research approach I used was iterative, joint, participatory and co-operative, and fostered co-learning between community and researchers. Community partners (including preschool teachers and service providers) were included early in the design of our intervention through meetings and workshops. Engaging partners in this way ensured they were empowered to contribute and guide each phase of the research to suit the needs of the community. I used a mixed methods approach to collect data, guided by the community-based participatory fundamentals as outlined by Israel et al (1998). With community participation, I developed and implemented a cross-sectional survey to collect the following data: quantitative data (demographic, IPV experience, substance misuse, help seeking behaviour); and qualitative data (attitudes and beliefs about IPV, drug misuse and help seeking behaviour). In addition, I documented observations and discussions during all field activities such as community meetings, training sessions for the survey delivery team, and workshops to develop the intervention. Analysis of the cross-sectional surveys found that IPV was present in the communities targeted, as was drug and alcohol misuse by fathers, and that use of available government services to address these issues was low. The reasons mothers experiencing IPV did not seek help included cultural or religious beliefs. The political settings in our study locations of Colombo and Galle influenced our data collection process, as did the long-term effects of living with trauma exhibited by members of our communities. Participation by fathers in the initial survey was low. To explore the reasons for this, and to inform future engagement of fathers, I undertook a literature review that aimed to: investigate how to successfully engage fathers in volunteer parenting interventions in low and lower-middle income countries; and to examine how to effectively retain fathers in such programs. Overall, this research found that improving the processes of designing, testing, and implementing the data collection and intervention by engaging the community early and at every phase using a community based participatory approach will support a better outcome. By engaging the community in this way, they are empowered through the process to increase control over their lives. The community should guide and lead projects that directly impact them, and delivery should be flexible in order to meet community needs. This research adds to the extremely limited evidence base for engaging fathers in voluntary well-being programs within complex social settings. Furthermore, the findings will be of practical use to field workers in the implementation of community-based programs in Sri Lanka and in similar settings internationally.
Open Access
Developing decision maker capabilities for robust and adaptive water planning
(2024) Rosello, Caroline
Decision makers in long-term water planning face the challenge of navigating "deep" uncertainty. Overcoming this challenge by being robust and adaptive requires deployment of appropriate capabilities and development of supporting tools and processes. This challenge is central to this thesis investigating "how to build decision makers' capabilities for robust and adaptive water planning". An interdisciplinary research (IDR) approach is used as a methodological framework, each chapter informing the next. A Dynamic Capabilities Project Design heuristic emerged organically throughout the thesis chapters, building on previously identified capabilities: 'absorptive capacity', 'creativity capability', 'agility capability' and 'resilience capability'. The approaches developed in the thesis are evaluated in terms of their contributions to deploying dynamic capabilities for robust and adaptive water planning. Chapter 2 sets the scene for river basin models to inform water planning. The historical perspective revealed the co-evolution of these models with societal changes and set the stage for understanding future challenges. These challenges informed a list of capabilities necessary for robust and adaptive planning. Chapter 3 focuses on augmenting predictive model capability for exploratory modelling uses. A Minimum Information Requirements (MIRs) approach is developed to augment model functionality and meet requirements of a robust and adaptive framework. The feasibility of MIRs was empirically validated for designing adaptive pathways using the Basin Futures software platform. MIRs appears valuable for rapid feedback early in the planning process, but additional mechanisms are needed to consider full user experience and support model uptake to inform planning. Chapter 4 introduces the Critical Appraisal Approach (CAA) to improve model uptake by enhancing the inclusion of model users in model software development processes. The CAA is expected to deal with some challenges to include model users by fostering shared understanding, coordinating development and design activities, and delivering market-based innovations. While promising, further mechanisms are required to consider differing contexts, challenges and requirements across scales and align information from decision-support tools with decision-making processes. Chapter 5 introduces a framework for operationalising scenario planning at finer and multiple scales (SPFMS). Developed by testing hypotheses regarding accounting for finer spatial and governance scales, SPFMS presents features suggesting potential contributions to polycentric governance systems, actionable decisions and dynamic capabilities for robust and adaptive water planning. However, the chapter emphasises the importance of considering institutional, societal and organisational contexts to assess their impact on the quality and proper use of outputs from decision-making processes to support robust and adaptive planning. Chapter 6 employs a capability approach to diagnose contextual barriers to capabilities for robust and adaptive water planning. This chapter underscores the pivotal role of good governance in enabling polycentric governance systems, actionable decisions, and overall dynamic capabilities for robust and adaptive water planning. The conclusion synthesises findings and describes the Dynamic Capabilities Project Design heuristic, derived from reflections on each chapter. Primary contributions of the thesis are 1) a set of tools and processes for managing deep uncertainty, and 2) a Dynamic Capabilities Project Design heuristic to couple and monitor complementary approaches for deploying capabilities for robust and adaptive planning.
Open Access
A Proposition towards A Praxis of Treaty with International Country | Portals out of The Garden of Non
(2024) Kimberley, Jonathan
'A Proposition towards A Praxis of Treaty with International Country | Portals out of The Garden of Non,' is a Creative-Practice-as-Research PhD thesis, seeking to decolonise Originary (so-called 'prehistoric') rock art (petroglyphs), towards the decolonisation of myself. The research question: "What is the truth-telling required of (post)Western culture in terms of revaluing the contemporary 'present' of Originary (so-called prehistoric) Neolithic petroglyphs in the UK and Europe, as portals of decolonisation?" The thesis is an artistic journey through the atemporal Originary of (Neolithic) petroglyphs at Ilkley Moor, West Yorkshire, UK; and South Tyrol, Northern Italy; guided through the paragon portal of First Nations' 'meenamatta petroglyphs' in lutruwita (Tasmania), Australia. My research in these three international locations is a solo praxis of transcultural responsibility, grounded in long-term collaborative art praxis with First Nations elders puralia meenamatta Jim Everett (plangermairreenner / pakana), and Gloria Andrews (pakana), in meenamatta country, lutruwita (Tasmania). A descendent of a First Fleet convict from the UK who became a free settler-coloniser of lutruwita in 1808, the project reflects on my personal sense of loss of deep-time ancestral knowledge within my cultural Originary in the UK and Europe. Archaeology dates petroglyphs in the UK and Europe as being made during the so-called Neolithic "transition" from hunter-gatherer to settler-farmer cultures (c.12,000-3,000BP). However, through the thesis, I suggest that this 10,000 year "transition" harbours far more complex cultural truths denatured through successive waves of Neolithic colonial invasion and contemporary nescience, resulting in an under-recognised deep-time cultural trauma within (post)Western contemporaneity. The result is what I call 'The Garden of Non'. A temporal plane of perpetual self-negation caused by a profound lack of truth-telling to Originary (proto)Western self, evident in the problematic term 'non-Aboriginal', which I argue is an inept deference to presumptive and premature (post)Western (post)coloniality and superficial decoloniality. Identifying and occupying this gap in (post)Western cultural gravitas through art praxis, the thesis advocates for a radical decolonisation of atemporal Originary cultural agency held within the petroglyphs of the UK and Europe, which I suggest can be understood as evidence of (de)colonial resistance during the Neolithic. The contemporary 'present' of Originary petroglyphs is paradoxically revalued within atemporal International Country, via extended journeys of pragmatic cultural pilgrimage through all three locations (UK, Italy, lutruwita) as integral to the generative development of the work. The resultant PhD thesis is One Work combining Writing and Exhibition. Grounded in the immersive immediacy of large-scale monochrome single-shot HD video projections, sound art and journal notes, combined with various forms of critical writing, a sculpture, and photography. The work is intended to evoke the open, rhythmic, recursive, non-definitive and searching form of creative praxis which interrogates dominant (post)Western modes of perceiving time and landscape. This exdisciplinary approach aims at dissolving methodological and cultural knowledge gaps created by the orthodoxies of (post)Western cultural disciplinarity and historicity. Inviting an artistic and cultural engagement 'through' the petroglyphs as portals for the decolonial dissolution of oneself 'into' International Country: 'being seen' by rock art as distinct from 'looking at' rock art.
Open Access
A national perspective on pandemics, plagues and preparedness in Australia
(2024) Lisson, Yasmin
In this thesis, I present the projects and activities that I undertook to fulfil the core competencies required for the Australian National University's Master of Philosophy in Applied Epidemiology (MAE) program during 2021 - 2022. During my MAE field placement, I was based at the Office of Health Protection at the Australian Government Department of Health and Aged Care. During this time, I completed four research projects that contributed to both local and national epidemiological work. I was involved in a range of public health activities and had the opportunity to work at the Australian Capital Territory Health Directorate (ACT Health) to support the COVID-19 response. The research projects comprise of an epidemiological study into national leptospirosis trends, an analysis of tuberculosis (TB) in the elderly, an outbreak investigation of SARS-CoV-2 in a childcare, and a feasibility study of influenza outbreak surveillance in residential aged care facilities in Australia. The following thesis also presents a selection of public health experiences and activities undertaken during the MAE program. This includes, conducting teaching activities, contributing to the COVID-19 response at the national and jurisdictional health authority level, undertaking a national analysis of TB notifications for the TB annual report, 2019 - 2020, and participating in routine activities within the communicable disease epidemiology and surveillance section. Together, these projects and public health experiences demonstrate my competency as a field epidemiologist and complete the requirements of the MAE program.
Open Access
The Reshaping of the Rules-based International order: Case Studies in Action
(2024) McNaughton, Anne
The term 'rules-based international order' has been used with increasing frequency over the past couple of decades almost as an aide-memoire to state and non-state actors alike, that global engagement is undertaken according to a particular set of rules. Yet there is little clarity about which ones or whose rules are operative or dominant. Hence, it is imperative that the issues around what is the rules-based international order and how it is being re-shaped be addressed. This thesis explores these questions and explicates the potential for a new sub-field of enquiry for the discipline of comparative law, embedded in a transdisciplinary framework. These analyses serve to demonstrate that the rules-based international order is a single framework to which comparative law and comparative lawyers are central to its interpretation. Acceptance of the fundamental principle that the most effective and desirable way of keeping the arbitrary abuse of political and economic power in check - and maintaining it that way - is through the existing rules-based international order which means that this offers the most effective way of a) Continuing to lift people out of poverty around the globe; b) Addressing the current challenges of climate change; c) Dealing positively with irregular migration; d) Countering pandemics such as the COVID 19 virus; and e) Protecting and promoting the values espoused in the order's core instruments. In order to facilitate this, effective communication of these fundamental principles is essential and especially so to those who currently feel excluded, 'left behind', unseen and unheard, disempowered and disenfranchised. Such communication requires flexibility and fluidity which is most efficacious in an environment freed from the constraints of disciplinary boundaries and open to an expansive lens on the rules-based international order with the potential of enlightening and useful perspectives. The thesis aims to investigate: a) The domestic consequences and disruption of globalisation and how these are to be scoped and understood (Chapters 3 - 6); and b) The potential contribution of a new conception of comparative law to the understanding of iterations arising from an evolving rules-based international order (chapters 7 - 8). The first aim is addressed through a series of case studies through which four foci of the thesis are identified: Institutions; Regulation; Integration; and Trust (Chapters 3 - 6). Building on the analyses derived from the eight case studies, the potential of a new sub-discipline of comparative law, namely international comparative law, to achieve a new understanding of the rules-based international order is explored. The central argument is that international comparative law has the potential to explain the collective commitment of non-traditional legal systems and thus offer fresh insights into how respect for the rule of law might be restored to the rules-based international order. IN adopting this approach the thesis also addresses the issues underlying this dissonance between aspirations at the international level and the sense of disempowerment and loss of agency increasingly felt locally in order to seek a way forward.
Open Access
Reintroductions through the lens of the refugee species concept, with case studies of Australian rodents
(2024) Smith, Kiarrah
Species reintroductions are a challenge that typically require significant resources to achieve success. In this thesis I argue that, for the special case of refugee species, conventional guidelines for reintroductions may contribute to the inefficient use of conservation and management resources. A refugee species is one that has become restricted to the subset of their formerly occupied habitats that are of suboptimal quality. As such, they may suffer poor conservation outcomes if only maintained in their currently occupied 'refuge' habitats. My overarching objective was to showcase how practitioners can reassess and approach the steps in a long-term reintroduction strategy in a way that could improve the conservation of these special cases. Chapter 2 tests the application of a Mini Safe Haven (MSH) approach in a trial reintroduction of a potential refugee species to inferred formerly occupied habitat. I hypothesised that providing a MSH would help a species to persist where it was naive to a key predation threat. I found that a MSH was more successful for supporting the persistence of released individuals than a more traditional soft-release approach. I highlight the broad applicability of MSHs as a complementary tool for wildlife conservation and pest impact-mitigation efforts, and recommend avenues for further refinement of the approach. In Chapter 3, I inform the design of reintroductions for a species through analysis of the hypothesis that its reproductive output in captivity was influenced by behavioural, demographic, experiential, pedigree, health, and physiological variables. This is a novel approach to formulating hypotheses to be tested in reintroduction trials and experiments. Although this method would be useful in a range of reintroduction contexts, it will be of particular benefit in cases where the focal species is a confirmed, or potential, refugee, because there is likely to be a high level of uncertainty around their post-release survival and reproduction. Chapter 4 tests a strategic translocation and assessment of microhabitat use, which included a biological interpretation of the null hypothesis that there is no difference in the focal species' microhabitat use between current refuge and inferred former habitats. I inferred insights to address ecological misconceptions and revise recommended restoration works and other release tactics for the focal species, as appropriate for the habitats assessed. Systematic implementation of this approach may help to reverse the impacts of shifting baseline syndrome (i.e., misconceptions of the norm that can arise when the knowledge of previous human generations is forgotten or ignored) that may pose an obstacle to the effective conservation of a refugee species. Finally, in the culmination of my thinking on refugee species throughout my candidature, Chapter 5 details a framework I developed to aid the identification and prioritisation of potential refugee species, which includes maps that could reduce the risk of ecological misconceptions attributable to shifting baseline syndrome. I found that approximately 60% of Australia's extant native rodents are potential refugee species; unrelated to their threatened status. I discuss the global applicability of this framework for complementing existing threatened species frameworks, and supporting ambitious (and potentially controversial) reintroductions.
Open Access
Design of Porous Metamaterials via GA-based Optimization Incorporating Geometry Constraints
(2024) Xiong, Cheng
Acoustic metamaterials exhibit unique bandgap characteristics that enable the manipulation of elastic waves at specific frequencies. The properties of these periodic metamaterials can be tailored by optimizing the material layout within the design domain. Many optimization methods have been proposed consisting of gradient_based and non_gradient_based methods. For gradient_based methods, establishing explicit mathematical formulas for optimization problems of acoustic wave propagation is usually challenging due to complex microstructures. In comparison, these explicit relationships are not required in non_gradient_based methods. Accordingly, genetic algorithms have become the most popular techniques. However, the major problem regarding this method is the enormous search space. This dramatically decreases the possibility of finding desired solutions in limited computational power. Additionally, ignoring the correlation information between elements gives rise to redundancy in searching. To cope with these drawbacks, a geometric_constrained strategy regarding connection of unit cell structure is proposed. The proposed framework has been proven effective in significantly decreasing the search space. The bandgap widths of optimized 2D structures employing the developed method under even 12*12 grids are much wider than those under 32*32 and 60*60 grids in conventional topology optimization. Three dimensional (3D) porous PnCs hold practical significance due to their omnidirectional absorption of acoustic waves. However, the increase in dimensionality results in a substantially larger search space and more complex connectivity issues. To address these challenges, the geometric constraint method developed for porous 2D PnCs is modified for designing porous 3D metamaterials. Besides, a pyramid symmetry is proposed for reducing the number of design variables. The effectiveness of the developed optimization framework has been demonstrated. Notably, optimization results have revealed that certain 3D structures, featuring only one type of mass lump, exhibit outstanding performance. These ultimately optimized structures are intricately linked to specific sequences of bandgaps. Compared with porous 3D single_phase PnCs, the increased configuration flexibility of porous 3D two_material PnCs indicates a broader range of potential for desired structures. However, the introduction of two materials in 3D PnCs leads to a significant search space than those with only one material. Meanwhile, there may be bonding issues at the boundary between two_material regions. To overcome these challenges, a method of 3D PnC construction by 2D mapping is proposed for reducing the number of design variables, and additional enclose constraints are proposed to handle different material property disparity. By incorporating these proposals into a genetic algorithm, the effectiveness of the optimization framework is demonstrated, showcasing its capability to reduce design variables and its applicability to two materials with various disparities. Hybrid metamaterials by combining acoustic and negative Poisson's ratio performance can offer multifunctionalities, making them adaptable to more application scenarios. Existing hybrid structures, however, usually exhibit narrow bandgaps that greatly restrict their potential engineering applications. Additionally, error_and_trial approaches commonly used are inefficient. Furthermore, widely utilized finite element analysis (FEA) renders high consumption of computational power due to its heavy reliance on mesh. To address these problems, an NSGA_ANN_based optimization framework is developed. The effectiveness and efficiency of the optimization framework have been verified. Compared to traditional FEA optimization, time consumption using ANN_based optimization is significantly decreased by 76%.
Open Access
Phylogenetic Model Selection via Machine Learning
(2024) Dong, Yanghe
Phylogenetic inference, which reconstructs evolutionary trees from DNA or amino acid sequences, is crucial for understanding the evolutionary histories of species on Earth. Model selection is a fundamental step in this process, determining the best-fit model for the data. However, classic maximum likelihood-based methods for model selection are computationally intensive. This study introduces a machine learning-based framework for amino acid model selection, consisting of three components: protFinder for selecting the best-fit substitution model, RHASFinder for identifying the appropriate rate heterogeneity model, and protFFinder for determining the use of empirical pre-estimated frequencies. Our framework is an order of magnitude faster than the widely used ModelFinder, while maintaining comparable accuracy.
Open Access
Captive breeding as a tool for species conservation
(2024) Bussolini, Laura
Conservation breeding programs and other forms of ex-situ management exist worldwide for a huge variety of taxa. These programs often have dual goals of preserving an insurance population in captivity and breeding individuals for release to supplement declining wild populations. Despite the popularity of ex-situ management, conservation breeding programs are costly, time-consuming, and have no guarantees of success. Species may fail to breed in captivity, develop deleterious adaptations to a captive environment, or survival post-release may be too low to contribute to wild population recovery. The goal of this thesis is to explore how conservation breeding programs are represented in the literature, understand what can be learnt from long-running programs, and utilise this knowledge to inform future recovery efforts. My primary study species is the orange-bellied parrot (Neophema chrysogaster), a critically endangered bird that has been bred in captivity since the mid-1980's. This thesis starts populating some of the gaps in the literature with the goal of asking important, real-world questions that could have direct implications on management and inform evidence-based decision-making both for this species and others. The first chapter of this thesis explains the background and study species in detail, framing how the subsequent research chapters contribute to these broader themes. Chapter 2 provides a scoping review of the literature, with a focus on understanding how conservation breeding and reintroduction programs are represented in the literature and highlighting research gaps. For any conservation breeding program to succeed, animals need to reproduce in captivity. Chapter 3 therefore attempts to understand what common factors could be influencing orange-bellied parrot reproductive success in a captive environment. To understand whether an early life in captivity might disadvantage a bird in future, in Chapter 4 I looked at physical growth of nestlings to determine what components of a individuals' early life might have carry-over effects on either physical growth or survival. This research demonstrates previously undetected carry-over effects of early life on survival, and potentially gives managers another tool to help improve first-year survival of both wild and captive-bred juveniles. Chapter 5 focuses on birds after they are released and how they integrate socially into the wild population. Social structure and integration are important both to have the safety of a large flock and for birds to learn important skills necessary for survival. I constructed social networks of wild orange-bellied parrots to determine whether captive-bred individuals differed socially from their wild conspecifics, and whether an individuals' social position impacts its probability of survival. Chapter 6 takes the themes and research explored in previous chapters and applies them to the future. I utilised data from existing conservation breeding programs to build a series of population models to gain a realistic understanding of how releasing individuals from captivity could impact the wild population of critically endangered swift parrots (Lathamus discolor). The final conclusion weaves together knowledge and insight from all the chapters with a focus on informing evidence-based decision-making processes regarding ex-situ conservation efforts.
Open Access
Auditors’ Evaluation of Subsequent Events: The Effects of Prior Commitment, Risk Factors, and Type of Accountability
(2016) Phang, Soon-Yeow
Recent international inspection reports indicate that there are deficiencies in the audits of subsequent events. What is less well understood is why these deficiencies occur. As the evaluation of subsequent events generally occurs toward the end of the audit process, this thesis examines whether auditors will commit to an initial view formed during the audit, and are therefore more likely to propose smaller audit adjustments to management in response to subsequent events. This thesis contains two studies. Study 1 examines the effects of prior commitment and risk of material misstatement on auditors’ evaluation of subsequent events. The findings from an experiment involving 87 auditors indicate that auditors propose a significantly smaller audit adjustment on a subsequent event when the event becomes known to them, after they have provided an initial view to management on the fair presentation of the financial statements. However, auditors are expected to be more skeptical when risk factors are present, so that they are more likely to adjust for subsequent events when the risk of material misstatement is high. Study 1 finds that when risk of material misstatement is high, auditors are less influenced by prior commitment. Therefore, they will propose to management a significantly larger amount of audit adjustment. Study 2 builds upon Study 1 by examining how accountability can mitigate auditors’ escalation behavior in evaluating subsequent events. The study specifically examines the effectiveness of two types of accountability—process versus outcome accountability—on auditors’ judgment decision-making. The results from an experiment involving 66 auditors demonstrate that auditors are more skeptical, by proposing a larger audit adjustment on a subsequent event when they are expected to justify their judgment process, than those who are expected to justify their judgment outcome. Study 2 provides evidence that auditors’ tendency to show escalation behavior is mitigated more by process accountability than by outcome accountability. That is, auditors’ proposed adjustments on subsequent events are less influenced by prior commitment to an initial view when the auditors are expected to justify their judgment process, rather than their judgment outcome. This study suggests a benefit of employing process accountability documentation in the audits of subsequent events.
Open Access
Applications of Computational Topology to Fusion Science
(2024) Bohlsen, Nicholas
Three novel applications of computational topology in the field of fusion science are developed. A procedure for the automatic classification of the orbits of magnetic field lines into topologically distinct classes using Vietoris-Rips persistent homology is presented and tested for a toy model of a perturbed tokamak. A method for estimating the distribution of the size of islands in the phase space of a Hamiltonian system or area-preserving map by sub-level set persistent homology is explored. This method is used to analyse the case of an accelerator mode island in the phase space of Chirikov's standard map and the possibility of detecting the self-similar island hierarchy responsible for anomalous transport in this model is investigated. Finally, it is suggested that TDA provides a toolset for the detection and characterisation of renormalisation group transformations which leave structures in Hamiltonian phase spaces invariant. The specific example of detecting the transform which leaves the neighborhood of a hyperbolic fixed point of the perturbed pendulum invariant is investigated using two different TDA approaches. Both of which are found to be partially sensitive to the symmetry in question but only weakly.

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