Medicine & Health

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Now showing 1 - 10 of 27
  • (2022) Cao, Jun
    Thesis
    This thesis focuses on the development and applications of magnetic resonance electrical properties tomography (MREPT), which is an emerging imaging modality to noninvasively obtain the electrical properties of tissues, such as conductivity and permittivity. Chapter 2 describes the general information about human research ethics, MRI scanner, MR sequence and the method of phase-based MREPT implemented in this thesis. Chapter 3 examines the repeatability of phase-based MREPT in the brain conductivity measurement using balanced fast field echo (bFFE) and turbo spin echo (TSE) sequences, and investigate the effects of compressed SENSE, whole-head B_1 shimming and video watching during scan on the measurement precision. Chapter 4 investigates the conductivity signal in response to short-duration visual stimulus, compares the signal and functional activation pathway with that of BOLD, and tests the consistency of functional conductivity imaging (funCI) with visual stimulation across participants. Chapter 5 extends the use of functional conductivity imaging to somatosensory stimulation and trigeminal nerve stimulation to evaluate the consistency of functional conductivity activation across different types of stimuli. In addition, visual adaptation experiment is performed to test if the repetition suppression effect can be observed using funCI. Chapter 6 explores if resting state conductivity networks can be reliably constructed using resting state funCI, evaluates the consistency of persistent homology architectures, and compares the links between nodes in the whole brain. Chapter 7 investigates the feasibility of prostate conductivity imaging using MREPT, and distinctive features in the conductivity distribution between healthy participants and participants with suspected abnormalities.

  • (2022) Aishah, Atqiya
    Thesis
    Obstructive sleep apnoea (OSA) pathogenesis is multifactorial with contributions from anatomical and non-anatomical endotypes. Current anatomical-orientated therapies are often inadequate or poorly tolerated with no pharmacotherapies available for OSA. Recent research shows that a combination of noradrenergic and anti-muscarinic agents increases upper-airway muscle activity (key non-anatomical endotype) and reduces OSA severity. Thus, my thesis aimed to investigate alternate therapies for OSA including novel pharmacotherapies targeted towards non-anatomical OSA endotypes as well as combining with existing anatomical approaches based on OSA endotype characterisation. Study 1 investigated the effects of the noradrenergic agent atomoxetine combined with 2 different anti-muscarinics (solifenacin or biperiden) with different receptor-selectivity profiles. Previous studies combined atomoxetine with the antimuscarinic oxybutynin which has broad receptor-selectivity. The goal was to gain mechanistic insight into specific antimuscarinic receptor subtypes for OSA pharmacotherapy which may also have a better side-effect profile versus oxybutynin. The different anti-muscarinics plus atomoxetine improved upper airway function and perceived next-day sleepiness in people with OSA albeit to a lesser extent compared to oxybutynin. This suggests broad or at least M2 muscarinic receptor selectivity may be important in mediating the efficacy of this drug combination for OSA pharmacotherapy. Previous studies with noradrenergic and antimuscarinic agents have been short term (≤1 week) and have not included different doses. Accordingly, in study 2, I investigated longer term (1-month) safety, tolerability, and efficacy of different doses of atomoxetine plus oxybutynin (ato-oxy) versus placebo. 1-month of ato-oxy was generally well-tolerated with a side effect profile consistent with the known profile of each agent alone. An 80/5 mg dosage combination of ato-oxy reduced key OSA severity metrics by ~50%. In study 3 I aimed to investigate if OSA endotype characterisation can be used to inform targeted therapy to resolve OSA in the clinically relevant group of patients who have an incomplete therapeutic response to oral appliance alone (~50% of patients). In these individuals, I systematically added existing anatomical therapies and emerging non-anatomical therapies (i.e., ato-oxy) according to OSA endotype characterisation. OSA was controlled in 50% of participants with addition of other existing anatomical interventions. Almost all the remaining participants were fully treated with the addition of non-anatomical pharmacotherapies. These novel findings provide important insight for the development of novel pharmacotherapy and combination therapy approaches informed by underlying physiological mechanisms for future treatment and management of OSA.

  • (2022) Ye, Pengpeng
    Thesis
    Introduction With rapid ageing of the population, falls have become a significant public health issue in China. Although falls prevention activities have been mandated in the National Essential Public Health Service Package since 2009, recommendations remain only as general advice and are not evidence-based. This thesis aims to generate an evidence base to support the integration of falls prevention programs for older people into the National Essential Public Health Service Package within the Chinese primary health care system. Methods This thesis contains five interrelated studies: an epidemiological study to understand the burden of falls among older people at the national and subnational level in mainland China from 1990 to 2019 using data from the Global Burden of Diseases, Injuries, and Risk Factors Study 2019; a scoping review to characterise existing evidence for fall-prevention interventions in community-dwelling older people in mainland China from 1990 to 2022; a policy review to document national healthy ageing-related policies from a health system perspective in mainland China from 2016 to 2020; a qualitative study to identify the perceptions of facilitators and barriers to implementation of falls prevention programs in primary health care settings in China; and a participatory design study to develop an implementation framework to support the integration of evidence-based falls prevention programs for older people into the National Essential Public Health Service Package. Results In mainland China, the incidence rate of falls in older adults increased substantially over the last three decades. Very few high-quality studies were identified to provide evidence on the effectiveness of existing interventions in China. The national policies on healthy ageing, including falls prevention, were fragmented and inadequate. At the primary health care level, major barriers, including the lack of confidence in delivering interventions, fragmentation in service delivery and limited multi-sectoral collaboration, posed challenges to the implementation of falls prevention in the National Essential Public Health Service Package. An implementation framework consisting of data, workforce, organisation, service and policy themes was jointly developed to support the integration of falls prevention into the National Essential Public Health Service Package. Conclusions In mainland China, falls remain as an ongoing health burden for older people. The challenges to preventing falls for older people primarily arise from low-quality evidence for intervention effectiveness, fragmented policy support and multiple barriers to implementation at the primary health care level. Establishing data-driven surveillance, generating high-quality evidence for the effectiveness of interventions, and creating a supportive environment are three key strategies to address these challenges and have the potential to integrate falls prevention into the National Essential Public Health Service Package within the Chinese primary health care system.

  • (2022) Subramanian, Shruthi
    Thesis
    Regulation of gene expression is crucial in establishing cell identity and function. Chromatin accessibility and binding of transcription factors to target sites in DNA and the assembly of protein complexes that regulate gene transcription is one of many levels of control. The protein products of such transcription may be components of a regulatory network that in turn influences the transcriptional output of itself and other genes. These gene regulatory networks (GRNs) establish and maintain cell-type-specific gene expression while their dynamic remodelling contributes to cell trajectories that direct differentiation of stem cells to more mature cell states. Human blood stem cells residing in the bone marrow continuously repopulate billions of mature circulating blood cells including red blood cells, white blood cells and platelets, each day throughout postnatal life. These haematopoietic stem cells (HSC) undergo a series of differentiating events to give rise to more mature and less stem-cell-like “progenitor” populations enroute to the production of mature circulating cells. Corruption of GRNs may lead to aberrant proliferation and differentiation of these progenitors resulting in bone marrow failure and/or leukaemia. As such, studying these networks in stem and progenitor populations in the bone marrow could provide vital information regarding normal blood cell development in humans. My study explores the interplay of a heptad of transcription factors- FLI1, ERG, GATA2, RUNX1, TAL1, LYL1 and LMO2, that play important roles during blood development. To map the binding patterns of these factors and construct gene regulatory networks in various primary stem and progenitor populations, I fractionated cells including HSCs, common myeloid progenitors (CMP), granulocyte monocyte progenitors (GMP) and megakaryocyte erythroid progenitors (MEP) using fluorescence-activated cell sorting and extracted chromatin from these populations for downstream assays. These included a) chromatin immunoprecipitation (ChIP) and ChIPmentation for genome-wide identification of active (H3K27ac, H3K4me3) and inactive (H3K27me3) histone marks, and transcription factor and co-factor (including CTCF and PU.1) binding. b) HiC to broadly classify the higher order 3D genome structures including compartments and topologically associated domains and c) H3K27Ac HiChIP to identify active looping structures between regulatory and promoter regions. I have shown that the heptad transcription factors exhibit shared and distinct patterns of binding across the stem and progenitor populations, with a preference for binding to regulator-like regions. These transcription factors exhibit combinatorial binding, with the binding of all seven factors showing highest significance. Interestingly, across lineage determining genes such as GATA1 and MPO, I noticed a dynamic accumulation of the heptad transcription factors at gene promoters as cells became more differentiated. Higher order genome architectures were conserved across the four cell types, while chromatin loops between gene promoters and distal regulatory regions showed cell type specificity. On resolving the regulatory network of the seven individual transcription factor genes, I found an interconnected network displaying combinatorial binding that was asymmetric across the four stem and progenitor populations. I was able to connect candidate distal gene regulatory regions with specific gene promoters and relate differential transcription factor binding to differential gene expression in relevant cell populations. Furthermore, I noticed patterns of binding that changed along the differentiation arc across the regulatory regions of genes expressed in mature cells. For example, at gene loci expressed in monocytes/granulocytes, there was an increase in GATA2, ERG, LYL1 and LMO2 and a decrease in TAL1 binding in GMP with respect to other populations. In contrast, at regulatory regions of genes expressed in erythroblasts/megakaryocytes, I noticed an increase in TAL1, GATA2, LYL1 and LMO2 and a concomitant decrease in ERG binding in MEP. Finally, by combining datasets generated in this study, I clustered 85,100 accessible regions present in HSPCs based on their regulatory potential and used transcription factor binding in stem and progenitor populations as a scaffold to map usage of candidate gene regulatory regions during hematopoietic stem cell differentiation. Taken together, my study provides a comprehensive characterisation of the genome wide gene regulatory landscape in rare human blood stem and progenitor cells. The results of this study constitute an important framework for accurate analysis of aberrant regulatory networks in leukemic cells and assist in devising better therapeutic strategies.

  • (2023) Bulbul, Latifa
    Thesis
    Normally, the neural control of the brain’s respiratory centre (ventral respiratory column – VRC) alters to accommodate ventilatory requirements in response to respiratory demand. Disruption of the tonic drive to the VRC has been implicated in several respiratory diseases, including chronic obstructive pulmonary disease. However, the pathophysiology of central respiratory circuit dysfunction and subsequent disruption of autonomic respiratory regulating mechanisms under these conditions is unknown. The altered brainstem peptidergic circuits could contribute to this disruption. Moreover, persistent inflammation is involved in the pathogenesis of chronic respiratory diseases, which are exacerbated by chronic hypercapnia and cigarette smoking. Therefore, we investigated the peptidergic alterations and inflammatory responses in mouse brain respiratory regions following hypercapnia and smoking. In Chapters 3 and 4, mice were exposed to hypercapnia or room air for 6 hours, 10 days, or 14 days. In Chapter 3, immunohistochemistry data revealed that galanin immunoreactivity levels remained unchanged in respiratory regions following 10 or 14 days of hypercapnia. Galanin terminals were closely apposite to neurons expressing excitatory Somatostatin (SST) or inhibitory Parvalbumin (PV) in the VRC. In Chapter 4, stress (CORT) and inflammatory responses (interleukin (IL) -6 and IL-1β) in the circulation and brain IL-1β were measured using ELISA. Plasma CORT levels were increased after 10 days but remained unchanged after 6 hours or 14 days of hypercapnia. Cytokine levels were unchanged in circulation but IL-1β levels were higher in the cerebellum following 6 hours and, in the hypothalamus, and VRC following 10 days of hypercapnia. In Chapter 5, dams and their adult offspring were exposed to 12 cigarettes per day or room air (dams for 6 weeks before mating until the offspring were weaned, and the adult offspring for 1-month) prior to culling. In the VRC, IL-1β levels were decreased in dams and increased in offspring following cigarette smoke. Overall, the close apposition of galanin terminals to PV and SST neurons in the VRC indicates that multiple mechanisms are used to generate respiratory rhythm. Hypercapnia or cigarette smoke induces inflammation in the respiratory neural circuits, demonstrating how these two factors may contribute to respiratory irregularities in patients with chronic respiratory diseases.

  • (2022) Truong, Tuan Kiet Peter
    Thesis
    Azacitidine (AZA) and Decitabine (DAC) are frontline hypomethylating agents (HMAs) effective at altering the natural course of Myelodysplastic Syndromes (MDS). Unfortunately, treatment resistance and failure are hallmarks of HMA therapy. Developing effective HMA combinatorial therapies is challenging as the underlying mechanisms governing AZA response remain uncertain. To address this, I leveraged genome-wide CRISPR-Cas9 dropout screening in a human MDS cell line to identify novel synthetic lethal gene-AZA relationships. First, I looked to ascertain a clinically relevant treatment dose of AZA in the MDS-L cell line through using a combination of cell viability, mass spectrometry, and transcriptomic approaches. I identified a concentration of AZA that exerted more anti-proliferative rather than direct cytotoxic effects, triggered global hypomethylation, and induced clinically relevant transcriptomic signatures. Using the defined dosage, I performed a genome-wide CRISPR-Cas9 screen in the MDS-L cell line where I identified and validated TOPORS as a bonafide target that confers hypersensitivity to AZA therapy. Given AZA is also for Acute Myeloid Leukemia (AML), I determined whether targeting TOPORS could be generalized. Targeting TOPORS significantly sensitized a panel of AML cell lines to AZA. Importantly this combinatorial approach did not functionally impair healthy CD34+ cells and was relatively less toxic compared to MDS cells. As TOPORS is implicated in regulating the DNA damage response through SUMOylation-dependent mechanisms and AZA is known to induce genome instability, I hypothesized that TOPORS contributed to genome stability in response to AZA. TOPORS-edited MDS-L were primed for apoptosis as they accumulated extensive DNA damage and arrested at a late S- G2/M checkpoint in response to AZA. Concordantly, transcriptomics and nuclear proteomics revealed a disruption in the DNA damage response. As there are currently no pharmacological inhibitors of TOPORS, to enable clinical translation I sought to target its key biological processes. Here I piloted the combination of TAK-981, a novel inhibitor of SUMOylation, with AZA or DAC. Combining TAK-981 and AZA was found to be additive in MDS-L and synergistic in MOLM-13, while TAK-981 synergized with DAC in both MDS-L and MOLM-13. Collectively, my data provides a framework for the translation of TAK-981 in combination with HMA as a potential therapeutic strategy for patients with MDS or AML.

  • (2023) Albanese, Bianca
    Thesis
    The incorrect use of child car restraint systems is a longstanding and widespread problem. While child restraints offer good protection, incorrect use increases the risk of death and injury to child occupants in a crash. Strategies to address incorrect use continue to be developed and implemented. However, no strategy has successfully addressed the complexity of interactions between the users i.e., the adult, the child, and the restraint. There is a need to engineer design-based solutions that target the ergonomics of child restraints from a user-centred approach. This thesis presents four interrelated studies evaluating the potential of targeted restraint design to reduce incorrect use. A multimethod, user-centred approach was used to identify restraint design features or clusters of design features with the lowest propensity for misuse by both adult and child users. A diverse range of methods were used to capture the breadth of interactions that occur between the child, the adult and the restraint. Methods include in-depth observation studies, a laboratory trial, a driving trial and the retrospective analysis of naturalistic driving data. Descriptive and complex multilevel statistical analysis techniques were used, including those that allow for the control of potential confounders and clustering of data, as well as content analysis for qualitative data. Results from this body of work demonstrate the substantial scope for reducing incorrect use of child restraints through attention to their design. To realise this reduction, there is a need to shift to user-centred design that recognises the usability of a restraint as a precedent to its utility. Design that incorporates features with a low propensity for misuse by both the adult and child users will ensure a system offers the level of crash protection for which it was designed. There is a need to further investigate different restraint systems, with different features, across all tasks of restraint use from a user-centred approach.

  • (2023) Epiu, Isabella
    Thesis
    Across the world, altered breathing states like shortness of breathing are common presentations, more recently with millions infected during the COVID-19 pandemic. However, most people with chronic pulmonary diseases have longstanding shortness of breath. Dyspnoeic patients may suddenly become cognitively aware of their breathing difficulty, often in association with underlying infection, hypoxemia and/or hypercapnia, which are triggers to seek medical care. However, some patients with asthma and Chronic Obstructive Pulmonary Disease (COPD) lose lung function very slowly, adapt to it and present late in the course of their disease, without a preceding sudden deterioration. Therefore, further investigations to understand neural processing of respiratory stimuli in various respiratory diseases is paramount. In this thesis, I focus on respiratory motor impairments in COPD, one of the leading causes of morbidity and mortality worldwide. Novel investigations included swallowing assessment, inspiratory muscle responses to sudden airway occlusion, and neural perception including airway sensation, and EEG studies. I also built a decision analytic cost-effectiveness analysis model. Using bedside swallowing tests, I found lower tongue strength in this Australian sample, compared to the published weighted averages. The swallowing capacity was lower in the COPD than control groups, which also had a higher respiratory rate. Around 30% of the COPD group showed clinical signs of airway invasion, and their inhibitory reflex was delayed. The COPD group also had a reduced perception of the airway loads that could predispose them to aspirate, further increasing the risk of complications like pneumonia or acute exacerbations, which together reduce the quality of life of patients with COPD, some of whom may require intensive care unit (ICU) admission for respiratory failure and infection. This thesis provides further evidence of the swallowing, respiratory and cognitive impairments in COPD for targeted approaches to improve the neural control of breathing in this group. From the cost-effectiveness swallowing and respiratory sensation assessment (SwaRSA) model, the four SwaRSA strategies were all effective in reducing COPD exacerbations. The questionnaire based swallowing score alongside a modelled rehabilitation was the most cost-effective strategy, saving $8800 AUD per QALY gained. In people with COPD, SwaRSA testing, and a subsequent intervention appears costeffective relative to no-SwaRSA screening. The SwaRSA model is ready to be studied in a randomised trial to enable its implementation in routine practice at respiratory clinics and/or critical care units.

  • (2021) Barnet, Megan
    Thesis
    Effective anti-cancer response to checkpoint inhibitors can be paired with systemic immune activation, manifesting as auto-immune toxicity. This may represent a host predisposition to response (and toxicity); a genetic equivalent to the paired increased in response and toxicity seen with combination drug treatment. Germline contribution to anti-PD1 response and toxicity, however, is not well studied. Nucleotide-binding oligomerisation domain 2 (NOD2) is an innate immune receptor involved in maintaining immune homeostasis and its impairment is associated with autoinflammatory and inflammatory disease, most notably Crohn’s Disease; a form of inflammatory bowel disease. Germline variation in NOD2 could predispose to heightened response to anti-PD1 treatment. I identified compound heterozygous mutations within NOD2 (expected general population genotype frequency ~1 in 10,000) in a patient who experienced systemic “abscopal” response of metastatic melanoma following focal radiotherapy, simultaneously with a flare of Crohn’s colitis. To further explore the concept of germline contribution to anti-cancer response following immune stimulation, I then recruited 144 patients treated with single-agent anti-PD1/PD-L1 for metastatic non-small cell lung cancer (NSCLC). I selected patients with “high response” (n=40) or “non-response” (n=10) for germline whole genome sequencing. In these 50 individuals, rare and common variants were analysed and compared to general population and patients with NSCLC. To further explore the genetic association, we generated a translational mouse model truncating the candidate gene, NOD2, using CRISPR-Cas9 gene targeting (Nod2fs). Mice were transplanted subcutaneously with a syngeneic, mismatch repair deficient tumour (MC38). Tumour regression and time to progression following treatment with anti-PD1 antibody was improved in Nod2fs compared with wild-type (Nod2wt) animals and was accompanied by more effector memory subtype tumour infiltrating CD4 and CD8 T cells. Single cell gene expression analysis of Nod2fs compared with Nod2wt splenocytes provided insight into potential mechanism of the observed effect. Host predisposition to response and toxicity to immunotherapy represents an extensive and largely unexplored area. Further work is needed to define the potential role of germline immune variants as biomarkers for response and/or toxicity and as therapeutic targets. Germline analysis should be performed where possible alongside tumour analysis in order to identify novel tolerance checkpoints such as NOD2 with potential to modulate immune response to cancer.

  • (2022) Kelly, Shane
    Thesis
    Autoimmune diseases represent a significant cause of morbidity and mortality, for which there is no cure. The pathogenesis of autoimmunity is unknown. Identifying and profiling antigen-specific lymphocytes has the potential to advance our knowledge of disease pathogenesis, and potentially offer more targeted therapy. The overall aim of this thesis was to identify antigen-specific cells in a range of autoimmune diseases and characterise them proteomically, transcriptomically and genomically using novel sequencing technologies. The experimental design comprised identifying pathogenic B cells from peripheral blood by flow cytometry, followed by single cell sorting and sequencing by G&T seq. Those cells confirmed as antigen-specific then underwent in depth genomic, transcriptomic and proteomic analysis. For the cryoglobulinaemia project I succesfully charcaterised antigen-specific B cells in a pateint who had a rare IgA RF-producing clone. It harboured nonsense mutations in TNFAIP3 and in BCL-10, both of which it is anticipated lead to increased NFKB signalling. For the MAG neuropathy project I successfully characterised antigen-specific B cells in all three patients. All had multiple IgM kappa clonal populations, although for two I was able to show that they arose from a common progenitor, despite being heavily mutated. Essentially all clones, irrespective of MAG specificity, harboured a MYD88p.L265P mutation. I also identified a number of other somatic mutations, including in CXCR4 in one patient, and in SIGLEC11 which was present in only one clonal branch of another patient. For the polyclonal models of autoimmunity project (ie PR3-AAV, MPO-AAV and Ro60+SjS) I was successful for two of the three diseases, although the cell frequency was exceedingly rare. In the one patient (who had PR3-AAV) where I isolated enough antigen-specific B cells to perform a meaningful analysis it was notable that they were enriched for IgG4, lambda, J6 gene usage, IGHE expression, and demonstrated low levels of somatic hypermutation. In summary in this thesis I was successful in most of my aims in identifying and multiomic profiling of antigen-specific B cells in a range of autoimmune diseases including cryoglobulinaemic vasculitis, MAG neuropathy and PR3-AAV. However given the significant challenges in isolating such cells in polyclonal models of autoimmunity, consideration needs to be given in sourcing alternative samples to peripheral blood and/or modifying the current experimental strategy.