Over the last 10 years we examined complex multidirectional interactions between the digestive system and osteoporotic fractures focusing on pathophysiological and clinical issues of liver-bone relationships. These included: vitamin D, vitamin K and parathyroid hormone in chronic liver and pancreatic diseases (2 papers: [1, 2]); associations between liver function, bone-mineral biomarkers, indices of iron metabolism and adipokines (leptin, adiponectin, resistin) in orthogeriatric patients (3 papers: [3-5]); diagnostic and prognostic indicators of osteoporosis, fractures, and in- hospital outcomes (5 papers: [6-10]). A shortened overview of our main findings is presented.

Gastric cancer (GC) is lethal, with standard treatments offering little benefit. The immune component of the tumour microenvironment has been shown to highly influence GC progression and response to immune checkpoint therapies (ICTs). Tumour-associated macrophages (TAMs), one of the most abundant immune infiltrates in GC, are known for their plasticity and multiplicity of function. An abundance of TAMs is commonly associated with poor survival of cancer patients. However, their influences on survival in the GC setting are inconsistent between studies possibly due to a range of activation states and phenotypes and require further investigation. In this study, a human GC cohort was interrogated by multiplex immunohistochemistry and analysed using comprehensive bioinformatic spatial and transcriptomic techniques to investigate the spectrum of TAMs in GC. Their spatial distribution within the tumour and association with tumour-infiltrating T lymphocytes (TILs), GC microenvironment and clinical outcomes were determined. In silico and in vivo models were used to validate these findings. Seven predominant TAM populations were identified in a complexed multi-dimensional spectrum model. Each TAM population exhibited a unique combination of cellular markers and correlated with a specific environmental signature resembling published characteristics of in vitro-polarised macrophages. The spatial distribution pattern of TAMs was highly-related to their distance to tumour cells but was independent of their overall densities. This distribution pattern was described as an overall decrease in CD206, and increases in IRF8, CD68 and CD163 as TAMs near the tumour cells. The CD163+ TAMs expressing concurrent high CD68 (CD68++CD163+) were associated with improved patient prognosis. These TAMs co-existed with the CD3+CD8+ TILs within the same tumour. NOX2 and PD1 were identified as functional markers for these immune populations, respectively, and an upregulation of these markers on corresponding cells was observed when the cells were in proximity with each other. Inclusion of these functional markers improved the survival predictive value of these immune populations compared to using overall cell density, and suggests that these immune cells may be functioning through the NOX2/PD1 axis. This may reflect the antigen-presentation ability and activation statues of the TAMs and TILs, respectively. TAMs is commonly correlated with high programmed death ligand 1 (PDL1) expression, a current ICT target, in the literature. In this study, the CD68-only and CD206+ TAMs were identified as specific TAM populations that exhibit high PDL1. This indicates that these TAMs may be particularly associated with immunosuppression and may serve as a complementary biomarker for ICTs in addition to PDL1. An in vivo macrophage depletion protocol was established in an immune-incompetent mouse model to further test these hypotheses on macrophage subtypes. Concentrations of different clodronate-liposome constructs were optimised for investigating tumour invasion and progression in the absence of overall and CD206+ macrophages. In conclusion, this Thesis (i) establishes methods which allow investigation and reveal the spatial heterogeneity of TAMs in human GC, and (ii) identifies a specific TAM/TIL pair and PDL1+ TAM populations that may be utilised as potential therapeutic targets and biomarkers of patient survival and response to ICT.

Traumatic brain injury (TBI) is a leading cause of death and morbidity worldwide, and is also associated with the later onset of other neurodegenerative conditions. However, the pathogenesis of TBI is poorly understood, and there is currently no treatment known to improve long-term outcomes. Hyperphosphorylated tau has been implicated in the pathogenesis of TBI, where the accumulation of hyperphosphorylated tau has been associated with long term neurological deficits. The presence of protein inclusions consisting of TAR DNA-binding protein 43kd (TDP-43) are a pathological hallmark in motor neuron diseases (MND). Notably, TBI is a risk factor in the development of MND, and motor neuron loss, corticospinal tract degeneration and TDP-43 abnormalities have also been observed in individuals with a history of TBI. While preliminary studies suggest that each of these proteinopathies may occur in the aftermath of TBI, the role of tau and TDP-43 remain poorly understood in the TBI context. In this thesis, I examined the role of tau and TDP-43 using wild type and transgenic animal models in the context of TBI and repeated mild TBI. It was found that TBI resulted in abnormalities in both tau and TDP-43, and this was associated with functional consequences. It was also found that that treatment with sodium selenate reduced hyperphosphorylated tau and improved pathological and functional outcomes in a model of repeated mild TBI. Taken together, tau and TDP-43 pathologies appear to have an important role in preclinical TBI and represent potential pharmaceutical targets to improve outcomes.

Successful epilepsy surgery transforms the lives of patients with drug-resistant epilepsy. Yet, the seizure recurrence seen in a significant proportion of patients calls for improved selection of surgical candidates. The findings of this study, focusing on the role of 18FDG-PET as a metabolic predictor of memory deficits and seizure outcomes in patients with drug-resistant mesial temporal lobe epilepsy (MTLE) following an anterior temporal lobe resection, demonstrated the laterality-specific differentiality of metabolic patterns, with significantly higher rates of bitemporal hypometabolism observed in right MTLE patients heralding a 5-fold increased risk of postoperative seizure recurrence, whereas left MTLE patients exhibited more extensive ipsitemporal hypometabolism. While the real-world clinical utility of 18FDG-PET in predicting memory deficits in patients with MTLE is limited, the study findings suggest the need for further research into the role of impaired arbitrary learning as a potential biomarker of bitemporal epileptic network involvement in patients with right MTLE as well as the need for using task-specific neurocognitive markers in the evaluation of epilepsy surgery candidates. Lastly, while the extent of the postoperative gliosis was not associated with late seizure recurrence, time-related postoperative changes could offer further insights into the role of glial astrocytes in epileptogenesis and neuroprotection. The study findings enhance our understanding of laterality specific epileptic networks and have the distinct potential to advance patient care by influencing the selection of surgical candidates and assisting with preoperative patient counselling.

In patients with chronic kidney disease (CKD), disordered mineral metabolism, deterioration in bone quality and extra-skeletal calcification constitute the clinical syndrome known as chronic kidney disease – mineral and bone disorder (CKD–MBD). Renal osteodystrophy (ROD) is the skeletal component of CKD-MBD, and refers to abnormalities of bone turnover, mineralisation, volume, linear growth or strength. The erosion of bone quality in CKD confers an excess fracture risk through stages of CKD, is not attenuated by kidney transplantation and can be associated with persistent hyperparathyroidism in kidney transplant recipients (KTRs). The currently available tools in clinical practice have limited utility in evaluating ROD and add to diagnostic and therapeutic uncertainty in this area. The mechanisms of bone loss after transplantation and their relationship with changes in bone structure and markers of mineral metabolism are poorly understood. Tackling these challenges requires an enhanced understanding of the pathophysiology of ROD and development of tools for accurate evaluation of renal bone disease. The advent of high-resolution (HR) imaging and newer biomarkers has provided greater insight and generated research interest in CKD-MBD. HR imaging studies of bone microarchitecture have highlighted the contribution of cortical bone structure to overall bone strength and its association with hyperparathyroidism and bone fragility in KTRs and patients with CKD. HR magnetic resonance imaging (MRI) using customised processing techniques has proven to be an excellent non-invasive tool for studying bone microarchitecture. My research explored prevalent bone and mineral metabolism abnormalities and the role of various contemporary imaging modalities, in particular MRI, in evaluation of ROD. Chapter 2, a cross-sectional study of histological abnormalities of bone in a relatively young cohort of potential KTRs, highlights severe deterioration of cortical microarchitecture but predominantly normal trabecular parameters, reinforcing the importance of comprehensive cortical bone evaluation in patients with CKD. Chapter 3 describes a proof-of-concept evaluation of bone microarchitecture in patients with CKD using MRI with findings correlated to those obtained by bone biopsy and other bone imaging techniques (Dual-energy X-ray absorptiometry, DXA; peripheral quantitative computed tomography, pQCT; trabecular bone score, TBS), to highlight advantages of MRI as a diagnostic tool in ROD. MRI demonstrated significant and relevant associations with important bone biopsy and DXA parameters but could not establish a reliable relationship with bone turnover. No associations were observed with bone turnover markers. This study also underlined the inherent heterogeneity of bone microarchitecture at differing skeletal sites and the pitfalls of assessing these and comparing imaging modalities with vastly different resolutions and protocols. The study described in Chapter 4 monitored changes in bone density and microarchitecture in KTRs over one year after transplantation using MRI, DXA, pQCT and TBS and biomarkers. Trabecular bone structure and connectivity deteriorated independent of changes in BMD but associated with PTH levels, complemented by significant reduction in TBS. Unlike in other contemporary studies, there was no progressive deterioration in cortical bone. Chapter 5 describes an exploration of mineral metabolism and clinical outcomes after transplantation in a large cohort of KTRs, focusing on the impact of discontinuation of cinacalcet on these parameters. Persistent post-transplantation hyperparathyroidism and hypercalcaemia, consistent with available data, was demonstrated, but the clinical significance of these mineral metabolism markers was unclear. Historically, aluminium deposition in bone was recognised as a major cause of adynamic bone disease but is now less relevant due to increasingly rare use and phasing out of aluminium-containing phosphate binders in clinical practice. However, many centres continue to routinely screen dialysis patients for aluminium levels. The study in Chapter 6 examined the utility of routine testing of serum aluminium levels in the haemodialysis population in our centre via a retrospective audit of tests performed on 755 patients over four years. Only 0.5% of 2058 test results matched criteria for toxic aluminium levels, with no evidence of clinical toxicity and progressive reduction in the proportion of elevated aluminium levels over the years. This led to cessation of routine testing of aluminium levels in our dialysis unit. In conclusion, clinical studies presented in this thesis add to the increasing body of literature about the bone abnormalities prevalent in CKD and highlight the novel use of MRI in assessing bone quality in CKD and in KTRs. Overall, non-invasive HR imaging, particularly MRI, has the potential to close the vast gap between screening of BMD using DXA and comprehensive diagnosis by bone biopsy. This needs validation in large trials with hard clinical endpoints and should be viewed in the context of a plethora of technical caveats and issues of high cost and availability. The utility of MRI (and other HR imaging) would be enhanced by more accurate and reliable non-invasive markers of bone turnover and mineralisation. These challenges are significant, but not insurmountable. A coordinated, multidisciplinary, patient-focused effort is needed from the nephrology research community to address the unmet needs of patients with ROD and CKD-MBD.

Plasmodium falciparum is a protozoan parasite that is responsible for the most severe and fatal form of human malaria. In addition to the canonical histones, the parasite possesses divergent and Apicomplexa-specific histone variants. The N-terminal tails of histones in P. falciparum are extensively acetylated and carry unique acetylation marks. P. falciparum relies on this network of histone post-translational modifications and interactive, chromatin-associated proteins to modulate its gene expression. Integral to this process are bromodomain (BRD) histone reader proteins which interact with acetylated lysine. The rapid emergence and development of human BRD inhibitors for the treatment of many diseases prompted our project to study P. falciparum BRD proteins (PfBDPs) and assess their value as potential, novel, antimalarial therapies. There are eight bromodomain proteins in P. falciparum. P. falciparum bromodomain protein 1 (PfBDP1) is critical for the coordinated regulation of invasion genes and is essential for parasite survival. In addition, a piggyBac transposon mutagenesis forward-genetic screen in P. falciparum showed that PfBDP2, PfGCN5 and PfTAF2 are essential for the parasite during the blood, asexual life cycle. Recent studies showed that PfBDPs can interact with histone acetylations and transcription factors as well as other chromatin-associated proteins to form a network of histone reader complexes. This thesis investigates the functions of PfBDP4 and PfBDP3 and their importance to parasite survival. Conditional disruption of PfBDP4 caused a growth defect from which an essential role in the blood stage, asexual life cycle was inferred. Chromatin immunoprecipitation sequencing (ChIP-seq) indicated that PfBDP4 was enriched upstream of highly expressed genes, especially genes that are important for parasite invasion. In addition, PfBDP4 shares genomic localisation with an Apicomplexa-specific transcription factor AP2-I and the BRD protein PfBDP1, confirming their interaction in a complex as observed in previous studies. PfBDP4 was also enriched upstream of genes that are involved in metabolic pathways such as proteolysis and phosphorylation which demonstrates that PfBDP4 likely regulates multiple critical pathways of the parasite. In contrast, parasite growth was not inhibited by knockdown of PfBDP3, which is consistent with previous studies. In trophozoites, PfBDP3 was enriched in heterochromatin or compact chromatin, where genes are generally silenced. As PfBDP3 has two BRDs, PfBDP3 may act as a scaffold for proteins that are associated with heterochromatin. Finally, hit compounds from collaborators biochemical screens of recombinant PfBDP BRDs were tested for P. falciparum in vitro growth inhibition. Potent hit compounds were identified. These confirmed hits should now be tested for specificity and selectivity to confirm that they are acting on-target and do not cause cytotoxic effects in human cells. Overall, this study showed that PfBDP4 is associated with active promoters of select processes and its BRD is essential for the parasite survival while PfBDP3 is associated with heterochromatin and is non-essential during the asexual life cycle. This work also highlighted PfBDPs as novel drug targets in P. falciparum and demonstrated the feasibility of identifying potent PfBDP inhibitors as candidates for future investigation.

Background: Dual energy X-ray absorptiometry (DXA), as the most established tool for the assessment of bone fragility, has limitations in identifying individuals with increased fracture risk. Peripheral quantitative computed tomography (pQCT) can provide additional information about bone fragility compared with DXA alone. The three-dimensional data acquired by peripheral quantitative computed tomography are a potential source to generate finite element analysis (FEA) models to further estimate bone mechanical properties. Aims: This doctoral project aimed to establish a FEA model based on pQCT data (pQCT-FEA) and to investigate its role in the assessment of bone fragility in three populations: older patients with low-trauma fracture, women following surgical menopause and young women with type 1 diabetes mellitus (T1DM). Methods: This project consisted of four parts. In the first study, FEA models were established using distal radius pQCT cross-sections and were validated against forearm failure load obtained from mechanical testing in laboratory. In the second study, variables of DXA, standard pQCT and pQCT-FEA were compared between older patients with low-trauma fracture and controls. Their ability to classify the two groups were also examined. In the third study, bone loss was examined between women who received and who did not receive hormone therapy following risk reducing bilateral salpingo-oophorectomy (RRBSO) and controls. In the fourth study, comparison was made in DXA, standard pQCT and pQCT-FEA variables between young women with T1DM and age-, height- and weight-matched controls. Results: For Study 1, high coefficient of determination (highest r2 = 0.86) was observed between pQCT-FEA stiffness variables and forearm failure load. For Study 2, there were significant difference in pQCT-FEA stiffness variables between fracture patients and controls. Enhanced area under the receiver operating characteristic curve (AUROC) was found in pQCT-FEA stiffness variables in both females (0.83 for shearing stiffness) and males (0.81 for bending stiffness) compared with DXA variables (0.71 and 0.62, respectively, for total hip areal bone density). For Study 3, an average 14.1% decrease was observed in bending stiffness by pQCT-FEA in women who did not receive hormone therapy following surgical menopause. Although DXA can also detect bone loss over the 24 months follow up, the change was smaller (up to 6.0% at the femoral neck). At the 24 months visit, pQCT-FEA variables differ between women following surgical menopause and controls. For Study 4, no difference was observed in DXA measurements between young women with T1DM (p >= 0.08) although there was a trend towards lower aBMD at the lumbar spine in T1DM subjects than in controls after adjustment for confounders (p = 0.053). Significantly lower stiffness by pQCT-FEA was detected in young women with T1DM. Conclusions: pQCT-FEA has good ability to predict bone failure load obtained from mechanical testing, which facilitates its application in clinical settings. It can provide additional information about bone strength deficits in patients with fragility fracture, women following surgical menopause and young women with T1DM. These findings warrant future study using pQCT-FEA for the assessment of bone fragility in other populations.

Abstract Background: Antimicrobial stewardship (AMS) programs are well established initiatives for the rationalisation and conservation of antimicrobial use. Surgical antimicrobial prophylaxis (SAP) has been identified as the most common indication for antimicrobial use in Australian hospitals, with low rates of appropriateness in both public and private hospitals. There is a paucity of literature targeting surgical AMS programs that are applicable to both sectors. Aims: The aim of this PhD is to explore challenges in SAP prescribing and strategies for the optimisation of SAP prescribing in Australia. Developing an understanding of current SAP prescribing practices and factors that influence SAP prescribing decisions, informs a framework for surgical AMS. The framework aims to address identified issues and support implementation and sustainability of surgical AMS across all Australian hospitals. Methods: A mixed-methods design integrating quantitative and qualitative research (within a pragmatic paradigm) constituted the overarching methodological approach in this thesis. Five projects were completed. In project 1, the implementability of the national SAP guidelines was assessed. In projects 2, 3 and 4, multiple logistic regression analyses were adopted across the Surgical National Antimicrobial Prescribing Survey dataset to investigate any potential association between patient, hospital and surgical factors’ and SAP appropriateness. Finally, in project 5, a qualitative case study explored the phenomenon of SAP decision-making across the professional groups involved in SAP prescribing and administration, i.e., surgeons, anaesthetists, theatre nurses and pharmacists. Barriers and enablers of prescribing decisions were identified through use of validated theoretical frameworks. Based on the integration and triangulation of all results, a framework for surgical AMS in Australia is proposed. Results: There are limited surgical AMS interventions identified in the current literature, and a framework to support surgical AMS (and outcome measures such as surgical site infection surveillance) in Australia does not currently exist. SAP prescribing practices continue to demonstrate high rates of inappropriateness across a range of surgical specialties and surgical procedures. Identified targets for improvement include; procedural dose timing, post-procedural prescription duration, and surgical procedures with noted high rates of inappropriateness, broad-spectrum antimicrobial use, and SAP administration when not required. The qualitative research identified six themes in clinicians’ perceptions about decision-making for antimicrobial use across surgical settings and highlighted the need for resources to support adequate documentation and communication about SAP prescribing decisions, engagement with senior clinicians who have significant influence upon their juniors’ prescribing practices, and the need for meaningful data addressing common fears and misperceptions regarding SAP durations to generate prescribing behaviour change. Conclusion: The surgical AMS framework provides a theoretical and evidence-based approach to improving patient quality of care and outcomes at a local level whilst also addressing the pressing issue of AMR at a national and global level. The implementation of surgical AMS is critical for the optimisation of antimicrobial use across public and private surgical settings in Australia. The framework for surgical AMS focuses on three key strategies; engagement and collaboration with stakeholders, advocating for a multi-disciplinary collaboration; development, implementation and evaluation of meaningful data and outcome measures; and the adoption of a multi-faceted quality improvement program.

Surgical and intensive care populations are ageing worldwide. Frailty, a state of increased vulnerability to stress, is increasingly common in older surgical and critically ill patients. In these cohorts, frailty predisposes to increased complications, mortality, and longer lengths of stay. Implementation of frailty screening can aid case finding, to select patients for more in-depth frailty measurement. This can assist identification of at-risk surgical and critically ill patients, and help identify which areas of health are more affected by frailty in these populations. Using routinely collected hospital data may allow construction of frailty indices, which can accurately and reproducibly measure frailty in granular detail, and help clarify the interplay between age, medical comorbidities, and frailty in individual patients. Aims of this PhD were to: 1. Review the role of frailty indices in the measurement of frailty in critically ill and surgical populations. 2. Determine which areas of health are adversely affected by frailty in surgical and intensive care patients. 3. Investigate the correlation between the screening Clinical Frailty Scale and multi-dimensional frailty measurement tools. 4. Explore whether frailty can be measured retrospectively from the clinical record. 5. Examine the prevalence and impact of frailty in intensive care unit populations in Australia and New Zealand. 6. To develop and validate a frailty index from medical admission data to measure frailty in surgical and intensive care unit patients. Phases of research and results The phases of research to accomplish these aims were: Phase 1: A systematic literature review was undertaken, assessing the role of frailty indices in the measurement of frailty in intensive care and surgery. Studies were identified through systematic review of MEDLINE, EMBASE, CINAHL databases, including studies which utilised a frailty index containing at least 30 health deficits. Outcomes assessed included mortality, complications, length of stay and discharge location. Study and frailty index quality were assessed, with findings narratively described. Phase 1 Results (Chapter 2): Thirteen studies utilising frailty indices were identified, nine prospective and four retrospective. Frailty index quality was high in 11 of the 13 studies. Frailty indices identified patients at risk of increased death, surgical complications, increased length of stay, and discharge to residential care. The term “frailty index” was found to be misapplied to a number of measurement tools not fulfilling criteria to be true frailty index scales. Phase 2: Two concurrent prospective cohort studies were conducted in a tertiary metropolitan hospital, in an intensive care unit and peri-operative department. Adult patients aged >/= 50 years (ICU) or >/= 65 years (surgery) admitted between February and June 2017 were eligible for inclusion. Frailty (Clinical Frailty Scale, Edmonton Frail Scale, Frailty Index) were measured at baseline. Outcomes included mortality, discharge to residential care, ICU and peri-operative complications, six-month mortality and residential location. Phase 2 Results (Chapters 4, 5, 8) : Three-hundred and thirty-six patients were enrolled in a four-month period, 160 ICU patients, 218 surgical patients, with 42 patients in both cohorts. Frailty prevalence (measured via the Edmonton Frail scale) was 36% in ICU patients, and 24% in surgical patients. Mortality in frail patients was higher in both ICU and surgical cohorts (ICU: 24% vs. 9%, p = 0.010; surgery = 10% vs. 2%, p = 0.019). Patients with frailty were less likely to be discharged home and more likely to be discharged to in-patient rehabilitation, and to be residing in assisted living facilities at six month follow up. Phase 3: Based on the results from the cohorts enrolled in Phase 2 above, the Clinical Frailty Scale was compared to the multi-dimensional Edmonton Frail Scale, with agreement measured via Kappa co-efficient, and correlation via Spearman’s correlation coefficient. The affected health domains of patients with frailty were compared with those of patients without frailty. Phase 3 Results (Chapter 4): Clinical Frailty Scale and Edmonton Frail Scales were highly correlated in ICU patients (Spearman correlation coefficient = 0.85; 95% CI, 0.81 to 0.88), with high agreement (kappa coefficient = 0.78; 95% CI, 0.68 to 0.88), and in surgical patients (Spearman correlation coefficient, 0.81; 95% CI, 0.77 to 0.86; kappa coefficient, 0.76; 95% CI, 0.70 to 0.81). Frail patients had worse health status across the full spectrum of frailty domains, in particular functional dependence, malnutrition, and prior hospital admissions. Phase 4: A secondary analysis of an existing dataset was conducted to examine the feasibility and inter-rater reliability of retrospectively determining a Clinical Frailty Scale from the medical record of critically ill patients. One-hundred and forty-four ICU patients had CFS scores independently assigned by four blinded investigators, with inter-rater agreement between CFS scores examined via quadratic weighted Cohen’s kappa coefficients. Phase 4 Results (Chapter 6): Of 144 enrolled patients, 137 (95%) were able to have a CFS score assigned retrospectively from the medical record. Cohen’s kappa coefficient for inter-rater reliability between frailty assessors was 0.67, confirming substantial agreement. Frailty measurement was thus deemed feasible from the ICU clinical record. Phase 5: A retrospective population-based cohort study was conducted, analysing data from the Australian and New Zealand Intensive Care Society Adult Patient Database. All patients aged >/= 80 years on admission to ICU between 1 January 2017 and 31 December 2018 were included in the study. The database was interrogated for the Clinical Frailty Scale on admission, with a mixed effects logistic regression fitted to the primary outcome of in-hospital mortality. Secondary outcomes were length of stay (hospital and ICU), re-admission to ICU, and discharge destination (including new chronic care or nursing home admission). Phase 5 Results (Chapter 7): 15,613 patients aged >/= 80 years were included from 131 ICUs; 6,203 patients (40%) were frail. Patients with frailty had higher illness severity, and were more likely to be admitted emergently to ICU with sepsis or respiratory failure. Mortality was higher in patients with frailty (17.6% vs. 8.2%, p < 0.001; adjusted mortality OR [95% CI] = 1.87 [1.65 – 2.11], p < 0.001). Patients with frailty had longer lengths of stay in-ICU and in-hospital, and were more likely to be newly discharged to nursing home/chronic care (4.9% vs. 2.8%, p < 0.001). Phase 6: Based on the results from the cohorts enrolled in Phase 2 above, I developed a frailty index from routine data collected on hospital admission, and tested in both surgical and ICU cohorts. The diagnostic performance of the frailty index against existing frailty tools for both screening (the Clinical Frailty Scale) and measurement (the Edmonton Frail Scale) was assessed. The discriminative ability of the frailty index for mortality was compared to existing risk predictions tools, including the Acute Physiology and Chronic Health Evaluation (APACHE) III score (ICU) and the P-POSSUM score (surgical patients). Phase 6 Results (Chapter 8): A 36-item frailty index was constructed, able to be completed for all patients. Correlation between Edmonton and Clinical Frailty scales was strong for both ICU and surgical patients. The frailty index had good discriminative ability for prediction of mortality, comparable with the performance of the APACHE-III illness severity score in ICU (AUC-ROC [95% CI] = 0.75 [0.64 – 0.85] vs. 0.80 [0.72 – 0.88]) and the P-POSSUM score in surgery (AUC-ROC = 0.76 [0.61 – 0.91] vs. 0.81 [0.71 – 0.92]). Conclusions Frailty is common in critically ill and surgical patients, affecting the full spectrum of health domains, and predisposing to poor outcomes. The Clinical Frailty Scale accurately screens for frailty in these cohorts, is able to be measured retrospectively from the clinical record, and can be used to determine frailty in critically ill patients at a population registry level. Frailty indices derived from routine hospital data are able to measure frailty in the peri-operative and ICU setting; electronic medical records show promise in automating such measurement.

Allogeneic haematopoietic stem cell transplantation (alloSCT) is a potent form of immunotherapy and an important treatment modality for patients with haematological malignancies. While alloSCT is a curative therapy for many patients, relapse remains a significant cause of treatment failure in a considerable proportion of patients. There is therefore an unmet need to improve the outcomes of patients after alloSCT by identifying patients at high risk of relapse and to develop effective strategies to prevent relapse in these patients. In addition, the outcome of patients with relapsed haematological malignancies after alloSCT remains poor and there is significant scope to develop novel strategies to treat relapse after alloSCT. In this thesis I investigate immunological biomarkers of relapse and explore novel strategies to prevent and treat relapse of haematological malignancies after alloSCT through two investigator initiated clinical trials. I describe that donor/recipient T-cell chimerism is significantly associated with relapse after both myeloablative and non-myeloablative alloSCT in a continuous fashion, however its utility is limited by poor sensitivity. In addition, there remains a subgroup of patients with low-risk disease who can remain in long-term remission despite mixed T-cell chimerism. In another piece of work, I explore the dynamics of T-cell receptor (TCR) repertoire reconstitution post-alloSCT and demonstrate that contrary to previous reports, a restricted TCR repertoire is not associated with early relapse of acute myeloid leukaemia (AML) after alloSCT. As an interesting aside, TCR diversity is significantly and adversely impacted by early cytomegalovirus (CMV) viremia and this effect persists late post-transplant. Therapeutic strategies to prevent relapse of haematological malignancies after alloSCT are required and in this context I explore the feasibility of low-dose lenalidomide to prevent relapse of AML and myelodysplastic syndromes (MDS) post-alloSCT. Preliminary results of this investigator-initiated phase 1 dose escalation study, which remains open to recruitment, have demonstrated that to date lenalidomide 5mg twice per week commencing at day 40 post-alloSCT is safe and tolerable. Finally, I describe the safety and efficacy of nivolumab, an inhibitor of the programmed death 1 (PD-1) receptor, for the treatment of relapsed haematological malignancies after alloSCT. In this investigator-initiated clinical trial, nivolumab induced highly potent alloimmune responses with complete remissions observed in highly refractory haematological malignancies albeit with a considerable risk of GVHD. Importantly, immunophenotypic and gene expression markers of T-cell activation may be able to identify patients who are primed to develop GVHD following nivolumab treatment and therefore guide the use of this powerful treatment strategy to those patients least likely to develop significant toxicities.

BACKGROUND: To date, the effects of extreme weather events (EWEs) on specific nutrients within the population’s diet have not been quantified. With climate change projected to increase the severity of extreme weather across the globe, it is necessary to understand how the global nutrient supply has historically responded, and which subpopulations are most at risk. One particular subpopulation of importance is Aboriginal and Torres Strait Islander people, who are already more susceptible to nutritional insult and metabolic syndrome than their non- Indigenous counterparts. While extreme weather is not the primary driving force in poor health outcomes, I hypothesise that it further exacerbates cardiometabolic health burdens globally, and especially among vulnerable populations. METHODS: In my first study, I conducted superposed epoch analysis to calculate the percentage change in nutrient supply during the year of an EWE relative to its five-year window. I composited the results globally and by United Nations designated low-income subgroups. I also reported changes in terms of Recommended Dietary Allowance (RDA) for children aged 1-3 years. In my second study, I constructed a holistic model with data from 104 Aboriginal and Tor- res Strait Islander communities in the Northern Territory from 2010-2015. I used varimax- rotated Principal Component Analysis to extract and condense information from 218 variables for physical environment, census, and climate data. I then conducted MM-estimator regression to model the extreme heat impacts on cardiometabolic-related rates for emergency room, inpatient admission, primary healthcare, and mortality. RESULTS: In the first study, most micronutrient supplies exhibited modest negative percentage change during the year of an EWE, including folate, magnesium, niacin, phosphorus, potassium, thiamin, vitamin B6, vitamin C, and zinc. Effects were magnified among Landlocked Developing Countries, which exhibited significant nutrient supply changes ranging from 1.6 – 8.0% of average supply. The observed nutrient supply deficits were found to be a large percentage (up to 41.5%) of what a healthy child’s average sufficient dietary intake level should be. The most compelling finding of the second study is that holding all else fixed, a unit in- crease in climate PC1 score is associated with a 77.8% change in emergency room rates, 6.7 percentage point increase in inpatient rates, and 9.3 percentage point increase in primary healthcare rates. Thus, a larger cardiometabolic health burden is strongly correlated with communities that experience relatively lower apparent temperature and humidity but greater maximum heatwave severity, e.g. Alice Springs area. CONCLUSION: The EWE effects on nutrient supply are modest in isolation; however, in the context of nutrient needs for healthy child development, the effects observed are substantial. Children are a particularly vulnerable subpopulation of interest, given how certain nutritional deficiencies during gestation and the first five years of life can have irrecoverable consequences for health, growth, and development. In the second study, I found that relative heat – or sudden rises in temperature above that of the recent past – poses the most significant threat to cardiometabolic health among Indigenous communities in northern Australia. Relative heat, rather than absolute heat, should therefore be the focus of public health preparation and response. Both studies echo previous literature in stressing the urgency with which the international community must tackle the issue of nutritional and metabolic health among vulnerable populations, especially because this health landscape is poised to worsen with climate change.

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia encountered in clinical practice in developed countries, with a rising incidence reaching epidemic proportions. Beyond adverse impacts on quality of life, AF is associated with significant morbidity, heart failure, stroke and a markedly higher risk of mortality. Current understanding incorporates contributions from focal triggers and remodelled atrial substrate, however the precise interactions between these mechanisms remain incompletely understood. The paradigm of AF management over the last decade has evolved to a more lifestyle directed and holistic approach rather than basic pharmacological rate versus rhythm control measures. However, the AF disease process is multifactorial and the optimal treatment of particularly persistent forms of AF continues to be elusive. This thesis aims to evaluate novel mechanisms and influences on electroanatomic atrial substrate contributing to AF which may form the basis for emerging strategies in personalised AF therapy. Initially, we assess the genetic predisposition to AF by effects on atrial substrate and post AF ablation outcomes. We explore the impact of novel pacing strategies and sex-differences on atrial substrate in patients with AF. Finally, we define the influence of AF on sinus node and crista terminalis characteristics. Chapter 1 delineates the role of genetics in AF, a rapidly progressive area in cardiovascular medicine. We then explore the evolving understanding of pathogenesis of the AF mechanism with an emphasis on the impact and importance of atrial substrate, sex-differences and sinus node remodelling. Chapter 2 investigates the impact of genetic susceptibility in patients with AF to electrical and structural remodelling and outcomes. Chapter 2 is a prospective cohort study of 102 patients undergoing AF ablation who undergo genetic sequencing for a 4q25 single nucleotide variant (SNV) and high-density electroanatomical mapping of their left atria. The genetic aspects were completed under the supervision of Prof Diane Fatkin’s Inherited Heart Diseases Laboratory at the Victor Chang Cardiac Research Institute. We document long-term outcomes 2 years post ablation utilising high intensity monitoring including insertable loop recorders and regular Holter monitors. We compare carriers and non-carriers to determine whether there are differences in electrophysiological and conduction properties between groups. We conclude that the 4q25 variants is associated with adverse atrial remodelling characterised by greater conduction heterogeneity and presence of complex fractionated signals with poorer long-term outcomes. Chapter 3 and 4 examine the impact of pacing strategies on electroanatomic atrial substrate in patients with AF. Chapter 3 describes rate-dependent conduction differences in maps created at different cycle-lengths in 56 patients with a history of AF. It observes globally greater atrial substrate at a faster cycle-length across multiple electrophysiologic parameters including voltage, conduction velocity and complex signals. Chapter 4 then evaluates the impact of direction-dependent conduction in 17 patients with AF when pacing from the pulmonary vein. It concludes a highly regional increase in atrial substrate posteriorly. Together, these data suggest the dynamic nature of atrial substrate maps with marked variation according to changes in pacing rate and direction. Chapter 5 focusses on the comparison of electrophysiologic properties underpinning sex-based differences in AF as despite having a lower incidence of AF compared with men, women carry higher risks of stroke and adverse AF-related outcomes. We perform a cross-sectional electroanatomic mapping study of 93 patients with AF and 45 control patients with SVT. Interestingly, in both patients with and without AF, women have a greater degree of atrial substrate when compared with men. Coupled with these substrate differences, we demonstrate that women had higher single and multi-procedure arrhythmia-recurrence following AF ablation. Chapter 6 presents an ultra high-density mapping study investigating the characteristics of the sinus node and anatomically-determined regions of right atrial substrate in relation to AF. We conduct a mapping study on 25 patients with AF and 25 age-matched controls undergoing SVT ablation. Key findings included more significant sinus node remodelling in patients with AF and persistent forms of AF in particular characterised by progressive caudal shifts in sinus node activation, loss of multicentricity, lower sinus node voltage and greater ‘latent’ substrate at the crista terminalis. Chapter 7 concludes the thesis by summarising the pertinent translational findings and implications for the clinical outlook of each study. Moreover, the future directions of novel mechanisms of AF may help pave the way for personalised AF strategies to better treat AF.