Addressing issues in sparseness, ecological bias and formulation of the adjacency matrix in Bayesian spatio-temporal analysis of disease counts

The main objective of this PhD was to further develop Bayesian spatio-temporal models (specifically the Conditional Autoregressive (CAR) class of models), for the analysis of sparse disease outcomes such as birth defects. The motivation for the thesis arose from problems encountered when analyzing a large birth defect registry in New South Wales. The specific components and related research objectives of the thesis were developed from gaps in the literature on current formulations of the CAR model, and health service planning requirements. Data from a large probabilistically-linked database from 1990 to 2004, consisting of fields from two separate registries: the Birth Defect Registry (BDR) and Midwives Data Collection (MDC) were used in the analyses in this thesis. The main objective was split into smaller goals. The first goal was to determine how the specification of the neighbourhood weight matrix will affect the smoothing properties of the CAR model, and this is the focus of chapter 6. Secondly, I hoped to evaluate the usefulness of incorporating a zero-inflated Poisson (ZIP) component as well as a shared-component model in terms of modeling a sparse outcome, and this is carried out in chapter 7. The third goal was to identify optimal sampling and sample size schemes designed to select individual level data for a hybrid ecological spatial model, and this is done in chapter 8. Finally, I wanted to put together the earlier improvements to the CAR model, and along with demographic projections, provide forecasts for birth defects at the SLA level. Chapter 9 describes how this is done. For the first objective, I examined a series of neighbourhood weight matrices, and showed how smoothing the relative risk estimates according to similarity by an important covariate (i.e. maternal age) helped improve the model’s ability to recover the underlying risk, as compared to the traditional adjacency (specifically the Queen) method of applying weights. Next, to address the sparseness and excess zeros commonly encountered in the analysis of rare outcomes such as birth defects, I compared a few models, including an extension of the usual Poisson model to encompass excess zeros in the data. This was achieved via a mixture model, which also encompassed the shared component model to improve on the estimation of sparse counts through borrowing strength across a shared component (e.g. latent risk factor/s) with the referent outcome (caesarean section was used in this example). Using the Deviance Information Criteria (DIC), I showed how the proposed model performed better than the usual models, but only when both outcomes shared a strong spatial correlation. The next objective involved identifying the optimal sampling and sample size strategy for incorporating individual-level data with areal covariates in a hybrid study design. I performed extensive simulation studies, evaluating thirteen different sampling schemes along with variations in sample size. This was done in the context of an ecological regression model that incorporated spatial correlation in the outcomes, as well as accommodating both individual and areal measures of covariates. Using the Average Mean Squared Error (AMSE), I showed how a simple random sample of 20% of the SLAs, followed by selecting all cases in the SLAs chosen, along with an equal number of controls, provided the lowest AMSE. The final objective involved combining the improved spatio-temporal CAR model with population (i.e. women) forecasts, to provide 30-year annual estimates of birth defects at the Statistical Local Area (SLA) level in New South Wales, Australia. The projections were illustrated using sixteen different SLAs, representing the various areal measures of socio-economic status and remoteness. A sensitivity analysis of the assumptions used in the projection was also undertaken. By the end of the thesis, I will show how challenges in the spatial analysis of rare diseases such as birth defects can be addressed, by specifically formulating the neighbourhood weight matrix to smooth according to a key covariate (i.e. maternal age), incorporating a ZIP component to model excess zeros in outcomes and borrowing strength from a referent outcome (i.e. caesarean counts). An efficient strategy to sample individual-level data and sample size considerations for rare disease will also be presented. Finally, projections in birth defect categories at the SLA level will be made.

Entering the era of post production the role visual effects will play in documentary

Creating an acceptance of Visual Effects (VFX) as an effective non-fiction communication tool has the potential to significantly boost return on investment for filmmakers producing documentary. Obtaining this acceptance does not necessarily mean rethinking the way documentary is defined, however, the need to address negative perceptions presently dominant within the production industry does exist; specifically, the misguided judgement that use of sequences which include visual effects discredits a filmmaker's attempt to represent reality. After completing a documentary utilising a traditional model of production for methodology, the question of how to increase this film's marketability is then examined by testing the specific assertion that Visual Effects is capable of increasing the level of appeal inherent within the documentary genre. Whilst this area of research is speculative, qualifying Visual Effects as an acceptable communication tool in non-fiction narratives will allow the documentary sector to benefit from increased production capabilities.

Examination of social demographic status, disease status, health behaviours and quality of life in older Australians using the theory of planned behaviour model

The increase of life expectancy worldwide during the last three decades has increased age-related disability leading to the risk of loss of quality of life. How to improve quality of life including physical health and mental health for older people and optimize their life potential has become an important health issue. This study used the Theory of Planned Behaviour Model to examine factors influencing health behaviours, and the relationship with quality of life. A cross-sectional mailed survey of 1300 Australians over 50 years was conducted at the beginning of 2009, with 730 completed questionnaires returned (response rate 63%). Preliminary analysis reveals that physiological changes of old age, especially increasing waist circumference and co morbidity was closely related to health status, especially worse physical health summary score. Physical activity was the least adherent behaviour among the respondents compared to eating healthy food and taking medication regularly as prescribed. Increasing number of older people living alone with co morbidity of disease may be the barriers that influence their attitude and self control toward physical activity. A multidisciplinary and integrated approach including hospital and non hospital care is required to provide appropriate services and facilities toward older people.

Delirium in early-stage Alzheimer's disease : enhancing cognitive reserve as a possible preventive measure

Delirium is a disorder of acute onset with fluctuating symptoms and is characterized by inattention, disorganized thinking, and altered levels of consciousness. The risk for delirium is greatest in individuals with dementia, and the incidence of both is increasing worldwide because of the aging of our population. Although several clinical trials have tested interventions for delirium prevention in individuals without dementia, little is known about the mechanisms for the prevention of delirium in early-stage Alzheimer’s disease (AD). The purpose of this article is to explore ways of preventing delirium and slowing the rate of cognitive decline in early-stage AD by enhancing cognitive reserve. An agenda for future research on interventions to prevent delirium in individuals with early-stage AD is also presented.

3D lung and rib cage reconstruction using low dose CT scans of adolescent idiopathic scoliosis pre and post anterior thoracoscopic correction

Adolescent Idiopathic Scoliosis (AIS) has been associated with reduced pulmonary function believed to be due to a restriction of lung volume by the deformed thoracic cavity. A recent study by our group examined the changes in lung volume pre and post anterior thoracoscopic scoliosis correction using pulmonary function testing (1), however the anatomical changes in ribcage shape and left/right lung volume after thoracoscopic surgery which govern overall respiratory capacity are unknown. The aim of this study was to use 3D rendering from CT scan data to compare lung and ribcage anatomical changes from pre to two years post thoracoscopic anterior scoliosis correction. The study concluded that 3D volumetric reconstruction from CT scans is a powerful means of evaluating changes in pulmonary and thoracic anatomy following surgical AIS correction. Most likely, lung volume changes following thoracoscopic scoliosis correction are multifactorial and affected by changes in height (due to residual growth), ribcage shape, diaphragm positioning, Cobb angle correction in the thoracic spine. Further analysis of the 3D reconstructions will be performed to assess how each of these factors affect lung volume in this patient cohort.

Social Participation of Community Dwelling Stroke Survivors [Published Abstract: From the Quality of Care and Outcomes Research in Cardiovascular Disease and Stroke Conference 2009]

Disability following a stroke can impose various restrictions on patients’ attempts at participating in life roles. The measurement of social participation, for instance, is important in estimating recovery and assessing quality of care at the community level. Thus, the identification of factors influencing social participation is essential in developing effective measures for promoting the reintegration of stroke survivors into the community. Data were collected from 188 stroke survivors (mean age 71.7 years) 12 months after discharge from a stroke rehabilitation hospital. Of these survivors, 128 (61 %) had suffered a first ever stroke, and 81 (43 %) had a right hemisphere lesion. Most (n = 156, 83 %) were living in their own home, though 32 (17 %) were living in residential care facilities. Path analysis was used to test a hypothesized model of participation restriction which included the direct and indirect effects between social, psychological and physical outcomes and demographic variables. Participation restriction was the dependent variable. Exogenous independent variables were age, functional ability, living arrangement and gender. Endogenous independent variables were depressive symptoms, state self-esteem and social support satisfaction. The path coefficients showed functional ability having the largest direct effect on participation restriction. The results also showed that more depressive symptoms, low state self-esteem, female gender, older age and living in a residential care facility had a direct effect on participation restriction. The explanatory variables accounted for 71% of the variance in explaining participation restriction. Prediction models have empirical and practical applications such as suggesting important factors to be considered in promoting stroke recovery. The findings suggest that interventions offered over the course of rehabilitation should be aimed at improving functional ability and promoting psychological aspects of recovery. These are likely to enhance stroke survivors resume or maximize their social participation so that they may fulfill productive and positive life roles.

Disease prevention and control

Globally, the main contributors to morbidity and mortality are chronic diseases, including cardiovascular disease and diabetes. Chronic diseases are costly and partially avoidable, with around sixty percent of deaths and nearly fifty percent of the global disease burden attributable to these conditions. By 2020, chronic illnesses will likely be the leading cause of disability worldwide. Existing health care systems, both national and international, that focus on acute episodic health conditions, cannot address the worldwide transition to chronic illness; nor are they appropriate for the ongoing care and management of those already afflicted with chronic diseases. International and Australian strategic planning documents articulate similar elements to manage chronic disease; including the need for aligning sectoral policies for health, forming partnerships and engaging communities in decision-making. The Australian National Chronic Disease Strategy focuses on four core areas for managing chronic disease; prevention across the continuum, early detection and treatment, integrated and coordinated care, and self-management. Such a comprehensive approach incorporates the entire population continuum, from the ‘healthy’, to those with risk factors, through to people suffering from chronic conditions and their sequelae. This chapter examines comprehensive approach to the prevention, management and care of the population with non-communicable, chronic diseases and communicable diseases. It analyses models of care in the context of need, service delivery options and the potential to prevent or manage early intervention for chronic and communicable diseases. Approaches to chronic diseases require integrated approaches that incorporate interventions targeted at both individuals and populations, and emphasise the shared risk factors of different conditions. Communicable diseases are a common and significant contributor to ill health throughout the world. In many countries, this impact has been minimised by the combined efforts of preventative health measures and improved treatment of infectious diseases. However in underdeveloped nations, communicable diseases continue to contribute significantly to the burden of disease. The aim of this chapter is to outline the impact that chronic and communicable diseases have on the health of the community, the public health strategies that are used to reduce the burden of those diseases and the old and emerging risks to public health from infectious diseases.

Generation next : post-cinema Australian moviemaking, innovation and implications for cultural policy

The Australian screen industries are a leading domestic creative industry sector at a crossroad. New production, distribution and exhibition technologies are challenging traditional models of ‘filmmaking’. For the screen industries to remain competitive they must renovate business models for an emerging marketplace. This paper is a preliminary examination of three key aspects of next generation filmmaking: post-cinema approaches to screen production, emerging production and business models, and issues for policy.

Post-WTO China : competition and technology transfer laws in the 'new' socialist market economy

China has been the focus of much academic and business scrutiny of late. Its economic climate is changing and its huge new market opportunities seem quite tantalizing to the would-be 'technology entrepreneur'. But China's market is a relatively immature one; it is still in the process of being opened up to real competition. The corollary of this is that, at this stage of the transitional process, there is still significant State control of market function. This article discusses Chinese competition law, the technology transfer system, how the laws are being reformed and how the technology entrepreneur fares under them. The bottom line is that while opportunities beckon, the wise entrepreneur will nevertheless continue to exercise caution.

Does quality of life among breast cancer survivors one year after diagnosis differ depending on urban and non-urban residence? A comparative study

Background: This study examined the quality of life (QOL), measured by the Functional Assessment of Cancer Therapy (FACT) questionnaire, among urban (n=277) and non-urban (n=323) breast cancer survivors and women from the general population (n=1140) in Queensland, Australia. ---------- Methods: Population-based samples of breast cancer survivors aged <75 years who were 12 months post-diagnosis and similarly-aged women from the general population were recruited between 2002 and 2007. ---------- Results: Age-adjusted QOL among urban and non-urban breast cancer survivors was similar, although QOL related to breast cancer concerns was the weakest domain and was lower among non-urban survivors than their urban counterparts (36.8 versus 40.4, P<0.01). Irrespective of residence, breast cancer survivors, on average, reported comparable scores on most QOL scales as their general population peers, although physical well-being was significantly lower among non-urban survivors (versus the general population, P<0.01). Overall, around 20%-33% of survivors experienced lower QOL than peers without the disease. The odds of reporting QOL below normative levels were increased more than two-fold for those who experienced complications following surgery, reported upper-body problems, had higher perceived stress levels and/or a poor perception of handling stress (P<0.01 for all). ---------- Conclusions: Results can be used to identify subgroups of women at risk of low QOL and to inform components of tailored recovery interventions to optimize QOL for these women following cancer treatment.

An examination of the base rates of post-concussion symptoms : the influence of demographics and depression

Post-concussion syndrome (PCS) is a controversial constellation of cognitive, emotional, and physical symptoms that some patients experience following a mild traumatic brain injury or concussion. PCS-like symptoms are commonly found in individuals with depression, pain, and stress, as well as healthy individuals. This study investigated the base rate of PCS symptoms in a healthy sample of 96 participants and examined the relationship between these symptoms, depression, and sample demographics. PCS symptoms were assessed using the British-Columbia Post-Concussion Symptom Inventory. Depression was measured using the Beck Depression Inventory II. Results demonstrated that: The base rate of PCS was very high; there was a strong positive relationship between depression and PCS; and demographic characteristics were not related to PCS in this sample. These findings are broadly consistent with literature suggesting a significant role for non-neurological factors in the expression of PCS symptomatology. This study adds to the growing body of literature that calls for caution in the clinical interpretation of results from PCS symptom inventories.

Low sodium haemodialysis reduces interdialytic fluid consumption but paradoxically increases post-dialysis thirst

Background Interdialytic weight gain (IDWG) can be reduced by lowering the dialysate sodium concentration ([Na]) in haemodialysis patients. It has been assumed that this is because thirst is reduced, although this has been difficult to prove. We compared thirst patterns in stable haemodialysis patients with high and low IDWG using a novel technique and compared the effect of low sodium dialysis (LSD) with normal sodium dialysis (NSD). Methods Eight patients with initial high IDWG and seven with low IDWG completed hourly visual analogue ratings of thirst using a modified palmtop computer during the dialysis day and the interdialytic day. The dialysate [Na] was progressively reduced by up to 5 mmol/l over five treatments. Dialysis continued at the lowest attained [Na] for 2 weeks and the measurements were repeated. The dialysate [Na] then returned to baseline and the process was repeated. Results Baseline interdialytic day mean thirst was higher than the dialysis day mean for the high IDWG group (49.9±14.0 vs 36.2±16.6) and higher than the low weight gain group (49.9±14.0 vs 34.1±14.6). This trend persisted on LSD, but there was a pronounced increase in post-dialysis thirst scores for both groups (high IDWG: 46±13 vs 30±21; low IDWG: 48±24 vs 33±18). The high IDWG group demonstrated lower IDWG during LSD than NSD (2.23±0.98 vs 2.86±0.38 kg; P<0.05). Conclusions Our results indicate that patients with high IDWG experience more intense feelings of thirst on the interdialytic day. LSD reduces their IDWG, but paradoxically increases thirst in the immediate post-dialysis period.

Differences in post-prandial responses to fat and carbohydrate loads in habitual high and low fat consumers (phenotypes).

The present study investigated metabolic responses to fat and carbohydrate ingestion in lean male individuals consuming an habitual diet high or low in fat. Twelve high-fat phenotypes (HF) and twelve low-fat phenotypes (LF) participated in the study. Energy intake and macronutrient intake variables were assessed using a food frequency questionnaire. Resting (RMR) and postprandial metabolic rate and substrate oxidation (respiratory quotient; RQ) were measured by indirect calorimetry. HF had a significantly higher RMR and higher resting heart rate than LF. These variables remained higher in HF following the macronutrient challenge. In all subjects the carbohydrate load increased metabolic rate and heart rate significantly more than the fat load. Fat oxidation (indicated by a low RQ) was significantly higher in HF than in LF following the fat load; the ability to oxidise a high carbohydrate load did not differ between the groups. Lean male subjects consuming a diet high in fat were associated with increased energy expenditure at rest and a relatively higher fat oxidation in response to a high fat load; these observations may be partly responsible for maintaining energy balance on a high-fat (high-energy) diet. In contrast, a low consumer of fat is associated with relatively lower energy expenditure at rest and lower fat oxidation, which has implications for weight gain if high-fat foods or meals are periodically introduced to the diet.

Application of data mining techniques in the prediction of coronary artery disease : use of anaesthesia time-series and patient risk factor data

The high morbidity and mortality associated with atherosclerotic coronary vascular disease (CVD) and its complications are being lessened by the increased knowledge of risk factors, effective preventative measures and proven therapeutic interventions. However, significant CVD morbidity remains and sudden cardiac death continues to be a presenting feature for some subsequently diagnosed with CVD. Coronary vascular disease is also the leading cause of anaesthesia related complications. Stress electrocardiography/exercise testing is predictive of 10 year risk of CVD events and the cardiovascular variables used to score this test are monitored peri-operatively. Similar physiological time-series datasets are being subjected to data mining methods for the prediction of medical diagnoses and outcomes. This study aims to find predictors of CVD using anaesthesia time-series data and patient risk factor data. Several pre-processing and predictive data mining methods are applied to this data. Physiological time-series data related to anaesthetic procedures are subjected to pre-processing methods for removal of outliers, calculation of moving averages as well as data summarisation and data abstraction methods. Feature selection methods of both wrapper and filter types are applied to derived physiological time-series variable sets alone and to the same variables combined with risk factor variables. The ability of these methods to identify subsets of highly correlated but non-redundant variables is assessed. The major dataset is derived from the entire anaesthesia population and subsets of this population are considered to be at increased anaesthesia risk based on their need for more intensive monitoring (invasive haemodynamic monitoring and additional ECG leads). Because of the unbalanced class distribution in the data, majority class under-sampling and Kappa statistic together with misclassification rate and area under the ROC curve (AUC) are used for evaluation of models generated using different prediction algorithms. The performance based on models derived from feature reduced datasets reveal the filter method, Cfs subset evaluation, to be most consistently effective although Consistency derived subsets tended to slightly increased accuracy but markedly increased complexity. The use of misclassification rate (MR) for model performance evaluation is influenced by class distribution. This could be eliminated by consideration of the AUC or Kappa statistic as well by evaluation of subsets with under-sampled majority class. The noise and outlier removal pre-processing methods produced models with MR ranging from 10.69 to 12.62 with the lowest value being for data from which both outliers and noise were removed (MR 10.69). For the raw time-series dataset, MR is 12.34. Feature selection results in reduction in MR to 9.8 to 10.16 with time segmented summary data (dataset F) MR being 9.8 and raw time-series summary data (dataset A) being 9.92. However, for all time-series only based datasets, the complexity is high. For most pre-processing methods, Cfs could identify a subset of correlated and non-redundant variables from the time-series alone datasets but models derived from these subsets are of one leaf only. MR values are consistent with class distribution in the subset folds evaluated in the n-cross validation method. For models based on Cfs selected time-series derived and risk factor (RF) variables, the MR ranges from 8.83 to 10.36 with dataset RF_A (raw time-series data and RF) being 8.85 and dataset RF_F (time segmented time-series variables and RF) being 9.09. The models based on counts of outliers and counts of data points outside normal range (Dataset RF_E) and derived variables based on time series transformed using Symbolic Aggregate Approximation (SAX) with associated time-series pattern cluster membership (Dataset RF_ G) perform the least well with MR of 10.25 and 10.36 respectively. For coronary vascular disease prediction, nearest neighbour (NNge) and the support vector machine based method, SMO, have the highest MR of 10.1 and 10.28 while logistic regression (LR) and the decision tree (DT) method, J48, have MR of 8.85 and 9.0 respectively. DT rules are most comprehensible and clinically relevant. The predictive accuracy increase achieved by addition of risk factor variables to time-series variable based models is significant. The addition of time-series derived variables to models based on risk factor variables alone is associated with a trend to improved performance. Data mining of feature reduced, anaesthesia time-series variables together with risk factor variables can produce compact and moderately accurate models able to predict coronary vascular disease. Decision tree analysis of time-series data combined with risk factor variables yields rules which are more accurate than models based on time-series data alone. The limited additional value provided by electrocardiographic variables when compared to use of risk factors alone is similar to recent suggestions that exercise electrocardiography (exECG) under standardised conditions has limited additional diagnostic value over risk factor analysis and symptom pattern. The effect of the pre-processing used in this study had limited effect when time-series variables and risk factor variables are used as model input. In the absence of risk factor input, the use of time-series variables after outlier removal and time series variables based on physiological variable values’ being outside the accepted normal range is associated with some improvement in model performance.

Immunogenicity and protective efficacy of an anti-Streptococcus pyogenes vaccine candidate in multiple animal species

Streptococcus pyogenes, also known as Group A Streptococcus (GAS) has been associated with a range of diseases from the mild pharyngitis and pyoderma to more severe invasive infections such as streptococcal toxic shock. GAS also causes a number of non-suppurative post-infectious diseases such as rheumatic fever, rheumatic heart disease and glomerulonephritis. The large extent of GAS disease burden necessitates the need for a prophylactic vaccine that could target the diverse GAS emm types circulating globally. Anti-GAS vaccine strategies have focused primarily on the GAS M-protein, an extracellular virulence factor anchored to GAS cell wall. As opposed to the hypervariable N-terminal region, the C-terminal portion of the protein is highly conserved among different GAS emm types and is the focus of a leading GAS vaccine candidate, J8-DT/alum. The vaccine candidate J8-DT/alum was shown to be immunogenic in mice, rabbits and the non-human primates, hamadryas baboons. Similar responses to J8-DT/alum were observed after subcutaneous and intramuscular immunization with J8-DT/alum, in mice and in rabbits. Further assessment of parameters that may influence the immunogenicity of J8-DT demonstrated that the immune responses were identical in male and female mice and the use of alum as an adjuvant in the vaccine formulation significantly increased its immunogenicity, resulting in a long-lived serum IgG response. Contrary to the previous findings, the data in this thesis indicates that a primary immunization with J8-DT/alum (50ƒÊg) followed by a single boost is sufficient to generate a robust immune response in mice. As expected, the IgG response to J8- DT/alum was a Th2 type response consisting predominantly of the isotype IgG1 accompanied by lower levels of IgG2a. Intramuscular vaccination of rabbits with J8-DT/alum demonstrated that an increase in the dose of J8-DT/alum up to 500ƒÊg does not have an impact on the serum IgG titers achieved. Similar to the immune response in mice, immunization with J8-DT/alum in baboons also established that a 60ƒÊg dose compared to either 30ƒÊg or 120ƒÊg was sufficient to generate a robust immune response. Interestingly, mucosal infection of naive baboons with a M1 GAS strain did not induce a J8-specific serum IgG response. As J8-DT/alum mediated protection has been previously reported to be due to the J8- specific antibody formed, the efficacy of J8-DT antibodies was determined in vitro and in vivo. In vitro opsonization and in vivo passive transfer confirmed the protective potential of J8-DT antibodies. A reduction in the bacterial burden after challenge with a bioluminescent M49 GAS strain in mice that were passively administered J8-DT IgG established that protection due to J8-DT was mediated by antibodies. The GAS burden in infected mice was monitored using bioluminescent imaging in addition to traditional CFU assays. Bioluminescent GAS strains including the ‘rheumatogenic’ M1 GAS could not be generated due to limitations with transformation of GAS, however, a M49 GAS strain was utilized during BLI. The M49 serotype is traditionally a ‘nephritogenic’ serotype associated with post-streptococcal glomerulonephritis. Anti- J8-DT antibodies now have been shown to be protective against multiple GAS strains such as M49 and M1. This study evaluated the immunogenicity of J8-DT/alum in different species of experimental animals in preparation for phase I human clinical trials and provided the ground work for the development of a rapid non-invasive assay for evaluation of vaccine candidates.