Bayesian mixtures for modelling complex medical data : a case study in Parkinson’s disease

Mixture models are a flexible tool for unsupervised clustering that have found popularity in a vast array of research areas. In studies of medicine, the use of mixtures holds the potential to greatly enhance our understanding of patient responses through the identification of clinically meaningful clusters that, given the complexity of many data sources, may otherwise by intangible. Furthermore, when developed in the Bayesian framework, mixture models provide a natural means for capturing and propagating uncertainty in different aspects of a clustering solution, arguably resulting in richer analyses of the population under study. This thesis aims to investigate the use of Bayesian mixture models in analysing varied and detailed sources of patient information collected in the study of complex disease. The first aim of this thesis is to showcase the flexibility of mixture models in modelling markedly different types of data. In particular, we examine three common variants on the mixture model, namely, finite mixtures, Dirichlet Process mixtures and hidden Markov models. Beyond the development and application of these models to different sources of data, this thesis also focuses on modelling different aspects relating to uncertainty in clustering. Examples of clustering uncertainty considered are uncertainty in a patient’s true cluster membership and accounting for uncertainty in the true number of clusters present. Finally, this thesis aims to address and propose solutions to the task of comparing clustering solutions, whether this be comparing patients or observations assigned to different subgroups or comparing clustering solutions over multiple datasets. To address these aims, we consider a case study in Parkinson’s disease (PD), a complex and commonly diagnosed neurodegenerative disorder. In particular, two commonly collected sources of patient information are considered. The first source of data are on symptoms associated with PD, recorded using the Unified Parkinson’s Disease Rating Scale (UPDRS) and constitutes the first half of this thesis. The second half of this thesis is dedicated to the analysis of microelectrode recordings collected during Deep Brain Stimulation (DBS), a popular palliative treatment for advanced PD. Analysis of this second source of data centers on the problems of unsupervised detection and sorting of action potentials or "spikes" in recordings of multiple cell activity, providing valuable information on real time neural activity in the brain.

A first stage test of Dunning's framework on multinational contracting into Australia : reviewing secondary data.

In response to the need to leverage private finance and the lack of competition in some parts of the Australian public sector infrastructure market, especially in the very large economic infrastructure sector procured using Pubic Private Partnerships, the Australian Federal government has demonstrated its desire to attract new sources of in-bound foreign direct investment (FDI). This paper aims to report on progress towards an investigation into the determinants of multinational contractors’ willingness to bid for Australian public sector major infrastructure projects. This research deploys Dunning’s eclectic theory for the first time in terms of in-bound FDI by multinational contractors into Australia. Elsewhere, the authors have developed Dunning’s principal hypothesis to suit the context of this research and to address a weakness arising in this hypothesis that is based on a nominal approach to the factors in Dunning's eclectic framework and which fails to speak to the relative explanatory power of these factors. In this paper, a first stage test of the authors' development of Dunning's hypothesis is presented by way of an initial review of secondary data vis-à-vis the selected sector (roads and bridges) in Australia (as the host location) and with respect to four selected home countries (China; Japan; Spain; and US). In doing so, the next stage in the research method concerning sampling and case studies is also further developed and described in this paper. In conclusion, the extent to which the initial review of secondary data suggests the relative importance of the factors in the eclectic framework is considered. It is noted that more robust conclusions are expected following the future planned stages of the research including primary data from the case studies and a global survey of the world’s largest contractors and which is briefly previewed. Finally, and beyond theoretical contributions expected from the overall approach taken to developing and testing Dunning’s framework, other expected contributions concerning research method and practical implications are mentioned.

A study of environmental and management drivers of non-CO2 greenhouse gas emissions in Australian agro-ecosystems

Australian climate, soils and agricultural management practices are significantly different from those of the northern hemisphere nations. Consequently, experimental data on greenhouse gas production from European and North American agricultural soils and its interpretation are unlikely to be directly applicable to Australian systems. A programme of studies of non-CO2 greenhouse gas emissions from agriculture has been established that is designed to reduce uncertainty of non-CO2 greenhouse gas emissions in the Australian National Greenhouse Gas Inventory and provide outputs that will enable better on-farm management practices for reducing non-CO2 greenhouse gas emissions, particularly nitrous oxide. The systems being examined and their locations are irrigated pasture (Kyabram Victoria), irrigated cotton (Narrabri, NSW), irrigated maize (Griffith, NSW), rain-fed wheat (Rutherglen, Victoria) and rain-fed wheat (Cunderdin, WA). The field studies include treatments with and without fertilizer addition, stubble burning versus stubble retention, conventional cultivation versus direct drilling and crop rotation to determine emission factors and treatment possibilities for best management options. The data to date suggest that nitrous oxide emissions from nitrogen fertilizer, applied to irrigated dairy pastures and rain-fed winter wheat, appear much lower than the average of northern hemisphere grain and pasture studies. More variable emissions have been found in studies of irrigated cotton/vetch/wheat rotation and substantially higher emissions from irrigated maize.

The association between maternal infant feeding practices and child weight at 11-17 months in first-time Australian mothers

Introduction: Emerging evidence reveals that early feeding practices are associated with child food intake, eating behaviour and weight status. This cross-sectional analysis examined the association between maternal infant feeding practices/beliefs and child weight in Australian infants aged 11-17 months. Methods: Participants were 293 first-time mothers of healthy term infants (144 boys, mean age 14±1 months) enrolled in the NOURISH RCT. Mothers self-reported infant feeding practices and beliefs using the Infant Feeding Questionnaire (Baughcum, 2001). Anthropometric data were also measured at baseline (infants aged 4 months). Multiple regression analysis was used, adjusting for infant age, gender, birth weight, infant feeding mode (breast vs. formula), maternal perceptions of infant weight status, pre-pregnancy weight, weight concern, age and education. Results: The average child weight-for-age z-score (WAZ) was 0.62±0.83 (range:-1.56 to 2.94) and the mean change in WAZ (WAZ change) from 4 to 14 months was 0.62±0.69 (range:-1.50 to 2.76). Feeding practices/beliefs partly explained child WAZ (R2=0.28) and WAZ change (R2=0.13) in the adjusted models. While child weight status at 14 months was inversely associated with responsive feeding (e.g. baby feeds whenever she wants, feeding to stop baby being unsettled) (β=-0.104, p=0.06) and maternal concern about the child becoming underweight (β=-0.224, p<0.001), it was positively associated with mother’s concern about child overweight (β=0.197, p<0.05). Birth weight, infant’s age, maternal weight concern and perceiving her child as overweight were significant covariates. WAZ change was only significantly associated with responsive feeding (β=-0.147, p<0.05). Conclusion: Responsive feeding may be an important strategy to promote healthy child weight.

Individuals in a mass market environment: Australian bequest donors seek better communication from charities

Swelling social need and competing calls on government funds have heightened the philanthropic dollar’s value. Yet, Australia is not regarded as having a robust giving culture: while 86% of adults give, a mere 16% plan their giving with those who do donating four times as much as spontaneous givers (Giving Australia, 2005). Traditionally, the prime planned giving example is a charitable bequest, a revenue stream not prevalent here (Baker, 2007). In fact, Baker’s Victorian probate data shows under 5% of estates provide a charitable bequest and just over 1% of estate assets is bequeathed. The UK, in contrast, sources 30% and the US 10% of charitable income through bequests (NCVO, 2004; Sargeant, Wymer and Hilton,2006). Australian charities could boost bequest giving. Understanding the donor market, which has or may remember them in their will is critical. This paper reports donor perceptions of Australian charities’ bequest communication/ marketing. The data forms part of a wider study of Australian donors’ bequest attitudes and behaviour. Charities spend heavily on bequest promotion, from advertising to personal selling to public relations and promotion. Infrastructure funds are scarce so guidance on what works for donors is important. Guy and Patton (1988) made their classic call for a nonprofit marketing perspective and identify the need for charities to better understand the motivations and behaviour of their supporters. In similar vein, this study aims to improve the way nonprofits and givers interact; and ultimately, enhance the giving experience and thus multiply planned giving participation. Academically, it offers insights to Australian bequest motivations and attitudes not studied empirically before.

An integrated approach for precise road reconstruction from aerial imagery and LiDAR data

Accurate and detailed road models play an important role in a number of geospatial applications, such as infrastructure planning, traffic monitoring, and driver assistance systems. In this thesis, an integrated approach for the automatic extraction of precise road features from high resolution aerial images and LiDAR point clouds is presented. A framework of road information modeling has been proposed, for rural and urban scenarios respectively, and an integrated system has been developed to deal with road feature extraction using image and LiDAR analysis. For road extraction in rural regions, a hierarchical image analysis is first performed to maximize the exploitation of road characteristics in different resolutions. The rough locations and directions of roads are provided by the road centerlines detected in low resolution images, both of which can be further employed to facilitate the road information generation in high resolution images. The histogram thresholding method is then chosen to classify road details in high resolution images, where color space transformation is used for data preparation. After the road surface detection, anisotropic Gaussian and Gabor filters are employed to enhance road pavement markings while constraining other ground objects, such as vegetation and houses. Afterwards, pavement markings are obtained from the filtered image using the Otsu's clustering method. The final road model is generated by superimposing the lane markings on the road surfaces, where the digital terrain model (DTM) produced by LiDAR data can also be combined to obtain the 3D road model. As the extraction of roads in urban areas is greatly affected by buildings, shadows, vehicles, and parking lots, we combine high resolution aerial images and dense LiDAR data to fully exploit the precise spectral and horizontal spatial resolution of aerial images and the accurate vertical information provided by airborne LiDAR. Objectoriented image analysis methods are employed to process the feature classiffcation and road detection in aerial images. In this process, we first utilize an adaptive mean shift (MS) segmentation algorithm to segment the original images into meaningful object-oriented clusters. Then the support vector machine (SVM) algorithm is further applied on the MS segmented image to extract road objects. Road surface detected in LiDAR intensity images is taken as a mask to remove the effects of shadows and trees. In addition, normalized DSM (nDSM) obtained from LiDAR is employed to filter out other above-ground objects, such as buildings and vehicles. The proposed road extraction approaches are tested using rural and urban datasets respectively. The rural road extraction method is performed using pan-sharpened aerial images of the Bruce Highway, Gympie, Queensland. The road extraction algorithm for urban regions is tested using the datasets of Bundaberg, which combine aerial imagery and LiDAR data. Quantitative evaluation of the extracted road information for both datasets has been carried out. The experiments and the evaluation results using Gympie datasets show that more than 96% of the road surfaces and over 90% of the lane markings are accurately reconstructed, and the false alarm rates for road surfaces and lane markings are below 3% and 2% respectively. For the urban test sites of Bundaberg, more than 93% of the road surface is correctly reconstructed, and the mis-detection rate is below 10%.

Analysis of ten years historical weather data in Australia

Typical reference year (TRY) weather data is often used to represent the long term weather pattern for building simulation and design. Through the analysis of ten year historical hourly weather data for seven Australian major capital cities using the frequencies procedure of descriptive statistics analysis (by SPSS software), this paper investigates: • the closeness of the typical reference year (TRY) weather data in representing the long term weather pattern; • the variations and common features that may exist between relatively hot and cold years. It is found that for the given set of input data, in comparison with the other weather elements, the discrepancy between TRY and multiple years is much smaller for the dry bulb temperature, relative humidity and global solar irradiance. The overall distribution patterns of key weather elements are also generally similar between the hot and cold years, but with some shift and/or small distortion. There is little common tendency of change between the hot and the cold years for different weather variables at different study locations.

Evaluating the economics of the Australian National Hand Hygiene Initiative

The National Hand Hygiene Initiative, implemented in Australia in 2009, is currently being evaluated for effectiveness and cost-effectiveness by a multidisciplinary team of researchers. Data from a wide range of sources are being harvested to address the research questions. The data are observational and appropriate statistical and economic modelling methods are being used. Decision makers will be provided with new knowledge about how hand hygiene interventions should be organised and what investment decisions are justified. This is novel research and the authors are unaware of any other evaluation of hand hygiene improvement initiatives. This paper describes the evaluation currently underway.

Australian children's experiences of parents' online mediation

This paper draws on the work of the ‘EU Kids Online’ network funded by the EC (DG Information Society) Safer Internet plus Programme (project code SIP-KEP-321803); see www.eukidsonline.net, and addresses Australian children’s online activities in terms of risk, harm and opportunity. In particular, it draws upon data that indicates that Australian children are more likely to encounter online risks — especially around seeing sexual images, bullying, misuse of personal data and exposure to potentially harmful user-generated content — than is the case with their EU counterparts. Rather than only comparing Australian children with their European equivalents, this paper places the risks experienced by Australian children in the context of the mediation and online protection practices adopted by their parents, and asks about the possible ways in which we might understand data that seems to indicate that Australian children’s experiences of online risk and harm differ significantly from the experiences of their Europe-based peers. In particular, and as an example, this paper sets out to investigate the apparent conundrum through which Australian children appear twice as likely as most European children to have seen sexual images in the past 12 months, but parents are more likely to filter their access to the internet than is the case with most children in the wider EU Kids Online study. Even so, one in four Australian children (25%) believes that what their parents do helps ‘a lot’ to improve their internet experience, and Australian children and their parents are a little less likely to agree about the mediation practices taking place in the family home than is the case in the EU. The AU Kids Online study was carried out as a result of the ARC Centre of Excellence for Creative Industries and Innovation’s funding of a small scale randomised sample (N = 400) of Australian families with at least one child, aged 9–16, who goes online. The report on Risks and safety for Australian children on the internet follows the same format and uses much of the contextual statement around these issues as the ‘county level’ reports produced by the 25 EU nations involved in EU Kids Online, first drafted by Livingstone et al. (2010). The entirely new material is the data itself, along with the analysis of that data.

A context sensitive model for querying linked scientific data

This thesis provides a query model suitable for context sensitive access to a wide range of distributed linked datasets which are available to scientists using the Internet. The model is designed based on scientific research standards which require scientists to provide replicable methods in their publications. Although there are query models available that provide limited replicability, they do not contextualise the process whereby different scientists select dataset locations based on their trust and physical location. In different contexts, scientists need to perform different data cleaning actions, independent of the overall query, and the model was designed to accommodate this function. The query model was implemented as a prototype web application and its features were verified through its use as the engine behind a major scientific data access site, Bio2RDF.org. The prototype showed that it was possible to have context sensitive behaviour for each of the three mirrors of Bio2RDF.org using a single set of configuration settings. The prototype provided executable query provenance that could be attached to scientific publications to fulfil replicability requirements. The model was designed to make it simple to independently interpret and execute the query provenance documents using context specific profiles, without modifying the original provenance documents. Experiments using the prototype as the data access tool in workflow management systems confirmed that the design of the model made it possible to replicate results in different contexts with minimal additions, and no deletions, to query provenance documents.

Mothers of young children with special health care needs : maternal well-being and engagement in work

This thesis reports research focused on the well-being and employment experiences of mothers who have a child with special health care needs. Data are drawn from Growing Up in Australia: The Longitudinal Study of Australian Children (LSAC). This is a public access database. The thesis uses the social ecological theory of Bronfenbrenner (1984) and the work of Zubrick et al. (2000) on human and social capital to inform the conceptual framework developed for the research. Four studies are reported. LSAC has a nationally representative sample of Australian children and their families. The study is tracking the development of 10,000 children, with data collected every two years, from 2004 to 2018. This thesis uses data from the Kindergarten Cohort of LSAC. The 4,983 children in the Kindergarten Cohort were aged 4 years at recruitment into the study in 2004. The analyses in this thesis use child and family data from Wave 1 (2004) and Wave 2 (2006) for a subsample of the children who are identified as having special health needs. This identification is based on a short screening questionnaire included in the Parent 1 Interview at each wave of the data collection. It is the children who are identified as having special health care needs which can be broadly defined as chronic health conditions or developmental difficulties. However, it is the well-being and employment experiences of the mothers of these children that are the primary focus in three of the four studies reported in this thesis.

Adults cycling on the footpath : what do the data show?

Recent increases in cycling have led to many media articles highlighting concerns about interactions between cyclists and pedestrians on footpaths and off-road paths. Under the Australian Road Rules, adults are not allowed to ride on footpaths unless accompanying a child 12 years of age or younger. However, this rule does not apply in Queensland. This paper reviews international studies that examine the safety of footpath cycling for both cyclists and pedestrians, and relevant Australian crash and injury data. The results of a survey of more than 2,500 Queensland adult cyclists are presented in terms of the frequency of footpath cycling, the characteristics of those cyclists and the characteristics of self-reported footpath crashes. A third of the respondents reported riding on the footpath and, of those, about two-thirds did so reluctantly. Riding on the footpath was more common for utilitarian trips and for new riders, although the average distance ridden on footpaths was greater for experienced riders. About 5% of distance ridden and a similar percentage of self-reported crashes occurred on footpaths. These data are discussed in terms of the Safe Systems principle of separating road users with vastly different levels of kinetic energy. The paper concludes that footpaths are important facilities for both inexperienced and experienced riders and for utilitarian riding, especially in locations riders consider do not provide a safe system for cycling.

Putting paid to prescribed roles : a new era for Australian women and philanthropy

In redefining our understanding of women’s roles in contemporary Australian philanthropy, the impact of major contextual and demographic changes, as well as changes in women’s roles, responsibilities and opportunities need to be considered. Although academic study of philanthropy and the wider third sector is increasing in Australia, literature searches have revealed little current data on the giving patterns and philanthropic drivers for contemporary Australian women, particularly emerging cohorts (one ABS survey looks at giving patterns – ABS, 2000b: 32). In contrast, there is increasing interest in the US, where it is acknowledged that more women are becoming independent holders of wealth; and that interested donors have specific needs, desires and motivations in terms of knowledge, power, marketing and response to their philanthropy (see for example, Grace 2000; McCarthy 2001; Women’s Philanthropy Institute 2002). These varied demographic, social and economic drivers, which could also be expected to encourage new cohorts of Australian women to give, will be examined within our definition of women in philanthropy, and a brief history of women’s philanthropy in Australia, in order to inform future in-depth analyses of Australian women donors.

Toward resolving deep neoaves phylogeny : data, signal enhancement, and priors

We report three developments toward resolving the challenge of the apparent basal polytomy of neoavian birds. First, we describe improved conditional down-weighting techniques to reduce noise relative to signal for deeper divergences and find increased agreement between data sets. Second, we present formulae for calculating the probabilities of finding predefined groupings in the optimal tree. Finally, we report a significant increase in data: nine new mitochondrial (mt) genomes (the dollarbird, New Zealand kingfisher, great potoo, Australian owlet-nightjar, white-tailed trogon, barn owl, a roadrunner [a ground cuckoo], New Zealand long-tailed cuckoo, and the peach-faced lovebird) and together they provide data for each of the six main groups of Neoaves proposed by Cracraft J (2001). We use his six main groups of modern birds as priors for evaluation of results. These include passerines, cuckoos, parrots, and three other groups termed “WoodKing” (woodpeckers/rollers/kingfishers), “SCA” (owls/potoos/owlet-nightjars/hummingbirds/swifts), and “Conglomerati.” In general, the support is highly significant with just two exceptions, the owls move from the “SCA” group to the raptors, particularly accipitrids (buzzards/eagles) and the osprey, and the shorebirds may be an independent group from the rest of the “Conglomerati”. Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes.

Australian children with special health care needs: Social-emotional and learning competencies in the early years

This study examined the relationship between special health care needs and social-emotional and learning competence in the early years, reporting on two waves of data from the Kindergarten Cohort of Growing up in Australia: The Longitudinal Study of Australian Children (LSAC). Six hundred and fifty children were identified through the 2-question Special Health Care Needs Screener as having special health care needs. Children with special health care needs were more likely to be male, to have been of low birth weight, to be taking prescription medications, to be diagnosed with a specific health condition and to be from families where the mother was less well educated. These children scored significantly lower on teacher-rated social-emotional and learning competencies prior to school compared to a control group of children without special health care needs. Multiple regression analyses indicated that being identified with a special health care need prior to school predicted lower social-emotional and learning competencies in the early years of school. Results are discussed in terms of the implications for policy and practice.