Latent variable models in statistical genetics

Understanding the complexities that are involved in the genetics of multifactorial diseases is still a monumental task. In addition to environmental factors that can influence the risk of disease, there is also a number of other complicating factors. Genetic variants associated with age of disease onset may be different from those variants associated with overall risk of disease, and variants may be located in positions that are not consistent with the traditional protein coding genetic paradigm. Latent Variable Models are well suited for the analysis of genetic data. A latent variable is one that we do not directly observe, but which is believed to exist or is included for computational or analytic convenience in a model. This thesis presents a mixture of methodological developments utilising latent variables, and results from case studies in genetic epidemiology and comparative genomics. Epidemiological studies have identified a number of environmental risk factors for appendicitis, but the disease aetiology of this oft thought useless vestige remains largely a mystery. The effects of smoking on other gastrointestinal disorders are well documented, and in light of this, the thesis investigates the association between smoking and appendicitis through the use of latent variables. By utilising data from a large Australian twin study questionnaire as both cohort and case-control, evidence is found for the association between tobacco smoking and appendicitis. Twin and family studies have also found evidence for the role of heredity in the risk of appendicitis. Results from previous studies are extended here to estimate the heritability of age-at-onset and account for the eect of smoking. This thesis presents a novel approach for performing a genome-wide variance components linkage analysis on transformed residuals from a Cox regression. This method finds evidence for a dierent subset of genes responsible for variation in age at onset than those associated with overall risk of appendicitis. Motivated by increasing evidence of functional activity in regions of the genome once thought of as evolutionary graveyards, this thesis develops a generalisation to the Bayesian multiple changepoint model on aligned DNA sequences for more than two species. This sensitive technique is applied to evaluating the distributions of evolutionary rates, with the finding that they are much more complex than previously apparent. We show strong evidence for at least 9 well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least 7 classes in an alignment of four mammals, including human. A pattern of enrichment and depletion of genic regions in the profiled segments suggests they are functionally significant, and most likely consist of various functional classes. Furthermore, a method of incorporating alignment characteristics representative of function such as GC content and type of mutation into the segmentation model is developed within this thesis. Evidence of fine-structured segmental variation is presented.

The conceptualisation, sensitivity and measurement of holding costs and other selected elements impacting housing affordability (Literature review and research methodology for confirmation of PhD candidature)

It is widely held that strong relationships exist between housing, economic status, and well being. This is exemplified by widespread housing stock surpluses in many countries which threaten to destabilise numerous aspects related to individuals and community. However, the position of housing demand and supply is not consistent. The Australian position provides a distinct contrast whereby seemingly inexorable housing demand generally remains a critical issue affecting the socio-economic landscape. Underpinned by high levels of immigration, and further buoyed by sustained historically low interest rates, increasing income levels, and increased government assistance for first home buyers, this strong housing demand ensures elements related to housing affordability continue to gain prominence. A significant, but less visible factor impacting housing affordability – particularly new housing development – relates to holding costs. These costs are in many ways “hidden” and cannot always be easily identified. Although it is only one contributor, the nature and extent of its impact requires elucidation. In its simplest form, it commences with a calculation of the interest or opportunity cost of land holding. However, there is significantly more complexity for major new developments - particularly greenfield property development. Preliminary analysis conducted by the author suggests that even small shifts in primary factors impacting holding costs can appreciably affect housing affordability – and notably, to a greater extent than commonly held. Even so, their importance and perceived high level impact can be gauged from the unprecedented level of attention policy makers have given them over recent years. This may be evidenced by the embedding of specific strategies to address burgeoning holding costs (and particularly those cost savings associated with streamlining regulatory assessment) within statutory instruments such as the Queensland Housing Affordability Strategy, and the South East Queensland Regional Plan. However, several key issues require investigation. Firstly, the computation and methodology behind the calculation of holding costs varies widely. In fact, it is not only variable, but in some instances completely ignored. Secondly, some ambiguity exists in terms of the inclusion of various elements of holding costs, thereby affecting the assessment of their relative contribution. Perhaps this may in part be explained by their nature: such costs are not always immediately apparent. Some forms of holding costs are not as visible as the more tangible cost items associated with greenfield development such as regulatory fees, government taxes, acquisition costs, selling fees, commissions and others. Holding costs are also more difficult to evaluate since for the most part they must be ultimately assessed over time in an ever-changing environment, based on their strong relationship with opportunity cost which is in turn dependant, inter alia, upon prevailing inflation and / or interest rates. By extending research in the general area of housing affordability, this thesis seeks to provide a more detailed investigation of those elements related to holding costs, and in so doing determine the size of their impact specifically on the end user. This will involve the development of soundly based economic and econometric models which seek to clarify the componentry impacts of holding costs. Ultimately, there are significant policy implications in relation to the framework used in Australian jurisdictions that promote, retain, or otherwise maximise, the opportunities for affordable housing.

Corruption and political interest : empirical evidence at the micro level

The topic of corruption has recently attracted a great deal of attention, yet there is still a lack of micro level empirical evidence regarding the determinates of corruption. Furthermore, the present literature has not investigated the effects of political interest on corruption despite the interesting potential of this link. We address these deficiencies by analysing a cross-section of individuals, using the World Values Survey. We explore the determinants of corruption through two dependant variables (perceived corruption and the justifiability of corruption). The impact of political interest on corruption is explored through three different proxies presenting empirical evidence at both the cross-country level and the within-country level.The results of the multivariate analysis suggest that political interest has an impact on corruption controlling for a huge number of factors.

Contesting ‘sustainability’ in infrastructure planning : The debate of the public interest in Brisbane’s Boggo Road Busway development

Sustainable infrastructure demands that declared principles of sustainability are enacted in the processes of its implementation. However, a problem arises if the concept of sustainability is not thoroughly scrutinised in the planning process. The public interest could be undermined when the rhetoric of sustainability is used to substantiate a proposed plan. This chapter analyses the manifestation of sustainable development in the Boggo Road Busway Plan in Brisbane, Australia against the sustainability agenda set in the South East Queensland Regional and Transport Plans. Although the construction of the Busway was intended to improve public transport access in the region, its implementation drew significant environmental concerns. Local community groups contested the ‘sustainability’ concept deployed in Queensland’s infrastructure planning. Their challenges resulted in important concessions in the delivery of the Busway plan. This case demonstrates that principles of sustainable infrastructure should be measurable and that local communities be better informed in order to fulfil the public interest in regional planning.

The effectiveness of a short-term group music therapy intervention for parents who have a child with a disability

The relationship between the quality of parent-child interactions and positive child developmental trajectories is well established (Guralnick, 2006; Shonkoff & Meissels, 2000; Zubrick et al., 2008). However, a range of parental, family, and socio-economic factors can pose risks to parents’ capacity to participate in quality interactions with their children. In particular, families with a child with a disability have been found to have higher levels of parenting stress, and are more likely to experience economic disadvantage, as well as social isolation. The importance of early interventions to promote positive parenting and child development for these families is widely recognised (Shonkoff & Meissels, 2000). However, to date, there is a lack of evidence about the effectiveness of early parenting programs for families who have a young child with a disability. This thesis investigates the impact of a music therapy parenting program, Sing & Grow, on 201 parent-child dyads who attended programs specifically targeted to parents who had a young child with a disability. Sing & Grow is an Australian national early parenting intervention funded by the Australian Government Department of Families, Housing, Community Services and Indigenous Affairs and delivered by Playgroup Queensland. It is designed and delivered by Registered Music Therapists for families with children aged from birth to three years. It aims to improve parenting skills and confidence, improve family functioning (positive parent-child interactions), enhance child development, and provide social networking opportunities to socially isolated families. The intervention targets a range of families in circumstances that have the potential to impact negatively on family functioning. This thesis uses data from the National Evaluation Study of Sing & Grow from programs which were targeted at families who had a young child with a disability. Three studies were conducted to address the objectives of this thesis. Study 1 examines the effects of the Sing & Grow intervention on parent reported pre and post parent mental health, parenting confidence, parenting skills, and child development, and other parent reported outcomes including social support, use of intervention resources, satisfaction with the intervention and perceived benefits of and barriers to participation. Significant improvements from pre to post were found for parent mental health and parent reported child communication and social skills, along with evidence that parents were very satisfied with the program and that it brought social benefits to families. Study 2 explored the pre to post effects of the intervention on children’s developmental skills and parent-child interactions using observational ratings made by clinicians. Significant pre to post improvements were found for parenting sensitivity, parental engagement with child and acceptance of child as well as for child responsiveness to parent, interest, and participation in the intervention, and social skills. Study 3 examined the nature of child and family characteristics that predicted better outcomes for families while taking account of the level of participation in the program. An overall outcome index was calculated and served as the dependent variable in a logistic regression analysis. Families who attended six or more sessions and mothers who had not completed high school were more likely to have higher outcome scores at post intervention than those who attended fewer sessions and those with more educated mothers respectively. The findings of this research indicate that the intervention had a positive impact on participants’ mental health, parenting behaviours and child development and that level of attendance was associated with better outcomes. There was also evidence that the program reached its target of high risk families (i.e., families in which mothers had lower educational levels) and that for these families better outcomes were achieved. There were also indications that the program was accessible and highly regarded by families and that it promoted social connections for participants. A theoretical model of how the intervention is currently working for families is proposed to explain the connections between early parenting, child development and maternal wellbeing. However, more research is required to further elucidate the mechanisms by which the intervention creates change for families. This research presents promising evidence that a short term group music therapy program can elicit important therapeutic benefits for families who have a child with a disability.

Renewable energy sources and frequency regulation : survey and new perspectives

As the use of renewable energy sources (RESs) increases worldwide, there is a rising interest on their impacts on power system operation and control. An overview of the key issues and new challenges on frequency regulation concerning the integration of renewable energy units into the power systems is presented. Following a brief survey on the existing challenges and recent developments, the impact of power fluctuation produced by variable renewable sources (such as wind and solar units) on sysstem frequency performance is also presented. An updated LFC model is introduced, and power system frequency response in the presence of RESs and associated issues is analysed. The need for the revising of frequency performance standards is emphasised. Finally, non-linear time-domain simulations on the standard 39-bus and 24-bus test systems show that the simulated results agree with those predicted analytically.

Modelling issues on the railway resource management process using multi-agent system

Many infrastructure and necessity systems such as electricity and telecommunication in Europe and the Northern America were used to be operated as monopolies, if not state-owned. However, they have now been disintegrated into a group of smaller companies managed by different stakeholders. Railways are no exceptions. Since the early 1980s, there have been reforms in the shape of restructuring of the national railways in different parts of the world. Continuous refinements are still conducted to allow better utilisation of railway resources and quality of service. There has been a growing interest for the industry to understand the impacts of these reforms on the operation efficiency and constraints. A number of post-evaluations have been conducted by analysing the performance of the stakeholders on their profits (Crompton and Jupe 2003), quality of train service (Shaw 2001) and engineering operations (Watson 2001). Results from these studies are valuable for future improvement in the system, followed by a new cycle of post-evaluations. However, direct implementation of these changes is often costly and the consequences take a long period of time (e.g. years) to surface. With the advance of fast computing technologies, computer simulation is a cost-effective means to evaluate a hypothetical change in a system prior to actual implementation. For example, simulation suites have been developed to study a variety of traffic control strategies according to sophisticated models of train dynamics, traction and power systems (Goodman, Siu and Ho 1998, Ho and Yeung 2001). Unfortunately, under the restructured railway environment, it is by no means easy to model the complex behaviour of the stakeholders and the interactions between them. Multi-agent system (MAS) is a recently developed modelling technique which may be useful in assisting the railway industry to conduct simulations on the restructured railway system. In MAS, a real-world entity is modelled as a software agent that is autonomous, reactive to changes, able to initiate proactive actions and social communicative acts. It has been applied in the areas of supply-chain management processes (García-Flores, Wang and Goltz 2000, Jennings et al. 2000a, b) and e-commerce activities (Au, Ngai and Parameswaran 2003, Liu and You 2003), in which the objectives and behaviour of the buyers and sellers are captured by software agents. It is therefore beneficial to investigate the suitability or feasibility of applying agent modelling in railways and the extent to which it might help in developing better resource management strategies. This paper sets out to examine the benefits of using MAS to model the resource management process in railways. Section 2 first describes the business environment after the railway 2 Modelling issues on the railway resource management process using MAS reforms. Then the problems emerge from the restructuring process are identified in section 3. Section 4 describes the realisation of a MAS for railway resource management under the restructured scheme and the feasible studies expected from the model.

A two-Dimensional finite volume method for variable density flow and solute transport through saturated-unsaturated media

Extensive groundwater withdrawal has resulted in a severe seawater intrusion problem in the Gooburrum aquifers at Bundaberg, Queensland, Australia. Better management strategies can be implemented by understanding the seawater intrusion processes in those aquifers. To study the seawater intrusion process in the region, a two-dimensional density-dependent, saturated and unsaturated flow and transport computational model is used. The model consists of a coupled system of two non-linear partial differential equations. The first equation describes the flow of a variable-density fluid, and the second equation describes the transport of dissolved salt. A two-dimensional control volume finite element model is developed for simulating the seawater intrusion into the heterogeneous aquifer system at Gooburrum. The simulation results provide a realistic mechanism by which to study the convoluted transport phenomena evolving in this complex heterogeneous coastal aquifer.

Models of collective cell spreading with variable cell aspect ratio : a motivation for degenerate diffusion models

Continuum diffusion models are often used to represent the collective motion of cell populations. Most previous studies have simply used linear diffusion to represent collective cell spreading, while others found that degenerate nonlinear diffusion provides a better match to experimental cell density profiles. In the cell modeling literature there is no guidance available with regard to which approach is more appropriate for representing the spreading of cell populations. Furthermore, there is no knowledge of particular experimental measurements that can be made to distinguish between situations where these two models are appropriate. Here we provide a link between individual-based and continuum models using a multi-scale approach in which we analyze the collective motion of a population of interacting agents in a generalized lattice-based exclusion process. For round agents that occupy a single lattice site, we find that the relevant continuum description of the system is a linear diffusion equation, whereas for elongated rod-shaped agents that occupy L adjacent lattice sites we find that the relevant continuum description is connected to the porous media equation (pme). The exponent in the nonlinear diffusivity function is related to the aspect ratio of the agents. Our work provides a physical connection between modeling collective cell spreading and the use of either the linear diffusion equation or the pme to represent cell density profiles. Results suggest that when using continuum models to represent cell population spreading, we should take care to account for variations in the cell aspect ratio because different aspect ratios lead to different continuum models.

Interest from Tertiary Educated Persons in Fostering Children with Higher Care needs under a Professional (Paid) Model Compared with General Foster Care

The number of Australian children requiring foster care due to abuse and neglect is increasing at a faster rate than suitable carers can be recruited. Currently increased numbers of foster children are presenting with higher care needs. Evidence suggests carers with a higher education could contribute to placement stability and ultimately provide more positive outcomes for this group of children. This paper explores the level of interest by tertiary educated persons toward a model of fostering for children with higher needs. Using a descriptive survey methodology, a convenience sample of 644 university undergraduate and postgraduate students within faculties of health sciences, and education, arts and social sciences was employed. Psychology students in the 17-26 year old age group showed greatest interest in a professional foster care model and this was statistically significant (p=0.002 955 CI .000-.010) when compared to other health professionals and other age groups. Education students held the highest interest in general fostering although not statistically significant. When these survey results were extrapolated to the total number of health professionals in Australia there could be 8,385 potential recruits for a model professional foster care. Focused campaigns are required to source professional as recruits to fostering with the benefit of servicing the placement needs of higher care needs children and contributing to general foster care resources.

User-driven saliency maps for evaluating Region-of-Interest detection

Detection of Region of Interest (ROI) in a video leads to more efficient utilization of bandwidth. This is because any ROIs in a given frame can be encoded in higher quality than the rest of that frame, with little or no degradation of quality from the perception of the viewers. Consequently, it is not necessary to uniformly encode the whole video in high quality. One approach to determine ROIs is to use saliency detectors to locate salient regions. This paper proposes a methodology for obtaining ground truth saliency maps to measure the effectiveness of ROI detection by considering the role of user experience during the labelling process of such maps. User perceptions can be captured and incorporated into the definition of salience in a particular video, taking advantage of human visual recall within a given context. Experiments with two state-of-the-art saliency detectors validate the effectiveness of this approach to validating visual saliency in video. This paper will provide the relevant datasets associated with the experiments.

A survey on the relationship between trust and interest similarity in online social networks

A remarkable growth in quantity and popularity of online social networks has been observed in recent years. There is a good number of online social networks exists which have over 100 million registered users. Many of these popular social networks offer automated recommendations to their users. This automated recommendations are normally generated using collaborative filtering systems based on the past ratings or opinions of the similar users. Alternatively, trust among the users in the network also can be used to find the neighbors while making recommendations. To obtain the optimum result, there must be a positive correlation exists between trust and interest similarity. Though the positive relations between trust and interest similarity are assumed and adopted by many researchers; no survey work on real life people’s opinion to support this hypothesis is found. In this paper, we have reviewed the state-of-the-art research work on trust in online social networks and have presented the result of the survey on the relationship between trust and interest similarity. Our result supports the assumed hypothesis of positive relationship between the trust and interest similarity of the users.