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.

Asia and the Commons : case studies 2008

A collection of case studies of individuals and organisations utilising open models in the Asia Pacific and associated regions. The case studies represent activities in nine countries, broader regions such as the Arab nations, and global efforts towards sustainability and social justice, revealing creative ways of participating in the commons. Featured are remix artists, performers, open source software programmers, film makers, collecting institutions and publishing houses focused on democracy and change, who demonstrate a diverse set of motivations to engage with the shared ideals of openness and community collaboration.

Building a successful partnership to increase affordable rental housing supply in Queensland

Accessibility to housing for low to moderate income groups in Australia has been experiencing a severe decline since 2001. On the supply side, the public sector has been reducing its commitment to the direct provision of public housing. Despite high demand for affordable housing, there has been limited supply generated by non-government housing providers. One possible solution to promote an increase in affordable housing supply, like other infrastructure, is through the development of multi-stakeholder partnerships and private financing. This research aims to identify current issues underlying decision-making criteria for building multi-stakeholder partnerships to deliver affordable housing projects. It also investigates strategies for minimising risk and ensuring the financial outcomes of these partnership arrangements. A mix of qualitative in-depth interviews and quantitative surveys has been used as the main method to explore stakeholder experiences regarding their involvement in partnership arrangements in the affordable housing sector in Queensland. Two sets of interviews were conducted following an exploratory pilot study: one set in 2003-2004 and the other in 2007-2008. There were nineteen respondents representing government, private and not-for-profit organisations in the first stage interviews and surveys. The second stage interviews were focussed on twenty-two housing providers in South East Queensland. Initial analyses have been conducted using thematic and statistical analyses. This study extends the use of existing decision making tools and combines the use of a Soft System Framework to analyse the ideal state questionnaires using qualitative thematic analysis. Soft System Methodology (SSM) has been used to analyse this unstructured complex problem by using systematic thinking to develop a conceptual model and carrying it to the real world situations to solve the problem. This research found that the diversity of stakeholder capability and their level of risk acceptance will allow partnerships to develop the best synergies and a degree of collaboration which achieves the required financial return within acceptable risk parameters. However, some of the negativity attached to future commitment to such partnerships has been found to be the anticipation of a worse outcome than that expected from independent action. Many interviewees agree that housing providers' fear of financial risk and community rejection has been central to dampening their enthusiasm for entering such investment projects. The creation of a mixed-use development structure will mitigate both risk and return as the commercial income will subsidise the affordable housing development and will normalise concentration of marginalised low-income people who live in a prime location with an award winning design. In addition, tenant support schemes and rent-to-buy incentive programs will encourage them to secure their tenancies and significantly reduce the risk of rent arrears and property damage. There is also a breakthrough investment vehicle offered by the social developer which sells the non-physical but financial product to individual and institutional investors to mitigate further financial risk. Finally, this study recommends modification of the current value-for-money framework in favour of broader partnership arrangements which are more closely aligned with risk minimisation strategies.

Elective foot and ankle surgery : activity and perioperative complications in Queensland public hospitals, Australia

Objective: To conduct an audit of elective foot and ankle surgery in Queensland public hospitals and to compare the frequency of these procedures performed to other states and territories of Australia. ---------- Methods: ICD-10-AM data was used to extract elective foot and ankle procedures from the Data Services Unit of Queensland Health, and the Australian Institute of Health and Welfare between the years of 2000 and 2004. ---------- Results During the 4-year audit period 3846 primary procedures were performed during the 4-year period with a complication rate of 2.2% during the hospital admission period. Mean length of stay was 1.7 days. Post-operative infection rates were 0.26%. With the exception of Tasmania and the Northern Territory, Queensland performs the least number of elective foot and ankle procedures per capita per year in Australia. ---------- Conclusions This is the first reported audit of elective foot and ankle surgery for Queensland public hospitals. Complication rates cannot be directly compared to the literature as this data could only capture complications within hospital admission period. Fewer elective foot and ankle procedures were performed in Queensland public hospitals compared to all other mainland states of Australia during the data collection period.

The impact of spin on Australian real estate journalism : a Queensland study

Regardless of ‘bear’ or ‘bull’ markets, the great Australian dream remains to own your own home. Central to this dream of home ownership is unflagging interest in the property market, reflected in bulging real estate news sections of newspapers in South East Queensland, the focus area for this thesis research. While there has been much scholarly research into other areas of public relations spin and its impact on news-gathering processes, there appears to be next to no research on real estate spin, how it is prepared and by whom, and journalism’s attitude to and the managing of the spin. Real estate spin remains an under-researched topic requiring further investigation not only in South East Queensland but Australia-wide given the ‘big bucks’ allotted to the promotion of real estate and the income it generates for news media outlets, particularly newspapers. This thesis examines the influence of public relations practitioners and journalists specialising in real estate spin through interviews, content analysis, and how real estate spin envelopes itself in today’s society. From content analyses and observations of journalism in the real estate rounds of the two major newspapers in South East Queensland, I found that journalists were using massive quantities of real estate spin supplied by PR practitioners and other associated industry sources. This spin is supplanting investigative newsroom journalism, thus allowing newspapers to operate with minimal staffing levels yet still able to publish large weekly real estate news sections. My research also revealed growing commercialisation of real estate news through increasing outsourcing of journalistic work to a writing bureau, which could jeopardise both the professions of journalism and public relations in the future.

Critical review of Queensland's Crime and Misconduct Commission Inquiry into abuse of children in foster care : social work's contribution to reform

This paper profiles Queensland's recent Crime and Misconduct Commission Inquiry into the abuse of children in foster care. The authors welcome the outcome as an opportunity to highlight the problems encountered by child protection jurisdictions in Australia and internationally, and they applaud some of the Inquiry's findings. However, the paper argues that the path to reform is hampered by insufficient accountability by government and management, and an inadequate challenge to the ideologies underpinning contemporary child protection policy and practice. The authors conclude with a call to value and assert social work's contribution to child protection systems so as to vastly improve outcomes for children and families.

E-commerce experiences in the real estate industry : a preliminary study in regional Queensland

Computer systems have become commonplace in most SMEs and technology is increasingly becoming a part of doing business. In recent years, the Internet has become readily available to businesses; consequently there has been growing pressure on SMEs to take up e-commerce. However, e-commerce is perceived by many as being unproven in terms of business benefit. This research aims to determine what, if any, benefits are derived from assimilating e-commerce technologies into SME business processes. This paper presents three in-depth case studies from the Real Estate industry in a regional setting. Overall, findings were positive and identified the following experiences: enhanced business efficiencies, cost benefits, improved customer interactions and increased business return on investment.

Current child restraint practice in Queensland, new legislation and future challenges

Correct use of child restraints reduces the risk of death and injury. Use of adult seat belts is better than being unrestrained but can result in injury to children who are too small. New Australian legislation extends the requirement for using child-specific restraints until children are 7 years old and thus requires more appropriate levels of protection for these children. As part of a larger study of injury prevention in Queensland, parents of children 0-9 years old were surveyed regarding their restraint practices before the introduction of the new legislation. The restraint status of 18% of the children would not be compliant with the new legislation, with the problem being more prevalent for 5-9 year olds (22%) than 0-4 year olds (16%). A high proportion of older children used an adult seat belt. Very few children aged 0-4 (1.3%) usually travelled in the front seat in contravention of the new requirement, but around 11% of this age group were reported as ever having done so. Usual travel in the front seat was higher among 5-9 year olds (8.5%), with more than half of the 5-9 year olds reported as ever having done so. Given the widespread use of adult seat belts by older children, there is a need to consider improving protection of children in the ‘gap’ between when the requirement for the child to use a booster ceases (effectively age 7) and when the adult belt is likely to actually fit the child (closer to age 9 or 10).

Place makers : contemporary Queensland architects

This article reviews Place Makers: Contemporary Queensland Architects held in the Gallery of Modern Art (GOMA), Brisbane, Queensland.

Dengue fever and el nino-southern oscillation in Queensland, Australia : a time series predictive model

Background It remains unclear over whether it is possible to develop an epidemic forecasting model for transmission of dengue fever in Queensland, Australia. Objectives To examine the potential impact of El Niño/Southern Oscillation on the transmission of dengue fever in Queensland, Australia and explore the possibility of developing a forecast model of dengue fever. Methods Data on the Southern Oscillation Index (SOI), an indicator of El Niño/Southern Oscillation activity, were obtained from the Australian Bureau of Meteorology. Numbers of dengue fever cases notified and the numbers of postcode areas with dengue fever cases between January 1993 and December 2005 were obtained from the Queensland Health and relevant population data were obtained from the Australia Bureau of Statistics. A multivariate Seasonal Auto-regressive Integrated Moving Average model was developed and validated by dividing the data file into two datasets: the data from January 1993 to December 2003 were used to construct a model and those from January 2004 to December 2005 were used to validate it. Results A decrease in the average SOI (ie, warmer conditions) during the preceding 3–12 months was significantly associated with an increase in the monthly numbers of postcode areas with dengue fever cases (β=−0.038; p = 0.019). Predicted values from the Seasonal Auto-regressive Integrated Moving Average model were consistent with the observed values in the validation dataset (root-mean-square percentage error: 1.93%). Conclusions Climate variability is directly and/or indirectly associated with dengue transmission and the development of an SOI-based epidemic forecasting system is possible for dengue fever in Queensland, Australia.

Managing the winds of change

Environmental impacts caused during Australia's comparatively recent settlement by Europeans are evident. Governments (both Commonwealth and States) have been largely responsible for requiring landholders – through leasehold development conditions and taxation concessions – to conduct clearing that is now perceived as damage. Most governments are now demanding resource protection. There is a measure of bewilderment (if not resentment) among landholders because of this change. The more populous States, where most overall damage has been done (i.e. Victoria and New South Wales), provide most support for attempts to stop development in other regions where there has been less damage. Queensland, i.e. the north-eastern quarter of the continent, has been relatively slow to develop. It also holds the largest and most diverse natural environments. Tree clearing is an unavoidable element of land development, whether to access and enhance native grasses for livestock or to allow for urban developments (with exotic tree plantings). The consequences in terms of regulations are particularly complex because of the dynamic nature of vegetation. The regulatory terms used in current legislation – such as 'Endangered' and 'Of concern' – depend on legally-defined, static baselines. Regrowth and fire damage are two obvious causes of change. A less obvious aspect is succession, where ecosystems change naturally over long timeframes. In the recent past, the Queensland Government encouraged extensive tree-clearing e.g. through the State Brigalow Development Scheme (mostly 1962 to 1975) which resulted in the removal of some 97% of the wide-ranging mature forests of Acacia harpophylla. At the same time, this government controls National Parks and other reservations (occupying some 4% of the State's 1.7 million km2 area) and also holds major World Heritage Areas (such as the Great Barrier Reef and the Wet Tropics Rainforest) promulgated under Commonwealth legislation. This is a highly prescriptive approach, where the community is directed on the one hand to develop (largely through lease conditions) and on the other to avoid development (largely by unusable reserves). Another approach to development and conservation is still possible in Queensland. For this to occur, however, a more workable and equitable solution than has been employed to date is needed, especially for the remote lands of this State. This must involve resident landholders, who have the capacity (through local knowledge, infrastructure and daily presence) to undertake most costeffectively sustainable land-use management (with suitable attention to ecosystems requiring special conservation effort), that is, provided they have the necessary direction, encouragement and incentive to do so.

A model for engaging and evaluating innovative cross-sectoral education reform : case studies from Queensland, Australia

This paper will explore how a general education can contribute successfully to vocational outcomes using both Participatory Action Research (PAR) and Program Theory methodology. The paper will focus on the development aspects of ‘marrying’ vocational and general education including engagement processes, student, teacher, institute and employer preparation and the pathway possibilities that emerge. Successful cases presented include the: Healthy Futures program (pathways into the Health and Allied industries); Accounting Pathways program (simultaneously studying a general Accounting subject and a Certificate III vocational qualification); and Sustainable Sciences initiative (development of a vocational qualification that focuses on the emerging renewable energy industry and is linked to school science programs). The case studies have been selected because they are unique in character and application and can be used as a basis for future program development in other settings or curriculum areas.

Coordinated research support services at Queensland University of Technology, Australia

Queensland University of Technology (QUT) is a large multidisciplinary university located in Brisbane, Queensland, Australia. QUT is increasing its research focus and is developing its research support services. It has adopted a model of collaboration between the Library, High Performance Computing and Research Support (HPC) and more broadly with Information Technology Services (ITS). Research support services provided by the Library include the provision of information resources and discovery services, bibliographic management software, assistance with publishing (publishing strategies, identifying high impact journals, dealing with publishers and the peer review process), citation analysis and calculating authors’ H Index. Research data management services are being developed by the Library and HPC working in collaboration. The HPC group within ITS supports research computing infrastructure, research development and engagement activities, researcher consultation, high speed computation and data storage systems , 2D/ 3D (immersive) visualisation tools, parallelisation and optimization of research codes, statistics/ data modeling training and support (both qualitative and quantitative) and support for the university’s central Access Grid collaboration facility. Development and engagement activities include participation in research grants and papers, student supervision and internships and the sponsorship, incubation and adoption of new computing technologies for research. ITS also provides other services that support research including ICT training, research infrastructure (networking, data storage, federated access and authorization, virtualization) and corporate systems for research administration. Seminars and workshops are offered to increase awareness and uptake of new and existing services. A series of online surveys on eResearch practices and skills and a number of focus groups was conducted to better inform the development of research support services. Progress towards the provision of research support is described within the context organizational frameworks; resourcing; infrastructure; integration; collaboration; change management; engagement; awareness and skills; new services; and leadership. Challenges to be addressed include the need to redeploy existing operational resources toward new research support services, supporting a rapidly growing research profile across the university, the growing need for the use and support of IT in research programs, finding capacity to address the diverse research support needs across the disciplines, operationalising new research support services following their implementation in project mode, embedding new specialist staff roles, cross-skilling Liaison Librarians, and ensuring continued collaboration between stakeholders.

Combining the parts to make the whole : integrated child and family services in Queensland

Over the past decade, the promotion of 'integrated child and family services' has emerged as a strong and consistent theme within Australian early childhood policy. Fuelling this trend is the belief that integrated service provision is more responsive to holistic family needs, offering better support to parents and thereby promoting better outcomes for young children. Adding further strength is the prevention and early intervention literature, and suggested social and economic benefits of 'effective' early years services and supports. States and territories are introducing new integrated child and family service models and Reflections is continuing to profile these. In this edition, we look at directions and new service models in Queensland, in particular, the new Early Years Centre service model.

Studies of the radiation chemistry and grafting of a fluoropolymer

The radiation chemistry and the grafting of a fluoropolymer, poly(tetrafluoroethylene-coperfluoropropyl vinyl ether) (PFA), was investigated with the aim of developing a highly stable grafted support for use in solid phase organic chemistry (SPOC). A radiation-induced grafting method was used whereby the PFA was exposed to ionizing radiation to form free radicals capable of initiating graft copolymerization of styrene. To fully investigate this process, both the radiation chemistry of PFA and the grafting of styrene to PFA were examined. Radiation alone was found to have a detrimental effect on PFA when irradiated at 303 K. This was evident from the loss in the mechanical properties due to chain scission reactions. This meant that when radiation was used for the grafting reactions, the total radiation dose needed to be kept as low as possible. The radicals produced when PFA was exposed to radiation were examined using electron spin resonance spectroscopy. Both main-chain (–CF2–C.F–CF2-) and end-chain (–CF2–C.F2) radicals were identified. The stability of the majority of the main-chain radicals when the polymer was heated above the glass transition temperature suggested that they were present mainly in the crystalline regions of the polymer, while the end-chain radicals were predominately located in the amorphous regions. The radical yield at 77 K was lower than the radical yield at 303 K suggesting that cage recombination at low temperatures inhibited free radicals from stabilizing. High-speed MAS 19F NMR was used to identify the non-volatile products after irradiation of PFA over a wide temperature range. The major products observed over the irradiation temperature 303 to 633 K included new saturated chain ends, short fluoromethyl side chains in both the amorphous and crystalline regions, and long branch points. The proportion of the radiolytic products shifted from mainly chain scission products at low irradiation temperatures to extensive branching at higher irradiation temperatures. Calculations of G values revealed that net crosslinking only occurred when PFA was irradiated in the melt. Minor products after irradiation at elevated temperatures included internal and terminal double bonds and CF3 groups adjacent to double bonds. The volatile products after irradiation at 303 K included tetrafluoromethane (CF4) and oxygen-containing species from loss of the perfluoropropyl ether side chains of PFA as identified by mass spectrometry and FTIR spectroscopy. The chemical changes induced by radiation exposure were accompanied by changes in the thermal properties of the polymer. Changes in the crystallinity and thermal stability of PFA after irradiation were examined using DSC and TGA techniques. The equilibrium melting temperature of untreated PFA was 599 K as determined using a method of extrapolation of the melting temperatures of imperfectly formed crystals. After low temperature irradiation, radiation- induced crystallization was prevalent due to scission of strained tie molecules, loss of perfluoropropyl ether side chains, and lowering of the molecular weight which promoted chain alignment and hence higher crystallinity. After irradiation at high temperatures, the presence of short and long branches hindered crystallization, lowering the overall crystallinity. The thermal stability of the PFA decreased with increasing radiation dose and temperature due to the introduction of defect groups. Styrene was graft copolymerized to PFA using -radiation as the initiation source with the aim of preparing a graft copolymer suitable as a support for SPOC. Various grafting conditions were studied, such as the total dose, dose rate, solvent effects and addition of nitroxides to create “living” graft chains. The effect of dose rate was examined when grafting styrene vapour to PFA using the simultaneous grafting method. The initial rate of grafting was found to be independent of the dose rate which implied that the reaction was diffusion controlled. When the styrene was dissolved in various solvents for the grafting reaction, the graft yield was strongly dependent of the type and concentration of the solvent used. The greatest graft yield was observed when the solvent swelled the grafted layers and the substrate. Microprobe Raman spectroscopy was used to map the penetration of the graft into the substrate. The grafted layer was found to contain both poly(styrene) (PS) and PFA and became thicker with increasing radiation dose and graft yield which showed that grafting began at the surface and progressively penetrated the substrate as the grafted layer was swollen. The molecular weight of the grafted PS was estimated by measuring the molecular weight of the non-covalently bonded homopolymer formed in the grafted layers using SEC. The molecular weight of the occluded homopolymer was an order of magnitude greater than the free homopolymer formed in the surrounding solution suggesting that the high viscosity in the grafted regions led to long PS grafts. When a nitroxide mediated free radical polymerization was used, grafting occurred within the substrate and not on the surface due to diffusion of styrene into the substrate at the high temperatures needed for the reaction to proceed. Loading tests were used to measure the capacity of the PS graft to be functionialized with aminomethyl groups then further derivatized. These loading tests showed that samples grafted in a solution of styrene and methanol had superior loading capacity over samples graft using other solvents due to the shallow penetration and hence better accessibility of the graft when methanol was used as a solvent.