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 vernacular terrain : Songzhang Art Museum, Beijing, China

The field was the curation of cross-cultural new media/ digital media practices within large-scale exhibition practices in China. The context was improved understandings of the intertwining of the natural and the artificial with respect to landscape and culture, and their consequent effect on our contemporary globalised society. The research highlighted new languages of media art with respect to landscape and their particular underpinning dialects. The methodology was principally practice-led. --------- The research brought together over 60 practitioners from both local and diasporic Asian, European and Australian cultures for the first time within a Chinese exhibition context. Through pursuing a strong response to both cultural displacement and re-identification the research forged and documented an enduring commonality within difference – an agenda further concentrated through sensitivities surrounding that year’s Beijing’s Olympics. In contrast to the severe threats posed to the local dialects of many of the world’s spoken and written languages the ‘Vernacular Terrain’ project evidenced that many local creative ‘dialects’ of the environment-media art continuum had indeed survived and flourished. --------- The project was co-funded by the Beijing Film Academy, QUT Precincts, IDAProjects and Platform China Art Institute. A broad range of peer-reviewed grants was won including from the Australia China Council and the Australian Embassy in China. Through invitations from external curators much of the work then traveled to other venues including the Block Gallery at QUT and the outdoor screens at Federation Square, Melbourne. The Vernacular Terrain catalogue featured a comprehensive history of the IDA project from 2000 to 2008 alongside several major essays. Due to the reputation IDA Projects had established, the team were invited to curate a major exhibition showcasing fifty new media artists: The Vernacular Terrain, at the prestigious Songzhang Art Museum, Beijing in Dec 07-Jan 2008. The exhibition was designed for an extensive, newly opened gallery owned by one of China's most important art historians Li Xian Ting. This exhibition was not only this gallery’s inaugural non-Chinese curated show but also the Gallery’s first new media exhibition. It included important works by artists such as Peter Greenway, Michael Roulier, Maleonn and Cui Xuiwen. --------- Each artist was chosen both for a focus upon their own local environmental concerns as well as their specific forms of practice - that included virtual world design, interactive design, video art, real time and manipulated multiplayer gaming platforms and web 2.0 practices. This exhibition examined the interconnectivities of cultural dialogue on both a micro and macro scale; incorporating the local and the global, through display methods and design approaches that stitched these diverse practices into a spatial map of meanings and conversations. By examining the contexts of each artist’s practice in relationship to the specificity of their own local place and prevailing global contexts the exhibition sought to uncover a global vernacular. Through pursuing this concentrated anthropological direction the research identified key themes and concerns of a contextual language that was clearly underpinned by distinctive local ‘dialects’ thereby contributing to a profound sense of cross-cultural association. Through augmentation of existing discourse the exhibition confirmed the enduring relevance and influence of both localized and globalised languages of the landscape-technology continuum.

Australian pelvic floor questionnaire : a validated interviewer-administered pelvic floor questionnaire for routine clinic and research

The aim of this study was to design and validate an interviewer-administered pelvic floor questionnaire that integrates bladder, bowel and sexual function, pelvic organ prolapse, severity, bothersomeness and condition-specific quality of life. Validation testing of the questionnaire was performed using data from 106 urogynaecological patients and a separately sampled community cohort of 49 women. Missing data did not exceed 2% for any question. It distinguished community and urogynaecological populations regarding pelvic floor dysfunction. The bladder domain correlated with the short version of the Urogenital Distress Inventory, bowel function with an established bowel questionnaire and prolapse symptoms with the International Continence Society prolapse quantification. Sexual function assessment reflected scores on the McCoy Female Sexuality Questionnaire. Cronbach’s α coefficients were acceptable in all domains. Kappa coefficients of agreement for the test–retest analyses varied from 0.5 to 1.0. The interviewer-administered pelvic floor questionnaire assessed pelvic floor function in a reproducible and valid fashion in a typical urogynaecological clinic.

Exponential asymptotics with multiple stokes lines

When asymptotic series methods are applied in order to solve problems that arise in applied mathematics in the limit that some parameter becomes small, they are unable to demonstrate behaviour that occurs on a scale that is exponentially small compared to the algebraic terms of the asymptotic series. There are many examples of physical systems where behaviour on this scale has important effects and, as such, a range of techniques known as exponential asymptotic techniques were developed that may be used to examinine behaviour on this exponentially small scale. Many problems in applied mathematics may be represented by behaviour within the complex plane, which may subsequently be examined using asymptotic methods. These problems frequently demonstrate behaviour known as Stokes phenomenon, which involves the rapid switches of behaviour on an exponentially small scale in the neighbourhood of some curve known as a Stokes line. Exponential asymptotic techniques have been applied in order to obtain an expression for this exponentially small switching behaviour in the solutions to orginary and partial differential equations. The problem of potential flow over a submerged obstacle has been previously considered in this manner by Chapman & Vanden-Broeck (2006). By representing the problem in the complex plane and applying an exponential asymptotic technique, they were able to detect the switching, and subsequent behaviour, of exponentially small waves on the free surface of the flow in the limit of small Froude number, specifically considering the case of flow over a step with one Stokes line present in the complex plane. We consider an extension of this work to flow configurations with multiple Stokes lines, such as flow over an inclined step, or flow over a bump or trench. The resultant expressions are analysed, and demonstrate interesting implications, such as the presence of exponentially sub-subdominant intermediate waves and the possibility of trapped surface waves for flow over a bump or trench. We then consider the effect of multiple Stokes lines in higher order equations, particu- larly investigating the behaviour of higher-order Stokes lines in the solutions to partial differential equations. These higher-order Stokes lines switch off the ordinary Stokes lines themselves, adding a layer of complexity to the overall Stokes structure of the solution. Specifically, we consider the different approaches taken by Howls et al. (2004) and Chap- man & Mortimer (2005) in applying exponential asymptotic techniques to determine the higher-order Stokes phenomenon behaviour in the solution to a particular partial differ- ential equation.

Clustering with random indexing K-tree and XML structure

This paper describes the approach taken to the clustering task at INEX 2009 by a group at the Queensland University of Technology. The Random Indexing (RI) K-tree has been used with a representation that is based on the semantic markup available in the INEX 2009 Wikipedia collection. The RI K-tree is a scalable approach to clustering large document collections. This approach has produced quality clustering when evaluated using two different methodologies.

Monitoring animal behaviour and environmental interactions : GPS collars and satellite remote sensing within a satellite remote sensing context

Remote monitoring of animal behaviour in the environment can assist in managing both the animal and its environmental impact. GPS collars which record animal locations with high temporal frequency allow researchers to monitor both animal behaviour and interactions with the environment. These ground-based sensors can be combined with remotely-sensed satellite images to understand animal-landscape interactions. The key to combining these technologies is communication methods such as wireless sensor networks (WSNs). We explore this concept using a case-study from an extensive cattle enterprise in northern Australia and demonstrate the potential for combining GPS collars and satellite images in a WSN to monitor behavioural preferences and social behaviour of cattle.

Monitoring animal behaviour and environmental interactions using wireless sensor networks, GPS collars and satellite remote sensing

Remote monitoring of animal behaviour in the environment can assist in managing both the animal and its environmental impact. GPS collars which record animal locations with high temporal frequency allow researchers to monitor both animal behaviour and interactions with the environment. These ground-based sensors can be combined with remotely-sensed satellite images to understand animal-landscape interactions. The key to combining these technologies is communication methods such as wireless sensor networks (WSNs). We explore this concept using a case-study from an extensive cattle enterprise in northern Australia and demonstrate the potential for combining GPS collars and satellite images in a WSN to monitor behavioural preferences and social behaviour of cattle.

Overview of the INEX 2009 XML mining track : clustering and classification of XML documents

This report explains the objectives, datasets and evaluation criteria of both the clustering and classification tasks set in the INEX 2009 XML Mining track. The report also describes the approaches and results obtained by the different participants.

Deposition of hydroxyapatite and calcium oxalate dihydrate on a heat exchanger tube

Most studies on the characterisation of deposits on heat exchangers have been based on bulk analysis, neglecting the fine structural features and the compositional profiles of layered deposits. Attempts have been made to fully characterise a fouled stainless steel tube obtained from a quintuple Roberts evaporator of a sugar factory using X-ray diffraction and scanning electron microscopy techniques. The deposit contains three layers at the bottom of the tube and two layers on the other sections and is composed of hydroxyapatite, calcium oxalate dihydrate and an amorphous material. The proportions of these phases varied along the tube height. Energy-dispersive spectroscopy and XRD analysis on the surfaces of the outermost and innermost layers showed that hydroxyapatite was the major phase attached to the tube wall, while calcium oxalate dihydrate (with pits and voids) was the major phase on the juice side. Elemental mapping of the cross-sections of the deposit revealed the presence of a mineral, Si-Mg-Al-Fe-O, which is probably a silicate mineral. Reasons for the defects in the oxalate crystal surfaces, the differences in the crystal size distribution from bottom to the top of the tube and the composite fouling process have been postulated.

Effect of poly(acrylic acid) end-group functionality on inhibition of calcium oxalate crystal growth

A number of series of poly(acrylic acids) (PAA) of differing end-groups and molecular weights prepared using atom transfer radical polymerization were used as inhibitors for the crystallization of calcium oxalate at 23 and 80°C. As measured by turbidimetry and conductivity and as expected from previous reports, all PAA series were most effective for inhibition of crystallization at molecular weights of 1500–4000. However, the extent of inhibition was in general strongly dependent on the hydrophobicity and molecular weight of the end-group. These results may be explicable in terms of adsorption/desorption of PAA to growth sites on crystallites. The overall effectiveness of the series didn't follow a simple trend with end-group hydrophobicity, suggesting self-assembly behavior or a balance between adsorption and desorption rates to crystallite surfaces may be critical in the mechanism of inhibition of calcium oxalate crystallization.

Effect of poly(acrylic acid) molecular mass and end-group functionality on calcium oxalate crystal morphology and growth

A number of series of poly(acrylic acids) (PAA) of differing end-groups and molecular mass were used to study the inhibition of calcium oxalate crystallization. The effects of the end-group on crystal speciation and morphology were significant and dramatic, with hexyl-isobutyrate end groups giving preferential formation of calcium oxalate dihydrate (COD) rather than the more stable calcium oxalate monohydrate (COM), while both more hydrophobic end-groups and less-hydrophobic end groups led predominantly to formation of the least thermodynamically stable form of calcium oxalate, calcium oxalate trihydrate. Conversely, molecular mass had little impact on calcium oxalate speciation or crystal morphology. It is probable that the observed effects are related to the rate of desorption of the PAA moiety from the crystal (lite) surfaces and that the results point to a major role for end-group as well as molecular mass in controlling desorption rate.

Formation of thermodynamically unstable calcium oxalate dihydrate in sugar mill evaporators

Calcium oxalate (CaOX) is the most intractable scale component to remove in sugar mill evaporators by either mechanical or chemical means. The operating conditions of sugar mill evaporators should preferentially favour the formation of the thermodynamically stable calcium oxalate monohydrate (COM), yet analysis of scale deposit from different sugar factories have shown that calcium oxalate dihydrate (COD) is usually the predominant phase, and in some cases is the only hydrate formed. The effects of trans-aconitic, succinic and acetic acids, all of which are present in sugarcane juice, and ethylenediamine tetraacetic acid disodium salt (EDTA) on the growth of CaOX crystals have been examined by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray powder diffraction (XRD) and thermogravimetric analysis (TGA). trans-Aconitic acid, which constitutes two-thirds of the organic acid component in sugarcane juice, in the presence of sugar resulted in the formation of COD and COM in a 3:1 ratio. EDTA was the most effective acid to promote the formation of COD followed by trans-aconitic acid, then acetic acid and lastly succinic acid.

The effect of friction on indenter force and pile-up in numerical simulations of bone nanoindentation

Nanoindentation is a useful technique for probing the mechanical properties of bone, and finite element (FE) modeling of the indentation allows inverse determination of elasto-plastic constitutive properties. However, FE simulations to date have assumed frictionless contact between indenter and bone. The aim of this study was to explore the effect of friction in simulations of bone nanoindentation. Two dimensional axisymmetric FE simulations were performed using a spheroconical indenter of tip radius 0.6m and angle 90°. The coefficient of friction between indenter and bone was varied between 0.0 (frictionless) and 0.3. Isotropic linear elasticity was used in all simulations, with bone elastic modulus E=13.56GPa and Poisson’s ratio =0.3. Plasticity was incorporated using both Drucker-Prager and von Mises yield surfaces. Friction had a modest effect on the predicted force-indentation curve for both von Mises and Drucker-Prager plasticity, reducing maximum indenter displacement by 10% and 20% respectively as friction coefficient was increased from zero to 0.3 (at a maximum indenter force of 5mN). However, friction has a much greater effect on predicted pile-up after indentation, reducing predicted pile-up from 0.27m to 0.11m with a von Mises model, and from 0.09m to 0.02m with Drucker-Prager plasticity. We conclude that it is important to include friction in nanoindentation simulations of bone.

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.