Bayesian models for longitudinal data

Longitudinal data, where data are repeatedly observed or measured on a temporal basis of time or age provides the foundation of the analysis of processes which evolve over time, and these can be referred to as growth or trajectory models. One of the traditional ways of looking at growth models is to employ either linear or polynomial functional forms to model trajectory shape, and account for variation around an overall mean trend with the inclusion of random eects or individual variation on the functional shape parameters. The identification of distinct subgroups or sub-classes (latent classes) within these trajectory models which are not based on some pre-existing individual classification provides an important methodology with substantive implications. The identification of subgroups or classes has a wide application in the medical arena where responder/non-responder identification based on distinctly diering trajectories delivers further information for clinical processes. This thesis develops Bayesian statistical models and techniques for the identification of subgroups in the analysis of longitudinal data where the number of time intervals is limited. These models are then applied to a single case study which investigates the neuropsychological cognition for early stage breast cancer patients undergoing adjuvant chemotherapy treatment from the Cognition in Breast Cancer Study undertaken by the Wesley Research Institute of Brisbane, Queensland. Alternative formulations to the linear or polynomial approach are taken which use piecewise linear models with a single turning point, change-point or knot at a known time point and latent basis models for the non-linear trajectories found for the verbal memory domain of cognitive function before and after chemotherapy treatment. Hierarchical Bayesian random eects models are used as a starting point for the latent class modelling process and are extended with the incorporation of covariates in the trajectory profiles and as predictors of class membership. The Bayesian latent basis models enable the degree of recovery post-chemotherapy to be estimated for short and long-term followup occasions, and the distinct class trajectories assist in the identification of breast cancer patients who maybe at risk of long-term verbal memory impairment.

Numerical modelling of industrial microwave heating

The numerical modelling of electromagnetic waves has been the focus of many research areas in the past. Some specific applications of electromagnetic wave scattering are in the fields of Microwave Heating and Radar Communication Systems. The equations that govern the fundamental behaviour of electromagnetic wave propagation in waveguides and cavities are the Maxwell's equations. In the literature, a number of methods have been employed to solve these equations. Of these methods, the classical Finite-Difference Time-Domain scheme, which uses a staggered time and space discretisation, is the most well known and widely used. However, it is complicated to implement this method on an irregular computational domain using an unstructured mesh. In this work, a coupled method is introduced for the solution of Maxwell's equations. It is proposed that the free-space component of the solution is computed in the time domain, whilst the load is resolved using the frequency dependent electric field Helmholtz equation. This methodology results in a timefrequency domain hybrid scheme. For the Helmholtz equation, boundary conditions are generated from the time dependent free-space solutions. The boundary information is mapped into the frequency domain using the Discrete Fourier Transform. The solution for the electric field components is obtained by solving a sparse-complex system of linear equations. The hybrid method has been tested for both waveguide and cavity configurations. Numerical tests performed on waveguides and cavities for inhomogeneous lossy materials highlight the accuracy and computational efficiency of the newly proposed hybrid computational electromagnetic strategy.

Monte Carlo modelling of X-ray absorptiometry and its application to body composition studies

This thesis applies Monte Carlo techniques to the study of X-ray absorptiometric methods of bone mineral measurement. These studies seek to obtain information that can be used in efforts to improve the accuracy of the bone mineral measurements. A Monte Carlo computer code for X-ray photon transport at diagnostic energies has been developed from first principles. This development was undertaken as there was no readily available code which included electron binding energy corrections for incoherent scattering and one of the objectives of the project was to study the effects of inclusion of these corrections in Monte Carlo models. The code includes the main Monte Carlo program plus utilities for dealing with input data. A number of geometrical subroutines which can be used to construct complex geometries have also been written. The accuracy of the Monte Carlo code has been evaluated against the predictions of theory and the results of experiments. The results show a high correlation with theoretical predictions. In comparisons of model results with those of direct experimental measurements, agreement to within the model and experimental variances is obtained. The code is an accurate and valid modelling tool. A study of the significance of inclusion of electron binding energy corrections for incoherent scatter in the Monte Carlo code has been made. The results show this significance to be very dependent upon the type of application. The most significant effect is a reduction of low angle scatter flux for high atomic number scatterers. To effectively apply the Monte Carlo code to the study of bone mineral density measurement by photon absorptiometry the results must be considered in the context of a theoretical framework for the extraction of energy dependent information from planar X-ray beams. Such a theoretical framework is developed and the two-dimensional nature of tissue decomposition based on attenuation measurements alone is explained. This theoretical framework forms the basis for analytical models of bone mineral measurement by dual energy X-ray photon absorptiometry techniques. Monte Carlo models of dual energy X-ray absorptiometry (DEXA) have been established. These models have been used to study the contribution of scattered radiation to the measurements. It has been demonstrated that the measurement geometry has a significant effect upon the scatter contribution to the detected signal. For the geometry of the models studied in this work the scatter has no significant effect upon the results of the measurements. The model has also been used to study a proposed technique which involves dual energy X-ray transmission measurements plus a linear measurement of the distance along the ray path. This is designated as the DPA( +) technique. The addition of the linear measurement enables the tissue decomposition to be extended to three components. Bone mineral, fat and lean soft tissue are the components considered here. The results of the model demonstrate that the measurement of bone mineral using this technique is stable over a wide range of soft tissue compositions and hence would indicate the potential to overcome a major problem of the two component DEXA technique. However, the results also show that the accuracy of the DPA( +) technique is highly dependent upon the composition of the non-mineral components of bone and has poorer precision (approximately twice the coefficient of variation) than the standard DEXA measurements. These factors may limit the usefulness of the technique. These studies illustrate the value of Monte Carlo computer modelling of quantitative X-ray measurement techniques. The Monte Carlo models of bone densitometry measurement have:- 1. demonstrated the significant effects of the measurement geometry upon the contribution of scattered radiation to the measurements, 2. demonstrated that the statistical precision of the proposed DPA( +) three tissue component technique is poorer than that of the standard DEXA two tissue component technique, 3. demonstrated that the proposed DPA(+) technique has difficulty providing accurate simultaneous measurement of body composition in terms of a three component model of fat, lean soft tissue and bone mineral,4. and provided a knowledge base for input to decisions about development (or otherwise) of a physical prototype DPA( +) imaging system. The Monte Carlo computer code, data, utilities and associated models represent a set of significant, accurate and valid modelling tools for quantitative studies of physical problems in the fields of diagnostic radiology and radiography.

Modelling of some biological materials using continuum mechanics

Continuum mechanics provides a mathematical framework for modelling the physical stresses experienced by a material. Recent studies show that physical stresses play an important role in a wide variety of biological processes, including dermal wound healing, soft tissue growth and morphogenesis. Thus, continuum mechanics is a useful mathematical tool for modelling a range of biological phenomena. Unfortunately, classical continuum mechanics is of limited use in biomechanical problems. As cells refashion the �bres that make up a soft tissue, they sometimes alter the tissue's fundamental mechanical structure. Advanced mathematical techniques are needed in order to accurately describe this sort of biological `plasticity'. A number of such techniques have been proposed by previous researchers. However, models that incorporate biological plasticity tend to be very complicated. Furthermore, these models are often di�cult to apply and/or interpret, making them of limited practical use. One alternative approach is to ignore biological plasticity and use classical continuum mechanics. For example, most mechanochemical models of dermal wound healing assume that the skin behaves as a linear viscoelastic solid. Our analysis indicates that this assumption leads to physically unrealistic results. In this thesis we present a novel and practical approach to modelling biological plasticity. Our principal aim is to combine the simplicity of classical linear models with the sophistication of plasticity theory. To achieve this, we perform a careful mathematical analysis of the concept of a `zero stress state'. This leads us to a formal de�nition of strain that is appropriate for materials that undergo internal remodelling. Next, we consider the evolution of the zero stress state over time. We develop a novel theory of `morphoelasticity' that can be used to describe how the zero stress state changes in response to growth and remodelling. Importantly, our work yields an intuitive and internally consistent way of modelling anisotropic growth. Furthermore, we are able to use our theory of morphoelasticity to develop evolution equations for elastic strain. We also present some applications of our theory. For example, we show that morphoelasticity can be used to obtain a constitutive law for a Maxwell viscoelastic uid that is valid at large deformation gradients. Similarly, we analyse a morphoelastic model of the stress-dependent growth of a tumour spheroid. This work leads to the prediction that a tumour spheroid will always be in a state of radial compression and circumferential tension. Finally, we conclude by presenting a novel mechanochemical model of dermal wound healing that takes into account the plasticity of the healing skin.

Real-time performance modelling of a sustained attention to response task

Vigilance declines when exposed to highly predictable and uneventful tasks. Monotonous tasks provide little cognitive and motor stimulation and contribute to human errors. This paper aims to model and detect vigilance decline in real time through participant’s reaction times during a monotonous task. A lab-based experiment adapting the Sustained Attention to Response Task (SART) is conducted to quantify the effect of monotony on overall performance. Then relevant parameters are used to build a model detecting hypovigilance throughout the experiment. The accuracy of different mathematical models are compared to detect in real-time – minute by minute - the lapses in vigilance during the task. We show that monotonous tasks can lead to an average decline in performance of 45%. Furthermore, vigilance modelling enables to detect vigilance decline through reaction times with an accuracy of 72% and a 29% false alarm rate. Bayesian models are identified as a better model to detect lapses in vigilance as compared to Neural Networks and Generalised Linear Mixed Models. This modelling could be used as a framework to detect vigilance decline of any human performing monotonous tasks.

Adaptive modelling of sustainable architecture design in entropy evolutionary

This paper argues a model of adaptive design for sustainable architecture within a framework of entropy evolution. The spectrum of sustainable architecture consists of efficient use of energy and material resource in the life-cycle of buildings, active involvement of the occupants into micro-climate control within the building, and the natural environment as the physical context. The interactions amongst all the parameters compose a complex system of sustainable architecture design, of which the conventional linear and fragmented design technologies are insufficient to indicate holistic and ongoing environmental performance. The latest interpretation of the Second Law of Thermodynamics states a microscopic formulation of an entropy evolution of complex open systems. It provides a design framework for an adaptive system evolves for the optimization in open systems, this adaptive system evolves for the optimization of building environmental performance. The paper concludes that adaptive modelling in entropy evolution is a design alternative for sustainable architecture.

The impact of nonlinear exposure risk relationships on seasonal time series data: modelling danish neonatal birth anthropometric data

Background Birth weight and length have seasonal fluctuations. Previous analyses of birth weight by latitude effects identified seemingly contradictory results, showing both 6 and 12 monthly periodicities in weight. The aims of this paper are twofold: (a) to explore seasonal patterns in a large, Danish Medical Birth Register, and (b) to explore models based on seasonal exposures and a non-linear exposure-risk relationship. Methods Birth weight and birth lengths on over 1.5 million Danish singleton, live births were examined for seasonality. We modelled seasonal patterns based on linear, U- and J-shaped exposure-risk relationships. We then added an extra layer of complexity by modelling weighted population-based exposure patterns. Results The Danish data showed clear seasonal fluctuations for both birth weight and birth length. A bimodal model best fits the data, however the amplitude of the 6 and 12 month peaks changed over time. In the modelling exercises, U- and J-shaped exposure-risk relationships generate time series with both 6 and 12 month periodicities. Changing the weightings of the population exposure risks result in unexpected properties. A J-shaped exposure-risk relationship with a diminishing population exposure over time fitted the observed seasonal pattern in the Danish birth weight data. Conclusion In keeping with many other studies, Danish birth anthropometric data show complex and shifting seasonal patterns. We speculate that annual periodicities with non-linear exposure-risk models may underlie these findings. Understanding the nature of seasonal fluctuations can help generate candidate exposures.

Physical activity, sitting and depression during pregnancy

Aims The aim of this cross sectional study is to explore levels of physical activity and sitting behaviour amongst a sample of pregnant Australian women (n = 81), and investigate whether reported levels of physical activity and/or time spent sitting were associated with depressive symptom scores after controlling for potential covariates. Methods Study participants were women who attended the antenatal clinic of a large Brisbane maternity hospital between October and November 2006. Data relating to participants. current levels of physical activity, sitting behaviour, depressive symptoms, demographic characteristics and exposure to known risk factors for depression during pregnancy were collected; via on-site survey, follow-up telephone interview (approximately one week later) and post delivery access to participant hospital records. Results Participants were aged 29.5 (¡¾ 5.6) years and mostly partnered (86.4%) with a gross household income above $26,000 per annum (88.9%). Levels of physical activity were generally low, with only 28.4 % of participants reporting sufficient total activity and 16% of participants reporting sufficient planned (leisure-time) activity. The sample mean for depressive symptom scores measured by the Hospital Anxiety and Depression Scale (HADS-D) was 6.38 (¡¾ 2.55). The mean depressive symptom scores for participants who reported total moderate-to-vigorous activity levels of sufficient, insufficient, and none, were 5.43 (¡¾ 1.56), 5.82 (¡¾ 1.77) and 7.63 (¡¾ 3.25), respectively. Hierarchical multivariable linear regression modelling indicated that after controlling for covariates, a statistically significant difference of 1.09 points was observed between mean depressive symptom scores of participants who reported sufficient total physical activity, compared with participants who reported they were engaging in no moderate-to-vigorous activity in a typical week (p = 0.05) but this did not reach the criteria for a clinically meaningful difference. Total physical activity was contributed 2.2% to the total 30.3% of explained variance within this model. The other main contributors to explained variance in multivariable regression models were anxiety symptom scores and the number of existing children. Further, a trend was observed between higher levels of planned sitting behaviour and higher depressive symptom scores (p = 0.06); this correlation was not clinically meaningful. Planned sitting contributed 3.2% to the total 31.3 % of explained variance. The number of regression covariates and limited sample size led to a less than ideal ratio of covariates to participants, probably attenuating this relationship. Specific information about the sitting-based activities in which participants engaged may have provided greater insight about the relationship between planned sitting and depressive symptoms, but these data were not captured by the present study. Conclusions The finding that higher levels of physical activity were associated with lower levels of depressive symptoms is consistent with the current body of existing literature in pregnant women, and with a larger body of evidence based in general population samples. Although this result was not considered clinically meaningful, the criterion for a clinically meaningful result was an a priori decision based on quality of life literature in non-pregnant populations and may not truly reflect a difference in symptoms that is meaningful to pregnant women. Further investigation to establish clinically meaningful criteria for continuous depressive symptom data in pregnant women is required. This result may have implications relating to prevention and management options for depression during pregnancy. The observed trend between planned sitting and depressive symptom scores is consistent with literature based on leisure-time sitting behaviour in general population samples, and suggests that further research in this area, with larger samples of pregnant women and more specific sitting data is required to explore potential associations between activities such as television viewing and depressive symptoms, as this may be an area of behaviour that is amenable to modification.

An approach to statistical lip modelling for speaker identification via chromatic feature extraction

This paper presents a novel technique for the tracking of moving lips for the purpose of speaker identification. In our system, a model of the lip contour is formed directly from chromatic information in the lip region. Iterative refinement of contour point estimates is not required. Colour features are extracted from the lips via concatenated profiles taken around the lip contour. Reduction of order in lip features is obtained via principal component analysis (PCA) followed by linear discriminant analysis (LDA). Statistical speaker models are built from the lip features based on the Gaussian mixture model (GMM). Identification experiments performed on the M2VTS¹ database, show encouraging results

Three-dimensional geological modelling and multivariate statistical analysis of water chemistry data to analyse and visualise aquifer structure and groundwater composition in the Wairau Plain, Marlborough District, New Zealand

Concerns regarding groundwater contamination with nitrate and the long-term sustainability of groundwater resources have prompted the development of a multi-layered three dimensional (3D) geological model to characterise the aquifer geometry of the Wairau Plain, Marlborough District, New Zealand. The 3D geological model which consists of eight litho-stratigraphic units has been subsequently used to synthesise hydrogeological and hydrogeochemical data for different aquifers in an approach that aims to demonstrate how integration of water chemistry data within the physical framework of a 3D geological model can help to better understand and conceptualise groundwater systems in complex geological settings. Multivariate statistical techniques(e.g. Principal Component Analysis and Hierarchical Cluster Analysis) were applied to groundwater chemistry data to identify hydrochemical facies which are characteristic of distinct evolutionary pathways and a common hydrologic history of groundwaters. Principal Component Analysis on hydrochemical data demonstrated that natural water-rock interactions, redox potential and human agricultural impact are the key controls of groundwater quality in the Wairau Plain. Hierarchical Cluster Analysis revealed distinct hydrochemical water quality groups in the Wairau Plain groundwater system. Visualisation of the results of the multivariate statistical analyses and distribution of groundwater nitrate concentrations in the context of aquifer lithology highlighted the link between groundwater chemistry and the lithology of host aquifers. The methodology followed in this study can be applied in a variety of hydrogeological settings to synthesise geological, hydrogeological and hydrochemical data and present them in a format readily understood by a wide range of stakeholders. This enables a more efficient communication of the results of scientific studies to the wider community.