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.

Exercise intensity influences NEAT in overweight and obese adults

PURPOSE: To determine the effect of acute bouts of moderate- and high-intensity walking exercise on non-exercise activity thermogenesis (NEAT) in overweight and obese adults. ---------- METHOD: 16 participants performed a single bout of either moderate-intensity walking exercise (MIE) or high-intensity walking exercise (HIE) on two separate occasions. The MIE consisted of walking for 60 minutes on a motorized treadmill at 6 km.h. The 60-minute HIE session consisted of walking in 5-min intervals at 6 km.h and 10% grade followed by 5-min at 0% grade. NEAT was assessed by accelerometer on three days before, the day of, and three days following the exercise sessions. ---------- RESULTS: There was no significant difference in NEAT vector magnitude (counts.min) between the pre-exercise period (days 1-3) and the exercise day (day 4) for either MIE or HIE protocol. In addition, there was no change in NEAT during the three days following the MIE session, however NEAT increased by 16% on day 7 (post-exercise) compared with exercise day (P = 0.32). However during the post-exercise period following the HIE session, NEAT was increased by 25% on day 7 compared with the exercise day (P = 0.08), and by 30-33% compared with pre-exercise period (day 1, day 2 and day 3); P = 0.03, 0.03, 0.02, respectively. ---------- CONCLUSION: A single bout of either MIE or HIE did not alter NEAT on the exercise day or on the first two days following the exercise session. However, monitoring NEAT on a third day allowed the detection of a 48-h delay in increased NEAT after performing HIE. A longer-term intervention is needed to determine the effect of accumulated exercise sessions over a week on NEAT.

An investigation of dose calculation accuracy in intensity-modulated radiotherapy of sites in the head & neck

Knowledge of the accuracy of dose calculations in intensity-modulated radiotherapy of the head and neck is essential for clinical confidence in these highly conformal treatments. High dose gradients are frequently placed very close to critical structures, such as the spinal cord, and good coverage of complex shaped nodal target volumes is important for long term-local control. A phantom study is presented comparing the performance of standard clinical pencil-beam and collapsed-cone dose algorithms to Monte Carlo calculation and three-dimensional gel dosimetry measurement. All calculations and measurements are normalized to the median dose in the primary planning target volume, making this a purely relative study. The phantom simulates tissue, air and bone for a typical neck section and is treated using an inverse-planned 5-field IMRT treatment, similar in character to clinically used class solutions. Results indicate that the pencil-beam algorithm fails to correctly model the relative dose distribution surrounding the air cavity, leading to an overestimate of the target coverage. The collapsed-cone and Monte Carlo results are very similar, indicating that the clinical collapsed-cone algorithm is perfectly sufficient for routine clinical use. The gel measurement shows generally good agreement with the collapsed-cone and Monte Carlo calculated dose, particularly in the spinal cord dose and nodal target coverage, thus giving greater confidence in the use of this class solution.

Incorporating weather into regionwide safety planning prediction models

Predicting safety on roadways is standard practice for road safety professionals and has a corresponding extensive literature. The majority of safety prediction models are estimated using roadway segment and intersection (microscale) data, while more recently efforts have been undertaken to predict safety at the planning level (macroscale). Safety prediction models typically include roadway, operations, and exposure variables—factors known to affect safety in fundamental ways. Environmental variables, in particular variables attempting to capture the effect of rain on road safety, are difficult to obtain and have rarely been considered. In the few cases weather variables have been included, historical averages rather than actual weather conditions during which crashes are observed have been used. Without the inclusion of weather related variables researchers have had difficulty explaining regional differences in the safety performance of various entities (e.g. intersections, road segments, highways, etc.) As part of the NCHRP 8-44 research effort, researchers developed PLANSAFE, or planning level safety prediction models. These models make use of socio-economic, demographic, and roadway variables for predicting planning level safety. Accounting for regional differences - similar to the experience for microscale safety models - has been problematic during the development of planning level safety prediction models. More specifically, without weather related variables there is an insufficient set of variables for explaining safety differences across regions and states. Furthermore, omitted variable bias resulting from excluding these important variables may adversely impact the coefficients of included variables, thus contributing to difficulty in model interpretation and accuracy. This paper summarizes the results of an effort to include weather related variables, particularly various measures of rainfall, into accident frequency prediction and the prediction of the frequency of fatal and/or injury degree of severity crash models. The purpose of the study was to determine whether these variables do in fact improve overall goodness of fit of the models, whether these variables may explain some or all of observed regional differences, and identifying the estimated effects of rainfall on safety. The models are based on Traffic Analysis Zone level datasets from Michigan, and Pima and Maricopa Counties in Arizona. Numerous rain-related variables were found to be statistically significant, selected rain related variables improved the overall goodness of fit, and inclusion of these variables reduced the portion of the model explained by the constant in the base models without weather variables. Rain tends to diminish safety, as expected, in fairly complex ways, depending on rain frequency and intensity.

Adherence to medicines in the older-aged with chronic conditions : does an intervention concerning adherence by an allied health professional help?

Adherence to medicines is a major determinant of the effectiveness of medicines. However, estimates of non-adherence in the older-aged with chronic conditions vary from 40 to 75%. The problems caused by non-adherence in the older-aged include residential care and hospital admissions, progression of the disease, and increased costs to society. The reasons for non-adherence in the older-aged include items related to the medicine (e.g. cost, number of medicines, adverse effects) and those related to person (e.g. cognition, vision, depression). It is also known that there are many ways adherence can be increased (e.g. use of blister packs, cues). It is assumed that interventions by allied health professions, including a discussion of adherence, will improve adherence to medicines in the older aged but the evidence for this has not been reviewed. There is some evidence that telephone counselling about adherence by a nurse or pharmacist does improve adherence, short- and long-term. However, face-to-face intervention counselling at the pharmacy, or during a home visit by a pharmacist, has shown variable results with some studies showing improved adherence and some not. Education programs during hospital stays have not been shown to improve adherence on discharge, but education programs for subjects with hypertension have been shown to improve adherence. In combination with an education program, both counselling and a medicine review program have been shown to improve adherence short-term in the older-aged. Thus, there are many unanswered questions about the most effective interventions to promote adherence. More studies are needed to determine the most appropriate interventions by allied health professions, and these need to consider the disease state, demographics, and socio-economic status of the older-aged subject, and the intensity and duration of intervention needed.

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.

Civic engagement and associationalism : the impact of group membership scope versus intensity of participation

The relationship between participation in civic and political activities and membership of voluntary associations is now well established. What is less clear is the relative impacts of how much time people spend on group activities (associational intensity), and the number and type of groups that individuals are involved with (associational scope). Does it matter in terms of civic engagement, for example, whether one is a member of a quilting-circle or trade union? Does it matter whether association ‘membership’ is simply an annual payment or a major commitment of time and energy? In this article, we use a large survey to explore these questions empirically by focusing on the membership patterns and civic engagement practices of 4,001 citizens drawn from eight suburbs across Greater Melbourne, Australia. Our findings indicate that, while associational intensity is positively related to civic engagement, associational scope (the number of group memberships per person), is a more influential determinant of the level of civic and political participation. The results also suggest that while all forms of associationalism are important in terms of fostering greater levels of civic activity, not all forms have the same impact.

Internet usage, internet marketing intensity and international marketing growth

This paper examines the role of the Internet in international marketing growth. Evidence of a positive relationship between e-mail, website usage, online marketing and advertising with international market growth was found, in terms of increased sales from new customers in new countries, new customers in existing countries, and existing customers.

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.