Bayesian latent trait modeling of migraine symptom data

Definition of disease phenotype is a necessary preliminary to research into genetic causes of a complex disease. Clinical diagnosis of migraine is currently based on diagnostic criteria developed by the International Headache Society. Previously, we examined the natural clustering of these diagnostic symptoms using latent class analysis (LCA) and found that a four-class model was preferred. However, the classes can be ordered such that all symptoms progressively intensify, suggesting that a single continuous variable representing disease severity may provide a better model. Here, we compare two models: item response theory and LCA, each constructed within a Bayesian context. A deviance information criterion is used to assess model fit. We phenotyped our population sample using these models, estimated heritability and conducted genome-wide linkage analysis using Merlin-qtl. LCA with four classes was again preferred. After transformation, phenotypic trait values derived from both models are highly correlated (correlation = 0.99) and consequently results from subsequent genetic analyses were similar. Heritability was estimated at 0.37, while multipoint linkage analysis produced genome-wide significant linkage to chromosome 7q31-q33 and suggestive linkage to chromosomes 1 and 2. We argue that such continuous measures are a powerful tool for identifying genes contributing to migraine susceptibility.

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.

Examination of the latent structure of the psychological sense of school membership scale

Despite its widespread use, there has been limited examination of the underlying factor structure of the Psychological Sense of School Membership (PSSM) scale. The current study examined the psychometric properties of the PSSM to refine its utility for researchers and practitioners using a sample of 504 Australian high school students. Results from exploratory and confirmatory factor analyses indicated that the PSSM is a multidimensional instrument. Factor analysis procedures identified three factors representing related aspects of students’ perceptions of their school membership: caring relationships, acceptance, and rejection

Estimating the latent demand for rail transit : a case study in Perth, Western Australia

This paper presents a study on estimating the latent demand for rail transit in Australian context. Based on travel mode-choice modelling, a two-stage analysis approach is proposed, namely market population identification and mode share estimation. A case study is conducted on Midland-Fremantle rail transit corridor in Perth, Western Australia. The required data mainly include journey-to-work trip data from Australian Bureau of Statistics Census 2006 and work-purpose mode-choice model in Perth Strategic Transport Evaluation Model. The market profile is analysed, such as catchment areas, market population, mode shares, mode specific trip distributions and average trip distances. A numerical simulation is performed to test the sensitivity of the transit ridership to the change of fuel price. A corridor-level transit demand function of fuel price is thus obtained and its characteristics of elasticity are discussed. This study explores a viable approach to developing a decision-support tool for the assessment of short-term impacts of policy and operational adjustments on corridor-level demand for rail transit.

Latent degradation indicators estimation and prediction : a Monte Carlo approach

Asset health inspections can produce two types of indicators: (1) direct indicators (e.g. the thickness of a brake pad, and the crack depth on a gear) which directly relate to a failure mechanism; and (2) indirect indicators (e.g. the indicators extracted from vibration signals and oil analysis data) which can only partially reveal a failure mechanism. While direct indicators enable more precise references to asset health condition, they are often more difficult to obtain than indirect indicators. The state space model provides an efficient approach to estimating direct indicators by using indirect indicators. However, existing state space models to estimate direct indicators largely depend on assumptions such as, discrete time, discrete state, linearity, and Gaussianity. The discrete time assumption requires fixed inspection intervals. The discrete state assumption entails discretising continuous degradation indicators, which often introduces additional errors. The linear and Gaussian assumptions are not consistent with nonlinear and irreversible degradation processes in most engineering assets. This paper proposes a state space model without these assumptions. Monte Carlo-based algorithms are developed to estimate the model parameters and the remaining useful life. These algorithms are evaluated for performance using numerical simulations through MATLAB. The result shows that both the parameters and the remaining useful life are estimated accurately. Finally, the new state space model is used to process vibration and crack depth data from an accelerated test of a gearbox. During this application, the new state space model shows a better fitness result than the state space model with linear and Gaussian assumption.

Beware of geeks bearing gifts? Online latent and untapped outlets for farmers' markets in South East Wales

This chapter sets out to identify related issues surrounding the use of Information and Computer Technology (ICT) in developing relationships between local food producers and consumers (both individuals and businesses). Three surveys were conducted in South- East Wales to consider the overlapping issues. The first concerned the role of ICT in relationships between farmers’ market (FMs) vendors and their traditional customers. The second survey examined potential new markets for farmers in the propensity of restaurants and hotels to buy locally, the types and sources of purchases made and the modes of advertising of these businesses. The final survey focused on the potential to expand local web- based selling of farmers’ produce in the future, by examining the potential market of high ICT- use small hotels. Despite the development of tailored ICT facilities, farmers’ market vendors and current individual customers are antipathetic to them. In addition, whilst there is a desire for more local produce particularly amongst independent local restaurants and hotels, this has not been capitalised upon and there is much work to be done even amongst high ICT-use small hotels, to expand the range and scope of farmers’ markets. This raises the need for creation and utilisation of enhanced logistics, payment and marketing management capacity available through a web- based presence, linked to promotion of FMs in business- to- business (B2B) links with local restaurants and hotels. This linked quantitative research highlights the potential value in substantial development of both web portals and supporting logistics to exploit this potential in the future.

Dynamics of railway wagons subjected to braking torques on defective tracks

It is well known that track defects cause profound effects to the dynamics of railway wagons; normally such problems are examined for cases of wagons running at a constant speed. Brake/traction torques affect the speed profile due to the wheel–rail contact characteristics but most of the wagon–track interaction models do not explicitly consider them in simulation. The authors have recently published a model for the dynamics of wagons subject to braking traction torques on a perfect track by explicitly considering the pitch degree of freedom for wheelsets. The model is extended for cases of lateral and vertical track geometry defects and worn railhead and wheel profiles. This paper presents the results of the analyses carried out using the model extended to the dynamics of wagons containing less ideal wheel profiles running on tracks with geometry defects and worn rails.

Trading spaces : on the lore and limitations of latent semantic analysis

Two decades after its inception, Latent Semantic Analysis(LSA) has become part and parcel of every modern introduction to Information Retrieval. For any tool that matures so quickly, it is important to check its lore and limitations, or else stagnation will set in. We focus here on the three main aspects of LSA that are well accepted, and the gist of which can be summarized as follows: (1) that LSA recovers latent semantic factors underlying the document space, (2) that such can be accomplished through lossy compression of the document space by eliminating lexical noise, and (3) that the latter can best be achieved by Singular Value Decomposition. For each aspect we performed experiments analogous to those reported in the LSA literature and compared the evidence brought to bear in each case. On the negative side, we show that the above claims about LSA are much more limited than commonly believed. Even a simple example may show that LSA does not recover the optimal semantic factors as intended in the pedagogical example used in many LSA publications. Additionally, and remarkably deviating from LSA lore, LSA does not scale up well: the larger the document space, the more unlikely that LSA recovers an optimal set of semantic factors. On the positive side, we describe new algorithms to replace LSA (and more recent alternatives as pLSA, LDA, and kernel methods) by trading its l2 space for an l1 space, thereby guaranteeing an optimal set of semantic factors. These algorithms seem to salvage the spirit of LSA as we think it was initially conceived.

Simulating a latent susceptible pool to examine the impact on cardiovascular mortality

The health effects of cold and hot temperatures are strongest in the frail and elderly. A large number of deaths in this "susceptible pool" after heat waves and cold snaps can cause mortality displacement, where an immediate increase in mortality is somewhat offset by a subsequent decrease in the following weeks. There may also be longer-term implications, as reductions in the pool caused by hot summers can reduce cold-related mortality in the following winter. A state-space model was used to simulate the numbers in the susceptible pool over time. We simulated the effects of harsh winters and heat waves, and varied the size of the susceptible pool. The larger the susceptible pool the smaller the mortality displacement. When 1% of the population were susceptible a harsh winter lead to an average of just 3 months of life lost per cold-related death, whereas a pool size of 10% meant that 24 months of life were lost per death. The impact of a cold spell on months of life lost was greater when the increased risk of death also applied to healthy people. The number of deaths caused by an August heat wave were reduced when there was a prior heat wave in June which reduced the susceptible pool. We were able to mimic some observed seasonal patterns in mortality using a simple state-space model. A better understanding of the size and dynamics of the susceptible pool will improve our understanding of the health effects of temperature.

Empirical IEEE 802.11p performance evaluation on test tracks

IEEE 802.11p is the new standard for inter-vehicular communications (IVC) using the 5.9 GHz frequency band; it is planned to be widely deployed to enable cooperative systems. 802.11p uses and performance have been studied theoretically and in simulations over the past years. Unfortunately, many of these results have not been confirmed by on-tracks experimentation. In this paper, we describe field trials of 802.11p technology with our test vehicles. Metrics such as maximum range, latency and frame loss are examined.

Explicit, latent and meta-criteria : types of criteria at play in professional judgement practice

This paper engages with debates about whether comprehensive prior specification of criteria and standards is sufficient for informed professional judgement. A preoccupation has emerged with the specificity and explication of criteria intended to regulate judgement. This has resulted in criteria-compliance in the use of defined standards to validate judgements and improve reliability and consistency. Compliance has become a priority, the consequence being the prominence of explicit criteria, to the lack of acknowledgement of the operation of latent and meta-criteria within judgement practice. This paper examines judgement as a process involving three categories of assessment criteria in the context of standards-referenced systems: explicit, latent and meta-criteria. These are understood to be wholly interrelated and interdependent. A conceptualisation of judgement involving the interplay of the three criteria types is presented with an exploration of how they function to focus or alter assessments of quality in judgements of achievement in English and Mathematics.