Comprehensive standardized data definitions for acute coronary syndrome research in emergency departments in Australasia

Patients with chest discomfort or other symptoms suggestive of acute coronary syndrome (ACS) are one of the most common categories seen in many Emergency Departments (EDs). While the recognition of patients at high-risk of ACS has improved steadily, identifying the majority of chest pain presentations who fall into the low-risk group remains a challenge. Research in this area needs to be transparent, robust, applicable to all hospitals from large tertiary centres to rural and remote sites, and to allow direct comparison between different studies with minimum patient spectrum bias. A standardised approach to the research framework using a common language for data definitions must be adopted to achieve this. The aim was to create a common framework for a standardised data definitions set that would allow maximum value when extrapolating research findings both within Australasian ED practice, and across similar populations worldwide. Therefore a comprehensive data definitions set for the investigation of non-traumatic chest pain patients with possible ACS was developed, specifically for use in the ED setting. This standardised data definitions set will facilitate ‘knowledge translation’ by allowing extrapolation of useful findings into the real-life practice of emergency medicine.

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.

Analysing Seasonal Health Data

Seasonal patterns have been found in a remarkable range of health conditions, including birth defects, respiratory infections and cardiovascular disease. Accurately estimating the size and timing of seasonal peaks in disease incidence is an aid to understanding the causes and possibly to developing interventions. With global warming increasing the intensity of seasonal weather patterns around the world, a review of the methods for estimating seasonal effects on health is timely. This is the first book on statistical methods for seasonal data written for a health audience. It describes methods for a range of outcomes (including continuous, count and binomial data) and demonstrates appropriate techniques for summarising and modelling these data. It has a practical focus and uses interesting examples to motivate and illustrate the methods. The statistical procedures and example data sets are available in an R package called ‘season’. Adrian Barnett is a senior research fellow at Queensland University of Technology, Australia. Annette Dobson is a Professor of Biostatistics at The University of Queensland, Australia. Both are experienced medical statisticians with a commitment to statistical education and have previously collaborated in research in the methodological developments and applications of biostatistics, especially to time series data. Among other projects, they worked together on revising the well-known textbook "An Introduction to Generalized Linear Models," third edition, Chapman Hall/CRC, 2008. In their new book they share their knowledge of statistical methods for examining seasonal patterns in health.

Data-driven background dataset selection for SVM-based speaker verification

The recently proposed data-driven background dataset refinement technique provides a means of selecting an informative background for support vector machine (SVM)-based speaker verification systems. This paper investigates the characteristics of the impostor examples in such highly-informative background datasets. Data-driven dataset refinement individually evaluates the suitability of candidate impostor examples for the SVM background prior to selecting the highest-ranking examples as a refined background dataset. Further, the characteristics of the refined dataset were analysed to investigate the desired traits of an informative SVM background. The most informative examples of the refined dataset were found to consist of large amounts of active speech and distinctive language characteristics. The data-driven refinement technique was shown to filter the set of candidate impostor examples to produce a more disperse representation of the impostor population in the SVM kernel space, thereby reducing the number of redundant and less-informative examples in the background dataset. Furthermore, data-driven refinement was shown to provide performance gains when applied to the difficult task of refining a small candidate dataset that was mis-matched to the evaluation conditions.

Exploiting multiple feature sets in data-driven impostor dataset selection for speaker verification

This study assesses the recently proposed data-driven background dataset refinement technique for speaker verification using alternate SVM feature sets to the GMM supervector features for which it was originally designed. The performance improvements brought about in each trialled SVM configuration demonstrate the versatility of background dataset refinement. This work also extends on the originally proposed technique to exploit support vector coefficients as an impostor suitability metric in the data-driven selection process. Using support vector coefficients improved the performance of the refined datasets in the evaluation of unseen data. Further, attempts are made to exploit the differences in impostor example suitability measures from varying features spaces to provide added robustness.

Performance pressure an empirical analysis using world and Euro cups data

There is a notable shortage of empirical research directed at measuring the magnitude and direction of stress effects on performance in a controlled environment. One reason for this is the inherent difficulties in identifying and isolating direct performance measures for individuals. Additionally most traditional work environments contain a multitude of exogenous factors impacting individual performance, but controlling for all such factors is generally unfeasible (omitted variable bias). Moreover, instead of asking individuals about their self-reported stress levels we observe workers' behavior in situations that can be classified as stressful. For this reason we have stepped outside the traditional workplace in an attempt to gain greater controllability of these factors using the sports environment as our experimental space. We empirically investigate the relationship between stress and performance, in an extreme pressure situation (football penalty kicks) in a winner take all sporting environment (FIFA World Cup and UEFA European Cup competitions). Specifically, we examine all the penalty shootouts between 1976 and 2008 covering in total 16 events. The results indicate that extreme stressors can have a positive or negative impact on Individuals' performance. On the other hand, more commonly experienced stressors do not affect professionals' performances.

Mobile data technologies and SME adoption and diffusion : an empirical study on barriers and facilitators

The technological environment in which Australian SMEs operate can be best described as dynamic and vital. The rate of technological change provides the SME owner/manager a complex and challenging operational context. Wireless applications are being developed that provide mobile devices with Internet content and e-business services. In Australia the adoption of e-commerce by large organisations has been relatively high, however the same cannot be said for SMEs where adoption has been slower than other developed countries. In contrast however mobile telephone adoption and diffusion is relatively high by SMEs. This exploratory study identifies attitudes, perceptions and issues for mobile data technologies by regional SME owner/managers across a range of industry sectors. The major issues include the sector the firm belongs to, the current adoption status of the firm, the level of mistrust of the IT industry, the cost of the technologies and the applications and attributes of the technologies.

Mobile data technology for small business : needs, uses, and adoption

The technological environment in which contemporary small and medium-sized enterprises (SMEs) operate can only be described as dynamic. The exponential rate of technological change, characterised by perceived increases in the benefits associated with various technologies, shortening product life cycles and changing standards, provides the SME a complex and challenging operational context. The primary aim of this research was to identify the needs of SMEs in regional areas for mobile data technologies (MDT). In this study a distinction was drawn between those respondents who were full-adopters of technology, those who were partial-adopters and those who were non-adopters and these three segments articulated different needs and requirements for MDT. Overall the needs of regional SMEs for MDT can be conceptualised into three areas where the technology will assist business practices, communication, e-commerce and security.

Exploring the needs for SMEs for mobile data technologies : the role of qualitative research techniques

The seemingly exponential nature of technological change provides SMEs with a complex and challenging operational context. The development of infrastructures capable of supporting the wireless application protocol (WAP) and associated 'wireless' applications represents the latest generation of technological innovation with potential appeals to SMEs and end-users alike. This paper aims to understand the mobile data technology needs of SMEs in a regional setting. The research was especially concerned with perceived needs across three market segments : non-adopters, partial-adopters and full-adopters of new technology. The research was exploratory in nature as the phenomenon under scrutiny is relatively new and the uses unclear, thus focus groups were conducted with each of the segments. The paper provides insights for business, industry and academics.

Mobile data technologies and small business adoption and diffusion : an empirical study of barriers and facilitators

The technological environment in which contemporary small- and medium-sized enterprises (SMEs) operate can only be described as dynamic. The exponential rate of technological change, characterised by perceived increases in the benefits associated with various technologies, shortening product life cycles and changing standards, provides for the SME a complex and challenging operational context. The primary aim of this research was to identify the needs of SMEs in regional areas for mobile data technologies (MDT). In this study a distinction was drawn between those respondents who were full-adopters of technology, those who were partial-adopters, and those who were non-adopters and these three segments articulated different needs and requirements for MDT. Overall, the needs of regional SMEs for MDT can be conceptualised into three areas where the technology will assist business practices; communication, e-commerce and security

Who needs it? An exploratory investigation into the reaction of small and medium enterprises to mobile data technologies

The technological environment in which contemporary small and medium-sized enterprises (SMEs) operate can only be described as dynamic. The seemingly exponential nature of technological change, characterised by perceived increases in the benefits associated with various technologies, shortening product life cycles and changing standards, provides for the small and medium-sized enterprise a complex and challenging operational context. The development of infrastructures capable of supporting the Wireless Application Protocol (WAP)and associated 'wireless' applications represents the latest generation of technological innovation with potential appeal to SMEs and end-users alike. The primary aim of this research was to understand the mobile data technology needs of SMEs in a regional setting. The research was especially concerned with perceived needs across three market segments; non-adopters of new technology, partial-adopters of new technology and full-adopters of new technology. Working with an industry partner, focus groups were conducted with each of these segments with the discussions focused on the use of the latest WP products and services. Some of the results are presented in this paper.

Data muling over underwater wireless sensor networks using an autonomous underwater vehicle

We present algorithms, systems, and experimental results for underwater data muling. In data muling a mobile agent interacts with static agents to upload, download, or transport data to a different physical location. We consider a system comprising an Autonomous Underwater Vehicle (AUV) and many static Underwater Sensor Nodes (USN) networked together optically and acoustically. The AUV can locate the static nodes using vision and hover above the static nodes for data upload. We describe the hardware and software architecture of this underwater system, as well as experimental data. © 2006 IEEE.

Augmenting RatSLAM using FAB-MAP-based visual data association

This paper investigates the use of the FAB-MAP appearance-only SLAM algorithm as a method for performing visual data association for RatSLAM, a semi-metric full SLAM system. While both systems have shown the ability to map large (60-70km) outdoor locations of approximately the same scale, for either larger areas or across longer time periods both algorithms encounter difficulties with false positive matches. By combining these algorithms using a mapping between appearance and pose space, both false positives and false negatives generated by FAB-MAP are significantly reduced during outdoor mapping using a forward-facing camera. The hybrid FAB-MAP-RatSLAM system developed demonstrates the potential for successful SLAM over large periods of time.

A rights management approach to securing data distribution in coalitions

As network capacity has increased over the past decade, individuals and organisations have found it increasingly appealing to make use of remote services in the form of service-oriented architectures and cloud computing services. Data processed by remote services, however, is no longer under the direct control of the individual or organisation that provided the data, leaving data owners at risk of data theft or misuse. This paper describes a model by which data owners can control the distribution and use of their data throughout a dynamic coalition of service providers using digital rights management technology. Our model allows a data owner to establish the trustworthiness of every member of a coalition employed to process data, and to communicate a machine-enforceable usage policy to every such member.

Development of rapid and highly resolving combinatorial genotyping schemes for Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni followed by Campylobacter coli contribute substantially to the economic and public health burden attributed to food-borne infections in Australia. Genotypic characterisation of isolates has provided new insights into the epidemiology and pathogenesis of C. jejuni and C. coli. However, currently available methods are not conducive to large scale epidemiological investigations that are necessary to elucidate the global epidemiology of these common food-borne pathogens. This research aims to develop high resolution C. jejuni and C. coli genotyping schemes that are convenient for high throughput applications. Real-time PCR and High Resolution Melt (HRM) analysis are fundamental to the genotyping schemes developed in this study and enable rapid, cost effective, interrogation of a range of different polymorphic sites within the Campylobacter genome. While the sources and routes of transmission of campylobacters are unclear, handling and consumption of poultry meat is frequently associated with human campylobacteriosis in Australia. Therefore, chicken derived C. jejuni and C. coli isolates were used to develop and verify the methods described in this study. The first aim of this study describes the application of MLST-SNP (Multi Locus Sequence Typing Single Nucleotide Polymorphisms) + binary typing to 87 chicken C. jejuni isolates using real-time PCR analysis. These typing schemes were developed previously by our research group using isolates from campylobacteriosis patients. This present study showed that SNP + binary typing alone or in combination are effective at detecting epidemiological linkage between chicken derived Campylobacter isolates and enable data comparisons with other MLST based investigations. SNP + binary types obtained from chicken isolates in this study were compared with a previously SNP + binary and MLST typed set of human isolates. Common genotypes between the two collections of isolates were identified and ST-524 represented a clone that could be worth monitoring in the chicken meat industry. In contrast, ST-48, mainly associated with bovine hosts, was abundant in the human isolates. This genotype was, however, absent in the chicken isolates, indicating the role of non-poultry sources in causing human Campylobacter infections. This demonstrates the potential application of SNP + binary typing for epidemiological investigations and source tracing. While MLST SNPs and binary genes comprise the more stable backbone of the Campylobacter genome and are indicative of long term epidemiological linkage of the isolates, the development of a High Resolution Melt (HRM) based curve analysis method to interrogate the hypervariable Campylobacter flagellin encoding gene (flaA) is described in Aim 2 of this study. The flaA gene product appears to be an important pathogenicity determinant of campylobacters and is therefore a popular target for genotyping, especially for short term epidemiological studies such as outbreak investigations. HRM curve analysis based flaA interrogation is a single-step closed-tube method that provides portable data that can be easily shared and accessed. Critical to the development of flaA HRM was the use of flaA specific primers that did not amplify the flaB gene. HRM curve analysis flaA interrogation was successful at discriminating the 47 sequence variants identified within the 87 C. jejuni and 15 C. coli isolates and correlated to the epidemiological background of the isolates. In the combinatorial format, the resolving power of flaA was additive to that of SNP + binary typing and CRISPR (Clustered regularly spaced short Palindromic repeats) HRM and fits the PHRANA (Progressive hierarchical resolving assays using nucleic acids) approach for genotyping. The use of statistical methods to analyse the HRM data enhanced sophistication of the method. Therefore, flaA HRM is a rapid and cost effective alternative to gel- or sequence-based flaA typing schemes. Aim 3 of this study describes the development of a novel bioinformatics driven method to interrogate Campylobacter MLST gene fragments using HRM, and is called ‘SNP Nucleated Minim MLST’ or ‘Minim typing’. The method involves HRM interrogation of MLST fragments that encompass highly informative “Nucleating SNPS” to ensure high resolution. Selection of fragments potentially suited to HRM analysis was conducted in silico using i) “Minimum SNPs” and ii) the new ’HRMtype’ software packages. Species specific sets of six “Nucleating SNPs” and six HRM fragments were identified for both C. jejuni and C. coli to ensure high typeability and resolution relevant to the MLST database. ‘Minim typing’ was tested empirically by typing 15 C. jejuni and five C. coli isolates. The association of clonal complexes (CC) to each isolate by ‘Minim typing’ and SNP + binary typing were used to compare the two MLST interrogation schemes. The CCs linked with each C. jejuni isolate were consistent for both methods. Thus, ‘Minim typing’ is an efficient and cost effective method to interrogate MLST genes. However, it is not expected to be independent, or meet the resolution of, sequence based MLST gene interrogation. ‘Minim typing’ in combination with flaA HRM is envisaged to comprise a highly resolving combinatorial typing scheme developed around the HRM platform and is amenable to automation and multiplexing. The genotyping techniques described in this thesis involve the combinatorial interrogation of differentially evolving genetic markers on the unified real-time PCR and HRM platform. They provide high resolution and are simple, cost effective and ideally suited to rapid and high throughput genotyping for these common food-borne pathogens.