Knowledge discovery using multiple sources of biological data

The primary aim of this dissertation is to develop data mining tools for knowledge discovery in biomedical data when multiple (homogeneous or heterogeneous) sources of data are available. The central hypothesis is that, when information from multiple sources of data are used appropriately and effectively, knowledge discovery can be better achieved than what is possible from only a single source. ^ Recent advances in high-throughput technology have enabled biomedical researchers to generate large volumes of diverse types of data on a genome-wide scale. These data include DNA sequences, gene expression measurements, and much more; they provide the motivation for building analysis tools to elucidate the modular organization of the cell. The challenges include efficiently and accurately extracting information from the multiple data sources; representing the information effectively, developing analytical tools, and interpreting the results in the context of the domain. ^ The first part considers the application of feature-level integration to design classifiers that discriminate between soil types. The machine learning tools, SVM and KNN, were used to successfully distinguish between several soil samples. ^ The second part considers clustering using multiple heterogeneous data sources. The resulting Multi-Source Clustering (MSC) algorithm was shown to have a better performance than clustering methods that use only a single data source or a simple feature-level integration of heterogeneous data sources. ^ The third part proposes a new approach to effectively incorporate incomplete data into clustering analysis. Adapted from K-means algorithm, the Generalized Constrained Clustering (GCC) algorithm makes use of incomplete data in the form of constraints to perform exploratory analysis. Novel approaches for extracting constraints were proposed. For sufficiently large constraint sets, the GCC algorithm outperformed the MSC algorithm. ^ The last part considers the problem of providing a theme-specific environment for mining multi-source biomedical data. The database called PlasmoTFBM, focusing on gene regulation of Plasmodium falciparum, contains diverse information and has a simple interface to allow biologists to explore the data. It provided a framework for comparing different analytical tools for predicting regulatory elements and for designing useful data mining tools. ^ The conclusion is that the experiments reported in this dissertation strongly support the central hypothesis.^

True real-time change data capture with web service database encapsulation

This research is investigating the claim that Change Data Capture (CDC) technologies capture data changes in real-time. Based on theory, our hypothesis states that real-time CDC is not achievable with traditional approaches (log scanning, triggers and timestamps). Traditional approaches to CDC require a resource to be polled, which prevents true real-time CDC. We propose an approach to CDC that encapsulates the data source with a set of web services. These web services will propagate the changes to the targets and eliminate the need for polling. Additionally we propose a framework for CDC technologies that allow changes to flow from source to target. This paper discusses current CDC technologies and presents the theory about why they are unable to deliver changes in real-time. Following, we discuss our web service approach to CDC and accompanying framework, explaining how they can produce real-time CDC. The paper concludes with a discussion on the research required to investigate the real-time capabilities of CDC technologies. © 2010 IEEE.

Real-time surface current data in the Ibiza Channel from January to October 2016

The data set consists of maps of total velocity of surface currents in the Ibiza Channel, derived from HF radar measurements.

On independent component analysis applied to unmixing hyperspectral data

One of the most challenging task underlying many hyperspectral imagery applications is the spectral unmixing, which decomposes a mixed pixel into a collection of reectance spectra, called endmember signatures, and their corresponding fractional abundances. Independent Component Analysis (ICA) have recently been proposed as a tool to unmix hyperspectral data. The basic goal of ICA is to nd a linear transformation to recover independent sources (abundance fractions) given only sensor observations that are unknown linear mixtures of the unobserved independent sources. In hyperspectral imagery the sum of abundance fractions associated to each pixel is constant due to physical constraints in the data acquisition process. Thus, sources cannot be independent. This paper address hyperspectral data source dependence and its impact on ICA performance. The study consider simulated and real data. In simulated scenarios hyperspectral observations are described by a generative model that takes into account the degradation mechanisms normally found in hyperspectral applications. We conclude that ICA does not unmix correctly all sources. This conclusion is based on the a study of the mutual information. Nevertheless, some sources might be well separated mainly if the number of sources is large and the signal-to-noise ratio (SNR) is high.

Quality-based benefit design in health insurance : the impact of a product benefit design change on the utilisation of oral health services by members of a private health insurance fund in regional and rural New South Wales, Australia

Objective: To examine the impact on dental utilisation following the introduction of a participating provider scheme (Regional and Rural Oral Health Program {RROHP)). In this model dentists receive higher third party payments from a private health insurance fund for delivering an agreed range of preventive and diagnostic benefits at no out-ofpocket cost to insured patients. Data source/Study setting: Hospitals Contribution Fund of Australia (HCF) dental claims for all members resident in New South Wales over the six financial years from l99811999 to 200312004. Study design: This cohort study involves before and after analyses of dental claims experience over a six year period for approximately 81,000 individuals in the intervention group (HCF members resident in regional and rural New South Wales, Australia) and 267,000 in the control group (HCF members resident in the Sydney area). Only claims for individuals who were members of HCF at 31 December 1997 were included. The analysis groups claims into the three years prior to the establishment of the RROHP and the three years subsequent to implementation. Data collection/Extraction methods: The analysis is based on all claims submitted by users of services for visits between 1 July 1988 and 30 June 2004. In these data approximately 1,000,000 services were provided to the intervention group and approximately 4,900,000 in the control group. Principal findings: Using Statistical Process Control (SPC) charts, special cause variation was identified in total utilisation rate of private dental services in the intervention group post implementation. No such variation was present in the control group. On average in the three years after implementation of the program the utilisation rate of dental services by regional and rural residents of New South Wales who where members of HCF grew by 12.6%, over eight times the growth rate of 1.5% observed in the control group (HCF members who were Sydney residents). The differences were even more pronounced in the areas of service that were the focus of the program: diagnostic and preventive services. Conclusion: The implementation of a benefit design change, a participating provider scheme, that involved the removal of CO-payments on a defined range of preventive and diagnostic dental services combined with the establishment and promotion of a network of dentists, appears to have had a marked impact on HCF members' utilisation of dental services in regional and rural New South Wales, Australia.

Re-imagining school through young people’s drawings

Children’s drawings provide rich qualitative data (Walker, 2008) and “valuable information for the assessment of children's environmental perceptions” (Barraza, 1999, p. 49). They are the primary data source being used to re-imagine school from a student perspective (Schratz & Steiner-Löffler, 1998) in a research project being carried out with primary school students in Queensland, Australia. This paper will report on the progress of this project which addresses a mostly unmet need for students’ perspectives to be included in school design (Rudduck & Flutter, 2004). Grade 5/6 students in a number of primary schools have been invited to submit annotated drawings with up to 200 words of text illustrating their ideal educational spaces. Using purpose-designed analytical tools, the submissions will be compared across student backgrounds and school types to obtain a better understanding of the needs and educational desires of young people in relation to changing learning environments. The findings will inform consideration of the design and use of educational spaces with all work exhibited through a dedicated website. The term ‘educational spaces’ avoids restrictive notions of what the concept of ‘school’ means, referring to any real or virtual space in which teaching and learning may occur or, as Ferguson and Seddon (2007) have referred to it, “the shifting imagery of education” that includes red brick schools and dispersed learning networks. The theoretical framework for this study is grounded in the work of Greene (1995) and Wright-Mills (2001) who cited the deployment of critical and empathic imagination in addressing education reform.

The causal effect of income on health: Evidence from German reunification

We investigate whether therewas a causal effect of income changes on the health satisfaction of East and West Germans in the years following reunification. Our data source is the German Socio-Economic Panel (GSOEP) between 1984 and 2002, and we fit a recently proposed fixed-effects ordinal estimator to our health measures and use a causal decomposition technique to account for panel attrition.We find evidence of a significant positive effect of income changes on health satisfaction, but the quantitative size of this effect is small. This is the case with respect to current income and a measure of ‘permanent’ income.

Socioeconomic inequalities in weight status among mid-aged adults : the contribution of perceptions of weight status and weight-control behaviours

Background Socioeconomically-disadvantaged adults in developed countries experience a higher prevalence of a number of chronic diseases, such as cardiovascular disease, type 2 diabetes, osteoarthritis and some forms of cancer. Overweight and obesity are major risk factors for these diseases. Lower socioeconomic groups have a greater prevalence of overweight and obesity and this may contribute to their higher morbidity and mortality. International studies suggest that socioeconomic groups may differ in their self-perceptions of weight status and their engagement in weightcontrol behaviours (WCBs). Research has shown that lower socioeconomic adults are more likely to underestimate their weight status, and are less likely to engage in WCBs. This may contribute (in part) to the marked inequalities in weight status observed at the population level. There are few, and somewhat limited, Australian studies that have examined the types of weight-control strategies people adopt, the barriers to their weight control, the determinants of their perceived weight status and WCBs. Furthermore, there are no known Australian studies that have examined socioeconomic differences in these factors to better understand the reasons for socioeconomic inequalities in weight status. Hence, the overall aim of this Thesis is to examine why socioeconomically-disadvantaged group experience a greater prevalence of overweight and obesity than their more-advantaged counterparts. Methods This Thesis used data from two sources. Men and women aged 45 to 60 years were examined from both data source. First, the longitudinal Australian Diabetes, Obesity and Lifestyle (AusDiab) Study were used to advance our knowledge and understanding of socioeconomic differences in weight change, perceived weight status and WCBs. A total of 2753 participants with measured weights at both baseline (1999-2000) and follow-up (2004-2005) were included in the analyses. Percent weight change over the five-year interval was calculated and perceived weight status, WCBs and highest attained education were collected at baseline. Second, the Candidate conducted a postal questionnaire from 1013 Brisbane residents (69.8 % response rate) to investigate the relationship between socioeconomic position, determinants of perceived weight status, WCBs, and barriers and reasons to weight control. A test-retest reliability study was conducted to determine the reliability of the new measures used in the questionnaire. Most new measures had substantial to almost perfect reliability when considering either kappa coefficient or crude agreement. Results The findings from the AusDiab Study (accepted for publication in the Australian and New Zealand Journal of Public Health) showed that low-educated men and women were more likely to be obese at baseline compared to their higheducated respondents (O.R. = 1.97, 95 % C.I. = 1.30-2.98 and O.R. = 1.52, 95 % C.I. = 1.03-2.25, respectively). Over the five year follow-up period (1999-2000 to 2004- 05) there were no socioeconomic differences in weight change among men, however socioeconomically-disadvantaged women had greater weight gains. Participants perceiving themselves as overweight gained less weight than those who saw themselves as underweight or normal weight. There was no relationship between engaging in WCBs and five-year weight change. The postal questionnaire data showed that socioeconomically-disadvantaged groups were less likely to engage in WCBs. If they did engage in weight control, they were less likely to adopt exercise strategies, including moderate and vigorous physical activities but were more likely to decrease their sitting time to control their weight. Socioeconomically-disadvantaged adults reported more barriers to weight control; such as perceiving weight loss as expensive, requiring a lot of cooking skills, not being a high priority and eating differently from other people in the household. These results have been accepted for publication in Public Health Nutrition. The third manuscript (under review in Social Science and Medicine) examined socioeconomic differences in determinants of perceived weight status and reasons for weight control. The results showed that lower socioeconomic adults were more likely to specify the following reasons for weight control: they considered themselves to be too heavy, for occupational requirements, on recommendation from their doctor, family members or friends. Conversely, high-income adults were more likely to report weight control to improve their physical condition or to look more attractive compared with those on lower-incomes. There were few socioeconomic differences in the determinants of perceived weight status. Conclusions Education inequalities in overweight/obesity among men and women may be due to mis-perceptions of weight status; overweight or obese individuals in loweducated groups may not perceive their weight as problematic and therefore may not pay attention to their energy-balance behaviours. Socioeconomic groups differ in WCBs, and their reasons and perceived barriers to weight control. Health promotion programs should encourage weight control among lower socioeconomic groups. More specifically, they should encourage the engagement of physical activity or exercise and dietary strategies among disadvantaged groups. Furthermore, such programs should address potential barriers for weight control that disadvantaged groups may encounter. For example, disadvantaged groups perceive that weight control is expensive, requires cooking skills, not a high priority and eating differently from other people in the household. Lastly, health promotion programs and policies aimed at reducing overweight and obesity should be tailored to the different reasons and motivations to weight control experienced by different socioeconomic groups. Weight-control interventions targeted at higher socioeconomic groups should use improving physical condition and attractiveness as motivational goals; while, utilising social support may be more effective for encouraging weight control among lower socioeconomic groups.

Analysing children’s drawings : applied imagination

This article centres on a research project in which freehand drawings provided a richly creative and colourful data source of children’s imagined, ideal learning environments. Issues concerning the analysis of the visual data are discussed, in particular how imaginative content was analysed and how the analytical process was dependent on an accompanying, secondary data source comprising brief, explanatory written texts.

Fundamental understanding on the use of Bluetooth MAC scanner for arterial travel time estimation

This report is the eight deliverable of the Real Time and Predictive Traveller Information project and the third deliverable of the Arterial Travel Time Information sub-project in the Integrated Traveller Information research Domain of the Smart Transport Research Centre. The primary objective of the Arterial Travel Time Information sub-project is to develop algorithms for real-time travel time estimation and prediction models for arterial traffic. Brisbane arterial network is highly equipped with Bluetooth MAC Scanners, which can provide travel time information. Literature is limited with the knowledge on the Bluetooth protocol based data acquisition process and accuracy and reliability of the analysis performed using the data. This report expands the body of knowledge surrounding the use of data from Bluetooth MAC Scanner (BMS) as a complementary traffic data source. A multi layer simulation model named Traffic and Communication Simulation (TCS) is developed. TCS is utilised to model the theoretical properties of the BMS data and analyse the accuracy and reliability of travel time estimation using the BMS data.

The hazards of starting and quitting smoking: Some Australian evidence

The empirical analysis employs individual level data from the Australian Health Survey combined with retrospective data on tobacco price matched to the age at which the individual started and quit smoking. Split-population hazard models are estimated for both starting and quitting smoking. The analysis suggests price plays a significant role in the decision to start smoking but not in the decision to quit. Further sensitivity analysis of different age groups and an alternative data source, questions the robustness of the significant role of price in the smoking initiation decision. From a policy perspective, the results indicate that increases in tobacco taxation can be an important instrument in reducing the incidence of smoking, but should be combined with other mechanisms such as mandating smoke-free environments and antismoking education. Our results strongly support the targeting of antismoking campaigns towards teenagers.

Workplace physical activity interventions : a systematic review

Objective. To assess the effectiveness of workplace interventions in improving physical activity. Data Source. EBSCO research database (and all subdatabases). Study Inclusion and Exclusion Criteria. Articles were published from 2000 to 2010 in English, had appropriate designs, and measured employees' physical activity, energy consumption, and/or body mass index (BMI) as primary outcomes. Articles that did not meet the inclusion criteria were excluded. Data Extraction. Data extracted included study design, study population, duration, intervention activities, outcomes, and results. Data Synthesis. Data were synthesized into one table. Results of each relevant outcome including p values were combined. Results. Twelve (60%) of 20 selected interventions reported an improvement in physical activity level, steps, or BMI, and there was one slowed step reduction in the intervention group. Among these, 10 were less than 6 months in duration; 9 used pedometers; 6 applied Internet-based approaches; and 5 included activities targeting social and environmental levels. Seven of 8 interventions with pre-posttest and quasi-experimental controlled design showed improvement on at least one outcome. However, 7 of 12 randomized controlled trials (RCTs) did not prove effective in any outcome. Conclusion. Interventions that had less rigorous research designs, used pedometers, applied Internet-based approaches, and included activities at social and environmental levels were more likely to report being effective than those without these characteristics.

Case Study 4: Education Doctoral Student - "An Exploratory Study of Online Social Networking within a Doctorate of Education Program"

Introduction The professional doctorate is specifically designed for professionals investigating real-world problems and relevant issues for a profession, industry, and/or the community. The focus is scholarly research into professional practices. The research programme bridges academia and the professions, and offers doctoral candidates the opportunity to investigate issues relevant to their own practices and to apply these understandings to their professional contexts. The study on which this article is based sought to track the scholarly skill development of a cohort of professional doctoral students who commenced the course in January 2008 at an Australian university. Because they hold positions of responsibility and are time-poor, many doctoral students have difficulty transitioning from professional practitioner to researcher and scholar. The struggle many experience is in the development of a theoretical or conceptual standpoint for argumentation (Lesham, 2007; Weese et al., 1999). It was thought that the use of a scaffolded learning environment that drew upon a blended learning approach incorporating face to face intensive blocks and collaborative knowledge-building tools such as wikis would provide a data source for understanding the development of scholarly skills. Wikis, weblogs and similar social networking software have the potential to support communities to share, learn, create and collaborate. The development of a wiki page by each candidate in the 2008 cohort was encouraged to provide the participants and the teaching team members with textual indicators of progress. Learning tasks were scaffolded with the expectation that the candidates would complete these tasks via the wikis. The expectation was that cohort members would comment on each other’s work, together with the supervisor and/or teaching team member who was allocated to each candidate. The supervisor is responsible for supervising the candidate’s work through to submission of the thesis for examination and the teaching team member provides support to both the supervisor and the candidate through to confirmation. This paper reports on the learning journey of a cohort of doctoral students during the first seven months of their professional doctoral programme to determine if there had been any qualitative shifts in understandings, expectations and perceptions regarding their developing knowledge and skills. The paper is grounded in the literature pertaining to doctoral studies and examines the structure of the professional doctoral programme. Following this is a discussion of the qualitative study that helped to unearth key themes regarding the participants’ learning journey.

Into darkness: A study of deviance in Star Trek

Purpose The purpose of this chapter is to analyse the deviant behaviour of individuals in organisations. Deviants are those who depart from organisational norms. A typology of perceived deviant behaviour is developed from the deviance literature, and subsequently tested. Methodology/approach Star Trek: Into Darkness text is qualitatively analysed as a data source. Three different character arcs are analysed in relation to organisational deviance. Starfleet is the specific, fictional, organisational context. Findings We found that the typology of deviance is conceptually robust, and facilitates categorisation of different types of deviant behaviour, over time. Research limitations/implications Deviance is socially ascribed; so better categorisation of such behaviour improves our understanding of how specific behaviour might deviate from organisational norms, and how different behaviours can mean individuals can be viewed positively or negatively over time. Further research might determine management responses to the different forms of deviance, and unpack the processes where individuals eschew ‘averageness’ and become deviants. Practical implications The typology advanced has descriptive validity to describe deviant behaviour. Social implications Social institutions such as organisations ascribe individual deviants, both negatively and positively. Originality/value This chapter extends our understanding of positive and negative deviance in organisations by developing a new typology of deviant behaviour. This typology has descriptive validity in understanding deviant behaviour. Our understanding of both positive and negative deviance in organisational contexts is enhanced, as well as the utility of science fiction literature in ethical analysis.

The high burden of injuries in South Africa

Objective To estimate the magnitude and characteristics of the injury burden in South Africa within a global context. Methods The Actuarial Society of South Africa demographic and AIDS model (ASSA 2002) – calibrated to survey, census and adjusted vital registration data – was used to calculate the total number of deaths in 2000. Causes of death were determined from the National Injury Mortality Surveillance System profile. Injury death rates and years of life lost (YLL) were estimated using the Global Burden of Disease methodology. National years lived with disability (YLDs) were calculated by applying a ratio between YLLs and YLDs found in a local injury data source, the Cape Metropole Study. Mortality and disability-adjusted life years’ (DALYs) rates were compared with African and global estimates. Findings Interpersonal violence dominated the South African injury profile with age-standardized mortality rates at seven times the global rate. Injuries were the second-leading cause of loss of healthy life, accounting for 14.3% of all DALYs in South Africa in 2000. Road traffic injuries (RTIs) are the leading cause of injury in most regions of the world but South Africa has exceedingly high numbers – double the global rate. Conclusion Injuries are an important public health issue in South Africa. Social and economic determinants of violence, many a legacy of apartheid policies, must be addressed to reduce inequalities in society and build community cohesion. Multisectoral interventions to reduce traffic injuries are also needed. We highlight this heavy burden to stress the need for effective prevention programmes.