Bayesian mixtures for modelling complex medical data : a case study in Parkinson’s disease

Mixture models are a flexible tool for unsupervised clustering that have found popularity in a vast array of research areas. In studies of medicine, the use of mixtures holds the potential to greatly enhance our understanding of patient responses through the identification of clinically meaningful clusters that, given the complexity of many data sources, may otherwise by intangible. Furthermore, when developed in the Bayesian framework, mixture models provide a natural means for capturing and propagating uncertainty in different aspects of a clustering solution, arguably resulting in richer analyses of the population under study. This thesis aims to investigate the use of Bayesian mixture models in analysing varied and detailed sources of patient information collected in the study of complex disease. The first aim of this thesis is to showcase the flexibility of mixture models in modelling markedly different types of data. In particular, we examine three common variants on the mixture model, namely, finite mixtures, Dirichlet Process mixtures and hidden Markov models. Beyond the development and application of these models to different sources of data, this thesis also focuses on modelling different aspects relating to uncertainty in clustering. Examples of clustering uncertainty considered are uncertainty in a patient’s true cluster membership and accounting for uncertainty in the true number of clusters present. Finally, this thesis aims to address and propose solutions to the task of comparing clustering solutions, whether this be comparing patients or observations assigned to different subgroups or comparing clustering solutions over multiple datasets. To address these aims, we consider a case study in Parkinson’s disease (PD), a complex and commonly diagnosed neurodegenerative disorder. In particular, two commonly collected sources of patient information are considered. The first source of data are on symptoms associated with PD, recorded using the Unified Parkinson’s Disease Rating Scale (UPDRS) and constitutes the first half of this thesis. The second half of this thesis is dedicated to the analysis of microelectrode recordings collected during Deep Brain Stimulation (DBS), a popular palliative treatment for advanced PD. Analysis of this second source of data centers on the problems of unsupervised detection and sorting of action potentials or "spikes" in recordings of multiple cell activity, providing valuable information on real time neural activity in the brain.

Towards semantic search and inference in electronic medical records : an approach using concept-based information retrieval

For more than a decade research in the field of context aware computing has aimed to find ways to exploit situational information that can be detected by mobile computing and sensor technologies. The goal is to provide people with new and improved applications, enhanced functionality and better use experience (Dey, 2001). Early applications focused on representing or computing on physical parameters, such as showing your location and the location of people or things around you. Such applications might show where the next bus is, which of your friends is in the vicinity and so on. With the advent of social networking software and microblogging sites such as Facebook and Twitter, recommender systems and so on context-aware computing is moving towards mining the social web in order to provide better representations and understanding of context, including social context. In this paper we begin by recapping different theoretical framings of context. We then discuss the problem of context- aware computing from a design perspective.

Driving for work : a series of organisational audit results

Previous research has indicated that road crashes are the most common form of work related fatalities (Haworth et al., 2000). Historically, industry has often taken a “silver bullet” approach developing and implementing a single countermeasure to address all their work related road safety issues, despite legislative requirements to discharge obligations through minimising risk and enhancing safety. This paper describes the results and implications from a series of work related road safety audits that were undertaken across five organisations to determine deficiencies in each organisation‟s safe driving management and practice. Researchers conducted a series of structured interviews, reviewed documentation relating to work related driving, and analysed vehicle related crash and incident records to determine each organisation‟s current situation in the management of work related road safety and driver behaviour. A number of consistent themes and issues across each organisation were identified relating to managing driver behaviour, organisational policies, incident recording and reporting, communication and education, and formalisation of key work related road safety strategies. Although organisations are required to undertake risk reduction strategies for all work related driving, the results of the research suggest that many organisations fail to systematically manage driver behaviour and mitigate work related road safety risk. Future improvements in work related road safety will require organisations to firstly acknowledge the high risk associated with drivers driving for work and secondly adopt comprehensive risk mitigation strategies in a similar manner to managing other workplace hazards.

Overlapping medical alarms are almost indiscriminable

Objective: We explore how accurately and quickly nurses can identify melodic medical equipment alarms when no mnemonics are used, when alarms may overlap, and when concurrent tasks are performed. Background: The international standard IEC 60601-1-8 (International Electrotechnical Commission, 2005) has proposed simple melodies to distinguish seven alarm sources. Previous studies with nonmedical participants reveal poor learning of melodic alarms and persistent confusions between some of them. The effects of domain expertise, concurrent tasks, and alarm overlaps are unknown. Method: Fourteen intensive care and general medical unit nurses learned the melodic alarms without mnemonics in two sessions on separate days. In the second half of Day 2 the nurses identified single alarms or pairs of alarms played in sequential, partially overlapping, or nearly completely overlapping configurations. For half the experimental blocks nurses performed a concurrent mental arithmetic task. Results: Nurses' learning was poor and was no better than the learning of nonnurses in a previous study. Nurses showed the previously noted confusions between alarms. Overlapping alarms were exceptionally difficult to identify. The concurrent task affected response time but not accuracy. Conclusion: Because of a failure of auditory stream segregation, the melodic alarms cannot be discriminated when they overlap. Directives to sequence the sounding of alarms in medical electrical equipment must be strictly adhered to, or the alarms must redesigned to support better auditory streaming. Application: Actual or potential uses of this research include the implementation of IEC 60601-1-8 alarms in medical electrical equipment.

Learnability and discriminability of melodic medical equipment alarms

Melodic alarms proposed in the IEC 60601-1-8 standard for medical electrical equipment were tested for learnability and discriminability. Thirty-three non-anaesthetist participants learned the alarms over two sessions of practice, with or without mnemonics suggested in the standard. Fewer than 30% of participants could identify the alarms with 100% accuracy at the end of practice. Confusions persisted between pairs of alarms, especially if mnemonics were used during learning (p = 0.011). Participants responded faster (p < 0.00001) and more accurately (p = 0.002) to medium priority alarms than to high priority alarms, even though they rated the high priority alarms as sounding more urgent (p < 0.00001). Participants with at least 1 year of formal musical training identified the alarms more accurately (p = 0.0002) than musically untrained participants, and found the task easier overall (p < 0.00001). More intensive studies of the IEC 60601-1-8 alarms are needed for their effectiveness to be determined.

Sri Lanka in global medical research: a scientific analysis of the Sri Lankan research output during 2000-2009

Background Scientific research is an essential component in guiding improvements in health systems. There are no studies examining the Sri Lankan medical research output at international level. The present study evaluated the Sri Lankan research performance in medicine as reflected by the research publications output between years 2000-2009. Methods This study was based on Sri Lankan medical research publication data, retrieved from the SciVerse Scopus® from January 2000 to December 2009. The process of article selection was as follows: Affiliation - 'Sri Lanka' or 'Ceylon', Publication year - 'January 2000 to December 2009' and Subject area - 'Life and Health Sciences'. The articles identified were classified according to disease, medical speciality, institutions, major international collaborators, authors and journals. Results Sri Lanka's cumulative medical publications output between years 2000-2009 was 1,740 articles published in 160 different journals. The average annual publication growth rate was 9.1%. Majority of the articles were published in 'International' (n = 950, 54.6%) journals. Most articles were descriptive studies (n = 611, 35.1%), letters (n-345, 19.8%) and case reports (n = 311, 17.9%). The articles were authored by 148 different Sri Lankan authors from 146 different institutions. The three most prolific local institutions were Universities of; Colombo (n = 547), Kelaniya (n = 246) and Peradeniya (n = 222). Eighty four countries were found to have published collaborative papers with Sri Lankan authors during the last decade. UK was the largest collaborating partner (n = 263, 15.1%). Malaria (n = 75), Diabetes Mellitus (n = 55), Dengue (n = 53), Accidental injuries (n = 42) and Lymphatic filariasis (n = 40) were the major diseases studied. The 1,740 publications were cited 9,708 times, with an average citation of 5.6 per paper. The most cited paper had 203 citations, while there were 597 publications with no citations. The Sri Lankan authors' contribution to the global medical research output during the last decade was only 0.086%. Conclusion The Sri Lankan medical research output during the last decade is only a small fraction of the global research output. There it is a necessity to setup an enabling environment for research, with a proper vision, support, funds and training. In addition, collaborations across the region need to be strengthened to face common regional health challenges. Keywords: Sri Lanka, Medical research, Publication, Analysis

Information sharing in Onesocialweb using a multiple profile manager to better informed medical decision making processes

The study shows an alternative solution to existing efforts at solving the problem of how to centrally manage and synchronise users’ Multiple Profiles (MP) across multiple discrete social networks. Most social network users hold more than one social network account and utilise them in different ways depending on the digital context (Iannella, 2009a). They may, for example, enjoy friendly chat on Facebook1, professional discussion on LinkedIn2, and health information exchange on PatientsLikeMe3 In this thesis the researcher proposes a framework for the management of a user’s multiple online social network profiles. A demonstrator, called Multiple Profile Manager (MPM), will be showcased to illustrate how effective the framework will be. The MPM will achieve the required profile management and synchronisation using a free, open, decentralized social networking platform (OSW) that was proposed by the Vodafone Group in 2010. The proposed MPM will enable a user to create and manage an integrated profile (IP) and share/synchronise this profile with all their social networks. The necessary protocols to support the prototype are also proposed by the researcher. The MPM protocol specification defines an Extensible Messaging and Presence Protocol (XMPP) extension for sharing vCard and social network accounts information between the MPM Server, MPM Client, and social network sites (SNSs). . Therefore many web users need to manage disparate profiles across many distributed online sources. Maintaining these profiles is cumbersome, time-consuming, inefficient, and may lead to lost opportunity. The writer of this thesis adopted a research approach and a number of use cases for the implementation of the project. The use cases were created to capture the functional requirements of the MPM and to describe the interactions between users and the MPM. In the research a development process was followed in establishing the prototype and related protocols. The use cases were subsequently used to illustrate the prototype via the screenshots taken of the MPM client interfaces. The use cases also played a role in evaluating the outcomes of the research such as the framework, prototype, and the related protocols. An innovative application of this project is in the area of public health informatics. The researcher utilised the prototype to examine how the framework might benefit patients and physicians. The framework can greatly enhance health information management for patients and more importantly offer a more comprehensive personal health overview of patients to physicians. This will give a more complete picture of the patient’s background than is currently available and will prove helpful in providing the right treatment. The MPM prototype and related protocols have a high application value as they can be integrated into the real OSW platform and so serve users in the modern digital world. They also provide online users with a real platform for centrally storing their complete profile data, efficiently managing their personal information, and moreover, synchronising the overall complete profile with each of their discrete profiles stored in their different social network sites.

Alcohol and other drugs in construction

Evidence from the infrastructure and building sectors suggests issues of drugs and alcohol and its association with safety risk on construction sites. While most Australian jurisdictions have identified this as a critical safety issue, information is limited regarding the prevalence of alcohol and other drugs in the workplace and there is limited evidential guidance on how to effectively and efficiently address such an issue. A nationally consistent collaborative approach across the construction workforce - involving employers and employees; clients, unions; contractors and sub-contractors is required to engender a cultural change in the construction workforce – in a similar manner to the on-going initiative in securing a cultural change to drink-driving in our society where peer intervention and support is encouraged. A study to address these issues has three key objectives. Firstly, using the standard World Health Organisation Alcohol Use Disorders Identification Test (AUDIT), and a wide ranging set of structured interviews, a national qualitative and quantitative assessment of the use of drugs and alcohol is being undertaken. Secondly, the development of an appropriate industry policy with an adoption of an educative and rehabilitative approach is planned in consultation with employers and employees across the infrastructure and building sectors, with an aim of national adoption. Finally, an industry-specific cultural change management program will be developed through a nationally collaborative approach to reducing the risk of impaired performance on construction sites and increasing workers’ commitment to drugs and alcohol safety. The study outcomes stand to benefit not only occupational health and safety, through a greater understanding of the safety impacts of alcohol and other drugs at work, but also alcohol and drug use as a wider community health issue. This presentation will provide an analysis and discussion of the data collected in objective 1 and how the final results will inform the subsequent phases of the study.

The role of education and awareness in workplace alcohol and drug use in the Australian construction industry : proposed program of research and preliminary results

The main aim of this paper is to outline a proposed program of research which will attempt to quantify the extent of the problem of alcohol and other drugs in the Australian construction industry, and furthermore, develop an appropriate industry-wide policy and cultural change management program and implementation plan to address the problem. This paper will also present preliminary results from the study. The study will use qualitative and quantitative methods (in the form of interviews and surveys, respectively) to evaluate the extent of the problem of alcohol and other drug use in this industry, to ascertain the feasibility of an industry-wide policy and cultural change management program, and to develop an appropriate implementation plan. The study will be undertaken in several construction organisations, at selected sites in South Australia, Victoria and Northern Territory. It is anticipated that approximately 500 employees from the participating organisations across Australia will take part in the study. The World Health Organisation’s Alcohol Use Disorders Identification Test (AUDIT) will be used to measure the extent of alcohol use in the industry. Illicit drug use, ‘‘readiness to change’’, impediments to reducing impairment, feasibility of proposed interventions, and employee attitudes and knowledge regarding workplace AOD impairment, will also be measured through a combination of interviews and surveys. Among the preliminary findings, for 51% (n=127) of respondents, score on the AUDIT indicated alcohol use at hazardous levels. Of the respondents who were using alcohol at hazardous levels, 76% reported (n97) that they do not have a problem with drinking and 54% (n=68) reported that it would be easy to ‘‘cut down’’ or stop drinking. Nearly half (49%) of all respondents (n=122) had used marijuana/cannabis at some time prior to being surveyed. The use of other illicit substances was much less frequently reported. Preliminary interview findings indicated a lack of adequate employee knowledge regarding the physical effects of alcohol and other drugs in the workplace. As for conclusions, the proposed study will address a major gap in the literature with regard to the extent of the problem of alcohol and other drug use in the construction industry in Australia. The study will also develop and implement a national, evidence-based workplace policy, with the aim of mitigating the deleterious effects of alcohol and other drugs in this industry.

Medical ultrasound imaging

Ultrasound is used extensively in the field of medical imaging. In this paper, the basic principles of ultrasound are explained using ‘everyday’ physics. Topics include the generation of ultrasound, basic interactions with material and the measurement of blood flow using the Doppler effect.