Statistical modeling of protein lysate array data

The protein lysate array is an emerging technology for quantifying the protein concentration ratios in multiple biological samples. It is gaining popularity, and has the potential to answer questions about post-translational modifications and protein pathway relationships. Statistical inference for a parametric quantification procedure has been inadequately addressed in the literature, mainly due to two challenges: the increasing dimension of the parameter space and the need to account for dependence in the data. Each chapter of this thesis addresses one of these issues. In Chapter 1, an introduction to the protein lysate array quantification is presented, followed by the motivations and goals for this thesis work. In Chapter 2, we develop a multi-step procedure for the Sigmoidal models, ensuring consistent estimation of the concentration level with full asymptotic efficiency. The results obtained in this chapter justify inferential procedures based on large-sample approximations. Simulation studies and real data analysis are used to illustrate the performance of the proposed method in finite-samples. The multi-step procedure is simpler in both theory and computation than the single-step least squares method that has been used in current practice. In Chapter 3, we introduce a new model to account for the dependence structure of the errors by a nonlinear mixed effects model. We consider a method to approximate the maximum likelihood estimator of all the parameters. Using the simulation studies on various error structures, we show that for data with non-i.i.d. errors the proposed method leads to more accurate estimates and better confidence intervals than the existing single-step least squares method.

Aerial surveys to monitor bluefin tuna abundance and track efficiency of management measures

Conservation and management measures for exploited fish species rely on our ability to monitor variations in population abundance. In the case of the eastern stock of Atlantic bluefin tuna (ABFT), recent changes in management policies have strongly affected the reliability of fishery-dependent indicators due to drastic changes in fishing season/area, fisheries selectivity and strategy. However, fishery-independent indices of abundance are rare for large pelagic fish, and obtaining them is often costly and labor intensive. Here, we show that scientific aerial surveys are an appropriate tool for monitoring juvenile bluefin tuna abundance in the Mediterranean. We present an abundance index based on 62 aerial surveys conducted since 2000, using 2 statistical approaches to deal with the sampling strategy: line and strip transects. Both approaches showed a significant increase in juvenile ABFT abundance in recent years, resulting from the recovery plan established in 2007. Nonetheless, the estimates from the line transect method appear to be more robust and stable. This study provides essential information for fisheries management. Expanding the spatial coverage to other nursery grounds would further increase the reliability and representativeness of this index.

On the efficiency of impingers with fritted nozzle tip for collection of ultrafine particles

The aim of this study was to determine the collection efficiency of ultrafine particles into an impinger fitted with a fritted nozzle tip as a means to increase contact surface area between the aerosol and the liquid. The influence of liquid sampling volume, frit porosity and the nature of the sampling liquid was explored and it was shown that all impact on the collection efficiency of particles smaller than 220 nm. Obtained values for overall collection efficiency were substantially higher (~30–95%) than have been previously reported, mainly due to the high deposition of particles in the fritted nozzle tip, especially in case of finer porosity frits and smaller particles. Values for the capture efficiency of the solvent alone ranged from 20 to 45%, depending on the type and the volume of solvent. Additionally, our results show that airstream dispersion into bubbles improves particle trapping by the liquid and that there is a difference in collection efficiencies based on the nature and volume of the solvent used.

An investigation into the barriers to the implementation of automation and robotics technologies in the construction industry

The rising problems associated with construction such as decreasing quality and productivity, labour shortages, occupational safety, and inferior working conditions have opened the possibility of more revolutionary solutions within the industry. One prospective option is in the implementation of innovative technologies such as automation and robotics, which has the potential to improve the industry in terms of productivity, safety and quality. The construction work site could, theoretically, be contained in a safer environment, with more efficient execution of the work, greater consistency of the outcome and higher level of control over the production process. By identifying the barriers to construction automation and robotics implementation in construction, and investigating ways in which to overcome them, contributions could be made in terms of better understanding and facilitating, where relevant, greater use of these technologies in the construction industry so as to promote its efficiency. This research aims to ascertain and explain the barriers to construction automation and robotics implementation by exploring and establishing the relationship between characteristics of the construction industry and attributes of existing construction automation and robotics technologies to level of usage and implementation in three selected countries; Japan, Australia and Malaysia. These three countries were chosen as their construction industry characteristics provide contrast in terms of culture, gross domestic product, technology application, organisational structure and labour policies. This research uses a mixed method approach of gathering data, both quantitative and qualitative, by employing a questionnaire survey and an interview schedule; using a wide range of sample from management through to on-site users, working in a range of small (less than AUD0.2million) to large companies (more than AUD500million), and involved in a broad range of business types and construction sectors. Detailed quantitative (statistical) and qualitative (content) data analysis is performed to provide a set of descriptions, relationships, and differences. The statistical tests selected for use include cross-tabulations, bivariate and multivariate analysis for investigating possible relationships between variables; and Kruskal-Wallis and Mann Whitney U test of independent samples for hypothesis testing and inferring the research sample to the construction industry population. Findings and conclusions arising from the research work which include the ranking schemes produced for four key areas of, the construction attributes on level of usage; barrier variables; differing levels of usage between countries; and future trends, have established a number of potential areas that could impact the level of implementation both globally and for individual countries.

Rural and remote road safety study : final report

• Introduction: Concern and action for rural road safety is relatively new in Australia in comparison to the field of traffic safety as a whole. In 2003, a program of research was begun by the Centre for Accident Research and Road Safety - Queensland (CARRS-Q) and the Rural Health Research Unit (RHRU) at James Cook University to investigate factors contributing to serious rural road crashes in the North Queensland region. This project was funded by the Premier’s Department, Main Roads Department, Queensland Transport, QFleet, Queensland Rail, Queensland Ambulance Service, Department of Natural Resources and Queensland Police Service. Additional funding was provided by NRMA Insurance for a PhD scholarship. In-kind support was provided through the four hospitals used for data collection, namely Cairns Base Hospital, The Townsville Hospital, Mount Isa Hospital and Atherton Hospital.----- The primary aim of the project was to: Identify human factors related to the occurrence of serious traffic incidents in rural and remote areas of Australia, and to the trauma suffered by persons as a result of these incidents, using a sample drawn from a rural and remote area in North Queensland.----- The data and analyses presented in this report are the core findings from two broad studies: a general examination of fatalities and casualties from rural and remote crashes for the period 1 March 2004 until 30 June 2007, and a further linked case-comparison study of hospitalised patients compared with a sample of non-crash-involved drivers.----- • Method: The study was undertaken in rural North Queensland, as defined by the Australian Bureau of Statistics (ABS) statistical divisions of North Queensland, Far North Queensland and North-West Queensland. Urban areas surrounding Townsville, Thuringowa and Cairns were not included. The study methodology was centred on serious crashes, as defined by a resulting hospitalisation for 24 hours or more and/or a fatality. Crashes meeting this criteria within the North Queensland region between 1 March 2004 and 30 June 2007 were identified through hospital records and interviewed where possible. Additional data was sourced from coroner’s reports, the Queensland Transport road crash database, the Queensland Ambulance Service and the study hospitals in the region.----- This report is divided into chapters corresponding to analyses conducted on the collected crash and casualty data.----- Chapter 3 presents an overview of all crashes and casualties identified during the study period. Details are presented in regard to the demographics and road user types of casualties; the locations, times, types, and circumstances of crashes; along with the contributing circumstances of crashes.----- Chapter 4 presents the results of summary statistics for all casualties for which an interview was able to be conducted. Statistics are presented separately for drivers and riders, passengers, pedestrians and cyclists. Details are also presented separately for drivers and riders crashing in off-road and on-road settings. Results from questionnaire data are presented in relation to demographics; the experience of the crash in narrative form; vehicle characteristics and maintenance; trip characteristics (e.g. purpose and length of journey; periods of fatigue and monotony; distractions from driving task); driving history; alcohol and drug use; medical history; driving attitudes, intentions and behaviour; attitudes to enforcement; and experience of road safety advertising.----- Chapter 5 compares the above-listed questionnaire results between on-road crash-involved casualties and interviews conducted in the region with non-crash-involved persons. Direct comparisons as well as age and sex adjusted comparisons are presented.----- Chapter 6 presents information on those casualties who were admitted to one of the study hospitals during the study period. Brief information is given regarding the demographic characteristics of these casualties. Emergency services’ data is used to highlight the characteristics of patient retrieval and transport to and between hospitals. The major injuries resulting from the crashes are presented for each region of the body and analysed by vehicle type, occupant type, seatbelt status, helmet status, alcohol involvement and nature of crash. Estimates are provided of the costs associated with in-hospital treatment and retrieval.----- Chapter 7 describes the characteristics of the fatal casualties and the nature and circumstances of the crashes. Demographics, road user types, licence status, crash type and contributing factors for crashes are presented. Coronial data is provided in regard to contributing circumstances (including alcohol, drugs and medical conditions), cause of death, resulting injuries, and restraint and helmet use.----- Chapter 8 presents the results of a comparison between casualties’ crash descriptions and police-attributed crash circumstances. The relative frequency of contributing circumstances are compared both broadly within the categories of behavioural, environmental, vehicle related, medical and other groupings and specifically for circumstances within these groups.----- Chapter 9 reports on the associated research projects which have been undertaken on specific topics related to rural road safety.----- Finally, Chapter 10 reports on the conclusions and recommendations made from the program of research.---- • Major Recommendations : From the findings of these analyses, a number of major recommendations were made: + Male drivers and riders - Male drivers and riders should continue to be the focus of interventions, given their very high representation among rural and remote road crash fatalities and serious injuries.----- - The group of males aged between 30 and 50 years comprised the largest number of casualties and must also be targeted for change if there is to be a meaningful improvement in rural and remote road safety.----- + Motorcyclists - Single vehicle motorcycle crashes constitute over 80% of serious, on-road rural motorcycle crashes and need particular attention in development of policy and infrastructure.----- - The motorcycle safety consultation process currently being undertaken by Queensland Transport (via the "Motorbike Safety in Queensland - Consultation Paper") is strongly endorsed. As part of this process, particular attention needs to be given to initiatives designed to reduce rural and single vehicle motorcycle crashes.----- - The safety of off-road riders is a serious problem that falls outside the direct responsibility of either Transport or Health departments. Responsibility for this issue needs to be attributed to develop appropriate policy, regulations and countermeasures.----- + Road safety for Indigenous people - Continued resourcing and expansion of The Queensland Aboriginal Peoples and Torres Strait Islander Peoples Driver Licensing Program to meet the needs of remote and Indigenous communities with significantly lower licence ownership levels.----- - Increased attention needs to focus on the contribution of geographic disadvantage (remoteness) factors to remote and Indigenous road trauma.----- + Road environment - Speed is the ‘final common pathway’ in determining the severity of rural and remote crashes and rural speed limits should be reduced to 90km/hr for sealed off-highway roads and 80km/hr for all unsealed roads as recommended in the Austroads review and in line with the current Tasmanian government trial.----- - The Department of Main Roads should monitor rural crash clusters and where appropriate work with local authorities to conduct relevant audits and take mitigating action. - The international experts at the workshop reviewed the data and identified the need to focus particular attention on road design management for dangerous curves. They also indicated the need to maximise the use of audio-tactile linemarking (audible lines) and rumble strips to alert drivers to dangerous conditions and behaviours.----- + Trauma costs - In accordance with Queensland Health priorities, recognition should be given to the substantial financial costs associated with acute management of trauma resulting from serious rural and remote crashes.----- - Efforts should be made to develop a comprehensive, regionally specific costing formula for road trauma that incorporates the pre-hospital, hospital and post-hospital phases of care. This would inform health resource allocation and facilitate the evaluation of interventions.----- - The commitment of funds to the development of preventive strategies to reduce rural and remote crashes should take into account the potential cost savings associated with trauma.----- - A dedicated study of the rehabilitation needs and associated personal and healthcare costs arising from rural and remote road crashes should be undertaken.----- + Emergency services - While the study has demonstrated considerable efficiency in the response and retrieval systems of rural and remote North Queensland, relevant Intelligent Transport Systems technologies (such as vehicle alarm systems) to improve crash notification should be both developed and evaluated.----- + Enforcement - Alcohol and speed enforcement programs should target the period between 2 and 6pm because of the high numbers of crashes in the afternoon period throughout the rural region.----- + Drink driving - Courtesy buses should be advocated and schemes such as the Skipper project promoted as local drink driving countermeasures in line with the very high levels of community support for these measures identified in the hospital study.------ - Programs should be developed to target the high levels of alcohol consumption identified in rural and remote areas and related involvement in crashes.----- - Referrals to drink driving rehabilitation programs should be mandated for recidivist offenders.----- + Data requirements - Rural and remote road crashes should receive the same quality of attention as urban crashes. As such, it is strongly recommended that increased resources be committed to enable dedicated Forensic Crash Units to investigate rural and remote fatal and serious injury crashes.----- - Transport department records of rural and remote crashes should record the crash location using the national ARIA area classifications used by health departments as a means to better identifying rural crashes.----- - Rural and remote crashes tend to be unnoticed except in relatively infrequent rural reviews. They should receive the same level of attention and this could be achieved if fatalities and fatal crashes were coded by the ARIA classification system and included in regular crash reporting.----- - Health, Transport and Police agencies should collect a common, minimal set of data relating to road crashes and injuries, including presentations to small rural and remote health facilities.----- + Media and community education programmes - Interventions seeking to highlight the human contribution to crashes should be prioritised. Driver distraction, alcohol and inappropriate speed for the road conditions are key examples of such behaviours.----- - Promotion of basic safety behaviours such as the use of seatbelts and helmets should be given a renewed focus.----- - Knowledge, attitude and behavioural factors that have been identified for the hospital Brief Intervention Trial should be considered in developing safety campaigns for rural and remote people. For example challenging the myth of the dangerous ‘other’ or ‘non-local’ driver.----- - Special educational initiatives on the issues involved in rural and remote driving should be undertaken. For example the material used by Main Roads, the Australian Defence Force and local initiatives.