Cellulosic ethanol from sugarcane bagasse in Australia : exploring industry feasibility through systems analysis, techno-economic assessment and pilot plant development

Overcoming many of the constraints to early stage investment in biofuels production from sugarcane bagasse in Australia requires an understanding of the complex technical, economic and systemic challenges associated with the transition of established sugar industry structures from single product agri-businesses to new diversified multi-product biorefineries. While positive investment decisions in new infrastructure requires technically feasible solutions and the attainment of project economic investment thresholds, many other systemic factors will influence the investment decision. These factors include the interrelationships between feedstock availability and energy use, competing product alternatives, technology acceptance and perceptions of project uncertainty and risk. This thesis explores the feasibility of a new cellulosic ethanol industry in Australia based on the large sugarcane fibre (bagasse) resource available. The research explores industry feasibility from multiple angles including the challenges of integrating ethanol production into an established sugarcane processing system, scoping the economic drivers and key variables relating to bioethanol projects and considering the impact of emerging technologies in improving industry feasibility. The opportunities available from pilot scale technology demonstration are also addressed. Systems analysis techniques are used to explore the interrelationships between the existing sugarcane industry and the developing cellulosic biofuels industry. This analysis has resulted in the development of a conceptual framework for a bagassebased cellulosic ethanol industry in Australia and uses this framework to assess the uncertainty in key project factors and investment risk. The analysis showed that the fundamental issue affecting investment in a cellulosic ethanol industry from sugarcane in Australia is the uncertainty in the future price of ethanol and government support that reduces the risks associated with early stage investment is likely to be necessary to promote commercialisation of this novel technology. Comprehensive techno-economic models have been developed and used to assess the potential quantum of ethanol production from sugarcane in Australia, to assess the feasibility of a soda-based biorefinery at the Racecourse Sugar Mill in Mackay, Queensland and to assess the feasibility of reducing the cost of production of fermentable sugars from the in-planta expression of cellulases in sugarcane in Australia. These assessments show that ethanol from sugarcane in Australia has the potential to make a significant contribution to reducing Australia’s transportation fuel requirements from fossil fuels and that economically viable projects exist depending upon assumptions relating to product price, ethanol taxation arrangements and greenhouse gas emission reduction incentives. The conceptual design and development of a novel pilot scale cellulosic ethanol research and development facility is also reported in this thesis. The establishment of this facility enables the technical and economic feasibility of new technologies to be assessed in a multi-partner, collaborative environment. As a key outcome of this work, this study has delivered a facility that will enable novel cellulosic ethanol technologies to be assessed in a low investment risk environment, reducing the potential risks associated with early stage investment in commercial projects and hence promoting more rapid technology uptake. While the study has focussed on an exploration of the feasibility of a commercial cellulosic ethanol industry from sugarcane in Australia, many of the same key issues will be of relevance to other sugarcane industries throughout the world seeking diversification of revenue through the implementation of novel cellulosic ethanol technologies.

Fuzzy methods for analysis of microarrays and networks

Bioinformatics involves analyses of biological data such as DNA sequences, microarrays and protein-protein interaction (PPI) networks. Its two main objectives are the identification of genes or proteins and the prediction of their functions. Biological data often contain uncertain and imprecise information. Fuzzy theory provides useful tools to deal with this type of information, hence has played an important role in analyses of biological data. In this thesis, we aim to develop some new fuzzy techniques and apply them on DNA microarrays and PPI networks. We will focus on three problems: (1) clustering of microarrays; (2) identification of disease-associated genes in microarrays; and (3) identification of protein complexes in PPI networks. The first part of the thesis aims to detect, by the fuzzy C-means (FCM) method, clustering structures in DNA microarrays corrupted by noise. Because of the presence of noise, some clustering structures found in random data may not have any biological significance. In this part, we propose to combine the FCM with the empirical mode decomposition (EMD) for clustering microarray data. The purpose of EMD is to reduce, preferably to remove, the effect of noise, resulting in what is known as denoised data. We call this method the fuzzy C-means method with empirical mode decomposition (FCM-EMD). We applied this method on yeast and serum microarrays, and the silhouette values are used for assessment of the quality of clustering. The results indicate that the clustering structures of denoised data are more reasonable, implying that genes have tighter association with their clusters. Furthermore we found that the estimation of the fuzzy parameter m, which is a difficult step, can be avoided to some extent by analysing denoised microarray data. The second part aims to identify disease-associated genes from DNA microarray data which are generated under different conditions, e.g., patients and normal people. We developed a type-2 fuzzy membership (FM) function for identification of diseaseassociated genes. This approach is applied to diabetes and lung cancer data, and a comparison with the original FM test was carried out. Among the ten best-ranked genes of diabetes identified by the type-2 FM test, seven genes have been confirmed as diabetes-associated genes according to gene description information in Gene Bank and the published literature. An additional gene is further identified. Among the ten best-ranked genes identified in lung cancer data, seven are confirmed that they are associated with lung cancer or its treatment. The type-2 FM-d values are significantly different, which makes the identifications more convincing than the original FM test. The third part of the thesis aims to identify protein complexes in large interaction networks. Identification of protein complexes is crucial to understand the principles of cellular organisation and to predict protein functions. In this part, we proposed a novel method which combines the fuzzy clustering method and interaction probability to identify the overlapping and non-overlapping community structures in PPI networks, then to detect protein complexes in these sub-networks. Our method is based on both the fuzzy relation model and the graph model. We applied the method on several PPI networks and compared with a popular protein complex identification method, the clique percolation method. For the same data, we detected more protein complexes. We also applied our method on two social networks. The results showed our method works well for detecting sub-networks and give a reasonable understanding of these communities.

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.

A Bayesian analysis of an agricultural field trial with three spatial dimensions

Modern technology now has the ability to generate large datasets over space and time. Such data typically exhibit high autocorrelations over all dimensions. The field trial data motivating the methods of this paper were collected to examine the behaviour of traditional cropping and to determine a cropping system which could maximise water use for grain production while minimising leakage below the crop root zone. They consist of moisture measurements made at 15 depths across 3 rows and 18 columns, in the lattice framework of an agricultural field. Bayesian conditional autoregressive (CAR) models are used to account for local site correlations. Conditional autoregressive models have not been widely used in analyses of agricultural data. This paper serves to illustrate the usefulness of these models in this field, along with the ease of implementation in WinBUGS, a freely available software package. The innovation is the fitting of separate conditional autoregressive models for each depth layer, the ‘layered CAR model’, while simultaneously estimating depth profile functions for each site treatment. Modelling interest also lay in how best to model the treatment effect depth profiles, and in the choice of neighbourhood structure for the spatial autocorrelation model. The favoured model fitted the treatment effects as splines over depth, and treated depth, the basis for the regression model, as measured with error, while fitting CAR neighbourhood models by depth layer. It is hierarchical, with separate onditional autoregressive spatial variance components at each depth, and the fixed terms which involve an errors-in-measurement model treat depth errors as interval-censored measurement error. The Bayesian framework permits transparent specification and easy comparison of the various complex models compared.

External orientation and business model adaptation in young and nascent firms : preliminary analysis from the CAUSSE project

Discovering factors that help or impede business model change is an important quest, both for researchers and practitioners. In this study we present preliminary findings based on the CAUSEE survey of young and nascent firms in Australia. In particular, we seek to determine an association between business model adaptation and external orientation among young and nascent firms within the random sample and amongst an oversample of high potential firms. The concept of external orientation is made operational by asking respondents whether, and to what extent, they rely on certain sources of advice and information. We find that high potential firms are more likely to have made at least some change to their business model, that greater use of external sources of advice is generally significantly associated with business model adaptation, but also that there appear to be different patterns of behaviour between the random sample and the over sample.

Confirmatory factor analysis of the Behaviour of Young Novice Drivers Scale (BYNDS)

The greatly increased risk of being killed or injured in a car crash for the young novice driver has been recognised in the road safety and injury prevention literature for decades. Risky driving behaviour has consistently been found to contribute to traffic crashes. Researchers have devised a number of instruments to measure this risky driving behaviour. One tool developed specifically to measure the risky behaviour of young novice drivers is the Behaviour of Young Novice Drivers Scale (BYNDS) (Scott-Parker et al., 2010). The BYNDS consists of 44 items comprising five subscales for transient violations, fixed violations, misjudgement, risky driving exposure, and driving in response to their mood. The factor structure of the BYNDS has not been examined since its development in a matched sample of 476 novice drivers aged 17-25 years. Method: The current research attempted to refine the BYNDS and explore its relationship with the self-reported crash and offence involvement and driving intentions of 390 drivers aged 17-25 years (M = 18.23, SD = 1.58) in Queensland, Australia, during their first six months of independent driving with a Provisional (intermediate) driver’s licence. A confirmatory factor analysis was undertaken examining the fit of the originally proposed BYNDS measurement model. Results: The model was not a good fit to the data. A number of iterations removed items with low factor loadings, resulting in a 36-item revised BYNDS which was a good fit to the data. The revised BYNDS was highly internally consistent. Crashes were associated with fixed violations, risky driving exposure, and misjudgement; offences were moderately associated with risky driving exposure and transient violations; and road-rule compliance intentions were highly associated with transient violations. Conclusions: Applications of the BYNDS in other young novice driver populations will further explore the factor structure of both the original and revised BYNDS. The relationships between BYNDS subscales and self-reported risky behaviour and attitudes can also inform countermeasure development, such as targeting young novice driver non-compliance through enforcement and education initiatives.

Geostatistical analysis of adult Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae) in wheat stored at constant temperatures

Insect monitoring and sampling programmes are used in the stored grains industry for the detection and estimation of insect pests. At the low pest densities dictated by economic and commercial requirements, the accuracy of both detection and abundance estimates can be influenced by variations in the spatial structure of pest populations over short distances. Geostatistical analysis of Rhyzopertha dominica populations in 2 dimensions showed that, in both the horizontal and vertical directions and at all temperatures examined, insect numbers were positively correlated over short (0-5cm) distances, and negatively correlated over longer (≥10cm) distances. Analysis in 3 dimensions showed a similar pattern, with positive correlations over short distances and negative correlations at longer distances. At 35°C, insects were located significantly further from the grain surface than at 25 and 30°C. Dispersion metrics showed statistically significant aggregation in all cases. This is the first research using small sample units, high sampling intensities, and a range of temperatures, to show spatial structuring of R. dominica populations over short distances. This research will have significant implications for sampling in the stored grains industry.

Three-dimensional geological modelling and multivariate statistical analysis of water chemistry data to analyse and visualise aquifer structure and groundwater composition in the Wairau Plain, Marlborough District, New Zealand

Concerns regarding groundwater contamination with nitrate and the long-term sustainability of groundwater resources have prompted the development of a multi-layered three dimensional (3D) geological model to characterise the aquifer geometry of the Wairau Plain, Marlborough District, New Zealand. The 3D geological model which consists of eight litho-stratigraphic units has been subsequently used to synthesise hydrogeological and hydrogeochemical data for different aquifers in an approach that aims to demonstrate how integration of water chemistry data within the physical framework of a 3D geological model can help to better understand and conceptualise groundwater systems in complex geological settings. Multivariate statistical techniques(e.g. Principal Component Analysis and Hierarchical Cluster Analysis) were applied to groundwater chemistry data to identify hydrochemical facies which are characteristic of distinct evolutionary pathways and a common hydrologic history of groundwaters. Principal Component Analysis on hydrochemical data demonstrated that natural water-rock interactions, redox potential and human agricultural impact are the key controls of groundwater quality in the Wairau Plain. Hierarchical Cluster Analysis revealed distinct hydrochemical water quality groups in the Wairau Plain groundwater system. Visualisation of the results of the multivariate statistical analyses and distribution of groundwater nitrate concentrations in the context of aquifer lithology highlighted the link between groundwater chemistry and the lithology of host aquifers. The methodology followed in this study can be applied in a variety of hydrogeological settings to synthesise geological, hydrogeological and hydrochemical data and present them in a format readily understood by a wide range of stakeholders. This enables a more efficient communication of the results of scientific studies to the wider community.

Australian Tax Analysis [8th Edition]

Now in its eighth edition, Australian Tax Analysis: Cases, Commentary, Commercial Applications and Questions has a proven track record as a high level work for students of taxation law written by a team of authors with many years of experience. Taking into account the fact that the volume of material needed to be processed by today’s taxation student can be overwhelming, the well-chosen extracts and thought-provoking commentary in Australian Tax Analysis, 8th edition, provide readers with the depth of knowledge, and reasoning and analytical skills that will be required of them as practitioners. As well as the carefully selected case extracts and the helpful commentary, each chapter is supplemented by engaging practice questions, involving problem-solving, commercial decision-making, legal analysis and quantitative application. All these elements combined make Australian Tax Analysis an invaluable aid to the understanding of a subject that can be both technical and complex.

Perceptions of visitor relationship marketing opportunities by destination marketers : an importance-performance analysis

Customer relationship marketing (CRM) initiatives are increasingly being adopted by businesses in the attempt to enhance brand loyalty and stimulate repeat purchases. The purpose of this study was to examine the extent to which destination marketing organisations (DMOs) around the world have developed a visitor relationship marketing (VRM) orientation. The proposition underpinning the study is that maintaining meaningful dialogue with previous visitors in some markets would represent a more efficient use of resources than above the line advertising to attract new visitors. Importance-performance analysis was utilised to measure destination marketers’ perceptions of the efficacy of CRM initiatives, and then rate their own organisation’s performance across the same range of initiatives. A key finding was that mean importance was higher than perceived performance for every item. While the small sample limits generalisability, in general there are appears to be a lack of strategic intent by DMOs to invest in VRM.

A case of community safety : displacing complex ‘social’ problems in Fortitude Valley

Public dialogue regarding the high concentration of drug use and crime in inner city locations is frequently legitimised through visibility of drug-using populations and a perception of high crime rates. The public space known as the Brunswick Street Mall (Valley mall), located in the inner city Brisbane suburb of Fortitude Valley, has long provided the focal point for discussions regarding the problem of illicit drug use and antisocial behaviour in Brisbane. During the late 1990s a range of stakeholders in Fortitude Valley became mobilised to tackle crime and illicit drugs. In particular they wanted to dismantle popular perceptions of the area as representing the dark and unsafe side of Brisbane. The aim of this campaign was to instil a sense of safety in the area and dislodge Fortitude Valley from its reputation as a =symbolic location of danger‘. This thesis is a case study about an urban site that became contested by the diverse aims of a range of stakeholders who were invested in an urban renewal program and community safety project. This case study makes visible a number of actors that were lured from their existing roles in an indeterminable number of heterogeneous networks in order to create a community safety network. The following analysis of the community safety network emphasises some specific actors: history, ideas, technologies, materialities and displacements. The case study relies on the work of Foucault, Latour, Callon and Law to draw out the rationalities, background contingencies and the attempts to impose order and translate a number of entities into the community safety project in Fortitude Valley. The results of this research show that the community safety project is a case of ontological politics. Specifically the data indicates that both the (reality) problem of safety and the (knowledge) solution to safety were created simultaneously. This thesis explores the idea that while violence continues to occur in the Valley, evidence that community safety got done is located through mapping its displacement and eventual disappearance. As such, this thesis argues that community safety is a =collateral reality‘.

Effects of Mobile Phone Distraction at the Onset of Amber Light: Analysis of Driving Simulator Data

Distraction whilst driving on an approach to a signalized intersection is particularly dangerous, as potential vehicular conflicts and resulting angle collisions tend to be severe. This study examines the decisions of distracted drivers during the onset of amber lights. Driving simulator data were obtained from a sample of 58 drivers under baseline and handheld mobile phone conditions at the University of IOWA - National Advanced Driving Simulator. Explanatory variables include age, gender, cell phone use, distance to stop-line, and speed. An iterative combination of decision tree and logistic regression analyses are employed to identify main effects, non-linearities, and interactions effects. Results show that novice (16-17 years) and younger (18-25 years) drivers’ had heightened amber light running risk while distracted by cell phone, and speed and distance thresholds yielded significant interaction effects. Driver experience captured by age has a multiplicative effect with distraction, making the combined effect of being inexperienced and distracted particularly risky. Solutions are needed to combat the use of mobile phones whilst driving.

Analysis of marine conflicts

The traffic conflict technique (TCT) is a powerful technique applied in road traffic safety assessment as a surrogate of the traditional accident data analysis. It has subdued the conceptual and implemental weaknesses of the accident statistics. Although this technique has been applied effectively in road traffic, it has not been practised well in marine traffic even though this traffic system has some distinct advantages in terms of having a monitoring system. This monitoring system can provide navigational information as well as other geometric information of the ships for a larger study area over a longer time period. However, for implementing the TCT in the marine traffic system, it should be examined critically to suit the complex nature of the traffic system. This paper examines the suitability of the TCT to be applied to marine traffic and proposes a framework for a follow up comprehensive conflict study.

Simple rules to contain an invasive species with a complex life cycle and high dispersal capacity

Designing practical rules for controlling invasive species is a challenging task for managers, particularly when species are long-lived, have complex life cycles and high dispersal capacities. Previous findings derived from plant matrix population analyses suggest that effective control of long-lived invaders may be achieved by focusing on killing adult plants. However, the cost-effectiveness of managing different life stages has not been evaluated. We illustrate the benefits of integrating matrix population models with decision theory to undertake this evaluation, using empirical data from the largest infestation of mesquite (Leguminosae: Prosopis spp) within Australia. We include in our model the mesquite life cycle, different dispersal rates and control actions that target individuals at different life stages with varying costs, depending on the intensity of control effort. We then use stochastic dynamic programming to derive cost-effective control strategies that minimize the cost of controlling the core infestation locally below a density threshold and the future cost of control arising from infestation of adjacent areas via seed dispersal. Through sensitivity analysis, we show that four robust management rules guide the allocation of resources between mesquite life stages for this infestation: (i) When there is no seed dispersal, no action is required until density of adults exceeds the control threshold and then only control of adults is needed; (ii) when there is seed dispersal, control strategy is dependent on knowledge of the density of adults and large juveniles (LJ) and broad categories of dispersal rates only; (iii) if density of adults is higher than density of LJ, controlling adults is most cost-effective; (iv) alternatively, if density of LJ is equal or higher than density of adults, management efforts should be spread between adults, large and to a lesser extent small juveniles, but never saplings. Synthesis and applications.In this study, we show that simple rules can be found for managing invasive plants with complex life cycles and high dispersal rates when population models are combined with decision theory. In the case of our mesquite population, focussing effort on controlling adults is not always the most cost-effective way to meet our management objective.

Association between prostinogen (KLK15) genetic variants and prostate cancer risk and aggressiveness in Australia and a meta-analysis of GWAS data

Background: Kallikrein 15 (KLK15)/Prostinogen is a plausible candidate for prostate cancer susceptibility. Elevated KLK15 expression has been reported in prostate cancer and it has been described as an unfavorable prognostic marker for the disease. Objectives: We performed a comprehensive analysis of association of variants in the KLK15 gene with prostate cancer risk and aggressiveness by genotyping tagSNPs, as well as putative functional SNPs identified by extensive bioinformatics analysis. Methods and Data Sources: Twelve out of 22 SNPs, selected on the basis of linkage disequilibrium pattern, were analyzed in an Australian sample of 1,011 histologically verified prostate cancer cases and 1,405 ethnically matched controls. Replication was sought from two existing genome wide association studies (GWAS): the Cancer Genetic Markers of Susceptibility (CGEMS) project and a UK GWAS study. Results: Two KLK15 SNPs, rs2659053 and rs3745522, showed evidence of association (p, 0.05) but were not present on the GWAS platforms. KLK15 SNP rs2659056 was found to be associated with prostate cancer aggressiveness and showed evidence of association in a replication cohort of 5,051 patients from the UK, Australia, and the CGEMS dataset of US samples. A highly significant association with Gleason score was observed when the data was combined from these three studies with an Odds Ratio (OR) of 0.85 (95% CI = 0.77-0.93; p = 2.7610 24). The rs2659056 SNP is predicted to alter binding of the RORalpha transcription factor, which has a role in the control of cell growth and differentiation and has been suggested to control the metastatic behavior of prostate cancer cells. Conclusions: Our findings suggest a role for KLK15 genetic variation in the etiology of prostate cancer among men of European ancestry, although further studies in very large sample sets are necessary to confirm effect sizes.