Approximate Bayesian computation using indirect inference

We present a novel approach for developing summary statistics for use in approximate Bayesian computation (ABC) algorithms by using indirect inference. ABC methods are useful for posterior inference in the presence of an intractable likelihood function. In the indirect inference approach to ABC the parameters of an auxiliary model fitted to the data become the summary statistics. Although applicable to any ABC technique, we embed this approach within a sequential Monte Carlo algorithm that is completely adaptive and requires very little tuning. This methodological development was motivated by an application involving data on macroparasite population evolution modelled by a trivariate stochastic process for which there is no tractable likelihood function. The auxiliary model here is based on a beta–binomial distribution. The main objective of the analysis is to determine which parameters of the stochastic model are estimable from the observed data on mature parasite worms.

Variability of input parameters related to pollutants build-up in stormwater quality modelling

The variability of input parameters is the most important source of overall model uncertainty. Therefore, an in-depth understanding of the variability is essential for uncertainty analysis of stormwater quality model outputs. This paper presents the outcomes of a research study which investigated the variability of pollutants build-up characteristics on road surfaces in residential, commercial and industrial land uses. It was found that build-up characteristics vary highly even within the same land use. Additionally, industrial land use showed relatively higher variability of maximum build-up, build-up rate and particle size distribution, whilst the commercial land use displayed a relatively higher variability of pollutant-solid ratio. Among the various build-up parameters analysed, D50 (volume-median-diameter) displayed the relatively highest variability for all three land uses.

Hierarchical Bayesian models for estimating the extent of plant pest invasions

Plant biosecurity requires statistical tools to interpret field surveillance data in order to manage pest incursions that threaten crop production and trade. Ultimately, management decisions need to be based on the probability that an area is infested or free of a pest. Current informal approaches to delimiting pest extent rely upon expert ecological interpretation of presence / absence data over space and time. Hierarchical Bayesian models provide a cohesive statistical framework that can formally integrate the available information on both pest ecology and data. The overarching method involves constructing an observation model for the surveillance data, conditional on the hidden extent of the pest and uncertain detection sensitivity. The extent of the pest is then modelled as a dynamic invasion process that includes uncertainty in ecological parameters. Modelling approaches to assimilate this information are explored through case studies on spiralling whitefly, Aleurodicus dispersus and red banded mango caterpillar, Deanolis sublimbalis. Markov chain Monte Carlo simulation is used to estimate the probable extent of pests, given the observation and process model conditioned by surveillance data. Statistical methods, based on time-to-event models, are developed to apply hierarchical Bayesian models to early detection programs and to demonstrate area freedom from pests. The value of early detection surveillance programs is demonstrated through an application to interpret surveillance data for exotic plant pests with uncertain spread rates. The model suggests that typical early detection programs provide a moderate reduction in the probability of an area being infested but a dramatic reduction in the expected area of incursions at a given time. Estimates of spiralling whitefly extent are examined at local, district and state-wide scales. The local model estimates the rate of natural spread and the influence of host architecture, host suitability and inspector efficiency. These parameter estimates can support the development of robust surveillance programs. Hierarchical Bayesian models for the human-mediated spread of spiralling whitefly are developed for the colonisation of discrete cells connected by a modified gravity model. By estimating dispersal parameters, the model can be used to predict the extent of the pest over time. An extended model predicts the climate restricted distribution of the pest in Queensland. These novel human-mediated movement models are well suited to demonstrating area freedom at coarse spatio-temporal scales. At finer scales, and in the presence of ecological complexity, exploratory models are developed to investigate the capacity for surveillance information to estimate the extent of red banded mango caterpillar. It is apparent that excessive uncertainty about observation and ecological parameters can impose limits on inference at the scales required for effective management of response programs. The thesis contributes novel statistical approaches to estimating the extent of pests and develops applications to assist decision-making across a range of plant biosecurity surveillance activities. Hierarchical Bayesian modelling is demonstrated as both a useful analytical tool for estimating pest extent and a natural investigative paradigm for developing and focussing biosecurity programs.

Early childhood teachers' mathematical content knowledge

The process of becoming numerate begins in the early years. According to Vygotskian theory (1978), teachers are More Knowledgeable Others who provide and support learning experiences that influence children’s mathematical learning. This paper reports on research that investigates three early childhood teachers mathematics content knowledge. An exploratory, single case study utilised data collected from interviews, and email correspondence to investigate the teachers’ mathematics content knowledge. The data was reviewed according to three analytical strategies: content analysis, pattern matching, and comparative analysis. Findings indicated there was variation in teachers’ content knowledge across the five mathematical strands and that teachers might not demonstrate the depth of content knowledge that is expected of four year specially trained early years’ teachers. A significant factor that appeared to influence these teachers’ content knowledge was their teaching experience. Therefore, an avenue for future research is the investigation of factors that influence teachers’ content numeracy knowledge.

Non-invasive assessment of tear film surface quality

The tear film plays an important role preserving the health of the ocular surface and maintaining the optimal refractive power of the cornea. Moreover dry eye syndrome is one of the most commonly reported eye health problems. This syndrome is caused by abnormalities in the properties of the tear film. Current clinical tools to assess the tear film properties have shown certain limitations. The traditional invasive methods for the assessment of tear film quality, which are used by most clinicians, have been criticized for the lack of reliability and/or repeatability. A range of non-invasive methods of tear assessment have been investigated, but also present limitations. Hence no “gold standard” test is currently available to assess the tear film integrity. Therefore, improving techniques for the assessment of the tear film quality is of clinical significance and the main motivation for the work described in this thesis. In this study the tear film surface quality (TFSQ) changes were investigated by means of high-speed videokeratoscopy (HSV). In this technique, a set of concentric rings formed in an illuminated cone or a bowl is projected on the anterior cornea and their reflection from the ocular surface imaged on a charge-coupled device (CCD). The reflection of the light is produced in the outer most layer of the cornea, the tear film. Hence, when the tear film is smooth the reflected image presents a well structure pattern. In contrast, when the tear film surface presents irregularities, the pattern also becomes irregular due to the light scatter and deviation of the reflected light. The videokeratoscope provides an estimate of the corneal topography associated with each Placido disk image. Topographical estimates, which have been used in the past to quantify tear film changes, may not always be suitable for the evaluation of all the dynamic phases of the tear film. However the Placido disk image itself, which contains the reflected pattern, may be more appropriate to assess the tear film dynamics. A set of novel routines have been purposely developed to quantify the changes of the reflected pattern and to extract a time series estimate of the TFSQ from the video recording. The routine extracts from each frame of the video recording a maximized area of analysis. In this area a metric of the TFSQ is calculated. Initially two metrics based on the Gabor filter and Gaussian gradient-based techniques, were used to quantify the consistency of the pattern’s local orientation as a metric of TFSQ. These metrics have helped to demonstrate the applicability of HSV to assess the tear film, and the influence of contact lens wear on TFSQ. The results suggest that the dynamic-area analysis method of HSV was able to distinguish and quantify the subtle, but systematic degradation of tear film surface quality in the inter-blink interval in contact lens wear. It was also able to clearly show a difference between bare eye and contact lens wearing conditions. Thus, the HSV method appears to be a useful technique for quantitatively investigating the effects of contact lens wear on the TFSQ. Subsequently a larger clinical study was conducted to perform a comparison between HSV and two other non-invasive techniques, lateral shearing interferometry (LSI) and dynamic wavefront sensing (DWS). Of these non-invasive techniques, the HSV appeared to be the most precise method for measuring TFSQ, by virtue of its lower coefficient of variation. While the LSI appears to be the most sensitive method for analyzing the tear build-up time (TBUT). The capability of each of the non-invasive methods to discriminate dry eye from normal subjects was also investigated. The receiver operating characteristic (ROC) curves were calculated to assess the ability of each method to predict dry eye syndrome. The LSI technique gave the best results under both natural blinking conditions and in suppressed blinking conditions, which was closely followed by HSV. The DWS did not perform as well as LSI or HSV. The main limitation of the HSV technique, which was identified during the former clinical study, was the lack of the sensitivity to quantify the build-up/formation phase of the tear film cycle. For that reason an extra metric based on image transformation and block processing was proposed. In this metric, the area of analysis was transformed from Cartesian to Polar coordinates, converting the concentric circles pattern into a quasi-straight lines image in which a block statistics value was extracted. This metric has shown better sensitivity under low pattern disturbance as well as has improved the performance of the ROC curves. Additionally a theoretical study, based on ray-tracing techniques and topographical models of the tear film, was proposed to fully comprehend the HSV measurement and the instrument’s potential limitations. Of special interested was the assessment of the instrument’s sensitivity under subtle topographic changes. The theoretical simulations have helped to provide some understanding on the tear film dynamics, for instance the model extracted for the build-up phase has helped to provide some insight into the dynamics during this initial phase. Finally some aspects of the mathematical modeling of TFSQ time series have been reported in this thesis. Over the years, different functions have been used to model the time series as well as to extract the key clinical parameters (i.e., timing). Unfortunately those techniques to model the tear film time series do not simultaneously consider the underlying physiological mechanism and the parameter extraction methods. A set of guidelines are proposed to meet both criteria. Special attention was given to a commonly used fit, the polynomial function, and considerations to select the appropriate model order to ensure the true derivative of the signal is accurately represented. The work described in this thesis has shown the potential of using high-speed videokeratoscopy to assess tear film surface quality. A set of novel image and signal processing techniques have been proposed to quantify different aspects of the tear film assessment, analysis and modeling. The dynamic-area HSV has shown good performance in a broad range of conditions (i.e., contact lens, normal and dry eye subjects). As a result, this technique could be a useful clinical tool to assess tear film surface quality in the future.

Influence of parameters on the heterogeneous photocatalytic degradation of pesticides and phenolic contaminants in wastewater : a short review

In recent years, the application of heterogeneous photocatalytic water purification process has gained wide attention due to its effectiveness in degrading and mineralizing the recalcitrant organic compounds as well as the possibility of utilizing the solar UV and visible light spectrum. This paper aims to review and summarize the recently published works on the titanium dioxide (TiO2) photocatalytic oxidation of pesticides and phenolic compounds, predominant in storm and waste water effluents. The effect of various operating parameters on the photocatalytic degradation of pesticides and phenols are discussed. Results reported here suggested that the photocatalytic degradation of organic compounds depends on the type of photocatalyst and composition, light intensity, initial substrate concentration, amount of catalyst, pH of the reaction medium, ionic components in water, solvent types, oxidizing agents/electron acceptors, catalyst application mode, and calcinations temperature in water environment. A substantial amount of research has focused on the enhancement of TiO2 photocatalysis by modification with metal, non-metal and ion doping. Recent developments in TiO2 photocatalysis for the degradation of various pesticides and phenols are also highlighted in this review. It is evident from the literature survey that photocatalysis has shown good potential for the removal of various organic pollutants. However, still there is a need to find out the practical utility of this technique on commercial scale.

A mathematical model of chlamydial infection incorporating movement of chlamydial particles

We present a spatiotemporal mathematical model of chlamydial infection, host immune response and spatial movement of infectious particles. The re- sulting partial differential equations model both the dynamics of the infection and changes in infection profile observed spatially along the length of the host genital tract. This model advances previous chlamydia modelling by incorporating spatial change, which we also demonstrate to be essential when the timescale for movement of infectious particles is equal to, or shorter than, the developmental cycle timescale. Numerical solutions and model analysis are carried out, and we present a hypothesis regarding the potential for treatment and prevention of infection by increasing chlamydial particle motility.

Towards a model for the analysis and description of mathematical knowledge and understanding

Mathematics education literature has called for an abandonment of ontological and epistemological ideologies that have often divided theory-based practice. Instead, a consilience of theories has been sought which would leverage the strengths of each learning theory and so positively impact upon contemporary educational practice. This research activity is based upon Popper’s notion of three knowledge worlds which differentiates the knowledge shared in a community from the personal knowledge of the individual, and Bereiter’s characterisation of understanding as the individual’s relationship to tool-like knowledge. Using these notions, a re-conceptualisation of knowledge and understanding and a subsequent re-consideration of learning theories are proposed as a way to address the challenge set by literature. Referred to as the alternative theoretical framework, the proposed theory accounts for the scaffolded transformation of each individual’s unique understanding, whilst acknowledging the existence of a body of domain knowledge shared amongst participants in a scientific community of practice. The alternative theoretical framework is embodied within an operational model that is accompanied by a visual nomenclature with which to describe consensually developed shared knowledge and personal understanding. This research activity has sought to iteratively evaluate this proposed theory through the practical application of the operational model and visual nomenclature to the domain of early-number counting, addition and subtraction. This domain of mathematical knowledge has been comprehensively analysed and described. Through this process, the viability of the proposed theory as a tool with which to discuss and thus improve the knowledge and understanding with the domain of mathematics has been validated. Putting of the proposed theory into practice has lead to the theory’s refinement and the subsequent achievement of a solid theoretical base for the future development of educational tools to support teaching and learning practice, including computer-mediated learning environments. Such future activity, using the proposed theory, will advance contemporary mathematics educational practice by bringing together the strengths of cognitivist, constructivist and post-constructivist learning theories.

Does sea-level rise have an impact on saltwater intrusion?

Climate change effects are expected to substantially raise the average sea level. It is widely assumed that this raise will have a severe adverse impact on saltwater intrusion processes in coastal aquifers. In this study we hypothesize that a natural mechanism, identified as the “lifting process” has the potential to mitigate or in some cases completely reverse the adverse intrusion effects induced by sea-level rise. A detailed numerical study using the MODFLOW-family computer code SEAWAT, was completed to test this hypothesis and to understand the effects of this lifting process in both confined and unconfined systems. Our conceptual simulation results show that if the ambient recharge remains constant, the sea-level rise will have no long-term impact (i.e., it will not affect the steady-state salt wedge) on confined aquifers. Our transient confined flow simulations show a self-reversal mechanism where the wedge which will initially intrude into the formation due to the sea-level rise would be naturally driven back to the original position. In unconfined systems, the lifting process would have a lesser influence due to changes in the value of effective transmissivity. A detailed sensitivity analysis was also completed to understand the sensitivity of this self-reversal effect to various aquifer parameters.

Latent degradation indicators estimation and prediction : a Monte Carlo approach

Asset health inspections can produce two types of indicators: (1) direct indicators (e.g. the thickness of a brake pad, and the crack depth on a gear) which directly relate to a failure mechanism; and (2) indirect indicators (e.g. the indicators extracted from vibration signals and oil analysis data) which can only partially reveal a failure mechanism. While direct indicators enable more precise references to asset health condition, they are often more difficult to obtain than indirect indicators. The state space model provides an efficient approach to estimating direct indicators by using indirect indicators. However, existing state space models to estimate direct indicators largely depend on assumptions such as, discrete time, discrete state, linearity, and Gaussianity. The discrete time assumption requires fixed inspection intervals. The discrete state assumption entails discretising continuous degradation indicators, which often introduces additional errors. The linear and Gaussian assumptions are not consistent with nonlinear and irreversible degradation processes in most engineering assets. This paper proposes a state space model without these assumptions. Monte Carlo-based algorithms are developed to estimate the model parameters and the remaining useful life. These algorithms are evaluated for performance using numerical simulations through MATLAB. The result shows that both the parameters and the remaining useful life are estimated accurately. Finally, the new state space model is used to process vibration and crack depth data from an accelerated test of a gearbox. During this application, the new state space model shows a better fitness result than the state space model with linear and Gaussian assumption.

Experimental investigation on extruded snack products from rice and Mung bean : optimization of parameters

Experiments were undertaken to study effect of initial conditions on the expansion ratio of two grains in a laboratory scale, single speed, single screw extruder at Naresuan University, Thailand. Jasmine rice and Mung bean were used as the material. Three different initial moisture contents were adjusted for the grains and classified them into three groups according to particle sizes. Mesh sizes used are 12 and 14. Expansion ratio was measured at a constant barrel temperature of 190oC. Response surface methodology was used to obtain optimum conditions between moisture content and particle size of the materials concerned.

Analysis of micro-structural changes and measurement of their parameters of a food material

Food microstructure represents the way their elements arrangement and their interaction. Researchers in this field benefit from identifying new methods of examination of the microstructure and analysing the images. Experiments were undertaken to study micro-structural changes of food material during drying. Micro-structural images were obtained for potato samples of cubical shape at different moisture contents during drying using scanning electron microscopy. Physical parameters such as cell wall perimeter, and area were calculated using an image identification algorithm, based on edge detection and morphological operators. The algorithm was developed using Matlab.

Application of an optimisation algorithm to configure an internal fixation device

Fractures of long bones are sometimes treated using various types of fracture fixation devices including internal plate fixators. These are specialised plates which are used to bridge the fracture gap(s) whilst anatomically aligning the bone fragments. The plate is secured in position by screws. The aim of such a device is to support and promote the natural healing of the bone. When using an internal fixation device, it is necessary for the clinician to decide upon many parameters, for example, the type of plate and where to position it; how many and where to position the screws. While there have been a number of experimental and computational studies conducted regarding the configuration of screws in the literature, there is still inadequate information available concerning the influence of screw configuration on fracture healing. Because screw configuration influences the amount of flexibility at the area of fracture, it has a direct influence on the fracture healing process. Therefore, it is important that the chosen screw configuration does not inhibit the healing process. In addition to the impact on the fracture healing process, screw configuration plays an important role in the distribution of stresses in the plate due to the applied loads. A plate that experiences high stresses is prone to early failure. Hence, the screw configuration used should not encourage the occurrence of high stresses. This project develops a computational program in Fortran programming language to perform mathematical optimisation to determine the screw configuration of an internal fixation device within constraints of interfragmentary movement by minimising the corresponding stress in the plate. Thus, the optimal solution suggests the positioning and number of screws which satisfies the predefined constraints of interfragmentary movements. For a set of screw configurations the interfragmentary displacement and the stress occurring in the plate were calculated by the Finite Element Method. The screw configurations were iteratively changed and each time the corresponding interfragmentary displacements were compared with predefined constraints. Additionally, the corresponding stress was compared with the previously calculated stress value to determine if there was a reduction. These processes were continued until an optimal solution was achieved. The optimisation program has been shown to successfully predict the optimal screw configuration in two cases. The first case was a simplified bone construct whereby the screw configuration solution was comparable with those recommended in biomechanical literature. The second case was a femoral construct, of which the resultant screw configuration was shown to be similar to those used in clinical cases. The optimisation method and programming developed in this study has shown that it has potential to be used for further investigations with the improvement of optimisation criteria and the efficiency of the program.