Addressing issues in sparseness, ecological bias and formulation of the adjacency matrix in Bayesian spatio-temporal analysis of disease counts

The main objective of this PhD was to further develop Bayesian spatio-temporal models (specifically the Conditional Autoregressive (CAR) class of models), for the analysis of sparse disease outcomes such as birth defects. The motivation for the thesis arose from problems encountered when analyzing a large birth defect registry in New South Wales. The specific components and related research objectives of the thesis were developed from gaps in the literature on current formulations of the CAR model, and health service planning requirements. Data from a large probabilistically-linked database from 1990 to 2004, consisting of fields from two separate registries: the Birth Defect Registry (BDR) and Midwives Data Collection (MDC) were used in the analyses in this thesis. The main objective was split into smaller goals. The first goal was to determine how the specification of the neighbourhood weight matrix will affect the smoothing properties of the CAR model, and this is the focus of chapter 6. Secondly, I hoped to evaluate the usefulness of incorporating a zero-inflated Poisson (ZIP) component as well as a shared-component model in terms of modeling a sparse outcome, and this is carried out in chapter 7. The third goal was to identify optimal sampling and sample size schemes designed to select individual level data for a hybrid ecological spatial model, and this is done in chapter 8. Finally, I wanted to put together the earlier improvements to the CAR model, and along with demographic projections, provide forecasts for birth defects at the SLA level. Chapter 9 describes how this is done. For the first objective, I examined a series of neighbourhood weight matrices, and showed how smoothing the relative risk estimates according to similarity by an important covariate (i.e. maternal age) helped improve the model’s ability to recover the underlying risk, as compared to the traditional adjacency (specifically the Queen) method of applying weights. Next, to address the sparseness and excess zeros commonly encountered in the analysis of rare outcomes such as birth defects, I compared a few models, including an extension of the usual Poisson model to encompass excess zeros in the data. This was achieved via a mixture model, which also encompassed the shared component model to improve on the estimation of sparse counts through borrowing strength across a shared component (e.g. latent risk factor/s) with the referent outcome (caesarean section was used in this example). Using the Deviance Information Criteria (DIC), I showed how the proposed model performed better than the usual models, but only when both outcomes shared a strong spatial correlation. The next objective involved identifying the optimal sampling and sample size strategy for incorporating individual-level data with areal covariates in a hybrid study design. I performed extensive simulation studies, evaluating thirteen different sampling schemes along with variations in sample size. This was done in the context of an ecological regression model that incorporated spatial correlation in the outcomes, as well as accommodating both individual and areal measures of covariates. Using the Average Mean Squared Error (AMSE), I showed how a simple random sample of 20% of the SLAs, followed by selecting all cases in the SLAs chosen, along with an equal number of controls, provided the lowest AMSE. The final objective involved combining the improved spatio-temporal CAR model with population (i.e. women) forecasts, to provide 30-year annual estimates of birth defects at the Statistical Local Area (SLA) level in New South Wales, Australia. The projections were illustrated using sixteen different SLAs, representing the various areal measures of socio-economic status and remoteness. A sensitivity analysis of the assumptions used in the projection was also undertaken. By the end of the thesis, I will show how challenges in the spatial analysis of rare diseases such as birth defects can be addressed, by specifically formulating the neighbourhood weight matrix to smooth according to a key covariate (i.e. maternal age), incorporating a ZIP component to model excess zeros in outcomes and borrowing strength from a referent outcome (i.e. caesarean counts). An efficient strategy to sample individual-level data and sample size considerations for rare disease will also be presented. Finally, projections in birth defect categories at the SLA level will be made.

Comparison of temporal processing and motion perception in emmetropes and myopes

While spatial determinants of emmetropization have been examined extensively in animal models and spatial processing of human myopes has also been studied, there have been few studies investigating temporal aspects of emmetropization and temporal processing in human myopia. The influence of temporal light modulation on eye growth and refractive compensation has been observed in animal models and there is evidence of temporal visual processing deficits in individuals with high myopia or other pathologies. Given this, the aims of this work were to examine the relationships between myopia (i.e. degree of myopia and progression status) and temporal visual performance and to consider any temporal processing deficits in terms of the parallel retinocortical pathways. Three psychophysical studies investigating temporal processing performance were conducted in young adult myopes and non-myopes: (1) backward visual masking, (2) dot motion perception and (3) phantom contour. For each experiment there were approximately 30 young emmetropes, 30 low myopes (myopia less than 5 D) and 30 high myopes (5 to 12 D). In the backward visual masking experiment, myopes were also classified according to their progression status (30 stable myopes and 30 progressing myopes). The first study was based on the observation that the visibility of a target is reduced by a second target, termed the mask, presented quickly after the first target. Myopes were more affected by the mask when the task was biased towards the magnocellular pathway; myopes had a 25% mean reduction in performance compared with emmetropes. However, there was no difference in the effect of the mask when the task was biased towards the parvocellular system. For all test conditions, there was no significant correlation between backward visual masking task performance and either the degree of myopia or myopia progression status. The dot motion perception study measured detection thresholds for the minimum displacement of moving dots, the maximum displacement of moving dots and degree of motion coherence required to correctly determine the direction of motion. The visual processing of these tasks is dominated by the magnocellular pathway. Compared with emmetropes, high myopes had reduced ability to detect the minimum displacement of moving dots for stimuli presented at the fovea (20% higher mean threshold) and possibly at the inferior nasal retina. The minimum displacement threshold was significantly and positively correlated to myopia magnitude and axial length, and significantly and negatively correlated with retinal thickness for the inferior nasal retina. The performance of emmetropes and myopes for all the other dot motion perception tasks were similar. In the phantom contour study, the highest temporal frequency of the flickering phantom pattern at which the contour was visible was determined. Myopes had significantly lower flicker detection limits (21.8 ± 7.1 Hz) than emmetropes (25.6 ± 8.8 Hz) for tasks biased towards the magnocellular pathway for both high (99%) and low (5%) contrast stimuli. There was no difference in flicker limits for a phantom contour task biased towards the parvocellular pathway. For all phantom contour tasks, there was no significant correlation between flicker detection thresholds and magnitude of myopia. Of the psychophysical temporal tasks studied here those primarily involving processing by the magnocellular pathway revealed differences in performance of the refractive error groups. While there are a number of interpretations for this data, this suggests that there may be a temporal processing deficit in some myopes that is selective for the magnocellular system. The minimum displacement dot motion perception task appears the most sensitive test, of those studied, for investigating changes in visual temporal processing in myopia. Data from the visual masking and phantom contour tasks suggest that the alterations to temporal processing occur at an early stage of myopia development. In addition, the link between increased minimum displacement threshold and decreasing retinal thickness suggests that there is a retinal component to the observed modifications in temporal processing.

A critical analysis of sperm donation practices : the personal and social effects of disrupting the unity of biological and social relatedness for the offspring

This thesis critically analyses sperm donation practices from a child-centred perspective. It examines the effects, both personal and social, of disrupting the unity of biological and social relatedness in families affected by donor conception. It examines how disruption is facilitated by a process of mediation which is detailed using a model provided by Sunderland (2002). This model identifies mediating movements - alienation, translation, re-contextualisation and absorption - which help to explain the powerful and dominating material, and social and political processes which occur in biotechnology, or in reproductive technology in this case. The understanding of such movements and mediation of meanings is inspired by the complementary work of Silverstone (1999) and Sunderland. This model allows for a more critical appreciation of the movement of meaning from previously inalienable aspects of life to alienable products through biotechnology (Sunderland, 2002). Once this mediation in donor conception is subjected to critical examination here, it is then approached from different angles of investigation. The thesis posits that two conflicting notions of the self are being applied to fertility-frustrated adults and the offspring of reproductive interventions. Adults using reproductive interventions receive support to maximise their genetic continuity, but in so doing they create and dismiss the corresponding genetic discontinuity produced for the offspring. The offspring’s kinship and identity are then framed through an experimental postmodernist notion, presenting them as social rather than innate constructs. The adults using the reproductive intervention, on the other hand, have their identity and kinship continuity framed and supported as normative, innate, and based on genetic connection. This use of shifting frameworks is presented as unjust and harmful, creating double standards and a corrosion of kinship values, connection and intelligibility between generations; indeed, it is put forward as adult-centric. The analysis of other forms of human kinship dislocation provided by this thesis explores an under-utilised resource which is used to counter the commonly held opinion that any disruption of social and genetic relatedness for donor offspring is insignificant. The experiences of adoption and the stolen generations are used to inform understanding of the personal and social effects of such kinship disruption and potential reunion for donor offspring. These examples, along with laws governing international human rights, further strengthen the appeal here for normative principles and protections based on collective knowledge and standards to be applied to children of reproductive technology. The thesis presents the argument that the framing and regulation of reproductive technology is excessively influenced by industry providers and users. The interests of these parties collide with and corrode any accurate assessments and protections afforded to the children of reproductive technology. The thesis seeks to counter such encroachments and concludes by presenting these protections, frameworks, and human experiences as resources which can help to address the problems created for the offspring of such reproductive interventions, thereby illustrating why these reproductive interventions should be discontinued.

Temporal-based support vector machines for facial expression recognition

When classifying a signal, ideally we want our classifier to trigger a large response when it encounters a positive example and have little to no response for all other examples. Unfortunately in practice this does not occur with responses fluctuating, often causing false alarms. There exists a myriad of reasons why this is the case, most notably not incorporating the dynamics of the signal into the classification. In facial expression recognition, this has been highlighted as one major research question. In this paper we present a novel technique which incorporates the dynamics of the signal which can produce a strong response when the peak expression is found and essentially suppresses all other responses as much as possible. We conducted preliminary experiments on the extended Cohn-Kanade (CK+) database which shows its benefits. The ability to automatically and accurately recognize facial expressions of drivers is highly relevant to the automobile. For example, the early recognition of “surprise” could indicate that an accident is about to occur; and various safeguards could immediately be deployed to avoid or minimize injury and damage. In this paper, we conducted initial experiments on the extended Cohn-Kanade (CK+) database which shows its benefits.

Dealing with temporal inconsistency in automated computer forensic profiling

Computer profiling is the automated forensic examination of a computer system in order to provide a human investigator with a characterisation of the activities that have taken place on that system. As part of this process, the logical components of the computer system – components such as users, files and applications - are enumerated and the relationships between them discovered and reported. This information is enriched with traces of historical activity drawn from system logs and from evidence of events found in the computer file system. A potential problem with the use of such information is that some of it may be inconsistent and contradictory thus compromising its value. This work examines the impact of temporal inconsistency in such information and discusses two types of temporal inconsistency that may arise – inconsistency arising out of the normal errant behaviour of a computer system, and inconsistency arising out of deliberate tampering by a suspect – and techniques for dealing with inconsistencies of the latter kind. We examine the impact of deliberate tampering through experiments conducted with prototype computer profiling software. Based on the results of these experiments, we discuss techniques which can be employed in computer profiling to deal with such temporal inconsistencies.

Description and evaluation of a Newton-based electronic appetite rating system for temporal tracking of appetite in human subjects

This study assessed the reliability and validity of a palm-top-based electronic appetite rating system (EARS) in relation to the traditional paper and pen method. Twenty healthy subjects [10 male (M) and 10 female (F)] — mean age M=31 years (S.D.=8), F=27 years (S.D.=5); mean BMI M=24 (S.D.=2), F=21 (S.D.=5) — participated in a 4-day protocol. Measurements were made on days 1 and 4. Subjects were given paper and an EARS to log hourly subjective motivation to eat during waking hours. Food intake and meal times were fixed. Subjects were given a maintenance diet (comprising 40% fat, 47% carbohydrate and 13% protein by energy) calculated at 1.6×Resting Metabolic Rate (RMR), as three isoenergetic meals. Bland and Altman's test for bias between two measurement techniques found significant differences between EARS and paper and pen for two of eight responses (hunger and fullness). Regression analysis confirmed that there were no day, sex or order effects between ratings obtained using either technique. For 15 subjects, there was no significant difference between results, with a linear relationship between the two methods that explained most of the variance (r2 ranged from 62.6 to 98.6). The slope for all subjects was less than 1, which was partly explained by a tendency for bias at the extreme end of results on the EARS technique. These data suggest that the EARS is a useful and reliable technique for real-time data collection in appetite research but that it should not be used interchangeably with paper and pen techniques.

The use of visual analogue scales to assess motivation to eat in human subjects: a review of their reliability and validity with an evaluation of new hand-held computerized stsytems for temporal tracking of appetite ratings.

This present paper reviews the reliability and validity of visual analogue scales (VAS) in terms of (1) their ability to predict feeding behaviour, (2) their sensitivity to experimental manipulations, and (3) their reproducibility. VAS correlate with, but do not reliably predict, energy intake to the extent that they could be used as a proxy of energy intake. They do predict meal initiation in subjects eating their normal diets in their normal environment. Under laboratory conditions, subjectively rated motivation to eat using VAS is sensitive to experimental manipulations and has been found to be reproducible in relation to those experimental regimens. Other work has found them not to be reproducible in relation to repeated protocols. On balance, it would appear, in as much as it is possible to quantify, that VAS exhibit a good degree of within-subject reliability and validity in that they predict with reasonable certainty, meal initiation and amount eaten, and are sensitive to experimental manipulations. This reliability and validity appears more pronounced under the controlled (but more arti®cial) conditions of the laboratory where the signal : noise ratio in experiments appears to be elevated relative to real life. It appears that VAS are best used in within-subject, repeated-measures designs where the effect of different treatments can be compared under similar circumstances. They are best used in conjunction with other measures (e.g. feeding behaviour, changes in plasma metabolites) rather than as proxies for these variables. New hand-held electronic appetite rating systems (EARS) have been developed to increase reliability of data capture and decrease investigator workload. Recent studies have compared these with traditional pen and paper (P&P) VAS. The EARS have been found to be sensitive to experimental manipulations and reproducible relative to P&P. However, subjects appear to exhibit a signi®cantly more constrained use of the scale when using the EARS relative to the P&P. For this reason it is recommended that the two techniques are not used interchangeably

Improving reflective writing in higher education : A social semiotic perspective

Reflective skills are widely regarded as a means of improving students’ lifelong learning and professional practice in higher education (Rogers 2001). While the value of reflective practice is widely accepted in educational circles, a critical issue is that reflective writing is complex, and has high rhetorical demands, making it difficult to master unless it is taught in an explicit and systematic way. This paper argues that a functional-semantic approach to language (Eggins 2004), based on Halliday’s (1978) systemic functional linguistics can be used to develop a shared language to explicitly teach and assess reflective writing in higher education courses. The paper outlines key theories and scales of reflection, and then uses systemic functional linguistics to develop a social semiotic model for reflective writing. Examples of reflective writing are analysed to show how such a model can be used explicitly to improve the reflective writing skills of higher education students.

Petri net modeling of spatial and temporal constraints in track allocation problem at railway stations

The track allocation problem (TAP) at a multi-track, multi-platform mainline railway station is defined by the station track layout and service timetable, which implies combinations of spatial and temporal conflicts. Feasible solutions are available from either traditional planning or advanced intelligent searching methods and their evaluations with respect to operational requirements are essential for the operators. To facilitate thorough analysis, a timed Coloured Petri Nets (CPN) model is presented here to encapsulate the inter-relationships of the spatial and temporal constraints in the TAP.

Fixed-wing attitude estimation using temporal tracking of the horizon and optical flow

In this paper, a method has been developed for estimating pitch angle, roll angle and aircraft body rates based on horizon detection and temporal tracking using a forward-looking camera, without assistance from other sensors. Using an image processing front-end, we select several lines in an image that may or may not correspond to the true horizon. The optical flow at each candidate line is calculated, which may be used to measure the body rates of the aircraft. Using an Extended Kalman Filter (EKF), the aircraft state is propagated using a motion model and a candidate horizon line is associated using a statistical test based on the optical flow measurements and the location of the horizon. Once associated, the selected horizon line, along with the associated optical flow, is used as a measurement to the EKF. To test the accuracy of the algorithm, two flights were conducted, one using a highly dynamic Uninhabited Airborne Vehicle (UAV) in clear flight conditions and the other in a human-piloted Cessna 172 in conditions where the horizon was partially obscured by terrain, haze and smoke. The UAV flight resulted in pitch and roll error standard deviations of 0.42◦ and 0.71◦ respectively when compared with a truth attitude source. The Cessna flight resulted in pitch and roll error standard deviations of 1.79◦ and 1.75◦ respectively. The benefits of selecting and tracking the horizon using a motion model and optical flow rather than naively relying on the image processing front-end is also demonstrated.

Temporal tissue patterns in bone healing of sheep

Secondary fracture healing in long bones leads to the successive formation of intricate patterns of tissues in the newly formed callus. The main aim of this work was to quantitatively describe the topology of these tissue patterns at different stages of the healing process and to generate averaged images of tissue distribution. This averaging procedure was based on stained histological sections (2, 3, 6, and 9 weeks post-operatively) of 64 sheep with a 3 mm tibial mid-shaft osteotomy, stabilized either with a rigid or a semi-rigid external fixator. Before averaging, histological images were sorted for topology according to six identified tissue patterns. The averaged images were obtained for both fixation types and the lateral and medial side separately. For each case, the result of the averaging procedure was a collection of six images characterizing quantitatively the progression of the healing process. In addition, quantified descriptions of the newly formed cartilage and the bone area fractions (BA/TA) of the bony callus are presented. For all cases, a linear increase in the BA/TA of the bony callus was observed. The slope was greatest in the case of the most rigid stabilization and lowest in the case of the least stiff. This topological description of the progression of bone healing will allow quantitative validation (or falsification) of current mechano-biological theories.