Computational fluid dynamics for improved bioreactor design and 3D culture

The complex relationship between the hydrodynamic environment and surrounding tissues directly impacts on the design and production of clinically useful grafts and implants. Tissue engineers have generally seen bioreactors as 'black boxes' within which tissue engineering constructs (TECs) are cultured. It is accepted that a more detailed description of fluid mechanics and nutrient transport within process equipment can be achieved by using computational fluid dynamics (CFD) technology. This review discusses applications of CFD for tissue engineering-related bioreactors -- fluid flow processes have direct implications on cellular responses such as attachment, migration and proliferation. We conclude that CFD should be seen as an invaluable tool for analyzing and visualizing the impact of fluidic forces and stresses on cells and TECs.

Dynamics of transformation and fragmentation of composite liquid nano-particles

Recent research on particle size distributions and particle concentrations near a busy road cannot be explained by the conventional mechanisms for particle evolution of combustion aerosols. Specifically they appear to be inadequate to explain the experimental observations of particle transformation and the evolution of the total number concentration. This resulted in the development of a new mechanism based on their thermal fragmentation, for the evolution of combustion aerosol nano-particles. A complex and comprehensive pattern of evolution of combustion aerosols, involving particle fragmentation, was then proposed and justified. In that model it was suggested that thermal fragmentation occurs in aggregates of primary particles each of which contains a solid graphite/carbon core surrounded by volatile molecules bonded to the core by strong covalent bonds. Due to the presence of strong covalent bonds between the core and the volatile (frill) molecules, such primary composite particles can be regarded as solid, despite the presence of significant (possibly, dominant) volatile component. Fragmentation occurs when weak van der Waals forces between such primary particles are overcome by their thermal (Brownian) motion. In this work, the accepted concept of thermal fragmentation is advanced to determine whether fragmentation is likely in liquid composite nano-particles. It has been demonstrated that at least at some stages of evolution, combustion aerosols contain a large number of composite liquid particles containing presumably several components such as water, oil, volatile compounds, and minerals. It is possible that such composite liquid particles may also experience thermal fragmentation and thus contribute to, for example, the evolution of the total number concentration as a function of distance from the source. Therefore, the aim of this project is to examine theoretically the possibility of thermal fragmentation of composite liquid nano-particles consisting of immiscible liquid v components. The specific focus is on ternary systems which include two immiscible liquid droplets surrounded by another medium (e.g., air). The analysis shows that three different structures are possible, the complete encapsulation of one liquid by the other, partial encapsulation of the two liquids in a composite particle, and the two droplets separated from each other. The probability of thermal fragmentation of two coagulated liquid droplets is discussed and examined for different volumes of the immiscible fluids in a composite liquid particle and their surface and interfacial tensions through the determination of the Gibbs free energy difference between the coagulated and fragmented states, and comparison of this energy difference with the typical thermal energy kT. The analysis reveals that fragmentation was found to be much more likely for a partially encapsulated particle than a completely encapsulated particle. In particular, it was found that thermal fragmentation was much more likely when the volume ratio of the two liquid droplets that constitute the composite particle are very different. Conversely, when the two liquid droplets are of similar volumes, the probability of thermal fragmentation is small. It is also demonstrated that the Gibbs free energy difference between the coagulated and fragmented states is not the only important factor determining the probability of thermal fragmentation of composite liquid particles. The second essential factor is the actual structure of the composite particle. It is shown that the probability of thermal fragmentation is also strongly dependent on the distance that each of the liquid droplets should travel to reach the fragmented state. In particular, if this distance is larger than the mean free path for the considered droplets in the air, the probability of thermal fragmentation should be negligible. In particular, it follows form here that fragmentation of the composite particle in the state with complete encapsulation is highly unlikely because of the larger distance that the two droplets must travel in order to separate. The analysis of composite liquid particles with the interfacial parameters that are expected in combustion aerosols demonstrates that thermal fragmentation of these vi particles may occur, and this mechanism may play a role in the evolution of combustion aerosols. Conditions for thermal fragmentation to play a significant role (for aerosol particles other than those from motor vehicle exhaust) are determined and examined theoretically. Conditions for spontaneous transformation between the states of composite particles with complete and partial encapsulation are also examined, demonstrating the possibility of such transformation in combustion aerosols. Indeed it was shown that for some typical components found in aerosols that transformation could take place on time scales less than 20 s. The analysis showed that factors that influenced surface and interfacial tension played an important role in this transformation process. It is suggested that such transformation may, for example, result in a delayed evaporation of composite particles with significant water component, leading to observable effects in evolution of combustion aerosols (including possible local humidity maximums near a source, such as a busy road). The obtained results will be important for further development and understanding of aerosol physics and technologies, including combustion aerosols and their evolution near a source.

Expert performance in sport and the dynamics of talent development

Research on expertise, talent identification and development has tended to be mono-disciplinary, typically adopting adopting neurogenetic deterministic or environmentalist positions, with an over-riding focus on operational issues. In this paper the validity of dualist positions on sport expertise is evaluated. It is argued that, to advance understanding of expertise and talent development, a shift towards a multi-disciplinary and integrative science focus is necessary, along with the development of a comprehensive multi-disciplinary theoretical rationale. Here we elucidate dynamical systems theory as a multi-disciplinary theoretical rationale for capturing how multiple interacting constraints can shape the development of expert performers. This approach suggests that talent development programmes should eschew the notion of common optimal performance models, emphasise the individual nature of pathways to expertise, and identify the range of interacting constraints that impinge on performance potential of individual athletes, rather than evaluating current performance on physical tests referenced to group norms.

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.

Southern theory : the global dynamics of knowledge in the social sciences

Up front I am impelled to acknowledge an intellectual debt to Raewyn Connell as one of my PhD supervisors about 20 years ago and as having a lasting influence on my own sociological approach to research. One of key themes of this book is that southern theorists are rarely read in the northern hemisphere. This is not the case for Connell, however, one of Australia’s most internationally renowned scholars. The tome reads as the creative outpouring of her lifelong thirst for social science. Its main claim is that southern theory ‘has as much intellectual power as metropolitan social thought, and more political relevance’ (p. xii). A big but compelling claim, as I will explain.

GPS fault detection with IMU and aircraft dynamics

Approaches with Vertical Guidance (APV) can provide greater safety and cost savings to general aviation through accurate GPS horizontal and vertical navigation. However, GPS needs augmentation to achieve APV fault detection requirements. Aircraft Based Augmentation Systems (ABAS) fuse GPS with additional sensors at the aircraft. Typical ABAS designs assume high-quality inertial sensors with Kalman filters but these are too expensive for general aviation. Instead of using high-quality (and expensive) sensors, the purpose of this paper is to investigate augmenting GPS with a low-quality MEMS IMU and Aircraft Dynamic Model (ADM). The IMU and ADM are fused together using a multiple model fusion strategy in a bank of Extended Kalman Filters (EKF) with the Normalized Solution Separation (NSS) fault detection scheme. A tightly-coupled configuration with GPS is used and frequent GPS updates are applied to the IMU and ADM to compensate for their errors. Based upon a simulated APV approach, the performance of this architecture in detecting a GPS ramp fault is investigated showing a performance improvement over a GPS-only “snapshot” implementation of the NSS method. The effect of fusing the IMU with the ADM is evaluated by comparing a GPS-IMU-ADM EKF with a GPS-IMU EKF where a small improvement in protection levels is shown.

Dynamics of in vitro polymer degradation of polycaprolactone-based scaffolds : accelerated versus simulated physiological conditions

The increasing use of biodegradable devices in tissue engineering and regenerative medicine means it is essential to study and understand their degradation behaviour. Accelerated degradation systems aim to achieve similar degradation profiles within a shorter period of time, compared with standard conditions. However, these conditions only partially mimic the actual situation, and subsequent analyses and derived mechanisms must be treated with caution and should always be supported by actual long-term degradation data obtained under physiological conditions. Our studies revealed that polycaprolactone (PCL) and PCL-composite scaffolds degrade very differently under these different degradation conditions, whilst still undergoing hydrolysis. Molecular weight and mass loss results differ due to the different degradation pathways followed (surface degradation pathway for accelerated conditions and bulk degradation pathway for simulated physiological conditions). Crystallinity studies revealed similar patterns of recrystallization dynamics, and mechanical data indicated that the scaffolds retained their functional stability, in both instances, over the course of degradation. Ultimately, polymer degradation was shown to be chiefly governed by molecular weight, crystallinity susceptibility to hydrolysis and device architecture considerations whilst maintaining its thermodynamic equilibrium.

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

A hidden Markov model and relative entropy rate approach to vision-based dim target detection for UAV sense-and-avoid

Uninhabited aerial vehicles (UAVs) are a cutting-edge technology that is at the forefront of aviation/aerospace research and development worldwide. Many consider their current military and defence applications as just a token of their enormous potential. Unlocking and fully exploiting this potential will see UAVs in a multitude of civilian applications and routinely operating alongside piloted aircraft. The key to realising the full potential of UAVs lies in addressing a host of regulatory, public relation, and technological challenges never encountered be- fore. Aircraft collision avoidance is considered to be one of the most important issues to be addressed, given its safety critical nature. The collision avoidance problem can be roughly organised into three areas: 1) Sense; 2) Detect; and 3) Avoid. Sensing is concerned with obtaining accurate and reliable information about other aircraft in the air; detection involves identifying potential collision threats based on available information; avoidance deals with the formulation and execution of appropriate manoeuvres to maintain safe separation. This thesis tackles the detection aspect of collision avoidance, via the development of a target detection algorithm that is capable of real-time operation onboard a UAV platform. One of the key challenges of the detection problem is the need to provide early warning. This translates to detecting potential threats whilst they are still far away, when their presence is likely to be obscured and hidden by noise. Another important consideration is the choice of sensors to capture target information, which has implications for the design and practical implementation of the detection algorithm. The main contributions of the thesis are: 1) the proposal of a dim target detection algorithm combining image morphology and hidden Markov model (HMM) filtering approaches; 2) the novel use of relative entropy rate (RER) concepts for HMM filter design; 3) the characterisation of algorithm detection performance based on simulated data as well as real in-flight target image data; and 4) the demonstration of the proposed algorithm's capacity for real-time target detection. We also consider the extension of HMM filtering techniques and the application of RER concepts for target heading angle estimation. In this thesis we propose a computer-vision based detection solution, due to the commercial-off-the-shelf (COTS) availability of camera hardware and the hardware's relatively low cost, power, and size requirements. The proposed target detection algorithm adopts a two-stage processing paradigm that begins with an image enhancement pre-processing stage followed by a track-before-detect (TBD) temporal processing stage that has been shown to be effective in dim target detection. We compare the performance of two candidate morphological filters for the image pre-processing stage, and propose a multiple hidden Markov model (MHMM) filter for the TBD temporal processing stage. The role of the morphological pre-processing stage is to exploit the spatial features of potential collision threats, while the MHMM filter serves to exploit the temporal characteristics or dynamics. The problem of optimising our proposed MHMM filter has been examined in detail. Our investigation has produced a novel design process for the MHMM filter that exploits information theory and entropy related concepts. The filter design process is posed as a mini-max optimisation problem based on a joint RER cost criterion. We provide proof that this joint RER cost criterion provides a bound on the conditional mean estimate (CME) performance of our MHMM filter, and this in turn establishes a strong theoretical basis connecting our filter design process to filter performance. Through this connection we can intelligently compare and optimise candidate filter models at the design stage, rather than having to resort to time consuming Monte Carlo simulations to gauge the relative performance of candidate designs. Moreover, the underlying entropy concepts are not constrained to any particular model type. This suggests that the RER concepts established here may be generalised to provide a useful design criterion for multiple model filtering approaches outside the class of HMM filters. In this thesis we also evaluate the performance of our proposed target detection algorithm under realistic operation conditions, and give consideration to the practical deployment of the detection algorithm onboard a UAV platform. Two fixed-wing UAVs were engaged to recreate various collision-course scenarios to capture highly realistic vision (from an onboard camera perspective) of the moments leading up to a collision. Based on this collected data, our proposed detection approach was able to detect targets out to distances ranging from about 400m to 900m. These distances, (with some assumptions about closing speeds and aircraft trajectories) translate to an advanced warning ahead of impact that approaches the 12.5 second response time recommended for human pilots. Furthermore, readily available graphic processing unit (GPU) based hardware is exploited for its parallel computing capabilities to demonstrate the practical feasibility of the proposed target detection algorithm. A prototype hardware-in- the-loop system has been found to be capable of achieving data processing rates sufficient for real-time operation. There is also scope for further improvement in performance through code optimisations. Overall, our proposed image-based target detection algorithm offers UAVs a cost-effective real-time target detection capability that is a step forward in ad- dressing the collision avoidance issue that is currently one of the most significant obstacles preventing widespread civilian applications of uninhabited aircraft. We also highlight that the algorithm development process has led to the discovery of a powerful multiple HMM filtering approach and a novel RER-based multiple filter design process. The utility of our multiple HMM filtering approach and RER concepts, however, extend beyond the target detection problem. This is demonstrated by our application of HMM filters and RER concepts to a heading angle estimation problem.

Perception of affordances in multi-scale dynamics as an alternative explanation for equivalence of analogical and inferential reasoning in animals and humans

Recent claims of equivalence of animal and human reasoning are evaluated and a study of avian cognition serves as an exemplar of weaknesses in these arguments. It is argued that current research into neurobiological cognition lacks theoretical breadth to substantiate comparative analyses of cognitive function. Evaluation of a greater range of theoretical explanations is needed to verify claims of equivalence in animal and human cognition. We conclude by exemplifying how the notion of affordances in multi-scale dynamics can capture behavior attributed to processes of analogical and inferential reasoning in animals and humans.