Special Issue on Spatial Moment Techniques for Modelling Biological Processes

Over the last two decades, there has been an increasing awareness of, and interest in, the use of spatial moment techniques to provide insight into a range of biological and ecological processes. Models that incorporate spatial moments can be viewed as extensions of mean-field models. These mean-field models often consist of systems of classical ordinary differential equations and partial differential equations, whose derivation, at some point, hinges on the simplifying assumption that individuals in the underlying stochastic process encounter each other at a rate that is proportional to the average abundance of individuals. This assumption has several implications, the most striking of which is that mean-field models essentially neglect any impact of the spatial structure of individuals in the system. Moment dynamics models extend traditional mean-field descriptions by accounting for the dynamics of pairs, triples and higher n-tuples of individuals. This means that moment dynamics models can, to some extent, account for how the spatial structure affects the dynamics of the system in question.

Modelling the movement of interacting cell populations: A moment dynamics approach

Mathematical models describing the movement of multiple interacting subpopulations are relevant to many biological and ecological processes. Standard mean-field partial differential equation descriptions of these processes suffer from the limitation that they implicitly neglect to incorporate the impact of spatial correlations and clustering. To overcome this, we derive a moment dynamics description of a discrete stochastic process which describes the spreading of distinct interacting subpopulations. In particular, we motivate our model by mimicking the geometry of two typical cell biology experiments. Comparing the performance of the moment dynamics model with a traditional mean-field model confirms that the moment dynamics approach always outperforms the traditional mean-field approach. To provide more general insight we summarise the performance of the moment dynamics model and the traditional mean-field model over a wide range of parameter regimes. These results help distinguish between those situations where spatial correlation effects are sufficiently strong, such that a moment dynamics model is required, from other situations where spatial correlation effects are sufficiently weak, such that a traditional mean-field model is adequate.

Numerical modelling of deformation behaviour of red blood cells in microvessels using the coupled SPH-DEM method

This thesis developed an advanced computational model to investigate the motion and deformation properties of red blood cells in capillaries. The novel model is based on the meshfree particle methods and is capable of modelling the large deformation of red blood cells moving through blood vessels. The developed model was employed to simulate the deformation behaviour of healthy and malaria infected red blood cells as well as the motion of red blood cells in stenosed capillaries.

The importance of modelling heterogeneity in complex disease: application to NIMH Schizophrenia Genetics Initiative data

As for other complex diseases, linkage analyses of schizophrenia (SZ) have produced evidence for numerous chromosomal regions, with inconsistent results reported across studies. The presence of locus heterogeneity appears likely and may reduce the power of linkage analyses if homogeneity is assumed. In addition, when multiple heterogeneous datasets are pooled, inter-sample variation in the proportion of linked families (alpha) may diminish the power of the pooled sample to detect susceptibility loci, in spite of the larger sample size obtained. We compare the significance of linkage findings obtained using allele-sharing LOD scores (LOD(exp))-which assume homogeneity-and heterogeneity LOD scores (HLOD) in European American and African American NIMH SZ families. We also pool these two samples and evaluate the relative power of the LOD(exp) and two different heterogeneity statistics. One of these (HLOD-P) estimates the heterogeneity parameter alpha only in aggregate data, while the second (HLOD-S) determines alpha separately for each sample. In separate and combined data, we show consistently improved performance of HLOD scores over LOD(exp). Notably, genome-wide significant evidence for linkage is obtained at chromosome 10p in the European American sample using a recessive HLOD score. When the two samples are combined, linkage at the 10p locus also achieves genome-wide significance under HLOD-S, but not HLOD-P. Using HLOD-S, improved evidence for linkage was also obtained for a previously reported region on chromosome 15q. In linkage analyses of complex disease, power may be maximised by routinely modelling locus heterogeneity within individual datasets, even when multiple datasets are combined to form larger samples.

An explicit finite element modelling method for masonry walls under out-of-plane loading

An explicit finite element modelling method is formulated using a layered shell element to examine the behaviour of masonry walls subject to out-of-plane loading. Masonry is modelled as a homogenised material with distinct directional properties that are calibrated from datasets of a “C” shaped wall tested under pressure loading applied to its web. The predictions of the layered shell model have been validated using several out-of-plane experimental datasets reported in the literature. Profound influence of support conditions, aspect ratio, pre-compression and opening to the strength and ductility of masonry walls is exhibited from the sensitivity analyses performed using the model.

The cost-effectiveness of exercise referral schemes

Background Exercise referral schemes (ERS) aim to identify inactive adults in the primary care setting. The primary care professional refers the patient to a third party service, with this service taking responsibility for prescribing and monitoring an exercise programme tailored to the needs of the patient. This paper examines the cost-effectiveness of ERS in promoting physical activity compared with usual care in primary care setting. Methods A decision analytic model was developed to estimate the cost-effectiveness of ERS from a UK NHS perspective. The costs and outcomes of ERS were modelled over the patient's lifetime. Data were derived from a systematic review of the literature on the clinical and cost-effectiveness of ERS, and on parameter inputs in the modelling framework. Outcomes were expressed as incremental cost per quality-adjusted life-year (QALY). Deterministic and probabilistic sensitivity analyses investigated the impact of varying ERS cost and effectiveness assumptions. Sub-group analyses explored the cost-effectiveness of ERS in sedentary people with an underlying condition. Results Compared with usual care, the mean incremental lifetime cost per patient for ERS was £169 and the mean incremental QALY was 0.008, generating a base-case incremental cost-effectiveness ratio (ICER) for ERS at £20,876 per QALY in sedentary individuals without a diagnosed medical condition. There was a 51% probability that ERS was cost-effective at £20,000 per QALY and 88% probability that ERS was cost-effective at £30,000 per QALY. In sub-group analyses, cost per QALY for ERS in sedentary obese individuals was £14,618, and in sedentary hypertensives and sedentary individuals with depression the estimated cost per QALY was £12,834 and £8,414 respectively. Incremental lifetime costs and benefits associated with ERS were small, reflecting the preventative public health context of the intervention, with this resulting in estimates of cost-effectiveness that are sensitive to variations in the relative risk of becoming physically active and cost of ERS. Conclusions ERS is associated with modest increase in lifetime costs and benefits. The cost-effectiveness of ERS is highly sensitive to small changes in the effectiveness and cost of ERS and is subject to some significant uncertainty mainly due to limitations in the clinical effectiveness evidence base.

Finite element modelling of lamb wave propagation in prestress concrete and effect of the prestress force on the wave’s characteristic

In order to assess the structural reliability of bridges, an accurate and cost effective Non-Destructive Evaluation (NDE) technology is required to ensure their safe and reliable operation. Over 60% of the Australian National Highway System is prestressed concrete (PSC) bridges according to the Bureau of Transport and Communication Economics (1997). Most of the in-service bridges are more than 30 years old and may experience a heavier traffic load than their original intended level. Use of Ultrasonic waves is continuously increasing for (NDE) and Structural Health Monitoring (SHM) in civil, aerospace, electrical, mechanical applications. Ultrasonic Lamb waves are becoming more popular for NDE because it can propagate long distance and reach hidden regions with less energy loses. The purpose of this study is to numerically quantify prestress force (PSF) of (PSC) beam using the fundamental theory of acoustic-elasticity. A three-dimension finite element modelling approach is set up to perform parametric studies in order to better understand how the lamb wave propagation in PSC beam is affected by changing in the PSF level. Results from acoustic-elastic measurement on prestressed beam are presented, showing the feasibility of the lamb wave for PSF evaluation in PSC bridges.

Modelling end-of-life care practices: Factors associated with critical care nurse engagement in care provision

Objective To identify factors associated with critical care nurses’ engagement in end-of-life care practices. Methods Multivariable regression modelling was undertaken on 392 responses to an online self-report survey of end-of-life care practices and factors influencing practice by Australian critical care nurses’. Univariate general linear models were built for six end-of-life care practice areas. Results Six statistically significant (p < 0.001) models were developed: Information sharing F(3, 377) = 40.53, adjusted R2 23.8%; Environmental modification F(5, 380) = 19.55, adjusted R2 19.4%; Emotional support F(10, 366) = 12.10, adjusted R2 22.8%; Patient and family centred decision making F(8, 362) = 17.61 adjusted R2 26.4%; Symptom management F(8, 376) = 7.10, adjusted R2 11.3%; and Spiritual support F(9, 367) = 14.66, adjusted R2 24.6%. Stronger agreement with values consistent with a palliative approach, and greater support for patient and family preferences were associated with higher levels of engagement in end-of-life care practices. Higher levels of preparedness and access to opportunities for knowledge acquisition were associated with engagement in the interpersonal practices of patient and family centred decision making and emotional support. Conclusion This study provides evidence for interventions to address factors associated with nurse engagement to increase participation in all end-of-life care practice areas.

Prediction of masonry compressive behaviour using a damage mechanics inspired modelling method

Masonry under compression is affected by the properties of its constituents and their interfaces. In spite of extensive investigations of the behaviour of masonry under compression, the information in the literature cannot be regarded as comprehensive due to ongoing inventions of new generation products – for example, polymer modified thin layer mortared masonry and drystack masonry. As comprehensive experimental studies are very expensive, an analytical model inspired by damage mechanics is developed and applied to the prediction of the compressive behaviour of masonry in this paper. The model incorporates a parabolic progressively softening stress-strain curve for the units and a progressively stiffening stress-strain curve until a threshold strain for the combined mortar and the unit-mortar interfaces is reached. The model simulates the mutual constraints imposed by each of these constituents through their respective tensile and compressive behaviour and volumetric changes. The advantage of the model is that it requires only the properties of the constituents and considers masonry as a continuum and computes the average properties of the composite masonry prisms/wallettes; it does not require discretisation of prism or wallette similar to the finite element methods. The capability of the model in capturing the phenomenological behaviour of masonry with appropriate elastic response, stiffness degradation and post peak softening is presented through numerical examples. The fitting of the experimental data to the model parameters is demonstrated through calibration of some selected test data on units and mortar from the literature; the calibrated model is shown to predict the responses of the experimentally determined masonry built using the corresponding units and mortar quite well. Through a series of sensitivity studies, the model is also shown to predict the masonry strength appropriately for changes to the properties of the units and mortar, the mortar joint thickness and the ratio of the height of unit to mortar joint thickness. The unit strength is shown to affect the masonry strength significantly. Although the mortar strength has only a marginal effect, reduction in mortar joint thickness is shown to have a profound effect on the masonry strength. The results obtained from the model are compared with the various provisions in the Australian Masonry Structures Standard AS3700 (2011) and Eurocode 6.

Mathematical modelling of human corneal oxygenation and cell kinetics in corneal epithelial wound healing

Healthy transparent cornea depends upon the regulation of fluid, nutrient and oxygen transport through the tissue to sustain cell metabolism and other critical processes for normal functioning. This research considers the corneal geometry and investigates oxygen distribution using a two-dimensional Monod kinetic model, showing that previous studies make assumptions that lead to predictions of near-anoxic levels of oxygen tension in the limbal regions of the cornea. It also considers the comparison of experimental spatial and temporal data with the predictions of novel mathematical models with respect to distributed mitotic rates during corneal epithelial wound healing.

A data fusion approach of multiple maintenance data sources for real-world reliability modelling

A central tenet in the theory of reliability modelling is the quantification of the probability of asset failure. In general, reliability depends on asset age and the maintenance policy applied. Usually, failure and maintenance times are the primary inputs to reliability models. However, for many organisations, different aspects of these data are often recorded in different databases (e.g. work order notifications, event logs, condition monitoring data, and process control data). These recorded data cannot be interpreted individually, since they typically do not have all the information necessary to ascertain failure and preventive maintenance times. This paper presents a methodology for the extraction of failure and preventive maintenance times using commonly-available, real-world data sources. A text-mining approach is employed to extract keywords indicative of the source of the maintenance event. Using these keywords, a Naïve Bayes classifier is then applied to attribute each machine stoppage to one of two classes: failure or preventive. The accuracy of the algorithm is assessed and the classified failure time data are then presented. The applicability of the methodology is demonstrated on a maintenance data set from an Australian electricity company.

Use of semi-active dampers in seismic mitigation of building structures

This research provides information for providing the required seismic mitigation in building structures through the use of semi active and passive dampers. The Magneto-Rheological (MR) semi-active damper model was developed using control algorithms and integrated into seismically excited structures as a time domain function. Linear and nonlinear structure models are evaluated in real time scenarios. Research information can be used for the design and construction of earthquake safe buildings with optimally employed MR dampers and MR-passive damper combinations.

Mathematical modelling and numerical simulation of phosphine flow during grain fumigation in leaky cylindrical silos

The phosphine distribution in a cylindrical silo containing grain is predicted. A three-dimensional mathematical model, which accounts for multicomponent gas phase transport and the sorption of phosphine into the grain kernel is developed. In addition, a simple model is presented to describe the death of insects within the grain as a function of their exposure to phosphine gas. The proposed model is solved using the commercially available computational fluid dynamics (CFD) software, FLUENT, together with our own C code to customize the solver in order to incorporate the models for sorption and insect extinction. Two types of fumigation delivery are studied, namely, fan- forced from the base of the silo and tablet from the top of the silo. An analysis of the predicted phosphine distribution shows that during fan forced fumigation, the position of the leaky area is very important to the development of the gas flow field and the phosphine distribution in the silo. If the leak is in the lower section of the silo, insects that exist near the top of the silo may not be eradicated. However, the position of a leak does not affect phosphine distribution during tablet fumigation. For such fumigation in a typical silo configuration, phosphine concentrations remain low near the base of the silo. Furthermore, we find that half-life pressure test readings are not an indicator of phosphine distribution during tablet fumigation.

Recapitulation in generating spatial layouts: Representations of embryogenesis in evolutionary design modelling

The noted 19th century biologist, Ernst Haeckel, put forward the idea that the growth (ontogenesis) of an organism recapitulated the history of its evolutionary development. While this idea is defunct within biology, the idea has been promoted in areas such as education (the idea of an education being the repetition of the civilizations before). In the research presented in this paper, recapitulation is used as a metaphor within computer-aided design as a way of grouping together different generations of spatial layouts. In most CAD programs, a spatial layout is represented as a series of objects (lines, or boundary representations) that stand in as walls. The relationships between spaces are not usually explicitly stated. A representation using Lindenmayer Systems (originally designed for the purpose of modelling plant morphology) is put forward as a way of representing the morphology of a spatial layout. The aim of this research is not just to describe an individual layout, but to find representations that link together lineages of development. This representation can be used in generative design as a way of creating more meaningful layouts which have particular characteristics. The use of genetic operators (mutation and crossover) is also considered, making this representation suitable for use with genetic algorithms.

Modelling user profiles for recommender systems

Recommender systems assist users in finding what they want. The challenging issue is how to efficiently acquire user preferences or user information needs for building personalized recommender systems. This research explores the acquisition of user preferences using data taxonomy information to enhance personalized recommendations for alleviating cold-start problem. A concept hierarchy model is proposed, which provides a two-dimensional hierarchy for acquiring user preferences. The language model is also extended for the proposed hierarchy in order to generate an effective recommender algorithm. Both Amazon.com book and music datasets are used to evaluate the proposed approach, and the experimental results show that the proposed approach is promising.