Model round-trip engineering

In the quest for shorter time-to-market, higher quality and reduced cost, model-driven software development has emerged as a promising approach to software engineering. The central idea is to promote models to first-class citizens in the development process. Starting from a set of very abstract models in the early stage of the development, they are refined into more concrete models and finally, as a last step, into code. As early phases of development focus on different concepts compared to later stages, various modelling languages are employed to most accurately capture the concepts and relations under discussion. In light of this refinement process, translating between modelling languages becomes a time-consuming and error-prone necessity. This is remedied by model transformations providing support for reusing and automating recurring translation efforts. These transformations typically can only be used to translate a source model into a target model, but not vice versa. This poses a problem if the target model is subject to change. In this case the models get out of sync and therefore do not constitute a coherent description of the software system anymore, leading to erroneous results in later stages. This is a serious threat to the promised benefits of quality, cost-saving, and time-to-market. Therefore, providing a means to restore synchronisation after changes to models is crucial if the model-driven vision is to be realised. This process of reflecting changes made to a target model back to the source model is commonly known as Round-Trip Engineering (RTE). While there are a number of approaches to this problem, they impose restrictions on the nature of the model transformation. Typically, in order for a transformation to be reversed, for every change to the target model there must be exactly one change to the source model. While this makes synchronisation relatively “easy”, it is ill-suited for many practically relevant transformations as they do not have this one-to-one character. To overcome these issues and to provide a more general approach to RTE, this thesis puts forward an approach in two stages. First, a formal understanding of model synchronisation on the basis of non-injective transformations (where a number of different source models can correspond to the same target model) is established. Second, detailed techniques are devised that allow the implementation of this understanding of synchronisation. A formal underpinning for these techniques is drawn from abductive logic reasoning, which allows the inference of explanations from an observation in the context of a background theory. As non-injective transformations are the subject of this research, there might be a number of changes to the source model that all equally reflect a certain target model change. To help guide the procedure in finding “good” source changes, model metrics and heuristics are investigated. Combining abductive reasoning with best-first search and a “suitable” heuristic enables efficient computation of a number of “good” source changes. With this procedure Round-Trip Engineering of non-injective transformations can be supported.

Identification of reduced models of power system areas using phasor measurement units

In this paper an approach is presented for identification of a reduced model for coherent areas in power systems using phasor measurement units to represent the inter-area oscillations of the system. The generators which are coherent in a wide range of operating conditions form the areas in power systems and the reduced model is obtained by representing each area by an equivalent machine. The reduced nonlinear model is then identified based on the data obtained from measurement units. The simulation is performed on three test systems and the obtained results show high accuracy of identification process.

Dynamic equivalent state estimation for multi-area power systems with synchronized phasor measurement units

This paper proposes a new approach for state estimation of angles and frequencies of equivalent areas in large power systems with synchronized phasor measurement units. Defining coherent generators and their correspondent areas, generators are aggregated and system reduction is performed in each area of inter-connected power systems. The structure of the reduced system is obtained based on the characteristics of the reduced linear model and measurement data to form the non-linear model of the reduced system. Then a Kalman estimator is designed for the reduced system to provide an equivalent dynamic system state estimation using the synchronized phasor measurement data. The method is simulated on two test systems to evaluate the feasibility of the proposed method.

Post-transcriptional regulation in the nucleus and cytoplasm: study of mean time to threshold (MTT) and narrow escape problem

Messenger RNAs (mRNAs) can be repressed and degraded by small non-coding RNA molecules. In this paper, we formulate a coarsegrained Markov-chain description of the post-transcriptional regulation of mRNAs by either small interfering RNAs (siRNAs) or microRNAs (miRNAs). We calculate the probability of an mRNA escaping from its domain before it is repressed by siRNAs/miRNAs via cal- culation of the mean time to threshold: when the number of bound siRNAs/miRNAs exceeds a certain threshold value, the mRNA is irreversibly repressed. In some cases,the analysis can be reduced to counting certain paths in a reduced Markov model. We obtain explicit expressions when the small RNA bind irreversibly to the mRNA and we also discuss the reversible binding case. We apply our models to the study of RNA interference in the nucleus, examining the probability of mRNAs escaping via small nuclear pores before being degraded by siRNAs. Using the same modelling framework, we further investigate the effect of small, decoy RNAs (decoys) on the process of post-transcriptional regulation, by studying regulation of the tumor suppressor gene, PTEN : decoys are able to block binding sites on PTEN mRNAs, thereby educing the number of sites available to siRNAs/miRNAs and helping to protect it from repression. We calculate the probability of a cytoplasmic PTEN mRNA translocating to the endoplasmic reticulum before being repressed by miRNAs. We support our results with stochastic simulations

Variational Bayes and the reduced dependence approximation for the autologistic model on an irregular grid with applications

Discrete Markov random field models provide a natural framework for representing images or spatial datasets. They model the spatial association present while providing a convenient Markovian dependency structure and strong edge-preservation properties. However, parameter estimation for discrete Markov random field models is difficult due to the complex form of the associated normalizing constant for the likelihood function. For large lattices, the reduced dependence approximation to the normalizing constant is based on the concept of performing computationally efficient and feasible forward recursions on smaller sublattices which are then suitably combined to estimate the constant for the whole lattice. We present an efficient computational extension of the forward recursion approach for the autologistic model to lattices that have an irregularly shaped boundary and which may contain regions with no data; these lattices are typical in applications. Consequently, we also extend the reduced dependence approximation to these scenarios enabling us to implement a practical and efficient non-simulation based approach for spatial data analysis within the variational Bayesian framework. The methodology is illustrated through application to simulated data and example images. The supplemental materials include our C++ source code for computing the approximate normalizing constant and simulation studies.

Reduced complexity on-line estimation of hidden Markov model parameters

In this paper we propose and study low complexity algorithms for on-line estimation of hidden Markov model (HMM) parameters. The estimates approach the true model parameters as the measurement noise approaches zero, but otherwise give improved estimates, albeit with bias. On a nite data set in the high noise case, the bias may not be signi cantly more severe than for a higher complexity asymptotically optimal scheme. Our algorithms require O(N3) calculations per time instant, where N is the number of states. Previous algorithms based on earlier hidden Markov model signal processing methods, including the expectation-maximumisation (EM) algorithm require O(N4) calculations per time instant.

An approximate method for the solution of an influence function foil rolling model

Fleck and Johnson (Int. J. Mech. Sci. 29 (1987) 507) and Fleck et al. (Proc. Inst. Mech. Eng. 206 (1992) 119) have developed foil rolling models which allow for large deformations in the roll profile, including the possibility that the rolls flatten completely. However, these models require computationally expensive iterative solution techniques. A new approach to the approximate solution of the Fleck et al. (1992) Influence Function Model has been developed using both analytic and approximation techniques. The numerical difficulties arising from solving an integral equation in the flattened region have been reduced by applying an Inverse Hilbert Transform to get an analytic expression for the pressure. The method described in this paper is applicable to cases where there is or there is not a flat region.

Relative entropy rate based multiple hidden Markov Model Approximation

This paper proposes a novel relative entropy rate (RER) based approach for multiple HMM (MHMM) approximation of a class of discrete-time uncertain processes. Under different uncertainty assumptions, the model design problem is posed either as a min-max optimisation problem or stochastic minimisation problem on the RER between joint laws describing the state and output processes (rather than the more usual RER between output processes). A suitable filter is proposed for which performance results are established which bound conditional mean estimation performance and show that estimation performance improves as the RER is reduced. These filter consistency and convergence bounds are the first results characterising multiple HMM approximation performance and suggest that joint RER concepts provide a useful model selection criteria. The proposed model design process and MHMM filter are demonstrated on an important image processing dim-target detection problem.

Establishment of a mouse model of colitis and its use to evaluate the anti-inflammatory effects of two ghrelin peptides

Ghrelin is a gut-brain peptide hormone that induces appetite, stimulates the release of growth hormone, and has recently been shown to ameliorate inflammation. Recent studies have suggested that ghrelin may play a potential role in inflammation-related diseases such as inflammatory bowel diseases (IBD). A previous study with ghrelin in the TNBS mouse model of colitis demonstrated that ghrelin treatment decreased the clinical severity of colitis and inflammation and prevented the recurrence of disease. Ghrelin may be acting at the immunological and epithelial level as the ghrelin receptor (GHSR) is expressed by immune cells and intestinal epithelial cells. The current project investigated the effect of ghrelin in a different mouse model of colitis using dextran sodium sulphate (DSS) – a luminal toxin. Two molecular weight forms of DSS were used as they give differing effects (5kDa and 40kDa). Ghrelin treatment significantly improved clinical colitis scores (p=0.012) in the C57BL/6 mouse strain with colitis induced by 2% DSS (5kDa). Treatment with ghrelin suppressed colitis in the proximal colon as indicated by reduced accumulative histopathology scores (p=0.03). Whilst there was a trend toward reduced scores in the mid and distal colon in these mice this did not reach significance. Ghrelin did not affect histopathology scores in the 40kDa model. There was no significant effect on the number of regulatory T cells or TNF-α secretion from cultured lymph node cells from these mice. The discovery of C-terminal ghrelin peptides, for example, obestatin and the peptide derived from exon 4 deleted proghrelin (Δ4 preproghrelin peptide) have raised questions regarding their potential role in biological functions. The current project investigated the effect of Δ4 peptide in the DSS model of colitis however no significant suppression of colitis was observed. In vitro epithelial wound healing assays were also undertaken to determine the effect of ghrelin on intestinal epithelial cell migration. Ghrelin did not significantly improve wound healing in these assays. In conclusion, ghrelin treatment displays a mild anti-inflammatory effect in the 5kDa DSS model. The potential mechanisms behind this effect and the disparity between these results and those published previously will be discussed.

Assessing the leanness in product design : a model for planned design reuse

Shrinking product lifecycles, tough international competition, swiftly changing technologies, ever increasing customer quality expectation and demanding high variety options are some of the forces that drive next generation of development processes. To overcome these challenges, design cost and development time of product has to be reduced as well as quality to be improved. Design reuse is considered one of the lean strategies to win the race in this competitive environment. design reuse can reduce the product development time, product development cost as well as number of defects which will ultimately influence the product performance in cost, time and quality. However, it has been found that no or little work has been carried out for quantifying the effectiveness of design reuse in product development performance such as design cost, development time and quality. Therefore, in this study we propose a systematic design reuse based product design framework and developed a design leanness index (DLI) as a measure of effectiveness of design reuse. The DLI is a representative measure of reuse effectiveness in cost, development time and quality. Through this index, a clear relationship between reuse measure and product development performance metrics has been established. Finally, a cost based model has been developed to maximise the design leanness index for a product within the given set of constraints achieving leanness in design process.

CYR61 (CCN1) protein expression during fracture healing in an ovine tibial model and its relation to the mechanical fixation stability

The formation of new blood vessels is a prerequisite for bone healing. CYR61 (CCN1), an extracellular matrix-associated signaling protein, is a potent stimulator of angiogenesis and mesenchymal stem cell expansion and differentiation. A recent study showed that CYR61 is expressed during fracture healing and suggested that CYR61 plays a significant role in cartilage and bone formation. The hypothesis of the present study was that decreased fixation stability, which leads to a delay in healing, would lead to reduced CYR61 protein expression in fracture callus. The aim of the study was to quantitatively analyze CYR61 protein expression, vascularization, and tissue differentiation in the osteotomy gap and relate to the mechanical fixation stability during the course of healing. A mid-shaft osteotomy of the tibia was performed in two groups of sheep and stabilized with either a rigid or semirigid external fixator, each allowing different amounts of interfragmentary movement. The sheep were sacrificed at 2, 3, 6, and 9 weeks postoperatively. The tibiae were tested biomechanically and histological sections from the callus were analyzed immunohistochemically with regard to CYR61 protein expression and vascularization. Expression of CYR61 protein was upregulated at the early phase of fracture healing (2 weeks), decreasing over the healing time. Decreased fixation stability was associated with a reduced upregulation of the CYR61 protein expression and a reduced vascularization at 2 weeks leading to a slower healing. The maximum cartilage callus fraction in both groups was reached at 3 weeks. However, the semirigid fixator group showed a significantly lower CYR61 immunoreactivity in cartilage than the rigid fixator group at this time point. The fraction of cartilage in the semirigid fixator group was not replaced by bone as quickly as in the rigid fixator group leading to an inferior histological and mechanical callus quality at 6 weeks and therefore to a slower healing. The results supply further evidence that CYR61 may serve as an important regulator of bone healing.

The influence of sensitivity to reward and punishment, propensity for sensation seeking, depression, and anxiety on the risky behaviour of novice drivers : a path model

Young novice drivers are significantly more likely to be killed or injured in car crashes than older, experienced drivers. Graduated driver licensing (GDL), which allows the novice to gain driving experience under less-risky circumstances, has resulted in reduced crash incidence; however, the driver's psychological traits are ignored. This paper explores the relationships between gender, age, anxiety, depression, sensitivity to reward and punishment, sensation-seeking propensity, and risky driving. Participants were 761 young drivers aged 17–24 (M= 19.00, SD= 1.56) with a Provisional (intermediate) driver's licence who completed an online survey comprising socio-demographic questions, the Impulsive Sensation Seeking Scale, Kessler's Psychological Distress Scale, the Sensitivity to Punishment and Sensitivity to Reward Questionnaire, and the Behaviour of Young Novice Drivers Scale. Path analysis revealed depression, reward sensitivity, and sensation-seeking propensity predicted the self-reported risky behaviour of the young novice drivers. Gender was a moderator; and the anxiety level of female drivers also influenced their risky driving. Interventions do not directly consider the role of rewards and sensation seeking, or the young person's mental health. An approach that does take these variables into account may contribute to improved road safety outcomes for both young and older road users.

The flammability of metallic materials in normal and reduced gravity

Metallic materials exposed to oxygen-enriched atmospheres – as commonly used in the medical, aerospace, aviation and numerous chemical processing industries – represent a significant fire hazard which must be addressed during design, maintenance and operation. Hence, accurate knowledge of metallic materials flammability is required. Reduced gravity (i.e. space-based) operations present additional unique concerns, where the absence of gravity must also be taken into account. The flammability of metallic materials has historically been quantified using three standardised test methods developed by NASA, ASTM and ISO. These tests typically involve the forceful (promoted) ignition of a test sample (typically a 3.2 mm diameter cylindrical rod) in pressurised oxygen. A test sample is defined as flammable when it undergoes burning that is independent of the ignition process utilised. In the standardised tests, this is indicated by the propagation of burning further than a defined amount, or „burn criterion.. The burn criterion in use at the onset of this project was arbitrarily selected, and did not accurately reflect the length a sample must burn in order to be burning independent of the ignition event and, in some cases, required complete consumption of the test sample for a metallic material to be considered flammable. It has been demonstrated that a) a metallic material.s propensity to support burning is altered by any increase in test sample temperature greater than ~250-300 oC and b) promoted ignition causes an increase in temperature of the test sample in the region closest to the igniter, a region referred to as the Heat Affected Zone (HAZ). If a test sample continues to burn past the HAZ (where the HAZ is defined as the region of the test sample above the igniter that undergoes an increase in temperature of greater than or equal to 250 oC by the end of the ignition event), it is burning independent of the igniter, and should be considered flammable. The extent of the HAZ, therefore, can be used to justify the selection of the burn criterion. A two dimensional mathematical model was developed in order to predict the extent of the HAZ created in a standard test sample by a typical igniter. The model was validated against previous theoretical and experimental work performed in collaboration with NASA, and then used to predict the extent of the HAZ for different metallic materials in several configurations. The extent of HAZ predicted varied significantly, ranging from ~2-27 mm depending on the test sample thermal properties and test conditions (i.e. pressure). The magnitude of the HAZ was found to increase with increasing thermal diffusivity, and decreasing pressure (due to slower ignition times). Based upon the findings of this work, a new burn criterion requiring 30 mm of the test sample to be consumed (from the top of the ignition promoter) was recommended and validated. This new burn criterion was subsequently included in the latest revision of the ASTM G124 and NASA 6001B international test standards that are used to evaluate metallic material flammability in oxygen. These revisions also have the added benefit of enabling the conduct of reduced gravity metallic material flammability testing in strict accordance with the ASTM G124 standard, allowing measurement and comparison of the relative flammability (i.e. Lowest Burn Pressure (LBP), Highest No-Burn Pressure (HNBP) and average Regression Rate of the Melting Interface(RRMI)) of metallic materials in normal and reduced gravity, as well as determination of the applicability of normal gravity test results to reduced gravity use environments. This is important, as currently most space-based applications will typically use normal gravity information in order to qualify systems and/or components for reduced gravity use. This is shown here to be non-conservative for metallic materials which are more flammable in reduced gravity. The flammability of two metallic materials, Inconel® 718 and 316 stainless steel (both commonly used to manufacture components for oxygen service in both terrestrial and space-based systems) was evaluated in normal and reduced gravity using the new ASTM G124-10 test standard. This allowed direct comparison of the flammability of the two metallic materials in normal gravity and reduced gravity respectively. The results of this work clearly show, for the first time, that metallic materials are more flammable in reduced gravity than in normal gravity when testing is conducted as described in the ASTM G124-10 test standard. This was shown to be the case in terms of both higher regression rates (i.e. faster consumption of the test sample – fuel), and burning at lower pressures in reduced gravity. Specifically, it was found that the LBP for 3.2 mm diameter Inconel® 718 and 316 stainless steel test samples decreased by 50% from 3.45 MPa (500 psia) in normal gravity to 1.72 MPa (250 psia) in reduced gravity for the Inconel® 718, and 25% from 3.45 MPa (500 psia) in normal gravity to 2.76 MPa (400 psia) in reduced gravity for the 316 stainless steel. The average RRMI increased by factors of 2.2 (27.2 mm/s in 2.24 MPa (325 psia) oxygen in reduced gravity compared to 12.8 mm/s in 4.48 MPa (650 psia) oxygen in normal gravity) for the Inconel® 718 and 1.6 (15.0 mm/s in 2.76 MPa (400 psia) oxygen in reduced gravity compared to 9.5 mm/s in 5.17 MPa (750 psia) oxygen in normal gravity) for the 316 stainless steel. Reasons for the increased flammability of metallic materials in reduced gravity compared to normal gravity are discussed, based upon the observations made during reduced gravity testing and previous work. Finally, the implications (for fire safety and engineering applications) of these results are presented and discussed, in particular, examining methods for mitigating the risk of a fire in reduced gravity.

Impact of a data warehouse model for improved decision-making process in healthcare

The health system is one sector dealing with a deluge of complex data. Many healthcare organisations struggle to utilise these volumes of health data effectively and efficiently. Also, there are many healthcare organisations, which still have stand-alone systems, not integrated for management of information and decision-making. This shows, there is a need for an effective system to capture, collate and distribute this health data. Therefore, implementing the data warehouse concept in healthcare is potentially one of the solutions to integrate health data. Data warehousing has been used to support business intelligence and decision-making in many other sectors such as the engineering, defence and retail sectors. The research problem that is going to be addressed is, "how can data warehousing assist the decision-making process in healthcare". To address this problem the researcher has narrowed an investigation focusing on a cardiac surgery unit. This research used the cardiac surgery unit at the Prince Charles Hospital (TPCH) as the case study. The cardiac surgery unit at TPCH uses a stand-alone database of patient clinical data, which supports clinical audit, service management and research functions. However, much of the time, the interaction between the cardiac surgery unit information system with other units is minimal. There is a limited and basic two-way interaction with other clinical and administrative databases at TPCH which support decision-making processes. The aims of this research are to investigate what decision-making issues are faced by the healthcare professionals with the current information systems and how decision-making might be improved within this healthcare setting by implementing an aligned data warehouse model or models. As a part of the research the researcher will propose and develop a suitable data warehouse prototype based on the cardiac surgery unit needs and integrating the Intensive Care Unit database, Clinical Costing unit database (Transition II) and Quality and Safety unit database [electronic discharge summary (e-DS)]. The goal is to improve the current decision-making processes. The main objectives of this research are to improve access to integrated clinical and financial data, providing potentially better information for decision-making for both improved from the questionnaire and by referring to the literature, the results indicate a centralised data warehouse model for the cardiac surgery unit at this stage. A centralised data warehouse model addresses current needs and can also be upgraded to an enterprise wide warehouse model or federated data warehouse model as discussed in the many consulted publications. The data warehouse prototype was able to be developed using SAS enterprise data integration studio 4.2 and the data was analysed using SAS enterprise edition 4.3. In the final stage, the data warehouse prototype was evaluated by collecting feedback from the end users. This was achieved by using output created from the data warehouse prototype as examples of the data desired and possible in a data warehouse environment. According to the feedback collected from the end users, implementation of a data warehouse was seen to be a useful tool to inform management options, provide a more complete representation of factors related to a decision scenario and potentially reduce information product development time. However, there are many constraints exist in this research. For example the technical issues such as data incompatibilities, integration of the cardiac surgery database and e-DS database servers and also, Queensland Health information restrictions (Queensland Health information related policies, patient data confidentiality and ethics requirements), limited availability of support from IT technical staff and time restrictions. These factors have influenced the process for the warehouse model development, necessitating an incremental approach. This highlights the presence of many practical barriers to data warehousing and integration at the clinical service level. Limitations included the use of a small convenience sample of survey respondents, and a single site case report study design. As mentioned previously, the proposed data warehouse is a prototype and was developed using only four database repositories. Despite this constraint, the research demonstrates that by implementing a data warehouse at the service level, decision-making is supported and data quality issues related to access and availability can be reduced, providing many benefits. Output reports produced from the data warehouse prototype demonstrated usefulness for the improvement of decision-making in the management of clinical services, and quality and safety monitoring for better clinical care. However, in the future, the centralised model selected can be upgraded to an enterprise wide architecture by integrating with additional hospital units’ databases.