Capacity determination and expansion models for rail networks

This thesis focused upon the development of improved capacity analysis and capacity planning techniques for railways. A number of innovations were made and were tested on a case study of a real national railway. These techniques can reduce the time required to perform decision making activities that planners and managers need to perform. As all railways need to be expanded to meet increasing demands, the presumption that analytical capacity models can be used to identify how best to improve an existing network at least cost, was fully investigated. Track duplication was the mechanism used to expanding a network's capacity, and two variant capacity expansion models were formulated. Another outcome of this thesis is the development and validation of bi objective models for capacity analysis. These models regulate the competition for track access and perform a trade-off analysis. An opportunity to develop more general mulch-objective approaches was identified.

Quantifying uncertainty in parameter estimates for stochastic models of collective cell spreading using approximate Bayesian computation

Wound healing and tumour growth involve collective cell spreading, which is driven by individual motility and proliferation events within a population of cells. Mathematical models are often used to interpret experimental data and to estimate the parameters so that predictions can be made. Existing methods for parameter estimation typically assume that these parameters are constants and often ignore any uncertainty in the estimated values. We use approximate Bayesian computation (ABC) to estimate the cell diffusivity, D, and the cell proliferation rate, λ, from a discrete model of collective cell spreading, and we quantify the uncertainty associated with these estimates using Bayesian inference. We use a detailed experimental data set describing the collective cell spreading of 3T3 fibroblast cells. The ABC analysis is conducted for different combinations of initial cell densities and experimental times in two separate scenarios: (i) where collective cell spreading is driven by cell motility alone, and (ii) where collective cell spreading is driven by combined cell motility and cell proliferation. We find that D can be estimated precisely, with a small coefficient of variation (CV) of 2–6%. Our results indicate that D appears to depend on the experimental time, which is a feature that has been previously overlooked. Assuming that the values of D are the same in both experimental scenarios, we use the information about D from the first experimental scenario to obtain reasonably precise estimates of λ, with a CV between 4 and 12%. Our estimates of D and λ are consistent with previously reported values; however, our method is based on a straightforward measurement of the position of the leading edge whereas previous approaches have involved expensive cell counting techniques. Additional insights gained using a fully Bayesian approach justify the computational cost, especially since it allows us to accommodate information from different experiments in a principled way.

Dynamic agent composition for large-scale agent-based models

PURPOSE: This paper describes dynamic agent composition, used to support the development of flexible and extensible large-scale agent-based models (ABMs). This approach was motivated by a need to extend and modify, with ease, an ABM with an underlying networked structure as more information becomes available. Flexibility was also sought after so that simulations are set up with ease, without the need to program. METHODS: The dynamic agent composition approach consists in having agents, whose implementation has been broken into atomic units, come together at runtime to form the complex system representation on which simulations are run. These components capture information at a fine level of detail and provide a vast range of combinations and options for a modeller to create ABMs. RESULTS: A description of the dynamic agent composition is given in this paper, as well as details about its implementation within MODAM (MODular Agent-based Model), a software framework which is applied to the planning of the electricity distribution network. Illustrations of the implementation of the dynamic agent composition are consequently given for that domain throughout the paper. It is however expected that this approach will be beneficial to other problem domains, especially those with a networked structure, such as water or gas networks. CONCLUSIONS: Dynamic agent composition has many advantages over the way agent-based models are traditionally built for the users, the developers, as well as for agent-based modelling as a scientific approach. Developers can extend the model without the need to access or modify previously written code; they can develop groups of entities independently and add them to those already defined to extend the model. Users can mix-and-match already implemented components to form large-scales ABMs, allowing them to quickly setup simulations and easily compare scenarios without the need to program. The dynamic agent composition provides a natural simulation space over which ABMs of networked structures are represented, facilitating their implementation; and verification and validation of models is facilitated by quickly setting up alternative simulations.

Improving robot vision models for object detection through interaction

We propose a method for learning specific object representations that can be applied (and reused) in visual detection and identification tasks. A machine learning technique called Cartesian Genetic Programming (CGP) is used to create these models based on a series of images. Our research investigates how manipulation actions might allow for the development of better visual models and therefore better robot vision. This paper describes how visual object representations can be learned and improved by performing object manipulation actions, such as, poke, push and pick-up with a humanoid robot. The improvement can be measured and allows for the robot to select and perform the `right' action, i.e. the action with the best possible improvement of the detector.

Building cross-scale models of epigenetic mechanisms

Epigenetic changes correspond to heritable modifications of the chromosome structure, which do not involve alteration of the DNA sequence but do affect gene expression. These mechanisms play an important role in normal cell differentiation, but aberration is associated also with several diseases, including cancer and neural disorders. In consequence, despite intensive studies in recent years, the contribution of modifications remains largely unquantified due to overall system complexity and insufficient data. Computational models can provide powerful auxiliary tools to experimentation, not least as scales from the sub-cellular through cell populations (or to networks of genes) can be spanned. In this paper, the challenges to development, of realistic cross-scale models, are discussed and illustrated with respect to current work.

Multi-parametric hydrogels support 3D in vitro bioengineered microenvironment models of tumour angiogenesis

Tumour microenvironment greatly influences the development and metastasis of cancer progression. The development of three dimensional (3D) culture models which mimic that displayed in vivo can improve cancer biology studies and accelerate novel anticancer drug screening. Inspired by a systems biology approach, we have formed 3D in vitro bioengineered tumour angiogenesis microenvironments within a glycosaminoglycan-based hydrogel culture system. This microenvironment model can routinely recreate breast and prostate tumour vascularisation. The multiple cell types cultured within this model were less sensitive to chemotherapy when compared with two dimensional (2D) cultures, and displayed comparative tumour regression to that displayed in vivo. These features highlight the use of our in vitro culture model as a complementary testing platform in conjunction with animal models, addressing key reduction and replacement goals of the future. We anticipate that this biomimetic model will provide a platform for the in-depth analysis of cancer development and the discovery of novel therapeutic targets.

Environmental conditions are important for establishing and evaluating pre-clinical models of GVHD

GVHD remains the major complication of allo-HSCT. Murine models are the primary system used to understand GVHD, and to develop potential therapies. Several factors are critical for GVHD in these models; including histo- compatibility, conditioning regimen, and T-cell number. We serendipitously found that environmental factors such as the caging system and bedding also significantly impact the kinetics of GVHD in these models. This is important because such factors may influence the experimental conditions required to cause GVHD and how mice respond to various treatments. Consequently, this is likely to alter interpretation of results between research groups, and the perceived effectiveness of experimental therapies.

The role of non-thermal plasma technique in {NOx} treatment: A review

Non-thermal plasma (NTP) has been introduced over the past several years as a promising method for nitrogen oxide (NOx) removal. The intent, when using NTP, is to selectively transfer input electrical energy to the electrons, and to not expend this in heating the entire gas stream, which generates free radicals through collisions, and promotes the desired chemical changes in the exhaust gases. The generated active species react with the pollutant molecules and decompose them. This paper reviews and summarizes relevant literature regarding various aspects of the application of {NTP} technology on {NOx} removal from exhaust gases. A comprehensive description of available scientific literature on {NOx} removal using {NTP} technology is presented, including various types of NTP, e.g. dielectric barrier discharge, corona discharge and electron beam. Furthermore, the combination of {NTP} with catalyst and adsorbent for better {NOx} removal efficiency is presented in detail. The removal of {NOx} from both simulated gases and real diesel engines is also considered in this review paper. As {NTP} is a new technique and is not yet commercialized, there is a need for more studies to be performed in this field.

Emergency department models of care in the context of care quality and cost: A systematic review

To identify current ED models of care and their impact on care quality, care effectiveness, and cost. A systematic search of key health databases (Medline, CINAHL, Cochrane, EMbase) was conducted to identify literature on ED models of care. Additionally, a focused review of the contents of 11 international and national emergency medicine, nursing and health economic journals (published between 2010 and 2013) was undertaken with snowball identification of references of the most recent and relevant papers. Articles published between 1998 and 2013 in the English language were included for initial review by three of the authors. Studies in underdeveloped countries and not addressing the objectives of the present study were excluded. Relevant details were extracted from the retrieved literature, and analysed for relevance and impact. The literature was synthesised around the study's main themes. Models described within the literature mainly focused on addressing issues at the input, throughput or output stages of ED care delivery. Models often varied to account for site specific characteristics (e.g. onsite inpatient units) or to suit staffing profiles (e.g. extended scope physiotherapist), ED geographical location (e.g. metropolitan or rural site), and patient demographic profile (e.g. paediatrics, older persons, ethnicity). Only a few studies conducted cost-effectiveness analysis of service models. Although various models of delivering emergency healthcare exist, further research is required in order to make accurate and reliable assessments of their safety, clinical effectiveness and cost-effectiveness.

BPMN Miner: Automated Discovery of BPMN Process Models with Hierarchical Structure

Existing techniques for automated discovery of process models from event logs gen- erally produce flat process models. Thus, they fail to exploit the notion of subprocess as well as error handling and repetition constructs provided by contemporary process modeling notations, such as the Business Process Model and Notation (BPMN). This paper presents a technique for automated discovery of hierarchical BPMN models con- taining interrupting and non-interrupting boundary events and activity markers. The technique employs functional and inclusion dependency discovery techniques in order to elicit a process-subprocess hierarchy from the event log. Given this hierarchy and the projected logs associated to each node in the hierarchy, parent process and subprocess models are then discovered using existing techniques for flat process model discovery. Finally, the resulting models and logs are heuristically analyzed in order to identify boundary events and markers. By employing approximate dependency discovery tech- niques, it is possible to filter out noise in the event log arising for example from data entry errors or missing events. A validation with one synthetic and two real-life logs shows that process models derived by the proposed technique are more accurate and less complex than those derived with flat process discovery techniques. Meanwhile, a validation on a family of synthetically generated logs shows that the technique is resilient to varying levels of noise.

Influence of the structural characteristic of pyrolysis products on thermal stability of styrene-butadiene rubber composites reinforced by different particle sized kaolinites

A series of rubber composites were prepared by blending styrene-butadiene rubber (SBR) latex and the different particle sized kaolinites. The thermal stabilities of the rubber composites were characterized using thermogravimetry, digital photography, scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, and Raman spectroscopy. Kaolinite SBR composites showed much greater thermal stability when compared with that of the pure SBR. With the increase of kaolinite particle size, the pyrolysis products became much looser; the char layer and crystalline carbon content gradually decreased in the pyrolysis residues. The pyrolysis residues of the SBR composites filled with the different particle sized kaolinites showed some remarkable changes in structural characteristics. The increase of kaolinite particle size was not beneficial to form the compact and stable crystalline carbon in the pyrolysis process, and resulted in a negative influence in improving the thermal stability of kaolinite/SBR composites.

Alive SMC^2: Bayesian model selection for low-count time series models with intractable likelihoods

In this paper we present a new method for performing Bayesian parameter inference and model choice for low count time series models with intractable likelihoods. The method involves incorporating an alive particle filter within a sequential Monte Carlo (SMC) algorithm to create a novel pseudo-marginal algorithm, which we refer to as alive SMC^2. The advantages of this approach over competing approaches is that it is naturally adaptive, it does not involve between-model proposals required in reversible jump Markov chain Monte Carlo and does not rely on potentially rough approximations. The algorithm is demonstrated on Markov process and integer autoregressive moving average models applied to real biological datasets of hospital-acquired pathogen incidence, animal health time series and the cumulative number of poison disease cases in mule deer.

Meltdown : a tool to help in the interpretation of thermal melt curves acquired by differential scanning fluorimetry

The output of a differential scanning fluorimetry (DSF) assay is a series of melt curves, which need to be interpreted to get value from the assay. An application that translates raw thermal melt curve data into more easily assimilated knowledge is described. This program, called “Meltdown,” conducts four main activities—control checks, curve normalization, outlier rejection, and melt temperature (Tm) estimation—and performs optimally in the presence of triplicate (or higher) sample data. The final output is a report that summarizes the results of a DSF experiment. The goal of Meltdown is not to replace human analysis of the raw fluorescence data but to provide a meaningful and comprehensive interpretation of the data to make this useful experimental technique accessible to inexperienced users, as well as providing a starting point for detailed analyses by more experienced users.

Performance evaluation of non-thermal plasma on particulate matter, ozone and CO2 correlation for diesel exhaust emission reduction

This study is seeking to investigate the effect of non-thermal plasma technology in the abatement of particulate matter (PM) from the actual diesel exhaust. Ozone (O3) strongly promotes PM oxidation, the main product of which is carbon dioxide (CO2). PM oxidation into the less harmful product (CO2) is the main objective whiles the correlation between PM, O3 and CO2 is considered. A dielectric barrier discharge reactor has been designed with pulsed power technology to produce plasma inside the diesel exhaust. To characterise the system under varied conditions, a range of applied voltages from 11 kVPP to 21kVPP at repetition rates of 2.5, 5, 7.5 and 10 kHz, have been experimentally investigated. The results show that by increasing the applied voltage and repetition rate, higher discharge power and CO2 dissociation can be achieved. The PM removal efficiency of more than 50% has been achieved during the experiments and high concentrations of ozone on the order of a few hundreds of ppm have been observed at high discharge powers. Furthermore, O3, CO2 and PM concentrations at different plasma states have been analysed for time dependence. Based on this analysis, an inverse relationship between ozone concentration and PM removal has been found and the role of ozone in PM removal in plasma treatment of diesel exhaust has been highlighted.

Applying metaethical and normative claims of moral relativism to (shareholder and stakeholder) models of corporate governance

There has, in recent decades, been considerable scholarship regarding the moral aspects of corporate governance,and differences in corporate governance practices around the world have been widely documented and investigated. In such a context, the claims associated with moral relativism are relevant. The purpose of this paper is to provide a detailed consideration of how the metaethical and normative claims of moral relativism in particular can be applied to corporate governance. This objective is achieved, firstly, by reviewing what is meant by metaethical moral relativism and identifying two ways in which the metaethical claim can be assessed. The possibility of a single, morally superior model of corporate governance is subsequently considered through an analysis of prominent works justifying the shareholder and stakeholder approaches, together with a consideration of academic agreement in this area. The paper then draws on the work of Wong (Moral relativity, University of California Press, Berkeley, CA, 1984, A companion to ethics, Blackwell, Malden, 1993, Natural moralities: A defense of pluralistic relativism,Oxford University Press, Oxford, 2006), firstly in providing an argument supporting metaethical moral relativism and secondly regarding values of tolerance and/or accommodation that can contribute to the normative claim. The paper concludes by proposing an argument that it is morally wrong to impose a model of corporate governance where there are differences in moral judgements relevant to corporate governance, or to interfere with a model in similar circumstances, and closes with consideration of the argument’s implications.