Exploring the boundaries of shallow phylogeny in the YESS group and the dynamics of gene cluster and operon formation in bacterial genomes

In this thesis I look at two different problems in bacterial genomic analysis. The first involves reconstructing the evolutionary history between a group of closely related bacteria. I addressed whether or not it is possible to separate such genomes into different genera, species and strains. Specifically, I addressed how different approaches such as the use of 16S rRNA phylogenetic trees, phylogenetic supertrees and concatenation of individual genes in order to construct phylogenetic trees compare with one another. What effect will problems associated with resolving shallow-phylogeny have on recovering a tree of life? Ultimately I show that for the group of genomes involved, different methods and data produce different results and that the true tree, if a tree-like structure does indeed exist for these genomes, is unrecoverable using such approaches. In the second part of my thesis I examine the phenomenon of gene clustering in bacterial genomes. I present a software program, GenClust, for the identification, analysis and visualisation of gene clusters. I show how GenClust can be used to recover and analyse clusters of genes involved in amino acid biosynthesis across a large !-proteobacterial dataset. Finally, I examine models of gene cluster and operon formation and test them with real data, using a combined approach of comparing clusters on both structural similarity and the underlying phylogenetic signals of the clustered genes. I provide a hypothesis for the selective forces driving cluster and operon formation in bacterial genomes

Challenges Experienced by Medical Device Software Organisations while following a Plan-driven SDLC

Medical device software organisations face challenges not faced by generic software development organisations. These challenges include the adherence to regulatory controls. Regulatory bodies require medical device software organisations to provide objective evidence that the software they are developing is safe and reliable. To produce this, regulatory bodies require a number of deliverables which must be achieved. However, they do not dictate which Software Development Life Cycle (SDLC) must be followed in order to achieve these deliverables. Despite not dictating which SDLC must be followed when developing medical device software, organisations typically develop their software in accordance with a Plan-Driven software development lifecycle. By conducting semi structured interviews with seven medical device software organisations, we gained a deeper insight into how the challenges experienced impact on the development of medical device software. The interviews also attempted to learn from the participants how they believe the challenges experienced can be overcome. The aim of this paper is to explain the methodology used to perform interviews with medical device software organisations and to present these interviews

Sequential Structural and Fluid Dynamics Analysis of Balloon-Expandable Coronary Stents: A Multivariable Statistical Analysis

Several clinical studies have identified a strong correlation between neointimal hyperplasia following coronary stent deployment and both stent-induced arterial injury and altered vessel hemodynamics. As such, the sequential structural and fluid dynamics analysis of balloon-expandable stent deployment should provide a comprehensive indication of stent performance. Despite this observation, very few numerical studies of balloon-expandable coronary stents have considered both the mechanical and hemodynamic impact of stent deployment. Furthermore, in the few studies that have considered both phenomena, only a small number of stents have been considered. In this study, a sequential structural and fluid dynamics analysis methodology was employed to compare both the mechanical and hemodynamic impact of six balloon-expandable coronary stents. To investigate the relationship between stent design and performance, several common stent design properties were then identified and the dependence between these properties and both the mechanical and hemodynamic variables of interest was evaluated using statistical measures of correlation. Following the completion of the numerical analyses, stent strut thickness was identified as the only common design property that demonstrated a strong dependence with either the mean equivalent stress predicted in the artery wall or the mean relative residence time predicted on the luminal surface of the artery. These results corroborate the findings of the large-scale ISAR-STEREO clinical studies and highlight the crucial role of strut thickness in coronary stent design. The sequential structural and fluid dynamics analysis methodology and the multivariable statistical treatment of the results described in this study should prove useful in the design of future balloon-expandable coronary stents

Computational Structural Modelling of Coronary Stent Deployment: A Review

The finite element (FE) method is a powerful investigative tool in the field of biomedical engineering, particularly in the analysis of medical devices such as coronary stents whose performance is extremely difficult to evaluate in vivo. In recent years, a number of FE studies have been carried out to simulate the deployment of coronary stents, and the results of these studies have been utilised to assess and optimise the performance of these devices. The aim of this paper is to provide a thorough review of the state-of-the-art research in this area, discussing the aims, methods and conclusions drawn from a number of significant studies. It is intended that this paper will provide a valuable reference for future research in this are

How Can Software SMEs Become Medical Device

The amount of software content within medical devices has grown considerably over recent years and will continue to do so as the level of complexity of medical devices increase. This is driven by the fact that software is introduced to produce sophisticated medical devices that would not be possible using only hardware. This therefore presents opportunities for software development SMEs to become medical device software development organisations. However, some obstacles need to be addressed and overcome in order to make the transition from being a generic software development organisation to becoming a medical device software development organisation. This paper describes these obstacles and how research that is currently being performed within the Regulated Software Research Group in Dundalk Institute of Technology may be used to assist with this transitio

Adopting Agile Practices When Developing Software for Use in the Medical Domain

Non-safety critical software developers have been reaping the benefits of adopting agile practices for a number of years. However, developers of safety critical software often have concerns about adopting agile practices. Through performing a literature review, this research has identified the perceived barriers to following agile practices when developing medical device software. A questionnaire based survey was also conducted with medical device software developers in Ireland to determine the barriers to adopting agile practices. The survey revealed that half of the respondents develop software in accordance with a plan driven software development lifecycle and that they believe that there are a number of perceived barriers to adopting agile practices when developing regulatory compliant software such as: being contradictory to regulatory requirements; insufficient coverage of risk management activities and the lack of up-front planning. In addition, a comparison is performed between the perceived and actual barriers. Based upon the findings of the literature review and survey, it emerged that no external barriers exist to adopting agile practices when developing medical device software and the barriers that do exists are internal barriers such as getting stakeholder buy in

Adopting Agile Practices when Developing Medical Device Software

Agile methods are gaining momentum amongst the developers of non-safety critical software. They offer the ability to improve development time, increase quality and reduce development costs. Despite this, the rate of adoption of agile methods within safety critical domains remains low. On face value agile methods appear to be contradictory to regulatory requirements. However while they may appear contradictory, they align on key values such as the development of the highest quality software. To demonstrate that agile methods could in fact be adopted when developing regulatory compliant software they were implemented on a medical device software development project. This implementation showed that not only can agile methods be successfully followed, but it also revealed that benefits were acquired. For example, the medical device software development project was completed 7% faster when following agile methods, when compared to if it had been completed in accordance with a plan-driven approach. While this implementation is confined to a single project, within a single organization it does strengthen the belief that adopting agile methods within regulated domains can reap the same benefits as those acquired in non-safety critical domains

Editorial: Capitalism(s) and the future of adult education policy

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Integrating Agile Practices with a Medical Device SDLC.

The rate at which agile software development practices are being adopted is growing rapidly. Agile software development practices and methodologies appear to offer the silver bullet which can solve the problems associated with following plan driven software development lifecycles. Agile software development practices offer the possibility of achieving lower development costs, increased efficiency and improved software quality. However, there is currently a low rate of publicly available information that suggests there is widespread adoption of agile practices within the medical device software domain. This is largely due to the fact that software developed for medical devices includes challenges not faced when developing non safety critical software. As a result of these challenges, medical device software is typically developed using plan driven software development lifecycles. However, such lifecycles are quite rigid and cannot accommodate changes easily. Previous research has revealed that medical device software development projects can benefit from adopting agile practices whilst still maintaining the discipline associated with following plan driven development lifecycles. This paper outlines the challenges faced by developers when developing medical device software and how shortcomings in both agile and plan driven approaches can be resolved by following a mixed method approach to medical device software developmen

Improving Safety in Medical Devices from Concept to Retirements

As with many domains the use of software within the healthcare industry is on the rise [1, 2] within the last 20 years