Prevalence and control of Clostridium difficile in patients with cystic fibrosis

The aim of this thesis was to investigate the high prevalence of Clostridium difficile in patients with cystic fibrosis (CF), and to control its dissemination. To determine the carriage rate of C. difficile in CF patients, 60 patients were tested for C. difficile and its toxin. In total, 50% of patients were found to be asymptomatic carriers of C. difficile despite toxin being detected in 31.66% of patients. Ribotyping of the C. difficile isolates revealed 16 distinct ribotypes, including the hyper virulent RT078. All isolates were sensitive to both Vancomycin and Metronidazole. The effect of CF and its treatment on the gut microbiota of CF patients was assessed by 16s sequencing of the gut microbiota of 68 CF patients. When compared to a healthy control group, CF patient gut microbiota was found to be less diverse and had an increased Firmicutes to Bacteriodetes ratio. Interestingly, CF patients who were carriers of C. difficile had a less diverse gut microbiota than C. difficile negative CF patients. Multilocus sequence typing was found to be comparable to PCR-ribotyping for typing C. difficile isolates from high risk patient groups. The sequence type ST 26 is potentially associated with CF patients as all seven isolates were found in this group and this sequence type has been previously reported in CF patients in a geographically distinct study. The bacteriophage ФCD6356 was assessed as a targeted antimicrobial against C. difficile in an ex-vivo model of the human distal colon. Despite reducing viable C. difficile by 1.75 logs over 24 hours, this bacteriophage was not suitable due to its lysogenic nature. Following treatment, all surviving C. difficile were immune to reinfection due to prophage integration. However, the ФCD6356 encoded endolysin was capable of reducing viable C. difficile by 2.9 over 2 hours in vitro after being cloned and expressed in Escherichia coli.

End-of-life care: identifying an appropriate legal framework for specialist palliative care in Ireland

This thesis argues that the legal framework in Ireland for specialist palliative care is inadequate and consequently a more appropriate legal framework must be identified. This research is guided by three central research questions. The first central research question examines the legitimacy of the distinction between specialist palliative care and euthanasia. The second central research question asks what legal framework currently exists in Ireland for specialist palliative care. The third central research question examines an alternative legal framework for specialist palliative. This thesis is composed of seven chapters. The first Chapter is an introduction to the thesis and defines the terminology and the central research questions. Chapter Two explores the development and practice of palliative care in Ireland. Chapter Three examines the distinction in criminal law between specialist palliative care practices and euthanasia. Chapter Four examines the human rights framework for specialist palliative care. Chapter Five critiques the regulatory framework in Ireland for specialist palliative care. Having gained a thorough understanding of palliative care and the related legal framework, this thesis then engages in comparative analysis of the Netherlands which is used as a source of ideas for reform in Ireland. Chapter Seven is the concluding chapter and, in it, the main findings of this thesis are summarised. The main findings being that: the distinction between specialist palliative care and euthanasia is not sufficiently supported by justifications such as a double effect or the acts and omissions distinction, there is no clear decision-making framework in Ireland for specialist palliative care, and the current legal framework lacks clarity and does not promote consistency between providers of specialist palliative care. This Chapter also proposes that detailed professional standards and guidelines are likely to be the most appropriate way to effect individual and institutional change in the provision of specialist palliative care.

Interactions between nematodes, potato and soil-borne micro-organisms and their effect on the management of potato cyst nematodes

Potato cyst nematodes (PCN) cause significant damage to the potato crop worldwide and growers experience economic losses related to yield loss and the cost of control measures. Experiments were set up to further elucidate the complex tritrophic PCNpotato-soil bacteria relationship. Bacterial strains isolated from the sugar beet rhizosphere were shown to be hatch active towards Globodera pallida and to be capable of successfully colonising the sugar beet rhizosphere when applied exogenously. A trap-crop system, based on these isolates, was proposed. Ridge and bulk soil taken from a commercial potato field were incubated with sterile potato root leachate (sPRL) and subsequent in vitro hatching assays showed that PCN hatch was influenced by microorganisms present in the ridge, but not in the bulk soil. Community level physiological profiling (CLPP) of ridge and bulk soil, using BIOLOG EcoplatesTM, demonstrated differences in bacterial functional diversity between the two soil types. An investigation of the inter-species competition between G. pallida and G. rostochiensis showed that G. pallida performed significantly better, in terms of multiplication rate, in competition with G. rostochiensis compared to its multiplication rate in single-species populations. Effectively removing the early hatch of G. rostochiensis in pot trials led to the removal of this competitive advantage of G. pallida suggesting that this advantage was due, at least in part, to morphological changes to the root caused by the early hatching of G. rostochiensis.

Learning to 'understand backwards' in time: children's temporal cognition and the primary history curriculum

This study examines children’s temporal ways of knowing and it highlights the centrality of temporal cognition in the development of children’s historical understanding. It explores how young children conceptualise time and it examines the provision for temporal cognition at the levels of the intended, enacted and received history curriculum in the Irish primary school context. Positioning temporality as a prerequisite second-order concept, the study recognises the essential role of both first-order and additional second-order concepts in historical understanding. While the former can be defined as the basic, substantive content to be taught, the latter refers to a number of additional key concepts that are deemed fundamental to children's capacity to make meaningful sense of history. The study argues for due recognition to be given to temporality, in the belief that both sets of knowledge, the content and skills, are required to develop historical thinking (Lévesque, 2011). The study addresses a number of key research questions, using a mixed methods research design, comprising an analysis of history textbooks, a survey among final year student teachers about their teaching of history, and school-based interviews with primary school children: What opportunities are available for children to develop temporal ways of knowing? How do student teachers experience being apprenticed into the available culture for teaching history and understanding temporality at primary level? What insights do the cognitive-developmental and sociocultural perspectives on learning provide for understanding the dynamics of children’s temporal ways of knowing? The study argues that the skill of developing a deeper understanding of time is a key prerequisite in connecting with, and constructing, understandings and frameworks of the past. The study advances a view of temporality as complex, multi-faceted and developmental. The findings have a potential contribution to make in influencing policy and pedagogy in establishing an elaborated and well-defined curriculum framework for developing temporal cognition at both national and international levels.

Investigation of electrically active defects at the interface of high-k dielectrics and compound semiconductors

As silicon based devices in integrated circuits reach the fundamental limits of dimensional scaling there is growing research interest in the use of high electron mobility channel materials, such as indium gallium arsenide (InGaAs), in conjunction with high dielectric constant (high-k) gate oxides, for Metal-Oxide-Semiconductor Field Effect Transistor (MOSFET) based devices. The motivation for employing high mobility channel materials is to reduce power dissipation in integrated circuits while also providing improved performance. One of the primary challenges to date in the field of III-V semiconductors has been the observation of high levels of defect densities at the high-k/III-V interface, which prevents surface inversion of the semiconductor. The work presented in this PhD thesis details the characterization of MOS devices incorporating high-k dielectrics on III-V semiconductors. The analysis examines the effect of modifying the semiconductor bandgap in MOS structures incorporating InxGa1-xAs (x: 0, 0.15. 0.3, 0.53) layers, the optimization of device passivation procedures designed to reduce interface defect densities, and analysis of such electrically active interface defect states for the high-k/InGaAs system. Devices are characterized primarily through capacitance-voltage (CV) and conductance-voltage (GV) measurements of MOS structures both as a function of frequency and temperature. In particular, the density of electrically active interface states was reduced to the level which allowed the observation of true surface inversion behavior in the In0.53Ga0.47As MOS system. This was achieved by developing an optimized (NH4)2S passivation, minimized air exposure, and atomic layer deposition of an Al2O3 gate oxide. An extraction of activation energies allows discrimination of the mechanisms responsible for the inversion response. Finally a new approach is described to determine the minority carrier generation lifetime and the oxide capacitance in MOS structures. The method is demonstrated for an In0.53Ga0.47As system, but is generally applicable to any MOS structure exhibiting a minority carrier response in inversion.

An analysis of selected secretion systems of Pseudomonas species

Direct secretion systems which deliver molecules from one cell to another have huge significance in shaping bacterial communities or in determining the outcome of bacterial associations with eukaryotic organisms. This work examines the roles of the Type III Secretion System (T3SS) and the Type VI Secretion System (T6SS) systems of Pseudomonas, a widespread genus including clinical pathogens and biocontrol strains. Bioinformatic analysis of T6SS phylogeny and associated gene content within Pseudomonas identified several T6SS phylogenetic groups, and linked T6SS components VgrG and Hcp encoded outside of T6SS gene loci with their cognate T6SS phylogenetic groups. Remarkably, such “orphan” vgrG and hcp genes were found to occur in diverse, horizontally transferred, operons often containing putative T6SS accessory components and effectors. The prevalence of a widespread superfamily of T6SS lipase effectors (Tle) was assessed in metagenomes from various environments. The abundance of the Tle superfamily and individual families varied between niches, suggesting there is niche specific selection and specialisation of Tle. Experimental work also discovered that P. fluorescens F113 uses the SPI-1 T3SS to avoid amoeboid grazing in mixed populations. This finding may represent a significant aspect of F113 rhizocompetence, and the rhizocompetence of other Rhizobacteria.

Childhood obesity treatment: integrating mobile health technology into a paediatric obesity service

Background: The management of childhood obesity is challenging. Aims: Thesis, i) reviews the evidence for lifestyle treatment of obesity, ii) explores cardiometabolic burden in childhood obesity, iii) explores whether changes in body composition predicts change in insulin sensitivity (IS), iv) develops and evaluates a lifestyle obesity intervention; v) develops a mobile health application for obesity treatment and vi) tests the application in a clinical trial. Methods: In Study 1, systematic reviews and meta-analyses of the 12‐month effects of lifestyle and mHealth interventions were conducted. In Study 2, the prevalence of cardiometabolic burden was estimated in a consecutive series of 267 children. In Study 3, body composition was estimated with bioelectrical impedance analysis (BIA) and dual x-ray absorptiometry (DXA) and linear regression analyses were used to estimate the extent to which each methods predicted change in IS. Study 4 describes the development of the Temple Street W82GO Healthy Lifestyle intervention for clinical obesity in children and a controlled study of treatment effect in 276 children is reported. Study 5 describes the development and testing of the Reactivate Mobile Obesity Application. Study 6 outlines the development and preliminary report from a clinical effectiveness trial of Reactivate. Results: In Study 1, meta--‐analyses BMI SDS changed by -0.16 (-0.24,‐0.07, p<0.01) and -0.03 (-0.13, 0.06, p=0.48). In study 2, cardiometabolic comorbidities were common (e.g. hypertension in 49%) and prevalence increased as obesity level increased. In Study 3, BC changes significantly predicted changes in IS. In Study 4, BMI SDS was significantly reduced in W82GO compared to controls (p<0.001). In Study 5, the Reactivate application had good usability indices and preliminary 6‐month process report data from Study 6, revealed a promising effect for Reactivate. Conclusions: W82GO and Reactivate are promising forms of treatment.

Education - research - practice

Through this paper we will look at links between architecture education, research and practice, using a current project as a vehicle to cover aspects of building, pilot and live project. The first aspect, the building project consists of the refurbishment and extension of a Parnell Cottage for a private client and is located near Cloyne, in East Cork, Ireland. The pilot project falls within the NEES Project, investigating the use of materials and services based on natural or recycled materials to improve the energy performance of new and existing buildings. The live project aims to hold a series of on site workshops and seminars for students of Architecture, Architects and interested parties, demonstrating the integration of the NEES best practice materials and techniques within the built project. The workshops, seminars and key project documents will be digitally recorded for dissemination through a web based publication. The small scale of the building project allowed for flexibility in the early conceptual design stages and the integration of the research and educational aspects.

A facilities maintenance management process based on degradation prediction using sensed data

Energy efficiency and user comfort have recently become priorities in the Facility Management (FM) sector. This has resulted in the use of innovative building components, such as thermal solar panels, heat pumps, etc., as they have potential to provide better performance, energy savings and increased user comfort. However, as the complexity of components increases, the requirement for maintenance management also increases. The standard routine for building maintenance is inspection which results in repairs or replacement when a fault is found. This routine leads to unnecessary inspections which have a cost with respect to downtime of a component and work hours. This research proposes an alternative routine: performing building maintenance at the point in time when the component is degrading and requires maintenance, thus reducing the frequency of unnecessary inspections. This thesis demonstrates that statistical techniques can be used as part of a maintenance management methodology to invoke maintenance before failure occurs. The proposed FM process is presented through a scenario utilising current Building Information Modelling (BIM) technology and innovative contractual and organisational models. This FM scenario supports a Degradation based Maintenance (DbM) scheduling methodology, implemented using two statistical techniques, Particle Filters (PFs) and Gaussian Processes (GPs). DbM consists of extracting and tracking a degradation metric for a component. Limits for the degradation metric are identified based on one of a number of proposed processes. These processes determine the limits based on the maturity of the historical information available. DbM is implemented for three case study components: a heat exchanger; a heat pump; and a set of bearings. The identified degradation points for each case study, from a PF, a GP and a hybrid (PF and GP combined) DbM implementation are assessed against known degradation points. The GP implementations are successful for all components. For the PF implementations, the results presented in this thesis find that the extracted metrics and limits identify degradation occurrences accurately for components which are in continuous operation. For components which have seasonal operational periods, the PF may wrongly identify degradation. The GP performs more robustly than the PF, but the PF, on average, results in fewer false positives. The hybrid implementations, which are a combination of GP and PF results, are successful for 2 of 3 case studies and are not affected by seasonal data. Overall, DbM is effectively applied for the three case study components. The accuracy of the implementations is dependant on the relationships modelled by the PF and GP, and on the type and quantity of data available. This novel maintenance process can improve equipment performance and reduce energy wastage from BSCs operation.

Sex offender risk assessment and management in Ireland

This research examined sex offender risk assessment and management in Ireland. It focused on the statutory agencies with primary responsibility (Garda Síochána and the Probation Service). The goal was to document the historical, contextual and current systems, in addition to identifying areas of concern/improvements. The research was a mixed-methods approach. Eight studies were conducted. This incorporated documentary reviews of four Commission to Inquire Reports, qualitative interviews/focus groups with Garda staff, Probation Service staff, statutory agencies, community stakeholders, various Non-Governmental Organisations (NGOs) and sex offenders. Quantitative questionnaires were also administered to Garda staff. In all over 70 interviews were conducted and questionnaires were forwarded to 270 Garda members. The overall findings are: •Sex offender management in Ireland has become formal only since 2001. Knowledge, skills and expertise is in its infancy and is still evolving. •Mixed reviews and questions regarding fitness for purpose of currently used risk assessments tools were noted. •The Sex Offender Act 2001 requires additional elements to ensure safe sex offender monitoring and public protection. A judicial review of the Sex Offender Act 2001 was recommended by many respondents. •Interagency working under SORAM was hugely welcomed. The sharing of information has been welcomed by managing agencies as the key benefit to improving sex offender management. •Respondents reported that in practice, sex offender management in Ireland is fragmented and unevenly implemented. The research concluded that an independent National Sex Offender Authority should be established as an oversight and regulatory body for policy, strategy and direction in sex offender management. Further areas of research were also highlighted: ongoing evaluation and audits of the joint agency process and systems in place; recidivism studies tracking the risk assessment ratings and subsequent offending; and an evaluation of the current status of sex offender housing in Ireland.

The impact of maternal inflammation and maternal stress in the regulation of neurodevelopment and physiological function

The mechanisms governing fetal development follow a tightly regulated pattern of progression such that interference at any one particular stage is likely to have consequences for all other stages of development in the physiological system that has been affected thereafter. These disturbances can take the form of many different events but two of the most common and widely implicated in causing detrimental effects to the developing fetus are maternal immune activation (MIA) and maternal stress. MIA has been shown to cause an increase in circulating proinflammatory cytokines in both the maternal and fetal circulation. This increase in proinflammatory mediators in the fetus is thought to occur by fetal production rather than through exchange between the maternal-fetal interface. In the case of maternal stress it is increased levels of stress related hormones such as cortisol/corticosterone which is thought to elicit the detrimental effects on fetal development. In the case of both maternal infection and stress the timing and nature of the insult generally dictates the severity and type of effects seen in affected offspring. We investigated the effect of a proinflammatory environment on neural precursor cells of which exposure resulted in a significant decrease in the normal rate of proliferation of NPCs in culture but did not have any effect on cell survival. These effects were seen to be age dependent. Using a restraint stress model we investigated the effects of prenatal stress on the development of a number of different physiological systems in the same cohort of animals. PNS animals exhibited a number of aberrant changes in cardiovascular function with altered responses to stress and hypertension, modifications in respiratory responses to hypercapnic and hypoxic challenges and discrepancies in gastrointestinal innervation. Taken together these findings suggest that both maternal infection and maternal stress are detrimental to the normal development of the fetus.

Intersections: proceedings of the youth work and music education symposium

The ‘Intersections: Youth Work and Music Education’ Symposium took place on Friday, 27th June 2014 in University College Cork. This event, held in association with the Institute of Social Sciences in the 21st Century (ISS21), was made possible thanks to funding from UCC’s Strategic Research Fund. The principle aim of this seed funding is to generate new research interests and this presented the ideal opportunity for developing collaborative relationships between youth work and music education lecturers, researchers and practitioners across the island of Ireland. This led to the formation of a new ‘Intersections’ research cluster, comprising representatives from four third-level institutions, each of which offers both youth work and music education undergraduate and/or postgraduate programmes, namely: University College Cork; National University of Ireland, Maynooth; Dundalk Institute of Technology; and, University of Ulster. This document presents some preliminary findings from primary research conducted through each of the participating institutions in their local areas. Data was also collected during the symposium, through engaging in small group discussions populated by the event’s participants. The publication and dissemination of this document was included in the original Strategic Research Fund proposal. Its intended audience includes youth workers, music educators, community-based practitioners, policy-makers and academics who are motivated and enthused by the possibilities of music-oriented youth work in Ireland and beyond.

Bioengineering of nisin to enhance functionality against dairy pathogens

The bacteriocin class of antimicrobial peptides have emerged as a viable alternative to at least partially fill the void created by the end of the golden age of antibiotic discovery. Along with this potential use in a clinical setting, bacteriocins also play an important role as bio-preservatives in the food industry. This thesis focuses on a specific bacteriocin group, the lantibiotics (Lanthionine-containing antibiotics). Their numerous methods of appliance in a food setting and how their gene-encoded nature can be modified to improve on overall bioactivity and functionality are explored here. The use of a lantibiotic (lacticin 3147) producing starter culture to control the Crohn’s disease-linked pathogen Mycobacterium paratuberculosis was assessed in a raw milk cheese. Although lacticin 3147 production did not effectively control the pathogen, the study provided an impetus to employ a variety of PCR-based mutagenesis techniques with a view to the creation of enhanced lantibiotic derivatives. Through the use of these techniques, a number of enhanced derivatives were generated from the ‘hinge’ region of the nisin peptide. Furthermore, a derivative in which the three hinge amino acids were replaced with three alanines represents the first enhanced derivative of nisin to have been designed through a rational process. This derivative also formed the backbone for the creation of an active, trypsin resistant, variant. Through the employment of further mutagenesis methods a derivative was created with potential use as an oral anti-bacterial in the future. Finally a number of lead nisin derivatives were investigated to assess their anti- Streptococcus agalactiae ability, a mastitis associated pathogen. Also a system was developed to facilitate the large scale production of these candidates, or other nisin derivatives, from dairy substrates.

Catalyst and substrate effects in enantioselective C–H insertion reactions of α-diazosulfones

This thesis describes a systematic investigation of the mechanistic and synthetic aspects of intramolecular reactions of a series of α-diazo-β-oxo sulfone derivatives using copper and, to a lesser extent, rhodium catalysts. The key reaction pathways explored were C–H insertion and cyclopropanation, with hydride transfer competing in certain instances. Significantly, up to 98% ee has been achieved in the C–H insertion processes using copper-NaBARF-bisoxazoline catalysts, with the presence of the additive NaBARF critical to the efficiency of the transformations. This novel synthetic methodology provides access to a diverse range of enantioenriched heterocyclic compounds including thiopyrans, sulfolanes, β- and γ-lactams, in addition to carbocycles such as fused cyclopropanes. The synthesis of the α-diazosulfones required for subsequent investigations is initially described. Of the twenty seven diazo sulfones described, nineteen are novel and are fully characterised in this work. The discussion is subsequently focused on a study of the copper and rhodium catalysed reactions of the α-diazosulfones with Chapter Four concentrated on highly enantioselective C–H insertion to form thiopyrans and sufolanes, Chapter Five focused on C–H insertion to form fused sulfolanes, Chapter Six focused on C–H insertion in sulfonyl α-diazoamides where both lactam formation and / or thiopyran / sulfolane formation can result from competing C–H insertion pathways, while Chapter Seven focuses on cyclopropanation to yield fused cyclopropane derviatives. One of the key outcomes of this work is an insight into the steric and / or electronic factors on both the substrate and the catalyst which control regio-, diastereo- and enantioselectivity patterns in these synthetically powerful transformations. Full experimental details for the synthesis and spectral characterisation of the compounds are included at the end of each Chapter, with details of chiral stationary phase HPLC analysis and assignment of absolute stereochemistry included in the appendix.