Users & use: An exploration of the interaction between the user and the digital archive

This thesis will examine the interaction between the user and the digital archive. The aim of the study is to support an in-depth examination of the interaction process, with a view to making recommendations and tools, for system designers and archival professionals, to promote digital archive domain development. Following a comprehensive literature review process, an urgent requirement for models was identified. The Model of Contextual Interaction presented in this thesis, aims to provide a conceptual model through which the interaction process, between the user and the digital archive, can be examined. Using the five-phased research development framework, the study will present a structured account of its methods, using a multi-method methodology to ensuring robust data collection and analysis. The findings of the study are presented across the Model of Contextual Interaction, and provide a basis on which recommendations and tools for system designers have been made. The thesis concludes with a summary of key findings, and a reflective account of how the findings and the Model of Contextual Interaction have impacted digital provision within the archive domain and how the model could be applied to other domains.

An exploration of the positive and negative relationships associated with the development of asthma and atopic disorders in primary school children in Cork

Childhood asthma, allergic rhinitis and eczema are complex heterogenic chronic inflammatory allergic disorders which constitute a major burden to children, their families. The prevalence of childhood allergic disorders is increasing worldwide and merely rudimentary understanding exists regarding causality, or the influence of the environment on disease expression. Phase Three of the International Study of Asthma and Allergy in Childhood (ISAAC) reported that Irish adolescents had the 4th highest eczema and rhinoconjunctivitis prevalence and 3rd highest asthma prevalence in the world. There are no ISAAC data pertaining to young Irish children. In 2002, Sturley reported a high prevalence of current asthma in Cork primary school children aged 6-9 years. This thesis comprises of three cross-sectional studies which examined the prevalence of and associations with childhood allergy and a quasi-retrospective cohort study which observed the natural history of allergy from 6-9 until 11-13 years. Although not part of ISAAC, data was attained by parentally completed ISAAC-based questionnaires, using the ISAAC protocol. The prevalence, natural history and risk factors of childhood allergy in Ireland, as described in this thesis, echo those in worldwide allergy research. The variations of prevalence in different populations worldwide and the recurring themes of associations between childhood allergy and microbial exposures, from farming environments and/or gastrointestinal infections, as shown in this thesis, strengthen the mounting evidence that microbial exposure on GALT may hold the key to the mechanisms of allergy development. In this regard, probiotics may be an area of particular interest in allergy modification. Although their effects in relation to allergy, have been investigated now for several years, our knowledge of their diversity, complex functions and interactions with gut microflora, remain rudimentary. Birth cohort studies which include genomic and microbiomic research are recommended in order to examine the underlying mechanisms and the natural course of allergic diseases.

Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation

Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet periodicity of ribosome profiling data to detect transitions in the translated reading frame. Application of this method to ribosome profiling data generated for human HeLa cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame. Since the initial publication of the ribosome profiling technique in 2009, there has been a proliferation of studies that have used the technique to explore various questions with respect to translation. A review of the many uses and adaptations of the technique is provided in Chapter 1. Indeed, owing to the increasing popularity of the technique and the growing number of published ribosome profiling datasets, we have developed GWIPS-viz (http://gwips.ucc.ie), a ribo-seq dedicated genome browser. Details on the development of the browser and its usage are provided in Chapter 3. One of the surprising findings of ribosome profiling of initiating ribosomes carried out in 3 independent studies, was the widespread use of non-AUG codons as translation initiation start sites in mammals. Although initiation at non-AUG codons in mammals has been documented for some time, the extent of non-AUG initiation reported by these ribo-seq studies was unexpected. In Chapter 4, I present an approach for estimating the strength of initiating codons based on the leaky scanning model of translation initiation. Application of this approach to ribo-seq data illustrates that initiation at non-AUG codons is inefficient compared to initiation at AUG codons. In addition, our approach provides a probability of initiation score for each start site that allows its strength of initiation to be evaluated.

Synthesis and reactivity of pyridine substituted α-diazocarbonyl compounds and exploration of rhodium carboxylates as asymmetric catalysts

The primary objective of this thesis was the preparation of a series of pyridine-containing α-diazocarbonyl compounds and subsequent investigation of the reactivity of these compounds on exposure to transition metal catalysts. In particular, the reactivity of the pyridyl α-diazocarbonyls was compared to that of the analogous phenyl α-diazocarbonyl compounds to ascertain the impact of replacement of the phenyl ring with pyridine. The first chapter initially provides a brief introduction into α-diazocarbonyl chemistry, comprising a compendium of well-established and recently developed methods in the preparation of these compounds, as well as an outline of the reactivity of these versatile substrates. The substantive element of this introductory chapter comprises a detailed review focused on transition metal-catalysed transformations of heterocyclic α-diazocarbonyl compounds, highlighting the extraordinary diversity of reaction products which can be accessed. This review is undertaken to set the work of this thesis in context. The results of this research are discussed in the second and third chapters together with the associated experimental details, including spectroscopic and analytical data obtained in the synthesis of all compounds during this research. The second chapter describes the preparation of a range of novel pyridine-containing α-diazocarbonyl compounds via a number of synthetic strategies including both acylation and diazo transfer methodologies. In contrast to the phenyl analogues, the generation of the pyridine α-diazocarbonyl substrates was complicated by a number of factors including the inherent basicity of the pyridine ring, tautomerism and existence of rotamers. Rhodium- and copper-mediated transformations of the pyridine-containing α-diazocarbonyl compounds is discussed in detail displaying very different reactivity patterns to those seen with the phenyl analogues; oxidation to 2,3- diketones, 1,2-hydride shift to form enones and oxonium and sulfonium ylide formation/rearrangement are prominent in the pyridyl series, with no evidence of aromatic addition to the pyridine ring. The third chapter focuses on exploration of novel chiral rhodium(II) catalysts, developed in the Maguire team, in both intermolecular cyclopropanations and intramolecular C–H insertion reactions. In this chapter, the studies are focused on standard α-diazocarbonyl compounds without heteroaryl substituents. The most notable outcome was the achievement of high enantiopurities for intramolecular C–H insertions, which were competitive with, and even surpassed, established catalyst systems in some cases. This work has provided insight into solvent and temperature effects on yields as well as enantio- and diastereoselectivity, thereby providing guidance for future development and design of chiral rhodium carboxylate catalysts. While this is a preliminary study, the significance of the results lie in the fact that these are the first reactions to give substantial asymmetric induction with these novel rhodium carboxylates. While the majority of the α-diazocarbonyl compounds explored in this work were α-diazoketones, a number of α-diazoesters are also described. Details of chiral stationary phase HPLC analysis, single crystal analysis and 2D NMR experiments are included in the Appendix (Appendix III-V).

An exploration through interview and drawings of the experiences of patients diagnosed with oral cancer across their cancer trajectory

Background: The treatment of oral cancer is complex and lengthy. Curative treatment implies a combination of surgery, radiotherapy and chemotherapy. The main goal of treatment is to guarantee long-term tumour free survival with as little functional and cosmetic damage. Despite progress in developing these strategies, cancers of the oral cavity continue to have high mortality rates that have not improved dramatically over the past ten years. Aim: The aim of this study was to uniquely explore the dynamic changes in the physical, psychological, social and existential experiences of newly diagnosed patients with oral cancer at two points across their cancer illness trajectory i.e. at the time of diagnosis and at the end of treatment. Methodology: A qualitative prospective longitudinal design was employed. Non-probability purposive sampling allowed the recruitment of 10 participants. The principal data collection method used was a digital audio taped semi-structured interview along with drawings produced by the participants. Analysis: Data was analysed using latent content analyses. Summary: Three ‘dynamic’ themes, physical, psychosocial and existential experiences were revealed that interact and influence each other in a complex and compound whole. These experiences are present at different degrees and throughout the entire trajectory of care. Patients have a number of specific concerns and challenges that cannot be compartmentalised into unitary or discrete aspects of their daily lives. Conclusion & Implications: An understanding of the patient’s experience of their illness at all stages of the disease trajectory, is essential to inform service providers’ decision making if the delivery of care is to be client centred. Dynamic and fluctuating changes in the patient’s personal experience of the cancer journey require dynamic, energetic and timely input from health care professionals.

The framework for REVIEWS: an exploration into design principles for an electronic medical early warning system observation chart

The observation chart is for many health professionals (HPs) the primary source of objective information relating to the health of a patient. Information Systems (IS) research has demonstrated the positive impact of good interface design on decision making and it is logical that good observation chart design can positively impact healthcare decision making. Despite the potential for good observation chart design, there is a paucity of observation chart design literature, with the primary source of literature leveraging Human Computer Interaction (HCI) literature to design better charts. While this approach has been successful, this design approach introduces a gap between understanding of the tasks performed by HPs when using charts and the design features implemented in the chart. Good IS allow for the collection and manipulation of data so that it can be presented in a timely manner that support specific tasks. Good interface design should therefore consider the specific tasks being performed prior to designing the interface. This research adopts a Design Science Research (DSR) approach to formalise a framework of design principles that incorporates knowledge of the tasks performed by HPs when using observation charts and knowledge pertaining to visual representations of data and semiology of graphics. This research is presented in three phases, the initial two phases seek to discover and formalise design knowledge embedded in two situated observation charts: the paper-based NEWS chart developed by the Health Service Executive in Ireland and the electronically generated eNEWS chart developed by the Health Information Systems Research Centre in University College Cork. A comparative evaluation of each chart is also presented in the respective phases. Throughout each of these phases, tentative versions of a design framework for electronic vital sign observation charts are presented, with each subsequent iteration of the framework (versions Alpha, Beta, V0.1 and V1.0) representing a refinement of the design knowledge. The design framework will be named the framework for the Retrospective Evaluation of Vital Sign Information from Early Warning Systems (REVIEWS). Phase 3 of the research presents the deductive process for designing and implementing V0.1 of the framework, with evaluation of the instantiation allowing for the final iteration V1.0 of the framework. This study makes a number of contributions to academic research. First the research demonstrates that the cognitive tasks performed by nurses during clinical reasoning can be supported through good observation chart design. Secondly the research establishes the utility of electronic vital sign observation charts in terms of supporting the cognitive tasks performed by nurses during clinical reasoning. Third the framework for REVIEWS represents a comprehensive set of design principles which if applied to chart design will improve the usefulness of the chart in terms of supporting clinical reasoning. Fourth the electronic observation chart that emerges from this research is demonstrated to be significantly more useful than previously designed charts and represents a significant contribution to practice. Finally the research presents a research design that employs a combination of inductive and deductive design activities to iterate on the design of situated artefacts.