Research Theses
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Item Childhood trauma and trauma-informed care in early intervention in psychosis(University College Cork, 2024) Hunt, Evan; Lambert, Sharon; Murphy, Mike; Lonergan, Edgar; O'Connor, Karen; Health Service ExecutiveThis doctoral thesis explores the integration of Trauma-Informed Care (TIC) within Mental Health Services (MHS) and examines the prevalence and impact of childhood trauma in individuals experiencing First-Episode Psychosis (FEP). Through a systematic review, the research identifies core principles and practices of TIC in MHS, leading to the development of a framework that encompasses therapeutic environment, sociocultural responsiveness, and workforce development, providing a blueprint for operationalising TIC within mental healthcare. Building on this foundation, an empirical study establishes the demographic and clinical profile of service users accessing an Early Intervention in Psychosis (EIP) service in Ireland. Findings reveal the complex and diverse needs of the population, including significant gender differences in age of onset, substance use, and functional impairments, emphasising the necessity for tailored interventions in EIP services. Further research investigates the prevalence of childhood trauma among FEP service users, revealing a high rate of trauma exposure (78%), with emotional abuse and neglect being most common. Gender differences were also found, with females reporting higher severity and cumulative trauma. These findings highlight the importance of integrating trauma-informed approaches into EIP services to address the multifaceted needs of individuals with psychosis. Finally, the thesis examines the longitudinal impact of childhood trauma on clinical outcomes in FEP. While trauma severity was linked to self-harm, it did not significantly affect other baseline clinical characteristics. Over the course of 12 months of treatment, significant improvements in symptomatology and functioning were observed, regardless of trauma history, highlighting the effectiveness of EIP services in supporting individuals with FEP. This research collectively emphasises the need for trauma-informed, individualised care to optimise outcomes for individuals with early psychosis.Item Digital Humanities: a bridge between computer vision and study of art(University College Cork, 2024) Xiao, Shuang; Murphy, Orla; Allen, Graham; China Scholarship CouncilFrom Humanities Computing to Digital Humanities, the development of digital technologies has brought many possibilities to the Humanities disciplines, including the exploration of painting research through deep learning. Such research currently focuses primarily on improving algorithmic performance, mainly derived from the field of computer vision, while technical barriers and disciplinary jargon make it difficult for Humanities scholars to engage in this type of research. However, effective interdisciplinary research requires communication and dialogue across multiple fields. On the one hand, the participation of Humanities scholars can make deep learning technologies more targeted in exploring painting research, thereby providing valuable research insights. On the other hand, Humanities scholars can critically examine deep learning, offering feasible suggestions for technological improvement, and identifying and avoiding potential ethical issues. Based on this research objective, this thesis conducts the following studies. The thesis first introduces the context of this research: “Digital Humanities,” “Artificial Intelligence,” “Computer Vision,” “Digital Art History,” and “Cultural Analytics.” and reviews existing research on deep learning in painting studies, critical research in Digital Humanities, and ethical issues in AI. Then, the thesis details the application process of deep learning in painting research in four parts: “Data Preparation,” “Model Training,” “Evaluation and Optimization,” and “Analysis and Interpretation,” each part including an introduction to basic knowledge, the application of technology (experiments), and reflections on deep learning. Chapter One, Data Preparation, introduces the basics of art image datasets, discussing how to assess, select, and clean image datasets. The experiment demonstrates how to organize datasets with code according to one’s research objectives, preparing for model training. The reflective section discusses the subjectivity and biases of datasets, the characteristics of art data itself, and the ethical, copyright, and technical limitations of datasets, proposing some targeted and feasible suggestions. Chapter Two, Model Training, uses CNNs as examples to introduce the internal structure of neural networks and various types of CNNs. The experiment demonstrates how to train a simple neural network model to predict the authors of paintings. Lastly, it reflects from a Humanities perspective on the potential issues that may arise during the model training process, including programming challenges, ethical issues and transparency of algorithms, the comparison between machine learning and human learning, and the effectiveness of transfer learning in art images. Chapter Three, Evaluation and Optimization, introduces methods for evaluating and optimizing models, and through experiments, evaluates and optimizes the model trained in Chapter Two. The reflection section discusses minimal computation, model accuracy, as well as issues with weights and biases. Chapter Four, Analysis and Interpretation, differentiates between model explanations from a computational perspective and model interpretations from a Humanities perspective. Based on the objectives and themes of painting research, it proposes five potential ways in which deep learning can assist painting research, including recognition of features and patterns, comparative studies, object detection, unsupervised clustering, and image generation, with detailed case explanations for each path. After completing the introduction and exploration of deep learning, this chapter ultimately suggests a research approach that combines Humanities and computing and discusses the value of AI-generated art based on current research trends. The biggest contribution of this thesis is in linking the fields of painting research and deep learning, which have vastly different research goals and methods, to form a research approach that allows for mutual communication and contribution. This approach represents a Digital Humanities research approach, promotes equal and dialogical exploration between Humanities research and Computer Science, where technology offers new insights and possibilities for Humanities research, and Humanities research provides critical suggestions for technological development.Item Differential regulation of the phosphorylated and dephosphorylated forms of the ubiquitin-conjugating enzyme Ubc6e(University College Cork, 2024) Burns, Stephanie; Fleming, John V (Eoin)The ubiquitin proteasome system (UPS) is a key stress response employed by cells to remove damaged and misfolded proteins that accumulate in the endoplasmic reticulum (ER) during energy deprivation, hypoxia, or viral infection. Ubc6e is an ER-localised ubiquitin-conjugating enzyme that plays an important role in the proteasomal degradation of misfolded proteins and can be phosphorylated at serine residue 184. Recent studies have demonstrated that Ubc6e is co-localised with p62/sequestrosome, which is a cargo receptor that delivers ubiquitinated cargo to autophagosomes for degradation. To further investigate the possible role that Ubc6e may play in autophagy, we aimed to investigate any protein-protein interactions between p62 and Ubc6e and we also aimed to investigate the effect of autophagic-related proteins, p62 and ULK1 on Ubc6e. From our research, we saw that Ubc6e levels are reduced when co-expressed with proteins that promote autophagy. Specifically for the autophagy inducer ULK1, we saw differential regulation between the phosphorylated and dephosphorylated forms of Ubc6e, suggesting that the S184 phosphorylation may protect the protein from autophagic degradation. Degradation of the dephosphorylated form, on the other hand, did not depend on S184 phosphorylation, or the catalytic activity of Ubc6e. Neither was it dependent absolutely on ER localisation. Finally, although ULK1 co-expression did not appear to specifically alter the ER/ perinuclear localisation of Ubc6e, it was noted that amino-terminal tagging with GFP led to a ULK1-related localisation of Ubc6e to intracellular vesicles. Together our results suggest that Ubc6e does play a role in autophagy however it is not mediated by the direct interaction with p62.Item Unravelling the role of Bacteroides and Phocaeicola in the human gut: exploring evolutionary dynamics, mother-to-infant vertical transmission, and functional characteristics(University College Cork, 2023) da Silva Morais, Emilene; Stanton, Catherine; Ross, R. Paul; Science Foundation Ireland; IFF - International Flavors & FragrancesThe human gut microbiota is composed of trillions of microrganims and plays a major role in human health and disease by performing a series of physiological functions, such as protection against pathogens, energy production, maintenance of intestinal barrier integrity, and regulation of the immune system. Bacteroides is one of the major genera present in the human gut. Bacteroides colonise the gut soon after birth in vaginally born babies and its abundance increases after weaning. However, different studies have shown that Bacteroides are missing or present in lower relative abundance in infants born by caesarean section (CS). Lower Bacteroides relative abundance has been associated with higher risk of atopic sensitization, especially in children of Asian heritage. Bacteroides and Phocaeicola have been linked to both health and disease. In the gut, Bacteroides is often associated with health benefits, but it can become an opportunistic pathogen in other body sites. Herein, this thesis explored a number of research topics aimed at gaining a better understanding of the role of Bacteroides and Phocaeicola in the human gut, such as production of metabolites, genetic and evolutionary features, vertical transfer, persistence and relative abundance of Bacteroides and Phocaeicola in early life. Characterization of a new species of Bacteroides and a potential Phocaeicola probiotic strain were also carried out. In Chapter 1, the current knowledge about the association of Bacteroides and Phocaeicola with health and disease was explored. Metabolic conditions associated with altered levels of these species, as well as their role as opportunistic pathogens and the challenges associated with the use of Bacteroides and Phocaeicola as probiotic were investigated. Numerous pre-clinical studies showed the benefits of strains of Bacteroides and Phocaeicola in various conditions, however, more clinical research is needed to evaluate if these benefits extend to humans. Chapter 2 explores Bacteroides and Phocaeicola in early life. Metagenomic analysis was carried out to compare the relative abundance of these species in vaginally delivered (VD) and CS-born infants during the first year of life. The presence of vertically transferred strains and strains that were persistent across different time points were also evaluated. Whole genome sequence (WGS) was carried out and the average nucleotide identity (ANI) was used to determine whether different isolates were the same strain. A blast comparison of the whole genome was also carried out. Metabolomics analyses and γ-aminobutyric acid (GABA) production was carried out in a subset of the isolates. Metagenomic analysis showed that Bacteroides are absent in CS children who were not exposed to antibiotics before birth, but present in CS-born children whose mothers were exposed to antibiotics during pregnancy and VD infants. Five groups of isolates that were vertically transferred and/or persistent across different timepoints were identified. The metabolomics profile showed that Bacteroides and Phocaeicola strains were able to produce organic acids and indole. On Chapter 3 a comparative analysis of the genomes of P. dorei and P. vulgatus were performed. Nearly 4000 assemblies were used to build the pan-genome of these species and to evaluate functional differences, like Carbohydrate-Active enZymes (CAZyme) content, antimicrobial resistance profile and mobile genetic elements. Both species have an open pan-genome and a similar antimicrobial resistance profile, but different CAZyme content, indicating they might have evolved to occupy different niches. We also hypothesised that P. dorei evolved from a larger than average subclade of P. vulgatus. Chapter 4 describes a novel Bacteroides species, Bacteroides sp. nov. (strain MSB163), which was isolated from a healthy mother 4 weeks after giving birth. The WGS, metabolomic profile, respiratory quinones, polar lipids, growth conditions and fermentation of different carbohydrate sources were analysed. Apart from differences in the genome, the main differences between MSB163 and its closest relatives, B. cellulosilyticus and B. intestinalis are the presence of phosphatidylglycerol on its cell membrane and the ability to ferment melezitose and sorbitol. In chapter 5, we characterize strain MSB026 (P. dorei), a bacteriocin producer and potential probiotic candidate. MSB026 was isolated from a VD infant, not exposed to antibiotics. WGS, growth conditions, 2’FL utilization, and production of compounds of interest were analysed. The production of health beneficial compounds, like GABA and SCFAs, associated with the strain’s technological robustness make it a potential probiotic candidate. Bacteroides and Phoceicola play a major role in the prevention and onset of different health conditions. They are present in the gut from the first days of life, producing numerous metabolites and interacting with the host in differen ways. The results outlined in this thesis expand on the knowledge of two important commensal genera of the human gut that have an important role in host health.Item Being a parent with a physical disability: an exploration of lived experiences(University College Cork, 2024) Dunne, Amanda; Ryan, Christian; Lennon, Aisling; Brennan, EmmaObjective: This thesis portfolio aims to (1) synthesise the qualitative literature exploring the parenting experiences of adults with both acquired and congenital physical disabilities, and (2) explore the parenting experiences of fathers with acquired physical disabilities. Methods: A systematic review and thematic synthesis were conducted to synthesise the qualitative literature exploring the parenting experiences of adults with physical disabilities. 11 studies were identified following searching of CINAHL, PsycINFO, PubMed, Scopus and Web of Science databases, in addition to backward snowballing. All studies were also subjected to quality appraisal. Seven fathers with acquired physical disabilities were also interviewed about their parenting experiences, with an interpretative phenomenological analysis being undertaken to analyse the data collected. Results: Each of the studies within the systematic review were deemed to be of high quality, with seven themes identified from the thematic synthesis: stigmatisation and the need to prove competence as a parent; feeling underrepresented as a parent with a physical disability; environmental limitations; experiences of accessing support; using skills and strategies to fulfil parenting role; children’s roles and reactions, and changes as they grow, and safety, wellness and health when parenting with a physical disability. Three group experiential themes were identified from the interpretative phenomenological analysis of seven fathers’ interviews: (1) the meaning of fatherhood, (2) navigating a complex emotional landscape, and (3) the dynamic nature of relationships. Conclusions: A number of clinical implications stemming from the findings of both studies are discussed, in addition to important areas for future research.