College of Science, Engineering and Food Science - Masters by Research Theses
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- ItemAutomated crack classification for underground tunnel infrastructure using deep learning(University College Cork, 2021-11-01) O'Brien, Darragh; Li, Zili; Osborne, John; Irish Centre for Applied Geoscience; CERNOne early sign of tunnel structure deterioration originates in the form of cracking, and therefore crack detection and resultant classification is integral for tunnel structural inspection and maintenance. Conventionally tunnel cracks are manually recorded and classified by trained professionals, which is costly, time-consuming and inevitably subjective. Recent advances in the deep learning space have allowed for automatic cracks detection algorithms to be developed and subsequently utilized in surface structural health assessment of surface buildings, bridges, roads and other civil infrastructure. Nevertheless, these methods of development underperform when implemented for a tunnel structure in an underground environment due to the disparity of illumination combined with the congested image data caused by pipes, steel mesh, wires, and other tunnel amenities. This thesis develops an intuitive crack directional classification approach that increases the accuracy, reduces time and subjectivity in comparison to traditional inspection methods. The detection of cracks by utilising CNN’s is antiquity investigated by in literature however little of the writings develop the algorithm further for classification purposes. The novel of this research is centred on the development of a crack classification algorithm that adheres to the directional classification rationale. The output information of the crack classification is correlated to the structural movement of the lining providing a deeper understanding of the tunnel behaviors. To surmount these challenges, this thesis constructs a Convolution Neural Network (CNN) image-based crack detection method accompanied by an innovative crack classification for underground infrastructure environment. Conventional CNN’s are developed from scratch, the proposed CNN incorporates transfer learning in the form of the VGG16 model with weights transferred from ImageNet. The transfer model was trained under various scenarios to determine the optimal model for the operational task in the tunnel environment. The various models are trained using over 10’000 images validated on 2’500 images all of which are 256 x 256 pixels in size, these models are all subsequently tested using 30 images 3072 x 4096 pixels in size. The transfer learning model used outperforms that of the traditional CNN training method of training from scratch. The optimum transfer model accomplished testing metrics of 96.6%,87.3%,92.4%,89.3% for Accuracy, Precision, Recall and F1 score respectively. The proposed CNN appraises images regarding the existence and subsequent location of cracks. Detected cracks are subjected to the secondary classification CNN where the crack is categorized into one of the four crack classes which include the three directional classes of Horizontal, vertical and diagonal with the last crack classes incorporated to represent complex crack regions. The secondary classification CNN attains an Accuracy of 92.3% a Precision of 83.9% a Recall value of 82.3 % and an F1 score of 81.5%. The performance of the manufactured integrated detection and classification method is analysed by performing a field test to evolve the research from a controlled theoretical setting into a realistic tunnel environment. The field test is performed on three separate tunnel sections with an amassed distance of 150 meters with the section testing the robustness, speed and ultimately prospect of application in the CERN inspection scenario. The outcome from this testing demonstrates that the established CNN crack detector/classifier can effectively overwhelm the unfavourable tunnel environment and accomplish results to a high standard.
- ItemHow do children and young people with intellectual and/or developmental disabilities experience the therapy process when engaging with occupational therapists, speech and language therapists, and physiotherapists?(University College Cork, 2022-03-26) Hynes, Patrick Joseph; Lynch, Helen; Robinson, KatieBackground: The UN Convention on the Rights of Persons with Disabilities (CRDP) was adopted by the United Nations General assembly in 2006 to protect, promote and ensure full equal enjoyment of all human rights and fundamental freedoms by all persons with disabilities. The right of all children to be heard and taken seriously constitutes one of the fundamental values of the United Nations Convention on the Rights of the Child (UNCRC). For children with disabilities the UNCRC applies, confirming the child’s right to have a voice in all matters that affect them. Children with disabilities face barriers to participation and threats to enactment of their rights, including in healthcare settings such as those provided by the disciplines of occupational therapy, speech and language therapy, and physiotherapy. Children with disabilities frequently access these services. These disciplines purport to deliver client centred services in line with human rights. However, little is known about children’s experiences of these therapies as voiced by children themselves. Aim/Objectives: Through the completion of a systematic review of qualitative evidence, this study aimed to explore how children with intellectual and/or developmental disabilities experience the therapy process when engaging with occupational therapists, speech and language therapists, and physiotherapists. Methods: A systematic search of seven databases was undertaken, and included studies were synthesised following the stages of meta-ethnography described by Noblit and Hare (1988). Databases searched were Academic Search Complete, AMED, CINAHL complete, MEDLINE, APA PsycINFO, APA PsycARTICLES, and Social Sciences Full Text (H.W. Wilson). The Preferred Reporting Items for Systemic Reviews and Meta-Analysis Protocols (PRISMA-P) checklist was used to illustrate the research strategy procedures. Searches were limited to English language publications. No limits were applied to date of publication. The Critical Skills Appraisal Skills Programme (CASP) Qualitative Studies Checklist was used to critically appraise the quality of the included papers. Findings: Sixteen studies were included in the synthesis. Four interrelated themes were identified; “Interpersonal experience of therapy”, “Who is in the driving seat? – Children’s experiences of power in therapy”, “The nuts and bolts of therapy: experiencing therapy in the here and now”, and “Making sense of therapy”. Conclusions: The value of qualitative research can be seen in this review due to the rich data that was extracted from a range of qualitative papers. Children with intellectual and/or developmental disabilities described how they experienced therapy sessions. Common experiences included having fun (and a desire for therapy to be more fun) and conversely boredom, discomfort and pain were also commonly experienced. Children described their interpersonal experiences and relationship with the therapist during therapy including their experiences of engagement, communication and trust and their experiences of therapist attunement. Children described how they understood therapy and its purpose, including their experiences of making progress in therapy or achieving outcomes and how therapy related to their view of themselves and their views of ability and disability. Children reported on their experiences of power in therapy, with finding suggesting that therapists often hold power over decisions and goals for therapy, and less frequently children hold power, often regarding smaller decisions. Findings point to the need for occupational therapists, speech and language therapists, and physiotherapists who work with children with intellectual and/or developmental disabilities to further create opportunities for children to be part of the decision-making process and goal setting process. Through interrogation and reflection on their practice, therapists have the potential to be poised for action to utilise a model such as Lundy’s model of participation (Lundy, 2007) to ensure that children experience the full participation in therapy of having their voice heard in all matters that affect them.
- ItemFeasibility study of reusing concrete gravity-based foundations designed for tidal energy converters(University College Cork, 2022) Dineen, Kate; Li, Zili; Ryan, Paraic; European Regional Development FundTidal energy converter devices have been developed to capture the enormous energy potential of the tides. These devices rely on robust mooring and foundation systems to ensure efficient energy extraction in operational conditions, and stability in extreme environmental conditions. Gravity-based foundations (GBF) are currently the most commonly used foundation type within the tidal energy industry. While tidal turbines are typically supported using bespoke carbon-steel tripod structures, concrete gravity-based foundations have been put forward by a number of studies as an alternative support solution. Several novel concrete GBF concepts exist and the developers of such concrete structures state that these foundations may be reused or relocated following decommissioning. Reuse of these massive concrete structures would greatly reduce construction and demolition (C&D) waste, and the need for new concrete GBFs for future devices, thus contributing significantly to the sustainability of the tidal energy industry. However, the concept of reusing concrete gravity-based foundations following long periods of deployment underwater has not been tested in real-world scenarios due to the nascent nature of the industry and long commissioning time periods. As highlighted from a related concept in the oil and gas industry, several safety issues may arise from reusing and relocating concrete GBFs, including geotechnical hazards and concrete degradation due to corrosion. Therefore, this study assessed the practicalities of reusing concrete foundations following decommissioning by designing a concrete GBF from first principles to be used for further analysis. This representative GBF was then extensively tested using Plaxis geotechnical software to investigate soil subsidence and differential settlement, assessing their impact on GBF relocation feasibility. Subsequently, the risk of corrosion to the steel reinforcement in the GBF was examined by, firstly, modelling the chloride concentration profile of the concrete, and secondly, investigating the interrelationship between oxygen availability and water saturation level. Thorough investigation into these study considerations can significantly contribute to the determination of whether it is practicable to reuse or relocate concrete gravity-based foundations in the tidal industry. The findings from the geotechnical analysis supports the possibility of reusing and relocating concrete GBFs for tidal turbines as both the total settlement and the tilt were significantly less than the allowable total settlement and tilt tolerance in a deployment site for which the GBF was designed and a contrasting site for which it was not. However, the findings from the concrete degradation analysis does not support the feasibility of reusing concrete GBFs. A chloride ingress analysis encapsulating three datasets indicated that the critical chloride threshold would be surpassed during a GBFs deployment period, meaning that the protective passive layer on the steel would be compromised leaving it vulnerable to corrosion should sufficient oxygen and water be present.
- ItemThe carbon sequestration potential of the Irish uplands(University College Cork, 2022-09-01) Swan, Sophia; Harrison, Simon; Sullivan, TimothyThe Irish uplands, which cover much of the western half of the country, have long been known as a bare, treeless landscape, used for grazing livestock. They are characterised by thin, peaty unproductive soils, and tend to provide poor economic returns to those farming them. A land use shift is currently occurring across the uplands, with many farmers ceasing actively to exploit the land and leaving the industry, a process exacerbated by isolation, poor incomes, and a lack of successors willing to continue farming the family landholdings. This comes at a time when Ireland is urgently seeking novel approaches to sequester carbon from the atmosphere, and offset GHG emissions from intensive agriculture. Expanding woodland cover onto degraded agricultural land is one of several potential methods being explored worldwide to increase terrestrial carbon sequestration and storage. This study aims to determine the future carbon sequestration potential of the Irish uplands, through the potential regeneration of native woodland, in the event that their land use shifts away from livestock grazing and the associated vegetation management of burning. We chose the Iveragh peninsular, Co. Kerry, SW Ireland as our study site. This is an area of extensive upland landscape, with a long history of extensive cattle and sheep grazing on the unenclosed land, including a considerable area of upland commonage. We used two approaches to estimate the potential carbon sequestration potential of regenerating woodland in the uplands. Firstly, we wished to determine the environmental and anthropogenic factors associated with woodland regeneration currently observed within the study site, so as to better predict the location and extent of any future woodland regrowth. This was achieved using a combination of online GIS mapping techniques, coupled with ground-truthing of the extent of tree regrowth. Secondly, we wished to establish the realistic nature of any potential future natural woodland cover, in terms of species composition, density and growth form of trees and in the soil composition underneath such woodland. We surveyed the woodland cover of a number of small, uninhabited and unexploited islands within lakes of the southwestern uplands. These islands were ascertained to have been ungrazed since at least the middle 19th century and likely for much longer, owing to their small size and inaccessibility to grazing animals. The vegetation and soil data were then used to calculate the potential carbon storage of any future woodland regeneration. GIS analysis revealed that slope, elevation, soil type, controlled burning practises and proximity to woodland seed source all influenced the current extent of tree regeneration in the study site. Significant differences were observed between the vegetative composition of the islands and adjacent mainland sites, with dense woodland cover consisting primarily of holly, rowan and birch observed across islands. This island vegetation sequestered ten times more carbon per hectare than adjacent mainland sites, which predominantly consisted of Molinia grassland, with no woodland growth noted. Soils in mainland sampling areas were consistently wetter and less carbon rich than those sampled on islands. Based on these factors, it was determined that within 40 years, 0.6% of the Irish uplands could show natural woodland regeneration, should barriers to re-growth (sheep grazing and vegetation burning) be removed. A higher percentage woodland regeneration could be achieved with additional proactive tree planting programme, which is likely necessary to establish woodland growth in areas remote from existing trees and which have been treeless for many centuries. Despite such a small, predicted increase in percentage tree cover via natural means, this still provides the potential to store over 600,000 tonnes of carbon, thus providing Ireland with valuable ways to offset carbon emissions, along with increasing biodiversity and reduce flood risk over the coming years.
- ItemGeneration of a CRISPR-Cas9 mediated knock-in reporter for the GRIA3 candidate gene for schizophrenia(University College Cork, 2022-09-27) Breen, Lisa; McCarthy, Tommie V.Glutamatergic neurotransmission impairment is considered a major feature of the neurobiology of Schizophrenia (SZ) and implicates genes in this pathway as potential candidates for the condition. A study on α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor genes found strong evidence of association between the Glutamate Ionotropic Receptor AMPA Type Subunit 3 (GRIA3) gene and SZ. Similarly, a recent report has identified a number of genes, including GRIA3, with ultra-rare disabling variants that promote SZ. The association of a rare disabling GRIA3 variant with SZ indicates that reduced expression of the gene predisposes people to SZ and suggests that increasing the expression GRIA3 could be a potential therapeutic avenue for treatment of the condition. The aim of this thesis was to establish a cell model enabling rapid analysis of GRIA3 expression. Such a model would be of high value and in addition to facilitating expression studies on GRIA3, would enable screening for new drugs that increase GRIA3 expression which could have therapeutic potential. This project aimed to modify the cell line using a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) - CRISPR associated protein 9 (Cas9) homology directed repair (HDR) approach so that a donor reporter vector containing the Gaussia secreted luciferase gene and linked green fluorescent protein (GFP) or neomycin resistance gene (Neo) gene would be integrated directly under the control of the endogenous promoter of the GRIA3 gene, in a manner that retains intact expression of the GRIA3 protein. This donor reporter vector was successfully constructed and has significant general use as it facilitates cloning of any pair of homology arms and the insertion of a reporter cassette into any target gene via CRISPR-Cas9 HDR. Flanking GRIA3 homology arms were inserted 5’ and 3’ of the reporter cassette for CRISPR-Cas9 HDR mediated insertion into the GRIA3 locus in human U87 glioblastoma cells. Luciferase activity was monitored post-transfection and was present at low levels suggesting successful HDR events. However, the presence of the donor cassette could not be demonstrated at the GRIA3 locus. It was not possible to distinguish if the luciferase activity resulted from read through of the donor plasmid or if a low number of targeted integration events had occurred. Further work involving isolation of individual clones of the targeted U87 cells and checking for the presence of the donor at the GRIA3 locus will be necessary to resolve this question. Overall, this reporter system should be of high value for targeting other loci and can be improved further by modifications to ensure luciferase is only active when inserted into the targeted locus.