UCC Theses

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UCC theses
CORA is the central repository for electronic copies of UCC postgraduate research theses. While we aim to provide full-text access, in certain circumstances theses may not have been provided by the graduate or may be embargoed in part or in full. To see details of all UCC theses in the UCC Library collections go to the UCC Library catalogue

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Now showing 1 - 20 of 2358

13.12.18
(University College Cork, 2019) D'Arcy, Kathy; Davis, Alex; O'Donoghue, Bernard; Irish Research Council
This piece takes the form of a long experimental poem in three parts followed by a ‘guidebook’ which is referenced throughout so that it can be read alongside. The poem is a heteroglossic exploration, using fictional voices and fragmented texts, of the blurred visibility (the ‘weighted silence’ as I have called it) of women in Irish history and literature, and an attempt to creatively problematise that omission. The first section begins in the mythological beginnings of Ireland, the second takes place in the first years of the hypermasculine ‘Irish State’, and the third occurs in the present. The various voices clash and coincide, speak over and beyond each other, and rise together in a palimpsest of re-articulation.
2000 - 2017 inventory of extreme weather events in Ireland
(2019-01-01) Pasik, Adam; Hickey, Kieran; Leahy, Paul; Environmental Protection Agency
Globally, extreme weather events are responsible for far more financial losses than the increase in mean temperature. In the context of climate change, attribution of the ever-increasing losses from these high-impact events is still contested. Some research finds climate change to drive the rising costs while other attributes this trend to socioeconomic factors such as higher population densities, demographical shift, accumulation of wealth and exposure of assets. As of yet no systematic inquiry into this matter has been carried out in Ireland. This research compiles a dataset of extreme weather events in Ireland between 2000 and 2017 based on an applied financial threshold of €30m. The overall annual losses are adjusted for inflation and emerging trends are identified and discussed. Population change and per capita GDP are considered as important variables in this research due to their potential to exacerbate losses even without any change in their frequency or climate. Temporal trends in population and per capita GDP are discussed as well as emerging spatial patterns in population distribution. Furthermore, loss values are normalized by adjusting them for inflation, population rise and GDP growth to better understand the relationship between losses from weather extremes and societal and economic factors. The results are contextualized in relevant peer-reviewed literature and compared to similar studies carried out elsewhere in the world. This study, in agreement with similar research implemented elsewhere, establishes an increasing trend in annual losses from weather extremes in Ireland, while also demonstrating that this trend is nullified by population rise and economic growth. During the study period population of Ireland has increased by 26.4%, resulting in 1 million new residents, meanwhile, the per capita GDP has more than doubled. Larger and wealthier populations hold more assets which can be potentially damaged. Losses from weather extremes in Ireland adjusted for population and wealth increase no longer show a rising trend, highlighting the importance of population densities and wealth accumulation as key factors driving the increase in financial damages stemming from weather and climatic extremes.
3D printing of dairy-based ingredients and investigation into Irish consumer acceptance of 3D food printing applications
(University College Cork, 2022-05-05) Ross, Megan M.; Kelly, Alan; Morrison, Alan P.; Crowley, Shane; Mccarthy, Mary; The Lauritzson Foundation
Three-dimensional (3D) food printing is a type of additive manufacture in which foods with certain rheological characteristics are mechanically layered to create 3D structures from a digitally model. 3D food printing can potentially offer consumers a range of benefits, such as personalised nutrition, customisable textures and unique structures and shapes. This multidisciplinary thesis outlines research completed in three key areas: engineering, food science and consumer science, reflecting the importance of evaluating 3D food printing in this holistic manner. The primary objectives of this work was three-fold: (1) to develop a practical 3D food printer design suitable for printing dairy-based ingredients; (2) to identify and develop suitable dairy-based recipes and investigate factors affecting their printability; and (3) to explore determinants of Irish consumer willingness to try 3D food printing applications. The rationale behind two selected 3D food printer designs (Cartesian and Delta), as well as a brief comparison between the functionality of both designs, are reported. The effects of printing parameters (i.e., nozzle diameter, distance to print bed, print speed etc.) on print quality are also discussed. Certain physicochemical factors such as pH and structural protein content were found to significantly affect the printability and texture of a basic processed cheese recipe. Samples with a higher pH (pH 5.8) tended to print less accurate grids and were significantly softer and less gummy, chewy and resilient than those with lower pH (≤ pH 5.6). Printed processed cheese recipes formulated with fresh curd (high structural protein content) resulted in significantly harder prints, yet printed grids inaccurately due to the material dragging during printing. Viscosity profiles were created for each processed cheese recipe using rheological methods and correlated with absolute printing precision values to identify a range of suitable recipes for accurate printing. The effect of various factors on the printability and functionality of Micellar Casein Concentrate (MCC) suspensions was also investigated. Increasing calcium chloride concentration (5 mM) of suspensions lead to significantly harder printed samples, which had lower dissolution and solubility rates than control or printed samples with lower calcium chloride concentration (1 mM). MCC suspensions printed in porous lattice structures were found to dissolve at a quicker rate than those printed in a hemisphere structure due to a higher surface area to volume ratio. An example of possible 3D-printed product concepts demonstrating the potential of MCC as a printing material is presented. In order to achieve a balanced and comprehensive understanding of 3D food printing technology from a number of perspectives, consumer acceptance research was incorporated into this study to compliment the food science and engineering narrative. Using qualitative methods, a series of themes were identified as forming Irish consumers’ perceptions of 3D food printing applications. Consumers’ affinity for naturalness and a strong association for unprocessed, homemade meals were considered barriers to acceptance of 3D-printed foods. As an extension of this study, data from quantitative research further revealed perceived personal relevance as a significant determinant affecting the dependent variable (i.e., willingness to try 3D food printing applications in the food service sector). Trust in science was found to diminish the negative effects of novel food technology neophobia on willingness to try. Potential solutions for negating factors affecting consumer acceptance are also discussed, which may be of benefit to those looking to market 3D food printing applications in the Irish marketplace. The findings from these studies present an opportunity for food sector stakeholders to utilise this knowledge as part of their foundation to build upon and create novel 3D food printer designs and printable formulations which are suitable for acceptance in the consumer market.
The Aarhus Convention and its implementation in Ireland: strengthening the role of NGOs in environmental governance
(University College Cork, 2015) Comerford, Phyllis; Ryall, Aine; Irish Research Council
One of the most striking features of the 1998 Aarhus Convention on Access to Information, Public Participation in Decision-making and Access to Justice in Environmental Matters is the leading role envisaged for environmental nongovernmental organisations (ENGOs) in furthering compliance with environmental law. The Convention aims to secure the special status of ENGOs in environmental governance procedures by guaranteeing procedural rights of access to information, participation in decision-making and access to review mechanisms. Although Ireland did not become a Party to the Convention until September 2012, the Aarhus procedural rights were already guaranteed under European Union (EU) law. The EU has been a Party to the Aarhus Convention since May 2005 and has adopted a number of legislative measures to implement the Convention. This thesis examines the evolving role of ENGOs in environmental governance in Ireland. It provides a doctrinal analysis of the impact of the Aarhus Convention and EU law on Irish law and governance arrangements involving ENGOs. The thesis considers the extent to which Ireland has delivered faithfully on the standards set by the Aarhus Convention to facilitate ENGOs to fulfil the role envisaged for them under the Convention.
Ab initio calculations of group 4 metallocene reaction mechanisms: atomic layer deposition and bond activation catalysis
(University College Cork, 2013) Zydor, Aleksandra; Elliott, Simon D.; European Commission; Enterprise Ireland
Thin film dielectrics based on titanium, zirconium or hafnium oxides are being introduced to increase the permittivity of insulating layers in transistors for micro/nanoelectronics and memory devices. Atomic layer deposition (ALD) is the process of choice for fabricating these films, as it allows for high control of composition and thickness in thin, conformal films which can be deposited on substrates with high aspect-ratio features. The success of this method depends crucially on the chemical properties of the precursor molecules. A successful ALD precursor should be volatile, stable in the gas-phase, but reactive on the substrate and growing surface, leading to inert by-products. In recent years, many different ALD precursors for metal oxides have been developed, but many of them suffer from low thermal stability. Much promise is shown by group 4 metal precursors that contain cyclopentadienyl (Cp = C5H5-xRx) ligands. One of the main advantages of Cp precursors is their thermal stability. In this work ab initio calculations were carried out at the level of density functional theory (DFT) on a range of heteroleptic metallocenes [M(Cp)4-n(L)n], M = Hf/Zr/Ti, L = Me and OMe, in order to find mechanistic reasons for their observed behaviour during ALD. Based on optimized monomer structures, reactivity is analyzed with respect to ligand elimination. The order in which different ligands are eliminated during ALD follows their energetics which was in agreement with experimental measurements. Titanocene-derived precursors, TiCp*(OMe)3, do not yield TiO2 films in atomic layer deposition (ALD) with water, while Ti(OMe)4 does. DFT was used to model the ALD reaction sequence and find the reason for the difference in growth behaviour. Both precursors adsorb initially via hydrogen-bonding. The simulations reveal that the Cp* ligand of TiCp*(OMe)3 lowers the Lewis acidity of the Ti centre and prevents its coordination to surface O (densification) during both of the ALD pulses. Blocking this step hindered further ALD reactions and for that reason no ALD growth is observed from TiCp*(OMe)3 and water. The thermal stability in the gas phase of Ti, Zr and Hf precursors that contain cyclopentadienyl ligands was also considered. The reaction that was found using DFT is an intramolecular α-H transfer that produces an alkylidene complex. The analysis shows that thermal stabilities of complexes of the type MCp2(CH3)2 increase down group 4 (M = Ti, Zr and Hf) due to an increase in the HOMO-LUMO band gap of the reactants, which itself increases with the electrophilicity of the metal. The reverse reaction of α-hydrogen abstraction in ZrCp2Me2 is 1,2-addition reaction of a C-H bond to a Zr=C bond. The same mechanism is investigated to determine if it operates for 1,2 addition of the tBu C-H across Hf=N in a corresponding Hf dimer complex. The aim of this work is to understand orbital interactions, how bonds break and how new bonds form, and in what state hydrogen is transferred during the reaction. Calculations reveal two synchronous and concerted electron transfers within a four-membered cyclic transition state in the plane between the cyclopentadienyl rings, one π(M=X)-to-σ(M-C) involving metal d orbitals and the other σ(C-H)-to-σ(X-H) mediating the transfer of neutral H, where X = C or N. The reaction of the hafnium dimer complex with CO that was studied for the purpose of understanding C-H bond activation has another interesting application, namely the cleavage of an N-N bond and resulting N-C bond formation. Analysis of the orbital plots reveals repulsion between the occupied orbitals on CO and the N-N unit where CO approaches along the N-N axis. The repulsions along the N-N axis are minimized by instead forming an asymmetrical intermediate in which CO first coordinates to one Hf and then to N. This breaks the symmetry of the N-N unit and the resultant mixing of MOs allows σ(NN) to be polarized, localizing electrons on the more distant N. This allowed σ(CO) and π(CO) donation to N and back-donation of π*(Hf2N2) to CO. Improved understanding of the chemistry of metal complexes can be gained from atomic-scale modelling and this provides valuable information for the design of new ALD precursors. The information gained from the model decomposition pathway can be additionally used to understand the chemistry of molecules in the ALD process as well as in catalytic systems.
Ability of early neurological assessment and continuous EEG to predict long term neurodevelopmental outcome at 5 years in infants following hypoxic-ischaemic encephalopathy
(University College Cork, 2018) O'Connor, Catherine M.; Murray, Deirdre M.; Boylan, Geraldine B.; Health Research Board
Hypoxic-ischaemic encephalopathy (HIE) symptoms evolve during the first days of life and their monitoring is critical for treatment decisions and long-term outcome predictions. This thesis aims to report the five-year outcome of a HIE cohort born in the pre-therapeutic hypothermia era and to evaluate the predictive value of (a) neonatal neurological and EEG markers and (b) development in the first 24 months, for outcome. Methods: Participants were recruited at age five from two birth cohorts; HIE and Comparison. Repeated neonatal neurological assessments using the Amiel-TisonNeurological-Assessment-at-Term, continuous video EEG monitoring in the first 72 hours, and Sarnat grading at 24 hours were recorded. EEG severity grades were assigned at 6, 12 and 24 hours. Development was assessed in the HIE cohort at 6, 12 and 24 months using the Griffiths Mental Development (0-2) Revised Scales. At age five, intellectual (WPPSI-IIIUK scale), neuropsychological (NEPSY-II scales), neurological and ophthalmic testing was completed. Results: 5-year outcomes were available for 81.5% (n=53) of HIE and 71.4% (n=30) of Comparison cohorts. In HIE, 47.2% (27% mild, 47% moderate, 83% severe Sarnat), had non-intact outcome vs. 3.3% of the Comparison cohort. Non-intact outcome rates by 6-hour EEG-grade were: grade0=3%, grade1=25%, grade2=54%, grade3/4=79%. In HIE, processing speed (p=0.01) and verbal short-term memory (p=0.005) were below test norms. No significant differences were found in IQ, NEPSY-II or ocular biometry scores between children following mild and moderate HIE. Median IQ scores for mild (99(94-112),p=grade 2) at 24hours had superior positive predictive value (74%; AUROC(95%CI)=0.70(0.55-0.85) for non-intact 5-year outcome than abnormal EEG at 6 hours (68%; AUROC(95%CI)=0.71(0.56-0.87). Within-child development scores were inconsistent across the first 24 months. Although all children with intact 24-month Griffiths quotient (n=30) had intact 5-year IQ, 8/30 had non-intact overall outcome. Conclusion: Predictive value of neonatal neurological assessments and an EEG grading system for outcome was confirmed. Intact early childhood outcomes post-HIE may mask subtle adverse neuropsychological sequelae into the school years. This thesis supports emerging evidence that mild-grade HIE is not a benign condition and its inclusion in studies of neuroprotective treatments for HIE is warranted.
Access to modified geiparvarins using Pd(0)-mediated C-C bond forming reactions
(University College Cork, 2014) Lynch, Denis; McCarthy, Daniel G.; Cork County Council; Irish Research Council for Science Engineering and Technology
Geiparvarin is a natural product which contains both a 3(2H)-furanone and a coumarin moiety in its structure. The aim of this project was to investigate the use of Pd(0)-mediated C–C bondforming reactions to produce structurally modified geiparvarins. Chapter 1 consists of a review of the relevant literature, including that pertaining to the syntheses of selected naturally occurring 3(2H)-furanones. The known syntheses of geiparvarin and closely related analogues are examined, along with the documented biological activity of these compounds. The synthetic routes which allow access to 4-substituted-3(2H)-furanones are also described. Chapter 2 describes in detail the synthesis of a variety of novel structurally modified geiparvarins by two complementary routes, both approaches utilising Pd(0)-mediated crosscoupling reactions, and discusses the characterisation of these compounds. The preparation of 5-ethyl-3(2H)-furanones is described, as is their incorporation into geiparvarin and the corresponding 5″-alkylgeiparvarin analogues via formation and dehydration of intermediate alcohols. Halogenation of 5-ethyl-3(2H)-furanones and the corresponding geiparvarin derivatives is discussed, along with further reactions of the resulting halides. Preparation of 3″-arylgeiparvarins involving both Suzuki–Miyura and Stille reactions, using the appropriate intermediate iodides and bromides, is described. The application of Stille and Heck conditions to give 3″-ethenylgeiparvarin analogues and Sonogashira conditions to produce 3″-ethynylgeiparvarin analogues, using the relevant intermediate iodides, is also extensively outlined. Chapter 3 contains all of the experimental data and details of the synthetic methods employed for the compounds prepared during the course of this research. All novel compounds prepared were fully characterised using NMR spectroscopy, IR spectroscopy, mass spectrometry and elemental analysis; the details of which are included.
Accommodating interruptions: a grounded theory of young people with asthma
(University College Cork, 2014) Hughes, Mary; Savage, Eileen; Andrews, Tom
Background: Accommodating Interruptions is a theory that emerged in the context of young people who have asthma. A background to the prevalence and management of asthma in Ireland is given to situate the theory. Ireland has the fourth highest incidence of asthma in the world, with almost one in five Irish young people having asthma. Although national and international asthma management guidelines exist it is accepted that the symptom control of asthma among the young people population is poor. Aim: The aim of this research is to investigate the lives of young people who have asthma, to allow for a deeper understanding of the issues affecting them. Methods: This research was undertaken using a Classic Grounded Theory approach. It is a systematic approach to allowing conceptual emergence from data in generating a theory that explains behaviour in resolving the participant’s main concern. The data were collected through in-depth interviews with young people aged 11-16 years who had asthma for over one year. Data were also collected from participant diaries. Constant comparative analysis, theoretical coding and memo writing were used to develop the theory. Results: The theory explains how young people resolve their main concern of being restricted, by maximizing their participation and inclusion in activities, events and relationships in spite of their asthma. They achieve this by accommodating interruptions in their lives in minimizing the effects of asthma on their everyday lives. Conclusion: The theory of accommodating interruptions explains young people’s asthma management behaviours in a new way. It allows us to understand how and why young people behave the way they do in order minimise the effect of asthma on their lives. The theory adds to the body of knowledge on young people with asthma and challenges some viewpoints regarding their behaviours.
The accountability of transnational armed groups under international law
(University College Cork, 2015) Brennan, Anna Marie; Donson, Fiona; Mullally, Siobhan; Irish Research Council
Terrorist attacks by transnational armed groups cause on average 15,000 deaths every year worldwide, with the law enforcement agencies of some states facing many challenges in bringing those responsible to justice. Despite various attempts to codify the law on transnational terrorism since the 1930s, a crime of transnational terrorism under International Law remains contested, reflecting concerns regarding the relative importance of prosecuting members of transnational armed groups before the International Criminal Court. However, a study of the emerging jurisprudence of the International Criminal Court suggests that terrorist attacks cannot be classified as a war crime or a crime against humanity. Therefore, using organisational network theory, this thesis will probe the limits of international criminal law in bringing members of transnational armed groups to justice in the context of changing methods of warfare. Determining the organisational structure of transnational armed groups, provides a powerful analytical framework for examining the challenges in holding members of transnational armed groups accountable before the International Criminal Court, in the context of the relationship between the commanders and the subordinate members of the group.
Accuracy of computer-aided design/computer-assisted manufacture (CAD/CAM) fabricated dental restorations: a comparative study
(University College Cork, 2015) Nasruddin, Mohd Faiz; Burke, Francis M.; Ray, Noel J.; Theocharopoulos, Antonios; Universiti Teknologi MARA, Malaysia
Introduction: Computer-Aided-Design (CAD) and Computer-Aided-Manufacture (CAM) has been developed to fabricate fixed dental restorations accurately, faster and improve cost effectiveness of manufacture when compared to the conventional method. Two main methods exist in dental CAD/CAM technology: the subtractive and additive methods. While fitting accuracy of both methods has been explored, no study yet has compared the fabricated restoration (CAM output) to its CAD in terms of accuracy. The aim of this present study was to compare the output of various dental CAM routes to a sole initial CAD and establish the accuracy of fabrication. The internal fit of the various CAM routes were also investigated. The null hypotheses tested were: 1) no significant differences observed between the CAM output to the CAD and 2) no significant differences observed between the various CAM routes. Methods: An aluminium master model of a standard premolar preparation was scanned with a contact dental scanner (Incise, Renishaw, UK). A single CAD was created on the scanned master model (InciseCAD software, V2.5.0.140, UK). Twenty copings were then fabricated by sending the single CAD to a multitude of CAM routes. The copings were grouped (n=5) as: Laser sintered CoCrMo (LS), 5-axis milled CoCrMo (MCoCrMo), 3-axis milled zirconia (ZAx3) and 4-axis milled zirconia (ZAx4). All copings were micro-CT scanned (Phoenix X-Ray, Nanotom-S, Germany, power: 155kV, current: 60µA, 3600 projections) to produce 3-Dimensional (3D) models. A novel methodology was created to superimpose the micro-CT scans with the CAD (GOM Inspect software, V7.5SR2, Germany) to indicate inaccuracies in manufacturing. The accuracy in terms of coping volume was explored. The distances from the surfaces of the micro-CT 3D models to the surfaces of the CAD model (CAD Deviation) were investigated after creating surface colour deviation maps. Localised digital sections of the deviations (Occlusal, Axial and Cervical) and selected focussed areas were then quantitatively measured using software (GOM Inspect software, Germany). A novel methodology was also explored to digitally align (Rhino software, V5, USA) the micro-CT scans with the master model to investigate internal fit. Fifty digital cross sections of the aligned scans were created. Point-to-point distances were measured at 5 levels at each cross section. The five levels were: Vertical Marginal Fit (VF), Absolute Marginal Fit (AM), Axio-margin Fit (AMF), Axial Fit (AF) and Occlusal Fit (OF). Results: The results of the volume measurement were summarised as: VM-CoCrMo (62.8mm3 ) > VZax3 (59.4mm3 ) > VCAD (57mm3 ) > VZax4 (56.1mm3 ) > VLS (52.5mm3 ) and were all significantly different (p presented as areas with different colour. No significant differences were observed at the internal aspect of the cervical aspect between all groups of copings. Significant differences (p< M-CoCrMo Internal Occlusal, Internal Axial and External Axial 2 ZAx3 > ZAx4 External Occlusal, External Cervical 3 ZAx3 < ZAx4 Internal Occlusal 4 M-CoCrMo > ZAx4 Internal Occlusal and Internal Axial The mean values of AMF and AF were significantly (p M-CoCrMo and CAD > ZAx4. Only VF of M-CoCrMo was comparable with the CAD Internal Fit. All VF and AM values were within the clinically acceptable fit (120µm). Conclusion: The investigated CAM methods reproduced the CAD accurately at the internal cervical aspect of the copings. However, localised deviations at axial and occlusal aspects of the copings may suggest the need for modifications in these areas prior to fitting and veneering with porcelain. The CAM groups evaluated also showed different levels of Internal Fit thus rejecting the null hypotheses. The novel non-destructive methodologies for CAD/CAM accuracy and internal fit testing presented in this thesis may be a useful evaluation tool for similar applications.
Acetylated microtubules are essential for touch sensation in mice
(University College Cork, 2016) Morley, Shane J.; Heppenstall, Paul; Rae, Mark
The sense of touch depends upon the transformation of mechanical energy into electrical signals by peripheral sensory neurons and associated cells in the skin. This conversion is thought to be mediated by a complex of proteins in which ion channels such as Piezo2 function as mechanotransducers. However, how mechanical energy is transmitted into mechanosensitive ion channel opening, and how cellular components such as the cytoskeleton influence this process, is largely unknown. Here we show that mice lacking the tubulin acetyltransferase, Atat1, in sensory neurons display profound deficits in their ability to detect mechanical touch and pain. In the absence of Atat1, behavioural responses to innocuous and noxious mechanical stimuli are strongly reduced in multiple assays while sensitivity of mice to thermal stimuli is unaltered. In ex vivo skin-nerve preparations, the mechanosensitivity of all low- and high- threshold mechanoreceptor subtypes innervating the skin is substantially decreased in Atat1 conditional knockout mice. In cultured dorsal root ganglion neurons, both slowly- and rapidly- adapting mechanically- activated currents are absent or reduced upon Atat1 deletion with no effect on other neuronal functions. We establish that this broad loss of mechanosensitivity is dependent upon the acetyltransferase activity of Atat1, and that by mimicking α-tubulin acetylation genetically by substituting the lysine amino acid for a structurally similar glutamine, mechanosensitivity can be restored in Atat1- deficient sensory neurons. Finally, we demonstrate that acetylated microtubules localize to a prominent band under the membrane of sensory neuron cell bodies and axons, and in the absence of Atat1 and acetylated α-tubulin, cultured sensory neurons display significant reductions in their membrane elasticity. Our results indicate that the microtubule cytoskeleton is an essential component of the mammalian mechanotransduction complex and that by influencing cellular stiffness, α-tubulin acetylation can tune mechanical sensitivity across the full range of mechanoreceptor subtypes.
Acoustic behaviour, ecology and social structure of bottlenose dolphins (Tursiops truncatus, Montagu 1821) in the North Atlantic
(University College Cork, 2014) Englund, Anneli; Rogan, Emer; Ingram, Simon N.; Irish Research Council for Science Engineering and Technology; National Parks and Wildlife Service, Ireland; Zoology, Ecology and Plant Science, College of Science, Engineering and Food Science, University College Cork
Communication is important for social and other behavioural interactions in most marine mammal species. The bottlenose dolphin (Tursiops truncatus, Montagu, 1821) is a highly social species that use whistles as communication calls to express identity and to initiate and maintain contact between socially interactive individuals. In this thesis, the degree of variability in whistle behaviour and whistle characteristics was examined between different habitats on a range of spatial scales. The whistle characteristics that best discriminated between different communities were investigated, along with exploration of whistle variation in relation to habitat type, levels of social interaction and relatedness. Finally, the use and variability of individually distinctive calls (signature whistles) within and between Irish and US waters were also examined. Relatively high levels of whistle variation were found within a genetically and socially isolated population of dolphins in the Shannon Estuary, reflecting the need for individual identification and distinctive whistles in a population with long term site fidelity and high levels of social cohesion. Variation between reproductively separate communities in Irish waters was relatively small except between animals in inshore compared with continental shelf waters. The greatest differences in whistle structure overall were evident between dolphins using inshore and offshore US waters, likely reflecting social isolation of the two distinct ecotypes that occur in these waters but also variation in behaviour or habitat conditions. Variation found among inshore communities in US waters reflected similarities in habitat use and levels of social interaction. These findings suggest that vocal variation is socially mediated, behaviourally maintained and dependent on levels of social contact between individuals. The findings contribute to our understanding of the interaction of factors influencing vocalisation behaviour in this behaviourally complex and ecologically plastic species.
The actinin family of actin crosslinking proteins: natural functions and potential applications in synthetic biology
(University College Cork, 2016) Murphy, Anita Catherine Honor; Young, Paul; Irish Research Council
Actinin and spectrin proteins are members of the Spectrin Family of Actin Crosslinking Proteins. The importance of these proteins in the cytoskeleton is demonstrated by the fact that they are common targets for disease causing mutations. In their most prominent roles, actinin and spectrin are responsible for stabilising and maintaining the muscle architecture during contraction, and providing shape and elasticity to the red blood cell in circulation, respectively. To carry out such roles, actinin and spectrin must possess important mechanical and physical properties. These attributes are desirable when choosing a building block for protein-based nanoconstruction. In this study, I assess the contribution of several disease-associated mutations in the actinin-1 actin binding domain that have recently been linked to a rare platelet disorder, congenital macrothrombocytopenia. I investigate the suitability of both actinin and spectrin proteins as potential building blocks for nanoscale structures, and I evaluate a fusion-based assembly strategy to bring about self-assembly of protein nanostructures. I report that the actinin-1 mutant proteins display increased actin binding compared to WT actinin-1 proteins. I find that both actinin and spectrin proteins exhibit enormous potential as nano-building blocks in terms of their stability and ability to self-assemble, and I successfully design and create homodimeric and heterodimeric bivalent building blocks using the fusion-based assembly strategy. Overall, this study has gathered helpful information that will contribute to furthering the advancement of actinin and spectrin knowledge in terms of their natural functions, and potential unnatural functions in protein nanotechnology.
Active learning in recommender systems: an unbiased and beyond-accuracy perspective
(University College Cork, 2020-12-05) Carraro, Diego; Bridge, Derek G.; O'Sullivan, Barry; Science Foundation Ireland; European Regional Development Fund
The items that a Recommender System (RS) suggests to its users are typically ones that it thinks the user will like and want to consume. An RS that is good at its job is of interest not only to its customers but also to service providers, so they can secure long-term customers and increase revenue. Thus, there is a challenge in building better recommender systems. One way to build a better RS is to improve the quality of the data on which the RS model is trained. An RS can use Active Learning (AL) to proactively acquire such data, with the goal of improving its model. The idea of AL for RS is to explicitly query the users, asking them to rate items which have not been rated yet. The items that a user will be asked to rate are known as the query items. Query items are different from recommendations. For example, the former may be items that the AL strategy predicts the user has already consumed, whereas the latter are ones that the RS predicts the user will like. In AL, query items are selected `intelligently' by an Active Learning strategy. Different AL strategies take different approaches to identify the query items. As with the evaluation of RSs, preliminary evaluation of AL strategies must be done offline. An offline evaluation can help to narrow the number of promising strategies that need to be evaluated in subsequent costly user trials and online experiments. Where the literature describes the offline evaluation of AL, the evaluation is typically quite narrow and incomplete: mostly, the focus is cold-start users; the impact of newly-acquired ratings on recommendation quality is usually measured only for those users who supplied those ratings; and impact is measured in terms of prediction accuracy or recommendation relevance. Furthermore, the traditional AL evaluation does not take into account the bias problem. As brought to light by recent RS literature, this is a problem that affects the offline evaluation of RS; it arises when a biased dataset is used to perform the evaluation. We argue that it is a problem that affects offline evaluation of AL strategies too. The main focus of this dissertation is on the design and evaluation of AL strategies for RSs. We first design novel methods (designated WTD and WTD_H) that `intervene' on a biased dataset to generate a new dataset with unbiased-like properties. Compared to the most similar approach proposed in the literature, we give empirical evidence, using two publicly-available datasets, that WTD and WTD_H are more effective at debiasing the evaluation of different recommender system models. We then propose a new framework for offline evaluation of AL for RS, which we believe facilitates a more authentic picture of the performances of the AL strategies under evaluation. In particular, our framework uses WTD or WTD_H to mitigate the bias, but it also assesses the impact of AL in a more comprehensive way than the traditional evaluation used in the literature. Our framework is more comprehensive in at least two ways. First, it segments users in more ways than is conventional and analyses the impact of AL on the different segments. Second, in the same way that RS evaluation has changed from a narrow focus on prediction accuracy and recommendation relevance to a wider consideration of so-called `beyond-accuracy' criteria (such as diversity, serendipity and novelty), our framework extends the evaluation of AL strategies to also cover `beyond-accuracy' criteria. Experimental results on two datasets show the effectiveness of our new framework. Finally, we propose some new AL strategies of our own. In particular, our new AL strategies, instead of focusing exclusively on prediction accuracy and recommendation relevance, are designed to also enhance `beyond-accuracy' criteria. We evaluate the new strategies using our more comprehensive evaluation framework.
Activity profiles of adults aged 50 - 70 years: functional data analysis
(University College Cork, 2019-10) Weedle, Richard; O'Sullivan, Kathleen (Catherine); Fitzgerald, Tony
Physical activity has a major impact on health. Questionnaires are the most common method of physical activity assessment. While cost effective, these are subjective and can correlate poorly with actual activity levels. Accelerometers have gained popularity given their accuracy, objectivity and ability to capture large amounts of data. Simple summary measures such as the total or average activity over the day are often used. However, these fail to exploit the longitudinal nature of the data and do not capture the variation in activity levels throughout the day. This study intends to capitalise on this nature by implementing a functional data analysis approach. Activity data was collected from a cohort of 475 people in Mitchelstown in 2011. The individuals wore wrist worn accelerometers in a free living environment for a week. This data was collapsed into 1 minute epochs and each epoch was then aggregated over the week to get an estimate of daily circadian activity. The discrete wavelet transform was chosen as the smoothing technique to reveal the underlying functional nature of the data. This allows every individual in the cohort to be represented by a smooth activity profile. This study aimed to identify and characterise subgroups within a cohort based on these activity profiles. Functional principal component analysis was applied to these activity profiles in order to explore the dominant patterns within the data. Each individual’s profile was approximated by a weighted sum of profiles and these weights were then used to perform a cluster analysis. Five distinct subgroups were identified. These differed from each other in both the magnitude of the activity and the times at which the activity occured. A more simplified approach, based purely on the distance between profiles, was also implemented. Two distinct clustering methods identified the exact same 5 subgroups in the cohort. To ensure their robustness, these results were subject to a sensitivity analysis with respect to the epoch length, smoothing technique and number of functional components utilised in the clustering. Other studies have clustered accelerometer data in terms of absolute activity volume, as in high or low activity groups. However, they do not place too much value in using the granularity of the data to determine what time of day people are active. In addition to the high, moderate and low activity subgroups, our analysis revealed two subgroups which have a propensity to be active in either the morning or evening. It is suggested that these are indicative of an individual’s biological rhythm or chronotype. The Mitchelstown cohort was re-screened 5 years later in 2016, which presents an exciting opportunity to examine changes in these profiles over time.
Acute hypoxia-induced diaphragm dysfunction is prevented by antioxidant pre-treatment
(University College Cork, 2016) O'Leary, Andrew J.; O'Halloran, Ken D.; Mackrill, John; Physiology, College of Medicine and Health, University College Cork; Strategic Research Fund, University College Cork
Diaphragm weakness is a strong predictor of poor outcome in patients. Acute hypoxia is a feature of respiratory conditions such as acute respiratory distress syndrome and ventilator-associated lung injury. However, the effects of acute hypoxia on the diaphragm are largely unknown despite the potential clinical relevance. C57BL6/J mice were exposed to 8hr of hypoxia (FiO2 = 0.10) or normoxia. A separate group of mice were administered N-acetyl cysteine (NAC; 200mg/kg, I.P.) immediately prior to acute hypoxia exposure. Ventilation was assessed using whole-body plethysmography. O2 consumption and CO2 production were measured as indices of metabolism. Diaphragm muscle contractile performance was determined ex-vivo. Gene expression was examined at 1, 4, and 8 hrs using qRT-PCR. Protein/phosphoprotein content was assessed using a sandwich immunoassay. Proteasome activity was measured using a spectrophotometric assay. Acute hypoxia decreased diaphragm force and fatigue. Ventilation during acute hypoxia was initially increased during the first 10 minutes, but quickly returned to normoxic levels for the duration of gas exposure. Metabolism was reduced by acute hypoxia, and gene expression driving mitochondrial uncoupling was increased. Acute hypoxia increased atrophic signalling, but not proteasome activity. Acute hypoxia increased hypertrophic and hypoxia protein signalling. NAC pre-treatment prevented the acute hypoxia-induced diaphragm weakness. Diaphragm weakness is reported in mechanically ventilated patients, which is primarily attributed to inactivity of the muscle, although this is controversial. The potential role of hypoxia in the development and/or exacerbation of ICU-related weakness is unclear. These data reveals that acute hypoxia is sufficient to cause diaphragm muscle weakness, likely relates to hypoxic stress. Muscle weakness was prevented by antioxidant supplementation, independent of the hypoxia-induced hypometabolic state. These findings highlight a potentially critical role for hypoxia in diaphragm muscle dysfunction observed in patients with acute respiratory diseases, and the potential benefits of NAC in preventing acute hypoxia-induced diaphragm dysfunction.
Adaptation and resilience in families of children with 22q11.2 deletion syndrome: a mixed methods study
(University College Cork, 2019-11-19) Caples, Maria; Savage, Eileen; Mccarthy, Bridie
Background: 22q11.2 deletion syndrome is a rare multisystem genetic disorder with over 200 associated characteristics, occurring in various combinations and severity, with an estimated incidence of 1 in 4,000 live births. The phenotype of syndrome is much varied, with some people more seriously affected then others. In addition, a rare disease can bring a range of challenges for those affected and their families which can result in people becoming marginalised psychologically, socially, culturally and economically. Extensive biomedical research has been undertaken on 22q11.2 deletion syndrome, however, there is a dearth of research on families’ experiences. Study Aim: To investigate the relationship between resilience factors and adaptation in families of children with 22q11.2 deletion syndrome. Methods: An explanatory sequential mixed methods design was used to investigate adaptation and resilience in families of children with 22q11.2 deletion syndrome. Families participated in a survey (n=64) and qualitative interviews (n=9). Quantitative data were analysed using IBM SPSS Statistics (Version 18) and qualitative data were analysed using content analysis. Results:Three variables that best explained adaptation in families of children with 22q11.2 deletion syndrome were identified: family hardiness, condition management effort, and condition management ability. Adaptation scores increased by 0.57 points (95% CI: 0.19 to 0.94) for every one-point increase in family hardiness score, by 0.95 (95% CI: 0.33 to 1.56) for every one-point increase in condition management ability score and decreased by 0.84 (95% CI: -1.55 to -0.13) for every one-point increase in effort scores. The qualitative data provided additional insights to the independent variables that were found to be significantly associated with adaptation for families of children with 22q11.2 deletion syndrome. These variables were condition management effort, condition management ability and family hardiness. Conclusion: This study provides insight to adaptation and resilience specific to families of children with 22q11.2 deletion syndrome. A key implication of the findings is the need for a family centered, integrated approach to care for families of children with 22q11.2 deletion syndrome.
An adaptive model for digital game based learning
(University College Cork, 2019) Cunningham, Larkin; Murphy, Orla; Cosgrave, Michael
Digital Game-based Learning (DGBL) has the potential to be a more effective means of instruction than traditional methods. However meta-analyses of studies on the effectiveness of DGBL have yielded mixed results. One of the challenges faced in the design and development of effective and motivating DGBL is the integration of learning and gameplay. A game that is effective at learning transfer, yet is no fun to play, is not going to engage learners for very long. This served as the motivation to devise a systematic approach to the design, development and evaluation of effective and engaging DGBL. A comprehensive literature review examined: how games can be made engaging and how the mechanics of learning can be mapped to the mechanics of gameplay; how learning can be designed to be universal to all; how learning analytics can empower learners and educators; and how an agile approach to the development of instructional materials leads to continuous improvement. These and other considerations led to the development of the Adaptive Model for Digital Game Based Learning (AMDGBL). To test how successful the model would be in developing effective, motivating and universal DGBL, a Virtual Reality (VR) game that teaches graph theory was designed, built and evaluated using the AMDGBL. An accompanying platform featuring an Application Programming Interface (API) for storing learner interaction data and a web-based learning analytics dashboard (LAD) were developed. A mixed methods approach was taken for a study of learners (N=20) who playtested the game and viewed visualizations in the dashboard. Observational and think aloud notes were recorded as they played and gameplay data was stored via the API. The participants also filled out a questionnaire. The notes taken were thematically analysed, and the gameplay data and questionnaire responses were statistically analysed. Triangulation of data improved confidence in findings and yielded new insights. The learner study became a case study for a second, qualitative study of DGBL practitioners (N=12). The VR game was demonstrated and a series of visualizations presented to the participants. They then completed a questionnaire featuring open questions about: the need for the model; the benefits of VR; and the embedding of learning analytics, universal design for learning, iteration with formative evaluation, and triangulation at the heart of the model. The responses were thematically analysed. The results of both studies supported the following assertions: that the AMDGBL would allow for iterative improvement of a DGBL prototype; that employing the AMDGBL would lead to an effective DGBL solution; that the inclusion of UDL would lead to a more universally-designed game; that the LAD would help learners with executive functions; and that VR would foster learner autonomy.
Addressing strategy and innovation in family business practice; a process of adaptive change
(University College Cork, 2018) Gleeson, Peter; Doyle, Eleanor
This Portfolio of Exploration documents the transformation in my management practice from an operational to a strategic orientation. The central research question revolves around the impact of a process of adaptive change on my management and a series of business implementation actions. My operational approach had reached its limits with the 2009 construction industry recession exposing the invalidation of the assumptions underlying my management practice. I engage in a process of adaptive change to formulate responses to the changed operating environment both in terms of strategy and innovation. The process is organised into a set of three essays. In Essay One, I engage in a Professional Development Review to trace the development of my meaning making and to surface the theories underlying my management practice. I reflect on how my background in family business and accountancy training has shaped my ‘hegemonic assumptions’ (Brookfield, 1995). I structure the review using the Adult Mental Development theory of Kegan (1994, Kegan & Lahey, 2009). I document my experiences since returning to manage the family business and outline the developmental goals pursued in the remainder of the Portfolio. In Essay Two, I explore the themes underlying my developmental goals by engaging with source thinkers in the Reading for Change Essay. The movement generated in my meaning making enables me to re-define my management practice. I apply an adaptive approach to reading Porter (1980, 1985, 2008) and to analyse my operating environment. Based on this re-reading, I develop a strategy for my business, incorporating advances in strategy since the launch of Porter. I examine the business model assumptions underlying my practice using Brookfield (1995) and Drucker (1994) and explore the role of assumptions in driving business models. I demonstrate the impact of my new management practice in Essay Three, Transforming Practice. Through a series of action research projects, I demonstrate how my practice has been transformed and the effect on the operations of my business. The action projects illustrate the application of previously unused productive managerial resources to business development. In the Portfolio Conclusion, I conclude that adopting a strategic perspective is essentially a higher-order mental demand and requires meaning making operating at that level. This work adds to knowledge in the family business and strategic management areas by demonstrating the impact of an adaptive change process on the effectiveness of management practice. It also reviews the impact of adaptive change on the innovative projects pursued. I set out the implications of this for my selected audience, i.e. practitioners operating in a family business environment and those operating in the SME sector of a commoditised industry with strong competitive forces along with researchers, advisors and policy makers in these areas.
Adolescence as a vulnerable period for the effects of intrinsic and extrinsic regulators of neurogenesis on cognitive behaviour
(University College Cork, 2017) O'Leary, James Daniel; Nolan, Yvonne M.; Cryan, John F.; O'Leary, Olivia; Science Foundation Ireland
Postnatal hippocampal neurogenesis is the birth of new neurons within the dentate gyrus that occurs throughout the lifespan. In adulthood, these new neurons have been shown to be necessary for cognitive tasks such as spatial and contextual memory. It is well established that adult hippocampal neurogenesis can be modulated by a number of intrinsic and extrinsic factors, such as intracellular signalling molecules, exercise, inflammation and stress. Moreover, levels of adult hippocampal neurogenesis do not remain constant throughout life. Indeed, levels of hippocampal neurogenesis and integration of new neurons within the dentate gyrus are up to four times higher during adolescence than during adulthood. The first aim of this thesis (addressed in Chapter 2) was to explore the extent and involvement of Tlx in motor, cognitive and anxietyrelated behaviour. A spontaneous deletion of Tlx, a key intrinsic regulator of neurogenesis, was demonstrated to impair motor, cognitive and anxiety-related behaviours during adolescence and adulthood. The second aim of this thesis (addressed in Chapters 3 and 4) was to investigate the impact of adolescent-initiated exercise on hippocampal plasticity and contextual and cued fear conditioning as well as pattern separation in adulthood. It was demonstrated that adult-initiated exercise enhanced both contextual and cued fear conditioning, while conversely, exercise that began in adolescence did not affect performance in these tasks and these differential effects were accompanied by differential expression of plasticity-related genes in the hippocampus in adulthood. Moreover, adult and adolescent-initiated exercise enhanced cognitive flexibility and dendritic complexity of immature neurons in the dentate gyrus. The third aim of this thesis (addressed in Chapter 5) was to examine the impact of chronically elevated IL-1β on adult hippocampal neurogenesis and pattern separation. It was shown that chronic lentiviral-mediated overexpression of IL-1β within the dorsal hippocampus impaired neurogenesis and performance in its associated cognition, while sparing neurogenesis independent cognition. Finally, the fourth aim of this thesis (addressed in Chapter 6) was to explore the impact of chronic IL-1β, chronic unpredictable stress exposure, or a combination of an initial chronic IL-1β insult was examined following exposure to chronic unpredictable stress on learning and memory and depressive-like behaviours. It was shown that exposure to chronically elevated IL1β and chronic stress independently impair certain types of learning and memory and increased depressive-like behaviour. However, exposure to a sequential ‘two-hit’ of chronically elevated hippocampal IL-1β and chronic stress did not produce an exacerbated phenotype. In summary (Chapter 7), disruption of intrinsic regulators of neurogenesis, such as Tlx, or exposure to extrinsic factors, such as exercise or adverse stimuli, like inflammation and stress, and the consequent effect on cognition may provide insight into why adolescence is a vital period for correct conditioning of hippocampal function in later life.

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