Digital signal processing and artificial intelligence for the automated classification of food allergy

As a by-product of the ‘information revolution’ which is currently unfolding, lifetimes of man (and indeed computer) hours are being allocated for the automated and intelligent interpretation of data. This is particularly true in medical and clinical settings, where research into machine-assisted diagnosis of physiological conditions gains momentum daily. Of the conditions which have been addressed, however, automated classification of allergy has not been investigated, even though the numbers of allergic persons are rising, and undiagnosed allergies are most likely to elicit fatal consequences. On the basis of the observations of allergists who conduct oral food challenges (OFCs), activity-based analyses of allergy tests were performed. Algorithms were investigated and validated by a pilot study which verified that accelerometer-based inquiry of human movements is particularly well-suited for objective appraisal of activity. However, when these analyses were applied to OFCs, accelerometer-based investigations were found to provide very poor separation between allergic and non-allergic persons, and it was concluded that the avenues explored in this thesis are inadequate for the classification of allergy. Heart rate variability (HRV) analysis is known to provide very significant diagnostic information for many conditions. Owing to this, electrocardiograms (ECGs) were recorded during OFCs for the purpose of assessing the effect that allergy induces on HRV features. It was found that with appropriate analysis, excellent separation between allergic and nonallergic subjects can be obtained. These results were, however, obtained with manual QRS annotations, and these are not a viable methodology for real-time diagnostic applications. Even so, this was the first work which has categorically correlated changes in HRV features to the onset of allergic events, and manual annotations yield undeniable affirmation of this. Fostered by the successful results which were obtained with manual classifications, automatic QRS detection algorithms were investigated to facilitate the fully automated classification of allergy. The results which were obtained by this process are very promising. Most importantly, the work that is presented in this thesis did not obtain any false positive classifications. This is a most desirable result for OFC classification, as it allows complete confidence to be attributed to classifications of allergy. Furthermore, these results could be particularly advantageous in clinical settings, as machine-based classification can detect the onset of allergy which can allow for early termination of OFCs. Consequently, machine-based monitoring of OFCs has in this work been shown to possess the capacity to significantly and safely advance the current state of clinical art of allergy diagnosis

Cultural revolution: reflections on an exchange

This paper considers an on-going exchange programme between the Boole Library, University College Cork (UCC) and Hangzhou Municipal Library, South East China. The authors describe the exchange and their impressions of working in a different library setting.

An evaluation of orogenic kinematic evolution utilizing crystalline and magnetic anisotropy in granitoids

The Silurian-Devonian Galway Granite Complex (GGC ~425-380Ma) is defined here as a suite of granitoid plutons that comprise the Main Galway Granite Batholith and the Earlier Plutons. The Main Batholith is a composite of the Carna Pluton in the west and the Kilkieran Pluton in the east and extends from Galway City ~130km to the west. The Earlier Plutons are spatially, temporally and structurally distinct, situated northwest of the Main Batholith and include the Roundstone, Omey, Inis and Letterfrack Plutons. The majority of isotopic and structural data currently available pertain to the Kilkieran Pluton, several tectonic models have already been devised for this part of the complex. These relate emplacement of the Kilkieran Pluton to extension across a large east-west Caledonian lineament, i.e. the Skird Rocks Fault, during late Caledonian transtension. No chronological data have been published that directly and accurately date the emplacement of the Carna Pluton or any of the Earlier Plutons. There is also a lack of data pertaining to the internal structure of these intrusions. Accordingly, no previous study has established the mechanisms of emplacement for the Earlier Plutons and only limited work is available for the Carna Pluton. As a consequense of this, constituents of the GGC have not previously been placed in a context relative to each other or to regional scale Silurio-Devonian kinematics. The current work focuses on the Omey, Roundstone and Carna Plutons. Here, results of detailed field and Anisotropy of Magnetic Susceptibiliy (AMS) fabric studies are presented. This work is complemented by geological mapping that focuses on fault dynamics and contact relationships. Interpretation of AMS data is aided by rock magnetic experiment data and petrographic microstructural evaluations of representative samples. A new geological map of the the Omey Pluton demonstrates that this intrusion has a defined roof and base which are gently inclined parallel to the fold hinge of the Connemara Antiform. AMS and petrographic data show the intrusion is cross cut by NNW-SSE shear zones that extend into the country rock. These pre-date and were active during magma emplacement. It is proposed that the Omey pluton was emplaced as a discordant phacolith. Pre-existing subvertical D5 faults in the host rock were reactived during emplacement, due to regional sinistral transpression, and served as centralised ascent conduits. A central portion of the Roundstone Pluton was mapped in detail for the first time. Two facies are identified, G1 forms the majority of the pluton and coeval G2 sheets cross cut G1 at the core of the pluton. NNW-SSE D5 faults mapped in the country rock extend across the pluton. These share a geometrical relationship with the distribution of submagmatic strain in the pluton and parallel the majoity of mapped subvertical G2 dykes. These data indicate that magma ascent was controlled by NNW-SSE conduits that are inherently related to those identifed in the Omey Pluton. It is proposed that the Roundstone Pluton is a punched laccolith, the symmetry and structure of which was controlled by pre-exising host rock structures and regional sinistral transpressive stress which presided during emplacement. Field relationships show the long axis of the Carna Pluton lies parallel to mulitple NNW-SSE shear zones. These are represented on a regional scale by the Clifden-Mace Fault which cross cuts the core of this intrusion. AMS and petrographic data show concentric emplacement fabrics were tectonically overprinted as magma cooled from the magmatic state due to this faulting. It is proposed that the Clifden-Mace Fault system was active during ascent and emplacement of the magma and that pluton inflation only terminated as this controlling structure went into compression due to the onset of regional transtension. U-Pb zircon laser ablation inductively coupled mass spectrometry (LA-ICP-MS) data has been compiled from four sample sites. New geochronological data from the Roundstone Pluton (RD1 = ± 3.2Ma) represent the oldest age determination obtained from any member of the GGC and demonstrates that this pluton predates the Carna Pluton by ~10Ma and probably intruded synchronously with the Omey Pluton (~422.5 ± 1.7Ma). Chronological data from the Carna Pluton (CN2 = 412.9 ± 2.5Ma; CN3 = 409.8 ± 7.2Ma; CN4 = 409.6 ± 3.6Ma) represent the first precise magma crystallisation age for this intrusion. This work shows this pluton is 10Ma older than the Kilkieran Pluton and that the supply of magma into the Carna Pluton had terminated by ~409Ma. Chronological, magnetic and field data have been utilised to evaluate the kinematic evolution of the Caledonides of western Ireland throughout the construction of the GGC. It is proposed that the GGC was constructed during four distinct episodes. The style of emplacement and the conduits used for magma transport to the site of emplacement was dependent on the orientation of local structures relative to the regional ambiant stress field. This philosophy is used to critically evaluate and progress existing hypotheses on the transition from regional transpression to regional transtension at the end of the Caledonian Orogeny.

Investigation of toll-like receptor tolerance in the regulation of inflammation

Inflammation is a complex and highly organised immune response to microbes and tissue injury. Recognition of noxious stimuli by pathogen recognition receptor families including Toll-like receptors results in the expression of hundreds of genes that encode cytokines, chemokines, antimicrobials and regulators of inflammation. Regulation of TLR activation responses is controlled by TLR tolerance which induces a global change in the cellular transcriptional expression profile resulting in gene specific suppression and induction of transcription. In this thesis the plasticity of TLR receptor tolerance is investigated using an in vivo, transcriptomics and functional approach to determine the plasticity of TLR tolerance in the regulation of inflammation. Firstly, using mice deficient in the negative regulator of TLR gene transcription, Bcl-3 (Bcl-3-/-) in a model of intestinal inflammation, we investigated the role of Bcl-3 in the regulation of intestinal inflammatory responses. Our data revealed a novel role for Bcl-3 in the regulation of epithelial cell proliferation and regeneration during intestinal inflammation. Furthermore this data revealed that increased Bcl-3 expression contributes to the development of inflammatory bowel disease (IBD). Secondly, we demonstrate that lipopolysaccharide tolerance is transient and recovery from LPS tolerance results in polarisation of macrophages to a previously un-described hybrid state (RM). In addition, we identified that RM cells have a unique transcriptional profile with suppression and induction of genes specific to this polarisation state. Furthermore, using a functional approach to characterise the outcomes of TLR tolerance plasticity, we demonstrate that cytokine transcription is uncoupled from cytokine secretion in macrophages following recovery from LPS tolerance. Here we demonstrate a novel mechanism of regulation of TLR tolerance through suppression of cytokine secretion in macrophages. We show that TNF-α is alternatively trafficked towards a degradative intracellular compartment. These studies demonstrate that TLR tolerance is a complex immunological response with the plasticity of this state playing an important role in the regulation of inflammation.

The musical enculturation of Irish traditional musicians: An ethnographic study of learning processes

The enculturation of Irish traditional musicians involves informal, non-formal, and sometimes formal learning processes in a number of different settings, including traditional music sessions, workshops, festivals, and classes. Irish traditional musicians also learn directly from family, peers, and mentors and by using various forms of technology. Each experience contributes to the enculturation process in meaningful and complementary ways. The ethnographic research discussed in this dissertation suggests that within Irish traditional music culture, enculturation occurs most effectively when learners experience a multitude of learning practices. A variety of experiences insures that novices receive multiple opportunities for engagement and learning. If a learner finds one learning practice ineffective, there are other avenues of enculturation. This thesis explores the musical enculturation of Irish traditional musicians. It focuses on the process of becoming a musician by drawing on methodologies and theories from ethnomusicology, education, and Irish traditional music studies. Data was gathered through multiple ethnographic methodologies. Fieldwork based on participant-observation was carried out in a variety of learning contexts, including traditional music sessions, festivals, workshops, and weekly classes. Additionally, interviews with twenty accomplished Irish traditional musicians provide diverse narratives and firsthand insight into musical development and enculturation. These and other methodologies are discussed in Chapter 1. The three main chapters of the thesis explore various common learning experiences. Chapter 2 explores how Irish traditional musicians learn during social and musical interactions between peers, mentors, and family members, and focuses on live music-making which occurs in private homes, sessions, and concerts. These informal and non-formal learning experiences primarily take place outside of organizations and institutions. The interview data suggests these learning experiences are perhaps the most pervasive and influential in terms of musical enculturation. Chapter 3 discusses learning experience in more organized settings, such as traditional music classes, workshops, summer schools, and festivals. The role of organizations such as Comhaltas Ceoltóirí Éireann and pipers’ clubs are discussed from the point of view of the learner. Many of the learning experiences explored in this chapter are informal, non-formal, and sometimes formal in nature, depending on the philosophy of the organization, institution, and individual teacher. The interview data and field observations indicate that learning in these contexts is common and plays a significant role in enculturation, particularly for traditional musicians who were born during and after the 1970s. Chapter 4 explores the ways Irish traditional musicians use technology, including written sources, phonography, videography, websites, and emerging technologies, during the enculturation process. Each type of technology presents different educational implications, and traditional musicians use these technologies in diverse ways and some more than others. For this, and other reasons, technology plays a complex role during the process of musical enculturation. Drawing on themes which emerge during Chapter 2, 3, and 4, the final chapter of this dissertation explores overarching patterns of enculturation within Irish traditional music culture. This ethnographic work suggests that longevity of participation and engagement in multiple learning and performance opportunities foster the enculturation of Irish traditional musicians. Through numerous and prolonged participation in music-making, novices become accustomed to and learn musical, social, and cultural behaviours. The final chapter also explores interconnections between learning experiences and also proposes directions for future research.

Health of the older worker in Ireland - occupational physical and psychosocial factors in the autumn of work life

Introduction: Worldwide, governments are striving to keep people in work to an older age. However, little is known about the effects of work on an older workforce. This thesis aims to investigate the importance of job characteristics to the antecedents and evolution of cardiovascular disease and functional limitations for the older worker (50+ years). Methods: Three studies were used in this thesis. The 5C (Cork Coronary Care Case- Control) Study investigated the association between job strain and a coronary event in males (n=208) 35-74 years old. The Mitchelstown Study examined the association between job characteristics and positive lifestyle behaviours and further, job characteristics and blood pressure for males and females 50-69 years (n=2,047). Finally, the Cork & Kerry Study investigated the physical effects of manual work and reported functional limitations/disabilities in a sample of 60-80 year olds (n=362). Results: Results from the 5C Study show a clear difference between younger (<50 years) and older (≥50 years) workers, with older workers who had a coronary event more likely to have high job strain and low job control. Data from the Mitchelstown Study showed workers with intermediate possibility for development or high quantitative demands (versus low) at work significantly more likely to have co-occurrence of positive lifestyle behaviours. Further, those who had high possibility for development were more likely to have high systolic blood pressure with no indication of recovery from this activation at night. Physically demanding work as reported by the participants of the Cork & Kerry Study was associated with functional limitations and activities of daily living disability for both the paid and unpaid worker. Discussion: The findings from this piece of work highlight the necessity to examine job characteristics and health outcomes in isolation for the over fifties. The challenge is to get this information into the workplace.

Characterisation of the microbiota of traditional fermented beverages and screening these and other populations for novel antimicrobial producers and gene clusters

To screen for novel ribosomally synthesised antimicrobials, in-silico genome mining was performed on all publically available fully sequenced bacterial genomes. 49 novel type 1 lantibiotic clusters were identified from a number of species, genera and phyla not usually associated with lantibiotic production, and indicates high prevalence. A crucial step towards the commercialisation of fermented beverages is the characterisation of the microbial content. To achieve this goal, we applied next-generation sequencing techniques to analyse the bacterial and yeast populations of the organic, symbiotically-fermented beverages kefir, water kefir and kombucha. A number of minor components were revealed, many of which had not previously been associated with these beverages. The dominant microorganism in each of the water kefir grains and fermentates was Zymomonas, an ethanol-producing bacterium that had not previously been detected on such a scale. These studies represent the most accurate description of these populations to date, and should aid in future starter design and in determining which species are responsible for specific attributes of the beverages. Finally, high-throughput robotics was applied to screen for the presence of antimicrobial producers associated with these beverages. This revealed a low frequency of bacteriocin production amongst the bacterial isolates, with only lactococcins A, B and LcnN of lactococcin M being identified. However, a proteinaceous antimicrobial produced by the yeast Dekkera bruxellensis, isolated from kombucha, was found to be active against Lactobacillus bulgaricus. This peptide was patially purified.

A study of diet and health in the elderly; the gut microbiota as a source of bioactive agents

The global proportion of older persons is increasing rapidly. Diet and the intestinal microbiota independently and jointly contribute to health in the elderly. The habitual dietary patterns and functional microbiota components of elderly subjects were investigated in order to identify specific effector mechanisms. A study of the dietary intake of Irish community-dwelling elderly subjects showed that the consumption of foods high in fat and/or sugar was excessive, while consumption of dairy foods was inadequate. Elderly females typically had a more nutrient- dense diet than males and a considerable proportion of subjects, particularly males, had inadequate intakes of calcium, magnesium, vitamin D, folate, zinc and vitamin C. The association between dietary patterns, glycaemic index and cognitive function was also investigated. Elderly subjects consuming ‘prudent’ dietary patterns had better cognitive function compared to those consuming ‘Western’ dietary patterns. Furthermore, fully-adjusted regression models revealed that a high glycaemic diet was associated with poor cognitive function, demonstrating a new link between nutrition and cognition. An extensive screening study of the elderly faecal-derived microbiota was also undertaken to examine the prevalence of antimicrobial production by intestinal bacteria. A number of previously characterised bacteriocins were isolated (gassericin T, ABP-118, mutacin II, enterocin L-50 and enterocin P) in this study. Interestingly, a Lactobacillus crispatus strain was found to produce a potentially novel antimicrobial compound. Full genome sequencing of this strain revealed the presence of three loci which exhibited varying degrees of homology with the genes responsible for helveticin J production in Lb. helveticus. An additional study comparing the immunomodulatory capacity of ‘viable’ and ‘non-viable’ Bifidobacterium strains found that Bifidobacterium-fermented milks (BFMs) containing ‘non-viable’ cells could stimulate levels of IL-10 and TNF-α in a manner similar to those stimulated by BFMs containing ‘viable’ cells in vitro.

Reasoning with sorted-pareto dominance and other qualitative and partially ordered preferences in soft constraints

In decision making problems where we need to choose a particular decision or alternative from a set of possible choices, we often have some preferences which determine if we prefer one decision over another. When these preferences give us an ordering on the decisions that is complete, then it is easy to choose the best or one of the best decisions. However it often occurs that the preferences relation is partially ordered, and we have no best decision. In this thesis, we look at what happens when we have such a partial order over a set of decisions, in particular when we have multiple orderings on a set of decisions, and we present a framework for qualitative decision making. We look at the different natural notions of optimal decision that occur in this framework, which gives us different optimality classes, and we examine the relationships between these classes. We then look in particular at a qualitative preference relation called Sorted-Pareto Dominance, which is an extension of Pareto Dominance, and we give a semantics for this relation as one that is compatible with any order-preserving mapping of an ordinal preference scale to a numerical one. We apply Sorted-Pareto dominance to a Soft Constraints setting, where we solve problems in which the soft constraints associate qualitative preferences to decisions in a decision problem. We also examine the Sorted-Pareto dominance relation in the context of our qualitative decision making framework, looking at the relevant optimality classes for the Sorted-Pareto case, which gives us classes of decisions that are necessarily optimal, and optimal for some choice of mapping of an ordinal scale to a quantitative one. We provide some empirical analysis of Sorted-Pareto constraints problems and examine the optimality classes that result.

College adjustment, depressive symptoms and peer support among undergraduate university students

Background: College adjustment is a developmental milestone that can be stressful and may lead to mental health problems such as depression. Support during this adjustment period is seen as essential, however it is unknown if informal peer support from fellow students has any impact on either college adjustment or depressive symptoms. Aim: To identify levels of social and personal college adjustment, depressive symptoms and peer support among students, and to examine the relationship between the variables. Design: A quantitative correlational design was used Instruments: Data were collected using two subscales of the Student Adaptation to College Questionnaire; the Centre for Epidemiology Depressive Symptoms Scale and a subscale of the Peer Support Evaluation Inventory. Sample: The sample consisted of 417, first (n=188), second (n=134) and fourth (n=94) year nursing and midwifery students from one University in Ireland. Findings: The findings indicated that 20% of participants were poorly personally adjusted and 9% poorly socially adjusted. Furthermore, 34% of participants experienced significant depressive symptoms. Most students had good levels of peer support. Statistically significant relationships were found between all key variables, the strongest of which were between personal adjustment and depressive symptoms and social adjustment and depressive symptoms. Differences in adjustment and depressive symptom scores were found based on year of study, with second year students experiencing more depressive symptoms and having poorer personal adjustment scores. Participants who had poor relationships with their father’s experienced greater depressive symptoms and had more difficulties personally and socially adjusting to college. The alcohol consumption of participants had a statistically significant correlation with college adjustment, depressive symptoms and peer support, with higher consumption having a positive impact on the variables.

Identification and characterization of innate immune receptor substrates of γ-secretase enzyme complex

The γ-secretase protease complexes and associated regulated intramembrane proteolysis play an important role in controlling receptor-mediated intracellular signalling events, which have a central role in Alzheimer’s disease, cancer progression and immune surveillance. It has previously been reported that the Interleukin-1 receptor, type 1, (IL-1R1) is a substrate for regulated intramembrane proteolysis, mediated by presenilin (PS)-dependent γ-secretase activity. The aims of this project were twofold. Firstly, to determine the conservation of regulated intramembrane proteolysis as a physiological occurrence amongst other cytokine receptors. In this regard, similar to IL-1R1, we identified the Tumour necrosis factor receptor type 1 (TNFR1) and the Toll like receptor 4 (TLR4) as novel γ-secretase substrates. Secondly, given that the diversity of signalling events mediated by the IL-1R1, TLR4 and TNFR1 are spatially segregated, we investigated the spatial distribution, subcellular trafficking and subcellular occurrence of regulated intramembrane proteolysis of IL-1R1, TLR4 and TNFR1. Using dynasore an inhibitor of clathrin-dependent receptor endocytosis, both ectodomain shedding and γ-secretase-mediated cleavage of IL-1R1 were observed post-internalization. In contrast, TNFR-1 underwent ectodomain shedding at the cell surface followed by endosomal γ-secretase-mediated cleavage. Furthermore, immortalised fibroblasts from PS1-deficient mice showed impaired γ-secretasemediated cleavage of IL-1R1 and TNFR1, indicating that both are cleaved by PS1-and not PS2-containing γ-secretase complexes. Subcellular fractionation and immunofluorescence studies revealed that the γ-secretase generated IL-1R1 ICD translocates to the nucleus on IL-1β stimulation. These observations further demonstrate the novel PS-dependent means of modulating IL-1β, LPS and TNFα- mediated immune responses by regulating IL-1R1/TLR4/TNFR1 protein levels within the cells.

Cryptographic coprocessors for embedded systems

In the field of embedded systems design, coprocessors play an important role as a component to increase performance. Many embedded systems are built around a small General Purpose Processor (GPP). If the GPP cannot meet the performance requirements for a certain operation, a coprocessor can be included in the design. The GPP can then offload the computationally intensive operation to the coprocessor; thus increasing the performance of the overall system. A common application of coprocessors is the acceleration of cryptographic algorithms. The work presented in this thesis discusses coprocessor architectures for various cryptographic algorithms that are found in many cryptographic protocols. Their performance is then analysed on a Field Programmable Gate Array (FPGA) platform. Firstly, the acceleration of Elliptic Curve Cryptography (ECC) algorithms is investigated through the use of instruction set extension of a GPP. The performance of these algorithms in a full hardware implementation is then investigated, and an architecture for the acceleration the ECC based digital signature algorithm is developed. Hash functions are also an important component of a cryptographic system. The FPGA implementation of recent hash function designs from the SHA-3 competition are discussed and a fair comparison methodology for hash functions presented. Many cryptographic protocols involve the generation of random data, for keys or nonces. This requires a True Random Number Generator (TRNG) to be present in the system. Various TRNG designs are discussed and a secure implementation, including post-processing and failure detection, is introduced. Finally, a coprocessor for the acceleration of operations at the protocol level will be discussed, where, a novel aspect of the design is the secure method in which private-key data is handled

Functional metagenomic analysis of the human gut microbiome to identify novel salt tolerance genes

The ability to adapt to and respond to increases in external osmolarity is an important characteristic that enables bacteria to survive and proliferate in different environmental niches. When challenged with increased osmolarity, due to sodium chloride (NaCl) for example, bacteria elicit a phased response; firstly via uptake of potassium (K+), which is known as the primary response. This primary response is followed by the secondary response which is characterised by the synthesis or uptake of compatible solutes (osmoprotectants). The overall osmotic stress response is much broader however, involving many diverse cellular systems and processes. These ancillary mechanisms are arguably more interesting and give a more complete view of the osmotic stress response. The aim of this thesis was to identify novel genetic loci from the human gut microbiota that confer increased tolerance to osmotic stress using a functional metagenomic approach. Functional metagenomics is a powerful tool that enables the identification of novel genes from as yet uncultured bacteria from diverse environments through cloning, heterologous expression and phenotypic identification of a desired trait. Functional metagenomics does not rely on any previous sequence information to known genes and can therefore enable the discovery of completely novel genes and assign functions to new or known genes. Using a functional metagenomic approach, we have assigned a novel function to previously annotated genes; murB, mazG and galE, as well as a putative brp/blh family beta-carotene 15,15’-monooxygenase. Finally, we report the identification of a completely novel salt tolerance determinant with no current known homologues in the databases. Overall the genes identified originate from diverse taxonomic and phylogenetic groups commonly found in the human gastrointestinal (GI) tract, such as Collinsella and Eggerthella, Akkermansia and Bacteroides from the phyla Actinobacteria, Verrucomicrobia and Bacteroidetes, respectively. In addition, a number of the genes appear to have been acquired via lateral gene transfer and/or encoded on a prophage. To our knowledge, this thesis represents the first investigation to identify novel genes from the human gut microbiota involved in the bacterial osmotic stress response.

Development of inversion-mode and junctionless Indium-Gallium-Arsenide MOSFETs

This PhD covers the development of planar inversion-mode and junctionless Al2O3/In0.53Ga0.47As metal-oxidesemiconductor field-effect transistors (MOSFETs). An implant activation anneal was developed for the formation of the source and drain (S/D) of the inversionmode MOSFET. Fabricated inversion-mode devices were used as test vehicles to investigate the impact of forming gas annealing (FGA) on device performance. Following FGA, the devices exhibited a subthreshold swing (SS) of 150mV/dec., an ION/IOFF of 104 and the transconductance, drive current and peak effective mobility increased by 29%, 25% and 15%, respectively. An alternative technique, based on the fitting of the measured full-gate capacitance vs gate voltage using a selfconsistent Poisson-Schrödinger solver, was developed to extract the trap energy profile across the full In0.53Ga0.47As bandgap and beyond. A multi-frequency inversion-charge pumping approach was proposed to (1) study the traps located at energy levels aligned with the In0.53Ga0.47As conduction band and (2) separate the trapped charge and mobile charge contributions. The analysis revealed an effective mobility (μeff) peaking at ~2850cm2/V.s for an inversion-charge density (Ninv) = 7*1011cm2 and rapidly decreasing to ~600cm2/V.s for Ninv = 1*1013 cm2, consistent with a μeff limited by surface roughness scattering. Atomic force microscopy measurements confirmed a large surface roughness of 1.95±0.28nm on the In0.53Ga0.47As channel caused by the S/D activation anneal. In order to circumvent the issue relative to S/D formation, a junctionless In0.53Ga0.47As device was developed. A digital etch was used to thin the In0.53Ga0.47As channel and investigate the impact of channel thickness (tInGaAs) on device performance. Scaling of the SS with tInGaAs was observed for tInGaAs going from 24 to 16nm, yielding a SS of 115mV/dec. for tInGaAs = 16nm. Flat-band μeff values of 2130 and 1975cm2/V.s were extracted on devices with tInGaAs of 24 and 20nm, respectively

Use of oxygen sensors for the non destructive measurement of oxygen in packaged food and beverage products and its impact on product quality and shelf life

The principal objective of this thesis was to investigate the ability of reversible optical O2 sensors to be incorporated into food/beverage packaging systems to continuously monitor O2 levels in a non-destructive manner immediately postpackaging and over time. Residual levels of O2 present in packs can negatively affect product quality and subsequently, product shelf-life, especially for O2-sensitive foods/beverages. Therefore, the ability of O2 sensors to continuously monitor O2 levels present within food/beverage packages was considered commercially relevant in terms of identifying the consequences of residual O2 on product safety and quality over time. Research commenced with the development of a novel range of O2 sensors based on phosphorescent platinum and palladium octaethylporphyrin-ketones (OEPk) in nano-porous high density polyethylene (HDPE), polypropylene (PP) polytetrafluoroethylene (PTFE) polymer supports. Sensors were calibrated over a temperature range of -10°C to +40°C and deemed suitable for food and beverage packaging applications. This sensor technology was used and demonstrated itself effective in determining failures in packaging containment. This was clearly demonstrated in the packaging of cheese string products. The sensor technology was also assessed across a wide range of packaged products; beer, ready-to-eat salad products, bread and convenience-style, muscle-based processed food products. The O2 sensor technology performed extremely well within all packaging systems. The sensor technology adequately detected O2 levels in; beer bottles prior to and following pasteurisation, modified atmosphere (MA) packs of ready-to-eat salad packs as respiration progressed during product storage and MA packs of bread and convenience-style muscle-based products as mycological growth occurred in food packs over time in the presence and absence of ethanol emitters. The use of the technology, in conjunction with standard food quality assessment techniques, showed remarkable usefulness in determining the impact of actual levels of O2 on specific quality attributes. The O2 sensing probe was modified, miniaturised and automated to screen for the determination of total aerobic viable counts (TVC) in several fish species samples. The test showed good correlation with conventional TVC test (ISO:4833:2003), analytical performance and ruggedness with respect to variation of key assay parameters (probe concentration and pipetting volume). Overall, the respirometric fish TVC test was simple to use, possessed a dynamic microbial range (104-107 cfu/g sample), had an accuracy of +/- one log(cfu/g sample) and was rapid. Its ability to assess highly perishable products such as fish for total microbial growth in <12 hr demonstrates commercial potential.