VictorJuiz/thesis huggingface dataset:
Carn Mor de Chlachan Beaga, A Large Cairn from Small Stones: Multivocality and Memory in Cape Breton Gaelic Singing
Keywords: Gaelic
Cape Breton
song
singing
tradition
musical transmission
memory
phenomenology
Scotland
Nova Scotia
ethnomusicology
folklore
archive
music and place
Turner
Ricoeur

Since the first Scottish Gaelic-speaking settlers arrived in Nova Scotia in the late 18th century, their Gaelic singing tradition has been an integral part of life in communities on Cape Breton Island. With the waning of the Gaelic language, however, came efforts to collect and preserve the song tradition, and the intention to pass it along intact. This dissertation eschews the consideration of Gaelic singing as a monolithic tradition with a common repertoire and experience, and instead examines it as a multifaceted process enacted by individuals in three main sites: home, public performance and the archive. It examines the various ways the practice manifests itself, concluding that memory and individual agency are constants, both for singers and listeners. Through interviews, participant-observer activity and archival research, this study demonstrates that Gaelic singers have been far from passive culture-bearers but have instead actively shaped their song practice by choosing repertoire, melody variants and texts. It also discusses the dynamic role of memory and social interaction in the transmission and performance of Gaelic song. Memories of other singers, discussion of the text, and contextual details draw singers and listeners into a community that is both synchronic and diachronic. This practice is chiefly oral, but is supported by recordings and printed songbooks as well as an array of objects – photo albums, clippings, tapes – which evoke the sense of previous performances and their singers. Despite their intention to transmit the songs with little or no change, singers have a flexible relationship with the material and in some cases subvert the authority of recorded or printed sources by turning instead to first-hand experiences. This simultaneous presence of past and present has tremendous implications for what it means to know a song, and one comes to understand it as a composite of multiple memories, performances and meanings.
Cognitive Rhythm Generators for Modelling and Modulation of Neuronal Electrical Activity
Keywords: Closed Loop
Cognitive Device
Complexity
Computer Model
Coupled Oscillators
Epilepsy
Neuromodulation
Nonlinear Dynamics
Neuronal Network
Seizure-Like Event
Seizure Transition
Therapeutic

An innovative mathematical architecture for modelling neuronal electrical activity is presented, called the cognitive rhythm generator (CRG), wherein the proposed architecture is a hybrid model comprised of three interconnected stages, namely: (1) a bank of neuronal modes; (2) a ring device (limit-cycle oscillator); and (3) a static output nonlinearity (mapper). Coupled CRG networks are employed to emulate and elucidate the dynamics of biological neural networks, including the recurrent networks in the hippocampus. Several species of ring devices are described and investigated, including the clock, labile clock, hourglass and multistable ring systems, and their applications to neuronal modelling explored. Complexity measures such as the maximum Lyapunov exponent, correlation dimension and detrended fluctuation analysis are applied to compare model and biological records and validate the CRG methodology. The basis of neural coding is also examined in mathematical detail, with particular regard to its description by Volterra-Wiener kernel formalism, from which the neuronal modes are derived. Applications to theta-gamma coding are discussed. Further on in the thesis, a CRG epileptiform network model of spontaneous seizure-like events (SLEs) is developed and used as a platform to test neuromodulation approaches for seizure abatement. (Neuromodulation mentioned here refers to methods involving electrical stimulation of neural tissue for therapeutic benefit). Spontaneous SLE transitions in the epileptiform network are shown to be related to the mechanism of intermittency, as determined by examining the state space dynamics of the model. The onset of SLEs is associated with increased network excitability and decreased stability, consistent with experimental results from the low-magnesium/high-potassium in vitro model of epilepsy. Lastly, a novel strategy for therapeutic neuromodulation is presented wherein a coupled CRG network (called the “therapeutic network”) is interfaced with the epileptiform network model, forming a closed loop for responsive, biomimetic neuromodulation of the epileptiform network. Relevance to clinical applications and future work is discussed.
The Role of PTEN in Pancreatic Beta Cells and Insulin Promoter-expressing Neurons in Modulating Glucose Metabolism and Energy Homeostasis
Keywords: type 2 diabetes
neuronal
PTEN
rat insulin promoter
insulin sensitivity
pancreatic beta cell mass and function

PI3K signaling in pancreatic β cells has been shown to be important in modulating β cell mass and function under basal condition. Evidence suggests that a specific group of insulin promoter-expressing neurons also modulates glucose metabolism and energy homeostasis through their PI3K signaling. Thus we hypothesize that PI3K activation via PTEN deletion under the control of rat insulin promoter (RIP) in pancreatic β cells and RIP-expressing neurons will protect against hyperglycemia and diabetes in experimentally induced mouse models of type 2 diabetes. In Chapter IV, we showed that RIP-mediated PTEN deletion in pancreatic β cells led to PI3K activation and subsequent increased β cell mass and function, thus protected the mice from high fat diet (HFD)-induced diabetes. Furthermore in the absence of global leptin signaling, β cell-specific PTEN deletion maintained β cell function in the setting of severe insulin resistance, therefore prevented diabetes development. Interestingly, RIP-mediated PTEN deletion also resulted in increased peripheral insulin sensitivity due to PI3K activation in central nervous system. In Chapter V, we showed this increased insulin sensitivity was maintained after HFD feeding, which also contributed to the protection against diabetes. These mice also showed increased visceral adipogenesis and subcutaneous adiposity on HFD, which were dramatically attenuated in the absence of leptin signaling, indicated the essential role of peripheral leptin action in mediating the insulin sensitive phenotype from neuronal RIP PTEN deletion. Finally, we demonstrated that the insulin sensitizing phenotype in these mice was not mediated through ventromedial hypothalamic nuclei (VMH), such that VMH-specific PTEN deletion did not alter energy homeostasis or glucose metabolism. Together, the data from this thesis points to an inhibitory role of PTEN in both central nervous system and pancreatic β cells in glycemic control. Therefore, PTEN may represent a potential target for diabetes prevention and treatment.
Control Strategies for the Next Generation Microgrids
Keywords: Power system
Microgrid
Control
Distributed generation
Distributed control
Trajectory shaping
Smart grid
Distributed energy resrouce

In the context of the envisioned electric power delivery system of the future, the smart grid, this dissertation focuses on control and management strategies for integration of distributed energy resources in the power system. This work conceptualizes a hierarchical framework for the control of microgrids---the building blocks of the smart grid---and develops the notion of potential functions for the secondary control for devising intermediate set points to ensure feasibility of operation of the system. A scalar potential function is defined for each controllable unit of the microgrid such that its minimization corresponds to achieving the control goal. The set points are dynamically updated using communication within the microgrid. This strategy is generalized to (i) include both local and system-wide constraints and (ii) allow a distributed implementation. This dissertation also proposes and evaluates a simple yet elaborate distributed strategy to mitigate the transients of controllable devices of the microgrid using local measurements. This strategy is based on response monitoring and is augmented to the existing controller of a power system device. This strategy can be implemented based on either set point automatic adjustment (SPAA) or set point automatic adjustment with correction enabled (SPAACE) methods. SPAA takes advantage of an approximate model of the system to calculate intermediate set points such that the response to each one is acceptable. SPAACE treats the device as a generic system and monitors its response and modulates its set point to achieve the desired trajectory. SPAACE bases its decisions on the trend of variations of the response and accounts for inaccuracies and unmodeled dynamics. Case studies using the PSCAD/EMTDC software environment and MATLAB programming environment are presented to demonstrate the application and effectiveness of the proposed strategies in different scenarios.
Functional Analysis of the Pseudoprotease iRhom2 and Nonsense-mediated mRNA Decay Factor Smg1 using Gene Deficient Mice
Keywords: iRhom2
Smg1
TNF
nonsense mediated RNA decay

This work involves the characterization of two genes using mouse models of gene deficiency and thus has two focuses: Focus I: Innate immune responses are vital for pathogen defence but can result in septic shock when excessive. A key mediator of septic shock is TNFα, which is shed into intercellular spaces after cleavage from the plasma membrane by the protease TACE. Here we report that the rhomboid family member iRhom2 interacts with TACE and regulates TNFα shedding in vitro and in vivo. Compared to controls, gene-targeted iRhom2-deficient mice showed reduced serum TNFα after LPS challenge survived a lethal LPS dose. Furthermore, iRhom2-deficient mice failed to adequately control the replication of Listeria monocytogenes and thus succumbed to even mild infections. Our study has identified iRhom2 as a novel regulator of innate immunity that may be an important target for modulating sepsis and pathogen defence. Focus II: Smg1 is a phosphatidylinositol 3-kinase-related kinase (PIKK) associated with multiple cellular functions, including DNA damage responses, telomere maintenance, and nonsense-mediated mRNA decay (NMD). NMD degrades transcripts that harbour premature termination codons (PTCs) due to events such as mutation or alternative splicing (AS). Recognition of PTCs during NMD requires the action of the Upstream frameshift protein Upf1, which must first be phosphorylated by Smg1. However, the physiological function of mammalian Smg1 is not known. Using a gene-trap model of Smg1 deficiency, we show that this kinase is essential for mouse embryogenesis such that Smg1 loss is lethal at embryonic day 8.5 (E8.5). High-throughput RNA sequencing (RNA-Seq) of RNA from cells of Smg1-deficient embryos revealed that Smg1 depletion led to pronounced accumulation of PTC-containing splice variant transcripts from ~9% of genes predicted to contain AS events capable of eliciting NMD. Among these genes are those involved in splicing itself, as well as genes not previously known to be subject to AS-coupled NMD, including several involved in transcription, intracellular signalling, membrane dynamics, cell death and metabolism. Our results demonstrate a critical role for Smg1 in early mouse development and link the loss of this NMD factor to major and widespread changes in the mammalian transcriptome.
Toward the Development of Nucleic Acid Assays Using Fluorescence Resonance Energy Transfer (FRET) and a Novel Label Free Molecular Switching Construct
Keywords: fluorescence
molecular switch
nucleic acid
thiazole orange

The research presented in this thesis introduces design criteria for development of a new type of self-contained optical biosensor. The study begins with evaluation of a dual label, fluorescence resonance energy transfer (FRET) bioassay format, and then goes on to demonstrate a signalling platform that uses an immobilized fluorescent intercalating dye so as to avoid labelling of both the target and probe strands. An extensive survey of FRET pairs that can be used to monitor hybridization events in solution and at solid interfaces was conducted in solution to provide a set of calculated Förster distances for the extrinsic labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethylrhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ) and Iowa Black RQ (IabRQ). FRET parameters using thiazole orange (TO) intercalating dye as a FRET donor for various acceptor dye-labelled DNA conjugates in solution were determined. Limitations associated with quenching mechanisms other than those mediated by FRET motivated the development of a molecular switch that contained intercalating dye. The four binding sites associated with Neutravidin served for assembly of the switch using biotin interactions. One binding site was used to immobilize an unlabelled oligonucleotide probe. The adjacent site was used to immobilize a novel biotinylated TO derivative that could physically reach the probe. On hybridization of the probe with target, the intercalating dye was captured by the hybrid, leading to a change of fluorescence. This reversible signalling mechanism offers a method without nucleic acid labelling to detect nucleic acid association at an interface. A SNP discrimination strategy involving TO and formamide was investigated, and SNP discrimination without the requirement of thermal denaturation was achieved for multiple target lengths, including a 141-base pair PCR amplicon in solution. It was determined that formamide could also provide improvements of signal-to-noise when using thiazole orange to detect hybridization.
Greening the City: Exploring Health, Well-being, Green Roofs, and the Perception of Nature in the Workplace
Keywords: Green roofs, health, nature, workplace, sense of place, Toronto, Chicago, Urban nature, green building, well-being, phenomenology, logistic regression

This five-paper thesis explores office workers perceptions of green roofs and how this influences their health/well-being in Toronto and Chicago. Paper 1 examines the underlying paradigms and world-views of major research programs that look at the human relationship to nature and health/well-being, showing that despite some convergence between their methods and integration of different paradigms, continued differences and lack of clarity on the normative assumptions underlying each approach leads to confusion in the specification of ‘nature’ in health/well-being and place research. Paper 2 is a comparative analysis of the implementation of green roof policies in Toronto and Chicago. Paper 2 demonstrates the importance of ‘selling’ green roofs by linking them to larger environmental programs and of the municipal power structure that influences how and if environmental programs are implemented. Paper 3 examines the awareness, attitudes, and feelings towards green roofs by office workers with access to them (visual or physical) from their workplace in Toronto and Chicago. Using a phenomenological analysis of semi-structured interviews (n=55), Paper 3 shows that the hinterland, expectations of different kinds of ‘nature’ and aesthetics in the city, and access all influence perceptions of green roofs and sense of place. Paper 4 explores office workers awareness of and attitudes towards green roofs and the possible influence on their well-being in Toronto and Chicago from a large survey (n = 903). Participants showed a high literacy on the environmental benefits of green roofs. Chi-square analysis showed mixed results for health, but a significant association between visual access to a green roof and improved concentration. Paper 5 tests whether the relationship found in Paper 4, improved concentration with visual access, was still significant when other confounding variables were added to the model. Using a logistic regression on the same survey population (subset n =505), results found that concentration was no longer significant but that there was a trend towards improved concentration.
Functional Development of Amygdalae and Anterior Cingulate Cortex in Emotion Processing
Keywords: Amygdala
Anterior Cingulate Cortex (ACC)
Emotion processing
Neuroimaging

Emotion processing involves specialised brain regions allowing for effective evaluation of the social environment and for the acquisition of social skills that emerge over childhood. In humans, an important aspect of normal development is the ability to understand the facial expressions of others that signal the nature and safety of the environment. Existing functional data, however, have not characterised the developmental trajectories associated with the differing neural and cognitive-behavioural development. The current thesis investigates the functional specialisation and development of the spatial and temporal patterns in neural activities during implicit processing of facial emotions from early childhood through adulthood. The first study identified brain regions engaged in implicit processing of emotional expressions using a simple emotion-processing paradigm (target detection task) with fourteen healthy adults using magnetoencephalography (MEG) recordings. Participants responded to a non-face target (a scrambled pattern) while ignoring the emotional face presented in a different hemifield. Results showed ACC and right-lateralised amygdala activations in early latencies in response to the unattended emotional faces related to rapid and implicit attention to the task-irrelevant facial emotions, specifically during the processing of the fearful emotion. Based on the findings in the first study, the second study investigated the developmental patterns and age-related differences in brain activities associated with the rapid and automatic processing of the emotional expressions in MEG with twelve children 7 – 10 years old, twelve adolescents 12 – 15 years old and twelve young adults (mean age 24.4 years) using the same paradigm. The results showed that emotion processing developed early in childhood in the amygdalae, whereas the processing of fear had later maturation engaging the ACC. The results further demonstrated an age-correlated increase in development in ACC activity and an age-related laterality shift in the amygdalae related to fear processing. The present thesis provides new evidence contributing to the understanding of the protracted but differing normal development in the emotional brain over the childhood into adulthood, and offers critical insights into understanding possible dysfunctions of these brain regions during development.
Reaction Dynamics of Alkyl Bromides at Silicon; Experiment and Theory
Keywords: Reaction dynamics
Silicon
Alkyl bromides
Scanning tuneling miscroscopy
Density funcitional theory

Physisorption and reaction at silicon surfaces of a series of brominated organic molecules: bromoethane, 1,2-dibromoethane, 1-bromopropane, 1-bromobutane and 1-bromopentane were examined by Scanning Tunneling Microscopy (STM). On Si(111)-7×7, a widely-spaced “one-per-corner-hole” pattern was observed, formed by the physisorption and reaction of several alkyl bromides. This “one-per-corner-hole” pattern suggested long-range repulsion between the adsorbates. Density Functional Theory (DFT) calculations, performed by others in parallel with these experiments, showed that this long-range repulsion was due to lateral charge transfer in the Si(111)-7×7 surface consequent on the physisorption of an alkyl bromide or chemisorption of a Br atom. The reaction rate of bromine ‘abstraction’ (transfer of a Br-atom from the adsorbate to the silicon) was examined for two physisorbed states of 1 bromopentane on Si(111)-7×7, one vertical and one horizontal, each distinguishable by STM. The energy barrier was found to be significantly lower for abstraction of Br-atom from the vertical than for the horizontal 1 bromopentane, both for thermal and electron-induced reaction. This finding accords with previous DFT calculations for methyl bromide, for which theory exhibited a clear preference for a vertical transition state in the bromination of Si(111)-7×7. The effect of alkyl chain-length on the rate of thermally-induced dissociative attachment reactions was investigated for a series of primary bromo-alkanes (bromoethane, 1-bromopropane and 1-bromobutane) on a different face of silicon; Si(100)-c(4×2). These three bromo-alkanes all physisorbed exclusively ‘inter-row’, bridging the gap between Si dimer-rows of Si(100)-c(4×2). Thermal reaction was highly ‘localized’, i.e. the chemisorbed Br-atom was formed directly below the parent bromo-alkane. The thermal barrier heights were found experimentally to increase systematically with chain length. This trend was interpreted, on the basis of DFT calculations performed by the author, as being due to the extra energy required to lift the alkyl group in going from the initial physisorbed state to the more-nearly vertical transition state.
Vitamin D Status and its Contribution to Multiple Sclerosis Risk: Insights Gained through the Study of Children with Central Nervous System Demyelination
Keywords: Vitamin D
Multiple Sclerosis
Nutrition
Pediatric
Autoimmune
Cholecalciferol
Calciferol
Bradford Hill
Sun exposure
Questionnaire
UVB

Acute demyelination in children may be a monophasic illness or the sentinel attack of multiple sclerosis (MS) – a chronic inflammatory neurodegenerative demyelinating disease. MS risk is largely determined during childhood and vitamin D may protect against MS. The primary objective of this thesis was to evaluate vitamin D status in children presenting with acute demyelinating syndromes (ADS) as a potential contributor to MS outcome. The LIAISON “25 OH Vitamin D TOTAL” assay was validated to assess the biomarker of vitamin D status – serum 25-hydroxyvitamin D (25(OH)D) concentrations. Consecutive patients (<16 y) were enrolled at presentation with ADS and prospectively evaluated at 23 Canadian centres. MS was defined by a second clinical demyelinating event or by MRI evidence of new lesions over time. Cox proportional hazards regression models assessed risk of MS outcome as a function of serum 25(OH)D tertiles, accounting for factors associated with either MS risk or vitamin D status – age, sex, season, and HLA-DRB1*15 status. Of 211 children with 25(OH)D measured in sera obtained a median of 9 days from onset (interquartile range, 5 – 17 d; maximum 36 days), 20% (n = 41) were diagnosed with MS after 3.7 mos. (3.1 – 7.3 mos.). Risk of MS was lower in children with 25(OH)D levels in the highest tertile (≥ 74 nmol/L) at ADS versus those in the lowest tertile (<50 nmol/L) (HR 0.41; 95% CI 0.18 to 0.97, adjusted model). Children with higher circulating 25(OH)D concentrations at ADS have a lower risk of MS. Further evidence for a role of vitamin D insufficiency during childhood and adolescence contributing to MS risk comes from three MS patients with suboptimally managed pseudo-vitamin D deficiency rickets. Finally, a sun exposure questionnaire was validated in the latter part of this thesis for use in future research into determinants of vitamin D status and their association with risk of MS.