VictorJuiz/thesis huggingface dataset:
Applications of Granger Causality to Magnetoencephalography Research, Short Trial Time Series Analysis, and the Study of Decision Making
Keywords: Neuroimaging
Causality analysis

Causality analysis is an approach to time series analysis that is being used increasingly to investigate neuroimaging data. The reason for its popularity is the useful perspective it provides in describing the ordered operations of various brain regions using indirectly and passively measured neurophysiological signals. Although there are numerous frameworks with which causality analysis can be performed, one concept in particular – termed Granger causality (GC) – is receiving much of the attention because of its ease of implementation and interpretability. GC makes use of the fact that a predictive relationship between the history of one signal and the future of another signal provides evidence for there being a causal relationship between the two signals, and as a result, the physical events underlying those signals. If such a relationship can be established across neural time series, causal dependencies between neural pathways can be inferred and their contribution to brain function can be studied. Several analysis frameworks exist for applying GC to neurophysiological questions but many of these frameworks have deficiencies that impede their application to large and highly multivariate neuroimaging datasets. To address some of these concerns, this study develops the theory and methods for a novel neural time series classification procedure – referred to as GC classification – based on concepts in GC analysis. Validation of this method in neuroimaging research is provided by showing that it can be applied to heterogeneous datasets, that it makes use of many parallel sources of information about causal relationships, and that it can be adapted to different types of preprocessing steps to uncover causal relationships in multivariate neural time series data. Application of this analysis method to human behavioural MEG data revealed that, during a cued button-pressing task, distinct causal relationships exist between sensory cortices and their downstream targets preceding the initiation of actions that differ by whether or not they were the result of a decision being made. These results provide evidence that the GC classification procedure is a useful and robust technique for studying causal relationships in neurophysiological time series.
Modelling of dissolution and bioremediation of chlorinated ethene DNAPL source zones
Keywords: groundwater modelling
groundwater contamination

This thesis investigated the dissolution of dense non aqueous phase liquids (DNAPL) source zones in the subsurface and the effectiveness of enhanced bioremediation for the treatment of chlorinated ethene DNAPLs, using numerical modeling. For this purpose, an existing multiphase numerical model was extended to include comprehensive models for the processes of dissolution and reaction. The first part of the thesis examined DNAPL dissolution. First, a thermodynamic-based dissolution model was validated using experimental data from two complex heterogeneous DNAPL releases. Model predictions for DNAPL spatial distribution and effluent concentrations agreed well with experimental measurements, without requiring calibration. This is the first successful application of a predictive dissolution model in the literature. Model results showed the important effects of relative permeability and interfacial areas on dissolution rates. Then, the thermodynamic dissolution model was compared to simpler models typically used in the literature. Five Sherwood-Gilland (SG) empirical correlations were evaluated and their limitations were illustrated. A new dissolution model was proposed that combined the predictive ability of the thermodynamic model and the simplicity of SG models, and is applicable for complex source zones. Lastly, the relationship between the DNAPL source architecture and downstream concentrations was investigated, focusing on multistage concentration profiles. A new upscaled model was proposed that is able to capture such complex behavior. In the second part of this thesis the thermodynamic dissolution model was combined with a model for reductive dechlorination of chlorinated ethenes to simulate DNAPL bioremediation. Simulations were conducted for simple DNAPL source zones to investigate the impact of dissolution-related processes on bioremediation effectiveness. Dissolution kinetics and back-partitioning of daughter products in the DNAPL were shown to affect dechlorination. Then, the investigation was extended to DNAPL source zones of complex architectures in heterogeneous domains, illustrating the importance of the source zone architecture for the effectiveness of DNAPL bioremediation. Overall, this thesis presents a comprehensive numerical model that will be an important research tool for evaluating the effectiveness of in-situ bioremediation for DNAPL source zones, and will provide the means for a better understanding and control of the critical factors affecting this technology in the field.
Analysis of Myosin VI in Drosophila melanogaster Synaptic Function and Development
Keywords: Myosin VI
nervous system

Myosin VI, encoded by jaguar (jar) in Drosophila melanogaster, is the only member of the myosin superfamily of actin-based motor proteins known to move towards the minus ends of actin filaments. In vitro studies demonstrate that Myosin VI has the ability to perform distinct functions as a cargo transporter and anchor in the cell, however which of these roles Myosin VI plays in the nervous system has yet to be determined. A locomotor defect, observed as sluggish movement in severe jar mutant larvae, was confirmed by behavioural assays. As this can indicate problems at the neuromuscular synapse, microscopy and electrophysiology were used to investigate neuromuscular junction (NMJ) structure and function in jar loss of function mutants of varying severity. Confocal imaging studies revealed a decrease in NMJ length, a reduction in bouton number per NMJ, alterations to the microtubule cytoskeleton and mislocalization of the synaptic vesicle protein Synaptotagmin in jar mutant boutons. FM dye labeling was consistent with the immunostaining data revealing vesicles endocytosed following electrical stimulation occupy the bouton centre in jar mutants. The data is indicative of a function for Myosin VI in maintaining proper peripheral vesicle localization. Electrophysiological experiments revealed a role for Myosin VI in basal synaptic transmission, with a reduction in low frequency nerve-evoked responses and spontaneous release in severe jar mutants. Changes in short-term synaptic plasticity were also observed in Myosin VI mutants by using both paired-pulse experiments to examine release probability and high-frequency stimulation paradigms to recruit vesicles from different functional pools. Taken together, the data suggest that Myosin VI functions as an anchor to peripherally localize vesicles within the bouton enabling their efficient release during nerve stimulation. Synaptic vesicles are mobile at the Drosophila NMJ; thus if Myosin VI is acting as a vesicle tether, it would normally be expected to restrain vesicle mobility at the synapse. FRAP analysis revealed a significant increase in synaptic vesicle mobility in jar mutant boutons. This study elucidates novel roles for Myosin VI function in the nervous system via regulation of the synaptic microtubule architecture and localization of synaptic vesicles within the nerve terminal.
Application of the HLD and NAC Models to the Formation and Stability of Emulsions
Keywords: Emulsions
Microemulsions
Hydrophilic-lipophilic deviation
Net-average curvature
aggregation
coalescence
formation
stability
Asphaltenes
Naphthenic amphiphiles
Bitumen

This thesis explored how asphaltene and naphthenic amphiphile species influence the formation (morphology and size) and stability of heavy crude oil (bitumen) emulsions. It was experimentally shown that asphaltenes produce water-in-oil emulsions. Naphthenic amphiphiles on the other hand flip the emulsion morphology to oil-in-water. It was further demonstrated that the size and stability of these emulsions is influenced by physicochemical effects such as the pH, solvent-bitumen-water ratios, solvent aromaticity, and temperature. In view of these findings, the hydrophilic-lipophilic deviation (HLD) and net-average curvature (NAC) models were looked at as potential means for predicting the formation and stability of emulsions. Owing to the complexity of bitumen emulsions, however, the HLD and NAC models were instead tested against well-defined sodium dihexyl sulfosuccinate-toluene-water emulsions. The morphologies of these emulsions were predicted as a function of the formulation salinity whereas corresponding droplet sizes were predicted as a function of the continuous phase density and interfacial tension (γow). Emulsion stability trends were in turn predicted using a collision-coalescence-separation assumption. From this assumption, emulsion stability was expressed as a function of the emulsion droplet collision frequency and activation energy. The key parameters of the highly scrutinized activation energy term included the γow, interfacial rigidity, and critical film thickness. In applying the same modeling approach to the stability of other emulsions already published in the literature, it was found that the rigidity of adsorbed multilayer/liquid crystal films cannot yet be fully accounted for. This shortcoming was the reason for which only minimum stability times were reported for bitumen emulsions.
Handle With Care Evaluation Project: Impact of a Mental Health Promotion Training Program on Child Care Practitioners' Knowledge and Practices
Keywords: child care
mental health promotion
Handle With Care
training
children
evaluation

This study explored the effectiveness of Handle With Care, a mental health promotion training program for child care practitioners working with children between birth to age 6. Handle With Care program content is based on research evidence. Training units are intended to deepen practitioners’ understanding of how children’s social-emotional development, centre and family connections and positive workplace activities link to children’s well-being and practitioners’ roles in these areas. Fifty-seven front-line practitioners from three different regional groups (Rural, Suburban, Urban) completed Handle With Care workshops and were compared to 56 comparison participants, matched according to region, who were not exposed to training. The evaluation utilized a time series repeated measures design and consisted of mixed quantitative and qualitative measures to determine training outcomes related to practitioner’s mental health promotion knowledge and practices. Findings indicated that child care practitioners who participated in Handle With Care training demonstrated increased mental health promotion knowledge. In particular, they acquired better comprehension of issues concerning practitioner and child attachment relationships, children’s self-esteem, emotion expression and regulation and peer relationships. Training participants significantly differed from comparison participants in their knowledge of these topics. In terms of practices, training participants also evidenced significantly improved practices relative to comparison participants. These gains were especially observed in relation to practitioners building trusting relationships with children, fostering children’s sense of self and competence, positive peer interactions and practitioners promoting their own mental health. In contrast, Handle With Care training did not show the intended consistent outcomes with respect to practitioners helping children with emotional communication, dealing with diversity, changes and transitions and practitioners building relationships with children’s parents. Results tended to be discrepant across regional groups, and in some instances, gains in mental health promotion and knowledge were not sustained over time. Overall, the study suggests that Handle With Care is a useful way to augment child care practitioners’ capacity to consider the mental health of all children in their care and flexibly implement strategies to help children reach their optimal potential. The study also provides important information concerning regional differences and areas of training content that may benefit from revision.
Evidence Based Strategic Decision Making in Ontario Public Hospitals
Keywords: evidence based management
strategic decision making

Context: A relatively recent focus on evidence based management has been influenced strongly by evidence based medicine. Healthcare administrators are encouraged to utilize similar principles to optimize their decision making. There are no known studies that address whether or not and how evidence is used by healthcare administrators in decision making practice and process. Objectives: This study explores how evidence is conceptualized by public hospital executives and whether or not, and how, evidence is brought to bear on strategic decision making. Design: The study undertook a qualitative design, using a grounded theory approach. The focus was to uncover how evidence is conceptualized by decision makers, whether or not and how evidence as defined is brought to bear, and under what conditions and why evidence is brought to bear. The study included four public hospitals in the Greater Toronto Area, two academic health sciences centres and two community teaching hospitals. Hospital CEOs were asked to identify three strategic decisions (one clinical expansion, one partnership, and one decision on prioritizing quality improvement). Interviews were conducted with 19 healthcare leaders and decision makers, and content analysis was undertaken for 64 supporting documents. Results: Strategic decision makers in this study bring an amalgam of evidence to bear on strategic decisions. Evidence comes from sources internal and external to the organization, and includes a series of types of evidence ranging from published research to local business evidence. The reasons for bringing evidence to bear are highly intertwined. Evidence was sought, developed, and brought to bear on decisions in a formalized manner, and was used in concert with conditions internal and externalto the organization, and informed by the decision maker characteristics. Conclusion: Evidence plays a prominent role in strategic decision making. Strategic decisions were supported by processes requiring evidence to be brought to bear.
Contraintes syntaxiques et sémantiques sur l'intensification implicite: un cas non standard de la construction intensive de conséquence
Keywords: construction
intensive
consequence
intensification
quantification
quantificateur
association
tardive
implicite
explicite
quantite
qualite
syntaxe
semantique
discours
gradation
gradabilite
mesurabilite
modification
francais
evaluation
correlation
tellement
si
assertion
comparaison
peripherie

Cette these porte sur differents aspects syntaxiques et semantiques de l'intensification implicite dans une construction du francais non standard du type "Marie est belle qu'on en reste ebahi". Cette construction se caracterise par la presence d'un modificateur propositionnel (la prop-que) jouant le role d'un evaluateur de mesures extremes liees au predicat de la proposition matrice ("belle"). Ce modificateur opere sur des echelles de mesures et delimite la mesure reelle en la mettant en rapport avec la consequence qu'il exprime. Comme ce type d'evaluation correlative definit aussi la construction intensive de consequence (CIC), ou l'intensification est lexicalement realisée par les marqueurs d'intensité "tellement", "si", etc., nous proposons que la construction non standard represente un type implicite de la CIC. La CIC-implicite constitue un nouvel objet d'etude pour la description et la formalisation dans le cadre de la grammaire generative (Chomsky 1993, 1995, 2000). L'objectif principal de cette these est de fournir une description detaillee des comportements de la CIC-implicite, d'identifier les contraintes qui la regissent et de proposer un lien derivationnel entre cette derniere et la CIC-explicite. Une comparaison systematique des proprietes des deux CIC montre que les realisations de la CIC-implicite sont plus restreintes. Les restrictions incluent, entre autres, l'impossibilite de l'enchassement par un verbe factif et l'absence de la force interrogative. Une ligne directe peut etre etablie entre les differentes restrictions en termes de la notion pragmatique d'assertion et de la presence du locuteur. Notre derivation de la CIC-implicite, basee sur l'analyse de la CIC-explicite par association tardive proposee par Bhatt et Pancheva (2004, 2007), formalise la notion d'assertion au niveau de la peripherie gauche avec une projection dediee (Haegeman 2006 ; Speas et Tenny 2003). Cette projection, ainsi que l'association de la prop-que modificatrice, permettent d'interpreter et de legitimer la categorie vide qui realise l'intensification dans la CIC-implicite.
CSI Feedback and Power Control in Wireless Networks
Keywords: Wireless Communications
Interference Networks
Quantization
Channel State Feedback
Power Control
Convex Optimization
Cooperative Networks
Resource Allocation

We investigate the effects of quantized channel state information (CSI) on the performance of resource allocation algorithms in wireless networks. The thesis starts with a brief overview of a specific type of quantizer, referred to as a conservative quantizer where we propose the optimality and sufficiency conditions as well as practical methods to find such quantizers. We apply this theory to the quantization of transmitter CSI in point-to-point Gaussian channels and transmission under short-term power constraints. Next, we show that in a multiple-node decode-and-forward (DF) cooperative network, the same structure for quantizer is close to op- timal for the sum-rate objective function. Based on a proposed upper bound on the rate loss in such scenarios, we also argue that the quantizer should assign uneven numbers of quantization bits to different links in the network. The simulation results show that given a target rate loss level, through quantization and bit allocation, there is, on average, 0.5−1 bits per link savings in CSI feedback requirements compared to the uniform and equal bit allocation approaches. Given the many benefits in non-uniform allocation of CSI rate in the network, we formulate a generalized bit allocation scheme which is extensible to arbitrary classes of network resource allocation problems. In the last part of this thesis, we focus on power control in an interference network and then, investigate the effects of CSI imperfections on the performance of power control algorithms. First, we propose an iterative power control algorithm based on a fixed-point iteration and prove its local convergence. Then, we show that for a centralized implementation of the power control algorithm, a uniform in dB (geometric) quantizer of channel power is efficient. Based on this choice of channel quantizer, we propose a bound on rate loss in terms of the resolution of the ii deployed quantizer, where a 3 dB in quantization error is shown to contribute to a maximum of 1 bit rate loss at each user. Similarly to the previous scenario, the upper bound suggests that an uneven assignment of numbers of quantization levels leads to smaller distortion. Based on this bound, we develop the corresponding bit allocation laws. We also investigate the effects of CSI errors on the performance of distributed power control algorithms and show that, compared to the centralized case, the distributed algorithm could lead to a further SINR loss of up to 3 dB for one or more transmitters. This error is due to the fact that because of CSI errors, the estimated interference level at each receiver is different from the induced interference wireless transmitters expect.
Controlling the Physical Properties of Organic Semiconductors through Siloxane Chemistry and other Organic Electronic Materials
Keywords: Siloxane
Triarylamine
Silicone
Organic Electronics
OLED
OPV
Semiconductors

Triarylamine type materials with vastly altered physical properties are synthesized by hybridizing organic semiconducting structures with silicone and siloxane groups. By altering the silicon content of these materials, we can tune their physical composition from free flowing liquids, to amorphous glasses, to cross-linked films. Much of this modification is enabled by the unique use of a metal-free Si-H activation chemistry; the Piers-Rubinsztajn reaction. This chemistry is demonstrated to be a general and rapid way to build up hybrid semiconducting structures. Key to the utility of these materials in electronic devices, it is shown that hybridization with silicon groups has a negligible effect on the useful electrochemical properties of the base materials. Building on this, it is shown that charge carrier mobility through a prototypical liquid organic semiconductor is similar to the base materials and transport is described by existing dispersive transport theories. Finally, two side projects in the area of organic electronics are discussed. New phthalonitrile based fluorophores are characterized and their utility as deep-blue emitting dopants in organic light emitting diodes is demonstrated. These same π-extended phthalonitriles can also be used as precursors to new red-shifted BsubPcs which display exceptional electrochemical stability and tuning.
Transcriptome Studies in Inflammatory Bowel Disease
Keywords: Transcriptome
IBD

Inflammatory bowel disease (IBD) is a composite classification for a range of gastrointestinal disorders. The two most common forms of IBD are Crohn’s disease (CD) and ulcerative colitis (UC). The chronicity of IBD has long-term consequences on the quality of life of affected individuals. However, therapies available today are applied with limited success. It is thought that interplay between environmental triggers and commensal bacteria can cause a dysregulated inflammatory response in genetically predisposed individuals, but the exact etiology is not understood. The objective of these studies was to identify the gene expression changes which associate with differential response to therapy and with recurrence of disease following surgery. The effects of genetic variation on gene expression were also evaluated. Tissue and blood samples were collected from eligible patients. Total RNA was extracted and measured on gene expression microarrays. The raw gene expression data were analyzed in a statistical framework against variables of interest in order to assess the significance of each association. Genes were evaluated individually as well as in biological networks. A few tens of genes were identified as differentially expressed in blood between UC patients who respond to intravenous corticosteroid therapy and those who do not. Some of these genes were also shown to have high predictive value. Differentially regulated genes were also found in UC patients who experience recurrence of disease after surgery, relative to those who remain disease-free. Specifically, gene networks responsible for the regulation of cellular transport were among the major players. A comparative analysis of genotype and gene expression in the human ileum indicated that the transcription of approximately 10% of genes is influenced by variations in the genome. Results from these studies have not only contributed to our understanding of disease mechanism, but could also have medical implications. With the advance of new and less costly transcriptome technologies on the clinical stage, panels of expression markers associated with therapy response and post-operative recurrence can be used as diagnostic and prognostic tools. Data on the relationship between genotype and gene expression are already shedding new light on the function of certain genetic IBD risk variants.