VictorJuiz/thesis huggingface dataset:
Development and Application of Methods for Real-time fMRI Neurofeedback
Keywords: fMRI
Neurofeedback

Improving stroke recovery is a topic of considerable interest in the developed world. Motor deficits following stroke can significantly impact quality of life, and motor rehabilitation strategies are urgently needed to promote brain recovery. One technique that has had therapeutic success in other domains is neurofeedback (NF), a strategy whereby a person is trained to gain volitional control of their neurological activity. The NF technique has proven efficacious in disorders ranging from epilepsy to attention deficit disorders based on feedback of electroencephalography (EEG) signals, and the potential exists for NF applications in the recovery of motor function following stroke. Using functional magnetic resonance imaging (fMRI), NF can be applied to precisely defined regions of interest (ROIs), facilitating the targeted treatment of affected functional areas. The combination of fMRI and NF is still relatively new, and much work remains in the characterization and optimization of fMRI NF strategies. In a two-pronged approach, this thesis focuses on the application of ROI-based NF to the motor system using traditional fMRI measurements and also the development and analysis of acquisition strategies intended for use in ROI-based NF. First, a study of the mechanisms governing the successful application of NF in primary motor cortex ROIs is presented, using kinaesthetic motor imagery (imagining the sensation and execution of movement) to engage the motor system. Second, an investigation of fMRI signal contrast enhancement properties using multi-echo fMRI acquisition methods in dense sampling regimes is considered. Third, a novel acquisition method is introduced, designed using parallel MRI principles to provide fast and detailed sampling of fMRI signals in selected ROIs, called Constrained Source Space Imaging (CSSI). To conclude, the potential future directions for fMRI NF research and the CSSI technique are discussed, including thoughts toward the continued development of NF as a potential motor therapy for stroke patients.
Rubato and Climax Projection in Two Piano Sonatas by Scriabin
Keywords: Rubato
Climax
Scriabin

Alexander Scriabin (1872-1915) is well known as a composer for his inventive tonal language and as a performer for his approach to rubato. As is evident through his piano roll recordings, Scriabin's pianism epitomizes the performance practice of the early twentieth century and raises significant issues for the modern interpreter of Scriabin’s scores. The diversity in Scriabin's compositional style has prompted a variety of analytic approaches. Chapter one surveys Scriabin’s stylistic development in terms of his piano music and explores relevant analytic and interpretive approaches. Chapter two explores Scriabin's pianism as described by his close friends, pupils, and critics of the time. These reports characterize Scriabin's playing as rhythmically flexible, sensitive to different layers of voicing, and subtle in its dynamic nuances. In Chapter three, the two central topics of the dissertation—rubato and climax—are explored in general and in relation to Scriabin’s music. In Scriabin’s early piano music the indication for rubato correlates with a specific melodic contour, and the broader connection between rubato and melodic contour is explored. The study of climax draws on Austin T. Patty’s theory of pacing, in which climaxes of different types arise through different handling of various musical parameters. The musical components of Scriabin’s climaxes evolve during his output. Chapters four and five examine the Piano Sonata No. 4, Op. 30, and Piano Sonata No. 10, Op. 70, respectively. These case studies provide a formal-thematic overview of each work, consider the use of rubato and the handling of climaxes with respect to the theoretical frameworks established in Chapter three, and assess performance choices with reference to several recorded performances. This dissertation provides an alternative outlook to the performance of Scriabin's music. Tempo graphs reveal the pacing between phrases and sections and permit comparisons among artists from different generations. The recordings surveyed for both sonatas indicate that the flexibility in timing within individual phrases or thematic sections is much greater in the earlier recordings compared to more recent ones, as is the degree of tempo contrast between slow and fast sections.
Development and Application of High-throughput Chemical Genomic Screens for Functional Studies of Cancer Therapeutics
Keywords: Chemical Genomics
Anticancer Agents

Chemotherapeutic agents act by targeting rapidly dividing cancer cells. The full extent of their cellular mechanisms, which is essential to balance efficacy and toxicity, is often unclear. In addition, the use of many anticancer drugs is limited by dose-limiting toxicities as well as the development of drug resistance. The work presented in this thesis aims to address the basic biology that underlies these issues through the development and application of chemical genomic tools to probe mechanisms of current and novel anticancer compounds. Chemical genomic screens in the yeast Saccharomyces cerevisiae have been used to successfully identify targets and pathways related to a compound’s mode of action. I applied these screens to examine the mode of action of potential anticancer drugs: a class of platinum-acridine compounds and the apoptosis-inducing compound elesclomol. By analogy to the yeast screens, I developed an RNAi-mediated chemical genomic screen in human cells which has the potential to reveal novel targets and drug mechanisms. This screen was applied to further understand doxorubicin’s mode of action. In parallel with the loss-of-function assays, our lab developed a human ORF overexpression screen in human cells. I applied this gain-of-function screen to identify those genes that, when overexpressed, are toxic to cells. Characterization of such genes that cause toxicity can provide insight into human diseases where gene amplification is prevalent.
Graphical Epitome Processing
Keywords: machine learning
computer vision
graphical models

This thesis introduces principled, broadly applicable, and efficient patch-based models for data processing applications. Recently, "epitomes" were introduced as patch-based probability models that are learned by compiling together a large number of examples of patches from input images. This thesis describes how epitomes can be used to model video data and a significant computational speedup is introduced that can be incorporated into the epitome inference and learning algorithm. In the case of videos, epitomes are estimated so as to model most of the small space-time cubes from the input data. Then, the epitome can be used for various modelling and reconstruction tasks, of which we show results for video super-resolution, video interpolation, and object removal. Besides computational efficiency, an interesting advantage of the epitome as a representation is that it can be reliably estimated even from videos with large amounts of missing data. This ability is illustrated on the task of reconstructing the dropped frames in a video broadcast using only the degraded video. Further, a new patch-based model is introduced, that when applied to epitomes, accounts for the varying geometric configurations of object features. The power of this model is illustrated on tasks such as multiple object registration and detection and missing data interpolation, including a difficult task of photograph relighting.
Investigating Mechanical Performance and Water Absorption Behavior of Organo-nanoclay Modified Biofiber Plastic Composites
Keywords: Biofiber plastic composites
water absorption
mechanical performance
organo-nanoclay

Hydrophobic Surface modification of biofibers to reduce water/moisture absorption of the biofiber or biofiber-plastic composites has attracted many researchers. In order to reduce the moisture sensitivity of kraft and mechanical pulp fibers, organo-nanoclay particles were adsorbed on the biofiber surfaces. Surface hydrophobicity, in terms of moisture absorption, water uptake, water contact angle and surface energy of the modified fibers were tested. The treated fibers had nano-scale surface roughness and substantially lower surface energy. The thermal stability of the mechanical pulp fibers increased after the nanoclay modification. The organo-nanoclay treated kraft and mechanical pulp fibers were used to make biofiber reinforced high density polyethylene (HDPE) composites. The organo-nanoclay treated kraft fibers had a more uniform dispersion in the HDPE matrix and the resulting composites had a higher Young’s modulus and thermal stability. Similar trend was observed for the mechanical pulp fiber-HDPE composites. The adhesion between the kraft fibers and matrix was greatly improved after adding maleic anhydride polyethylene (MAPE) as a compatibilizer, therefore, improvements in tensile strength, Young’s modulus, and thermal stability of both treated and untreated fiber composites were observed. However, this improvement was more significant for the composites containing the treated fibers. In addition, water absorption was decreased by incorporating the organo-nanoclay treated mechanical pulp fibers in the HDPE composites. The treated kraft fiber-HDPE-MAPE composites also showed a decrease in water absorption. The crystallization behaviors of the organo-nanoclay treated and untreated kraft fiber-HDPE composites with and without MAPE compatibilizer were studied. It was found by differential scanning calorimetry (DSC) analysis that both organo-nanoclay treated and untreated kraft fibers could act as nucleating agents. All composites crystallized much faster than the neat HDPE, while their crystallinity levels were lower. The organo-nanoclay treatment of the kraft fibers increased the nucleation rate. However, both the crystallinity level and the nucleation rate of the treated kraft fiber composites were increased by the addition of the MAPE compatibilizer. X-ray diffraction (XRD) analysis reveled that MAPE could also increase the d-spacing of the organo-nanoclay layers in the composites. When the fiber loading was 40 wt% in the composites, exfoliation of the nanoclays in the composites was observed.
Pb-Pb Isotopic and X-ray Tomographic Constraints on the Origin of Chondrules
Keywords: geochemistry
geochronology
lead
uranium
meteorite
chondrule
tomography
dating
ISA
TIMS
mass spectrometry
accelerator mass spectrometry
freeze thaw
cosmochemistry

207Pb*/206Pb* chronometry was used to obtain the ages of Ca,Al-rich inclusions (CAIs) and chondrules found in ancient meteorites. Assuming a 238U/235U=137.88, Pb/Pb ages of chondrules in NWA801 (a CR2 meteorite) are 4564.6±1.0 Ma, chondrules in Mokoia (a CV3 chondrite) are 4564.2±1.1Ma, and CAIs in Mokoia are 4567.9±5.4 Ma. The Pb/Pb age of NWA801 chondrules is concordant with 26Al/26Mg ages of CR chondrules. However if a 238U/235U < 137.88 is used, the age for NWA801 chondrules becomes younger by ~1Ma and discordant with 26Al/26Mg ages of CR chondrules. This suggests either a discrepancy with the U compositions or the initial Mg isotopic compositions of NWA801 chondrules. The shapes of NWA801 chondrules, and blebs of FeNi metal in the meteorite matrix, were further studied by 3D X-ray micro-computed tomography (CT). Most chondrules (92%) were ‘armoured’ with one discontinuous layer of FeNi metal. Two layers of FeNi metal (one on the exterior and one concentric through the interior separated by silicate) were rare <8%. Chondrules and matrix blebs occur as oblates, prolate, spheres and triaxial spheroids. It is proposed that the shapes were made free-floating in the nebula likely by flash-melting precursors into molten droplets that were vibrating as harmonic oscillators that ‘froze-in’ their shapes during cooling. Parent-body metamorphism and shock are not likely processes affecting the matrix-bleb and chondrule shapes. Chondrules with ≥2 FeNi metal layers were likely formed by mergers and not by successive deposition and annealing of metal in multiple flash-melting events. Attempts to obtain 207Pb*/206Pb* ages from chondrules and CAIs by thermal extraction (TE)- TIMS were unsuccessful. However LA-ICP-MS was shown to be useful for rapidly determining Pb isotopic trends in meteorites and unknown objects. In particular, it was shown that 137La (T1/2=60ky) should be detectable in recently fallen meteorites using LaF−4 to suppress the 137Ba isobar during tandem accelerator mass spectrometry combined with a novel instrumental technique for isobar separation.
A Method for Selective Concentrating of DNA Targets by Capillary Affinity Gel Electrophoresis
Keywords: Capillary Affinity Gel Electrophoresis
DNA Purification
Sample Enrichment

A method for the selective concentrating of DNA targets using capillary affinity gel electrophoresis is presented. Complementary ssDNA targets are retained through hybridization with oligonucleotide probes immobilized within polyacrylamide gels while non-complementary targets are removed. The captured DNA targets were concentrated by step elution, where a localized thermal zone was applied in small steps along the capillary. Evaluation of the selective capture of a 150 nt DNA target in a complicated mixture was carried out by factorial analysis. Gels with a smaller average pore size were found to retain a higher amount of complementary targets. This was thought to be due to the ssDNA target migrating through the gel by reptation, eliminating hairpin structures, making the complementary region of the target available for hybridization. This method was applied to a series of DNA targets of different lengths, 19 nt, 150 nt, 250 nt and 400 nt. The recovery of the method ranged from 0.5 to 4% for the PCR targets, and 13 to 18% for the 19 nt oligonucleotide target. The purity was calculated to be up to 44% for the PCR targets and up to 86% for the 19 nt target. This was an improvement in purity of up to 15 times and 1100 times in comparison to the original samples for the PCR targets and 19 nt oligonucleotide, respectively. The 19 nt targets were selective concentrated and delivered into a microfluidic based DNA biosensing platform. The purity of the sample improved from 0.01% to 50% while recovery decreased from 100% to 20% for a sample with 0.5 nM complementary and 1 μM non-complementary targets. An improvement in the response of the sensing platform was demonstrated on 19 nt oligonucleotide targets delivered by selective concentration versus concentration alone into the microfluidic biosensing system.
Relationships in Three Ontario Elementary Public School Councils: Patterns of Interaction
Keywords: school councils
administration
elementary
parent involvement

Historically there has been tension between local parent and community control and professional and centralized control in public school decision making. Provincial regulations in Ontario and in many other jurisdictions require the establishment of site-based school councils to bring together educational professionals with parents and community representatives. Ontario regulations confirm the advisory role of school councils in their mandate to improve student achievement and ensure school accountability to parents. This qualitative study examined the patterns of interaction between parents and school staff in three school councils. Semi-structured interviews were conducted with principals, vice principals, teachers, non-teaching staff and parents. Information was also obtained from participant interviews, school council minutes policy documentation and my attendance at each site-based school council meeting. The study revealed that although tensions continue to exist between home and school, the individual school context, leadership style of the principal and the relationship between the council chair and principal influence the vitality of the council. Factors that contribute to the vitality of a school council include communication strategies, characteristics of the membership, interactions at council meetings, a shared sense of purpose and practices that reflect a variety of forms of site based management. This research reveals an understanding of the relationships, strategies and processes that are important to school councils to move members towards democratic collaboration and participation. Implications for policy, school based practices and further research are described.
Ecological, Physiological and Molecular Population Genetics of a Single-locus Leaf Shape Cline in Ivyleaf Morning Glory, Ipomoea hederacea
Keywords: Ipomoea hederacea
ecological genetics
leaf shape
polymorphism
cline
natural selection
ecophysiology
population genetics

Leaf shape is remarkably variable among plants, and hence likely has major consequence for ecological function and fitness. My thesis addresses the ecological significance of clinal variation for a leaf shape polymorphism in Ipomoea hederacea (lobed leaves dominate the north, entire-shaped leaves restricted to the south), and investigates the role of adaptation and demography in shaping its evolutionary history in its eastern North American range. To evaluate the adaptive value of the cline, I surveyed leaf shape genotypes from 77 populations , and found a steep latitudinal leaf shape cline that was not reflected in 173 neutral genetic markers. Furthermore, the leaf shape locus was a genomic outlier, implicating divergent selection in generating or maintaining the cline. I investigated the thermoregulatory and freezing tolerance properties of the leaf shape genotypes, and discovered that lobed leaves remain marginally warmer at night, and a 1&deg;C decrease separated mildly damaged and severely frost damaged tissue, potentially suggesting that a critical ambient temperature could drive differential leaf shape damage. I further explored three additional hypothesized selective agents (insect herbivores, flowering phenology and growth), and showed that these putative agents impose selection on I. hederacea, but do not differentiate between leaf shapes. These studies highlighted the challenge of identifying selective agents, even for a polymorphic trait with hypothesized selective mechanisms. To understand the contribution of adaptation and demography in shaping I. hederacea&rsquo;s evolutionary history, I sequenced 7 nuclear loci from 192 individuals sampled from 24 populations and characterized patterns of nucleotide diversity. I demonstrated that I. hederacea is genetically structured in patches consistent with long-distance dispersal, genetically depauperate, and undergoing range expansion, suggesting a recent founder event or metapopulation dynamics. My thesis represents a comprehensive evaluation of the key processes affecting a polymorphism that influences plant morphology, geographical distribution, and population history.
Zebrafish Shoaling Behavior: Its Development, Quantification, Neuro-chemical Correlates, and Application in a Disease Model
Keywords: Zebrafsh
behavioral neuroscience
FASD
neurochemistry

Abnormal social behavior is a symptom of many human conditions, including Fetal Alcohol Spectrum Disorders (FASD). The zebrafish may be an excellent model to study embryonic alcohol effects, owing to the ease of drug administration. In recent decades, zebrafish have become increasingly popular in behavioral neuroscience, and their elaborate behavioral repertoire can provide insights in brain functioning and social behavior in response to teratogens or pharmaceutical agents. Shoaling is the zebrafish&rsquo;s most notable behavioral feature, but has not been well characterized. I have started this characterization by describing the ontogeny of shoaling behavior. Embryonic exposure to low doses of ethanol has been shown to impair social behavior without any gross morphological alterations in zebrafish. However, this has not been studied in freely moving groups (shoals). Validation for using a shoaling task in behavioral testing, and potentially for high throughput analyses in the future, hinges on thorough characterization of the behavioral effects, however subtle in alcohol treated zebrafish. In my studies, I have shown that social behavior is impaired in zebrafish in a group setting after one time embryonic ethanol exposure. I have also discovered that this impairment is accompanied by a reduction of dopamine, serotonin, DOPAC and 5HIAA, neurochemicals measured in whole brain samples using HPLC. I have developed refined methods of measuring shoaling behavior in ten member zebrafish groups, laying the foundation for high throughput screening of adult zebrafish. Zebrafish are an economical model, and therefore lend themselves particularly well for high throughput screening. However, current paradigms are still labor intensive and require substantial human capital. By refining current behavioral tests and deploying new analytical tools, high throughput screening is starting to become within reach.
Thermodynamics and the Sustainability of Cities
Keywords: Sustainable Cities
Thermodynamic Sustainability
Exergy
Efficiency
Resilience
Urban Energy Economics

Cities interact with and rely on energy in complex ways. Fundamentally cities rely upon high quality energy and outputs of low quality for their very existence. The energy flows and transformations enabling cities are tied to physical limits imposed by thermodynamics. Understanding of these limits and the relationships among energy and cities, it is revealed herein, is of vital importance to the sustainability of cities. Four contributions to this understanding are provided. The first articulates how the thermodynamic forces driving cities, together with the dynamic environment within which cities reside, stipulates what type of activities within cities are sustainable. Second, a model depicting the scaling relationship between urban energy use and economic output is devised, and it’s fit to historical data demonstrated via nonlinear regression. By differentiating between energy used to grow and energy used to maintain economic output the model illustrates how reductions in these values on a per dollar basis abets growth while the reverse delays growth, or stops it altogether when energy needs for maintenance become too high. Third, an exergy network conceptualization of cities is developed that reveals the structure of the exergy flows in a city. The topology of the network drastically alters the city’s ability to maximize usefulness of imported energy as well as alter that variability in the amount of usefulness extracted. Finally, the resilience of cities with respect to energy is presented by considering the energy storage and buffer capacity of the urban metabolism. The city of Toronto is shown to have adequate flexibility in food and transport fuels to withstand operation for days without undue interruption of typical activities. Together these differing aspects of the open non-equilibrium details of cities establish an improved prescription of the sustainable city.