VictorJuiz/thesis huggingface dataset:
Biochemical Studies of the CTCF Insulator Protein: Determination of Protein Interactions with CTCF using Tandem Affinity Purification, Characterization of its Post-translational Modification by the Small Ubiquitin-like Modifier Proteins and Studies of CTCF DNA Looping Ability

The CTCF protein is involved in several important aspects of gene regulation including transcriptional activation, transcriptional repression and insulator ability. It is also involved in the regulation of epigenetic processes including X-chromosome inactivation and the maintenance of genomic imprinting. CTCF has been shown to bind to approximately 15 000 sites in the mammalian genome and has been implicated in nuclear organization. The CTCF protein mediates long-range chromatin interactions and is believed to form DNA loops. It also acts to block the communication of an enhancer with a promoter by acting as an insulator. Despite its importance in gene regulation, the molecular mechanisms that govern CTCF’s ability to perform its myriad functions remain enigmatic. In this thesis, I add insight into our understanding of the mechanisms behind CTCF’s function. I show that CTCF is post-translationally modified by the Small Ubiquitin-like Modifier proteins and that this post-translational modification contributes to its repressive ability at the c-myc P2 promoter. I also show that CTCF is localized to the sub-nuclear compartment called the Polycomb bodies. The Polycomb protein Pc2 acts as an E3 ligase to enhance the SUMOylation of CTCF by SUMOs 2 and 3. These findings help to explain CTCF’s ability to act as a transcriptional repressor. I also report biochemical evidence to support the role for CTCF in forming an unusual DNA structure, possibly a loop. I hypothesize that a single CTCF binding site is able to form DNA loops. These findings suggest mechanisms by which CTCF is able to organize the mammalian genome and to function as an insulator protein. In addition to these findings I have also purified CTCF interacting proteins through the use of the tandem affinity purification technique. The interacting proteins contain many chromatin and DNA binding proteins further suggesting a role for CTCF in chromatin organization. The results in this thesis enhance our knowledge of the molecular mechanisms of CTCF function and provide a basis for the improved understanding of CTCF mediated gene expression.

Keywords: CTCF
Epigenetics
Advisor: Sadowski, Paul
MRI Based Imaging of Current Densities and Tissue Conductivities

Magnetic resonance imaging (MRI) is an imaging modality that noninvasively measures magnetic fields by selectively exciting the magnetization of protons inside the body. When combined with an understanding of electromagnetic theory, MRI can be used in a novel way to provide a powerful tool for measuring the electromagnetic fields and electrical properties of biological tissues. This thesis presents the analytical, numerical, processing and experimental components of a successful implementation of Low-Frequency Current Density Impedance Imaging (LF-CDII), an impedance imaging method based on MRI measurements. The accuracy, stability and noise tolerance of this technique are examined. The first in-vivo LF-CDII experiment was conducted with a clinical MRI scanner, and the conductivity distribution of the heart of a live piglet was obtained. Both the simulation and experimental results show that LF-CDII can be used as a reliable tool for accurate noninvasive, quantitative imaging of tissue conductivities. This thesis also presents new data processing algorithms, imaging procedures and hardware development for the measurement of electromagnetic fields at radio frequencies, based on Polar Decomposition Radio Frequency Current Density Imaging (PD-RFCDI). The method was tested on both numerical models and experiments on phantoms. The results show that the techniques presented here are able to successfully image current density fields without the strict restrictions on the direction and magnitude of the currents required in previous versions of RFCDI.

Keywords: Current Density Imaging
Electrical properties
Magnetic Resonance Imaging
Current Density Impedance Imaging
Advisor: Joy, Michael
Nachman, Adrian
Low and Mid-level Shape Priors for Image Segmentation

Perceptual grouping is essential to manage the complexity of real world scenes. We explore bottom-up grouping at three different levels. Starting from low-level grouping, we propose a novel method for oversegmenting an image into compact superpixels, reducing the complexity of many high-level tasks. Unlike most low-level segmentation techniques, our geometric flow formulation enables us to impose additional compactness constraints, resulting in a fast method with minimal undersegmentation. Our subsequent work utilizes compact superpixels to detect two important mid-level shape regularities, closure and symmetry. Unlike the majority of closure detection approaches, we transform the closure detection problem into one of finding a subset of superpixels whose collective boundary has strong edge support in the image. Building on superpixels, we define a closure cost which is a ratio of a novel learned boundary gap measure to area, and show how it can be globally minimized to recover a small set of promising shape hypotheses. In our final contribution, motivated by the success of shape skeletons, we recover and group symmetric parts without assuming prior figure-ground segmentation. Further exploiting superpixel compactness, superpixels are this time used as an approximation to deformable maximal discs that comprise a medial axis. A learned measure of affinity between neighboring superpixels and between symmetric parts enables the purely bottom-up recovery of a skeleton-like structure, facilitating indexing and generic object recognition in complex real images.

Keywords: Perceptual Grouping
Image Segmentation
Superpixels
Symmetry
Closure
Advisor: Dickinson, Sven
Sminchisescu, Cristian
Singularity Formation in Nonlinear Heat and Mean Curvature Flow Equations

In this thesis we study singularity formation in two basic nonlinear equations in n dimensions: nonlinear heat equation (also known as reaction-diffusion equation) and mean curvature flow equation. For the nonlinear heat equation, we show that for an important or natural open set of initial conditions the solution will blowup in finite time. We also characterize the blowup profile near blowup time. For the mean curvature flow we show that for an initial surface sufficiently close, in the Sobolev norm with the index greater than [special characters omitted] + 1, to the standard n-dimensional sphere, the solution collapses in a finite time t∗, to a point. We also show that as t → t∗, it looks like a sphere of radius

Keywords: nonlinear heat equation
mean curvature flow
Advisor: Sigal, Israel Michael
The Production of Racial Logic In Cuban Education: An Anti-colonial Approach

This work brings an anti-colonial reading to the production and maintenance of racial logic in Cuban schooling, through conversations with, and surveys of Cuban teachers, as well as through analysis of secondary and primary documents. The study undertaken seeks to contribute to the limited existent research on race relations in Cuba, with a research focus on the Cuban educational context. Teasing and staking out a middle ground between the blinding and often hollow pro-Cuba fanaticism and the deafening anti -Cuban rhetoric from the left and right respectively, this project seeks a more nuanced, complete and dialogical understanding of race and race relations in Cuba, with a specific focus on the educational context. With this in mind, the learning objectives of this study are to investigate the following: 1) What role does racism play in Cuba currently and historically? 2) What is the role of education in the life of race and racism on the island? 3) What new questions and insights emerge from the Cuban example that might be of use to integrated anti-racism, anti-colonialism and class-oriented scholarship and activism? On a more specific level, the guiding research objectives of the study are to investigate the following: 1) How do teachers support and/or challenge dominant ideas of race and racism, and to what degree to do they construct their own meanings on these topics? 2) How do teachers understand the relevance of race and racism for teaching and learning? 3) How and why do teachers address race and racism in the classroom? The data reveal a complex process of meaning making by teachers who are at once produced by and producers of dominant race discourse on the island. Teachers are the front line race workers of the racial project, doing much of the heavy lifting in the ongoing struggle against racism, but are at the same time custodians of an approach to race relations which has on the whole failed to eliminate racism. This work investigates and explicates this apparent contradiction inherent in teachers’ work and discourse on the island, revealing a flawed and complex form of Cuban anti-racism.

Keywords: Cuban studies
anti-racism
anti-colonialism
education
teachers
race relations
Advisor: Dei, George Jerry Sefa
Artists Under Reform: An Analysis of Professional Chinese Guohua Painters' Relation to the State in the Post-Mao Era

This thesis is purposefully limited to examining the status of China’s professional guohua (Chinese national painting) painters and their relation to the Party-State. It tackles the above subject by studying the contents of important official documents issued by the party-state, by retelling the interactions between professional guohua painters and the party-state in several crucial social-political contexts, and by analysing the experiences, opinions, observations and critiques of four professional guohua painters. The time span of this study extends from 1949 to the late 1990s, while acknowledging the year of 1978, when China officially launched its reform program, as a critical dividing juncture for comparative reasons. This thesis finds that a new favorable partnership was forged between the party-state and the professional guohua painters in the reform era. This was due to the impact of China’s political culture, changes in the ideology and policies of the ruling elite, the commercialization of art, and an emerging need to preserve guohua that is more instrumental to promote China’s cultural heritage and national soft power. It argues that the sustainability of such a partnership has been reinforced through a conscious differentiation between categories of art -- elite and non-elite, official and non-official, high and popular, public and non-public -- by Chinese cultural authorities as well as the artists themselves. This thesis further asserts that the significantly improved economic conditions and the social status that professional guohua painters enjoyed in the 1980s and 1990s did not reflect on their cultural and political autonomy. Most of them consciously chose to be part of the institutional establishments under the party-state and showed limited aspiration in the quest for cultural and political autonomy. The “organized dependence” of professional guohua painters prior to the reform era was replaced by “conformity” of these artists towards the party-state. Finally it suggests that, although China’s changing political environment will eventually give way to economics and the scale of ideological movements and cultural control will continue to decline, many professional guohua painters are likely to stay within the ideological and aesthetic boundaries set by the party-state and to be part of official arts agencies and institutions.

Keywords: guohua, Chinese national painting, Chinese professional guohua painters, party-state, political autonomy,
Advisor: Falkenheim, Victor
Investigating Executive Functioning in Everyday Life using an Ecologically Oriented Virtual Reality Task

Commonly employed executive function measures may be of limited use due to their modest ecological validity. A novel task was developed - the Multitasking in the City Test (MCT) - in an attempt to improve ecological validity. The MCT involves task demands that resemble the demands of everyday activities. In study one, healthy participants were recruited in order to explore ‘normal’ performance on the MCT and its relationship with other cognitive measures. The MCT showed poor associations with executive tests and significant correlations with non-executive tests. This suggested the MCT may evaluate executive functioning in a different way from other executive measures such that it does not simply measure component executive processes but the integration of these components into meaningful behaviour. Patients with stroke and traumatic brain injury were recruited for study two to further explore the ecological validity and MCT performance characteristics. Only the MCT and a semantic fluency task demonstrated good ecological validity via significant relationships with a behavioural rating scale. Patients and normals made qualitatively similar types of errors although patients made these errors more frequently. Patients demonstrated better planning ability but completed fewer tasks than normals on the MCT. This discrepancy was attributed to impaired initiation. In study three, the MCT and verbal fluency tasks were administered to brain-injured individuals both pre- and post-executive function rehabilitation to evaluate their utility as treatment outcome measures and to assess ecological validity via a different behavioural rating scale from the one used in study two. Strategies trained during treatment generalized to MCT but not verbal fluency performance. Both MCT and semantic fluency performance were found to have good ecological validity. Overall, the findings from this research project suggest the MCT and semantic fluency tasks have good ecological validity. They further suggest that several common executive function measures lack adequate ecological validity and may not be predictive of real world behaviour. Moreover, these results support the concept of an executive function ‘system’ that can be fractionated into a variety of executive processes and that impairments in one process (e.g., initiation) can exist alongside intact functioning in other processes (e.g., planning).

Keywords: neuropsychology
executive function
ecological validity
virtual reality
Advisor: Zakzanis, Konstantine
Probing Early and Late Inflations Beyond Tilted LambdaCDM

The topic of this thesis is about cosmic inflations, including the early-universe inflation that seeds the initial inhomogeneities of our universe, and the late-time cosmic acceleration triggered by dark energy. The two inflationary epochs have now become part of the standard ΛCDM cosmological model. In the standard paradigm, dark energy is a cosmological constant or vacuum energy, while the early-universe inflation is driven by a slowly rolling scalar field. Currently the minimal ΛCDM model with six parameters agrees well with cosmological observations. If the greatest achievement of the last twenty golden years of cosmology is the ΛCDM model, the theme of future precision cosmology will be to search for deviations from the minimal ΛCDM paradigm. It is in fact expected that the upcoming breakthroughs of cosmology will be achieved by observing the subdominant anomalies, such as nonGaussianities in the Cosmic Microwave Background map. The aim of this thesis is then to make theoretical predictions from models beyond ΛCDM, and confront them with cosmological observations. These models include: 1) a new dark energy parametrization based on quintessence models; 2) reconstructing early-universe inflationary trajectories, going beyond the slow-roll assumption; 3) non-Gaussian curvature fluctuations from preheating after the early-universe inflation; 4) infra-red cascading produced by particle production during inflation; 5) preheating after Modular inflation; 6) decaying cold dark matter. We update the cosmological data sets – Cosmic Microwave Background, Type Ia supernova, weak gravitational lensing, galaxy power spectra, and Lyman-α forest – to the most current catalog, and run Monte Carlo Markov Chain calculations to obtain the likelihood of parameters. We also simulate mock data to forecast future observational constraints.

Keywords: cosmology
Inflation
dark energy
preheating
dark matter
non-Gaussianity
Advisor: Bond, J. Richard
Kofman, Lev
Learning Language-vision Correspondences

Given an unstructured collection of captioned images of cluttered scenes featuring a variety of objects, our goal is to simultaneously learn the names and appearances of the objects. Only a small fraction of local features within any given image are associated with a particular caption word, and captions may contain irrelevant words not associated with any image object. We propose a novel algorithm that uses the repetition of feature neighborhoods across training images and a measure of correspondence with caption words to learn meaningful feature configurations (representing named objects). We also introduce a graph-based appearance model that captures some of the structure of an object by encoding the spatial relationships among the local visual features. In an iterative procedure we use language (the words) to drive a perceptual grouping process that assembles an appearance model for a named object. We also exploit co-occurrences among appearance models to learn hierarchical appearance models. Results of applying our method to three data sets in a variety of conditions demonstrate that from complex, cluttered, real-world scenes with noisy captions, we can learn both the names and appearances of objects, resulting in a set of models invariant to translation, scale, orientation, occlusion, and minor changes in viewpoint or articulation. These named models, in turn, are used to automatically annotate new, uncaptioned images, thereby facilitating keyword-based image retrieval.

Keywords: image annotation
object recognition
Advisor: Dickinson, Sven
Stevenson, Suzanne
Potentiometric pH Measurements in the Pressure Acid Leaching of Nickel Laterites

An electrochemical cell consisting of a flow-through yttria-stabilized zirconia (YSZ) sensor and a flow-through Ag/AgCl reference electrode has been employed to measure pH of high-temperature acidic sulphate solutions relevant to the pressure acid leaching (PAL) of nickel laterites. In a previous study, this cell was used to measure pH of H2SO4, Al2(SO4)3-H2SO4 and MgSO4-Al2(SO4)3-H2SO4 solutions at 250oC. In this work, the solutions range in complexity from the binary MgSO4-H2SO4, NiSO4-H2SO4, and Al2(SO4)3-H2SO4, through the ternary MgSO4-Al2(SO4)3-H2SO4 and NiSO4-Al2(SO4)3-H2SO4, to the PAL process solutions, whereas the temperature ranges from 200oC to 250oC. The measured and theoretical pH values typically agree within less than 0.1 pH unit and 0.2 pH units in synthetic solutions and PAL solutions, respectively. This is an improvement over the results of the previous study in synthetic solutions, which show differences between theory and experiment as high as 0.4 pH units. The conversion of measured potentials into pH values is based on the new mixed-solvent electrolyte (MSE) speciation model of the OLI Systems software calibrated independently based on solubility measurements. Both Henderson’s equation and the exact definition of the diffusion potential were employed in treating the obtained experimental data. Experimental pH values calculated using the diffusion potentials evaluated by either approach are essentially the same. This finding suggests that Henderson’s equation, which is based on readily available limiting ionic mobilities, can be effectively used. Lithium chloride is found to be a suitable alternative to sodium chloride as the reference electrode solution for the measurement of pH of aluminium-containing solutions, because it did not induce precipitation of aluminium as an alunite-type compound. The experimental results indicate that the high-temperature behaviour of Ni, Co and Mn sulphates can be satisfactorily approximated with that of MgSO4. The experimental findings also support the postulation that acid should be added to a PAL process so that the solution pH is around 1 at the leach temperature, regardless of the feed composition. The cell can be used for hydrometallurgical process research and development on a laboratory scale with very satisfactory performance, provided that a well-behaved YSZ sensor is available.

Keywords: pH measurement
Pressure Acid Leaching
Advisor: Papangelakis, Vladimiros G.
A Modeling Study of Seasonal and Inter-annual Variations of the Arctic Black Carbon and Sulphate Aerosols

The modeling results of current global aerosol models agree, generally within a factor of two, with the measured surface concentrations of black carbon (BC) and sulphate (SF) aerosols in rural areas across the northern continents. However, few models are able to capture the observed seasonal cycle of the Arctic aerosols. In general, the observed seasonality of the Arctic aerosols is determined by complex processes, including transport, emissions and removal processes. In this work, the representations of aerosol deposition processes (i.e., dry deposition, in-cloud and below-cloud scavenging) within the framework of the Canadian Global Air Quality Model – GEM-AQ are first enhanced. Through the enhancements in GEM-AQ, the seasonality of the Arctic BC and SF is reproduced, and the improvement in model performance extends to the rest of the globe as well. Then, the importance of these deposition processes in governing the Arctic BC and SF seasonality is investigated. It is found that the observed seasonality of the Arctic BC and SF is mainly caused by the seasonal changes in aerosol wet scavenging, as well as the seasonal injection of aerosols from surrounding source regions. Being able to reproduce the seasonality of the Arctic BC, the enhanced GEM-AQ allows more accurate assessment of the contributions of anthropogenic sources to the BC abundance in the Arctic air and deposition to the Arctic surface. Simulating results on regional contributions to the Arctic BC show a strong dependence on altitude. The results reinforce the previous finding of Eurasia being the dominant contributor to the surface BC in the Arctic, and suggest a significant contribution from Asian Russia. In addition to the seasonality of the Arctic aerosols, the inter-annual variation in the Arctic BC surface concentration is also investigated. To complement the 3-D GEM-AQ model, the atmospheric backward trajectory analysis, together with estimated BC emissions, is implemented as a computational effective approach to reconstruct BC surface concentrations observed at the Canadian high Arctic station, Alert. Strong correlations are found between the reconstructed and the measured BC in the cold season at Alert between 1990 and 2005, which implies that atmospheric transport and emissions are the major contributors to the observed inter-annual variations and trends in BC. The regional contributions estimated annually from 1990 through 2005 suggest that Eurasia is the major contributor in winter and spring to the near-surface BC level at Alert with a 16-year average contribution of over 85% (specifically 94% in winter and 70% in spring). A decreasing trend in the Eurasian contribution to the Arctic is found in this study, which is mainly due to regional emission reduction. However, the inter-annual variation in the North American contribution shows no clear trend.

Keywords: Arctic
aerosol
black carbon
sulphate
seasonal variation
inter-annual variation
Advisor: Jia, Charles Q.
Gong, Sunling