VictorJuiz/thesis huggingface dataset:
South-South-North Research Partnerships: A Transformative Development Modality?

This thesis investigates development assistance programming in the research activities of higher education institutions by studying the case of the Norwegian Programme for Education, Research and Development (NUFU) and its activities in two sub-Saharan African (SSA) nations. In this thesis, North-South Research Partnerships (NSRPs) are conceptualized through the construction of an ideal-type based on the historical record of NSRP progrmaming. A conceptual framework and analytical tool are developed in order to present the dominant norms associated with mainstream North-South research programming over the past sixty years, as firmly embedded in exploitative core-periphery dynamics. The main research questions ask to what extent the NUFU model differs from other NSRP programs, including South-South collaborative opportunities, and to what extent the program creates spaces for endogenous research needs and priorities to take precedent over exogenous demands and targets. A qualitative investigation is used to gather data from textual analysis, participant observation and key informant interviews in order to investigate how the NUFU program establishes demand-driven programs in Southern universities while negotiating the Norwegian and global political economies. A case study of a single NUFU North-South-South project demonstrates how the program framework influences the construction of the partnership modality. The findings indicate that the North-South component of the model presents significant opportunities for demand-driven research, but that changing trends in Norway are placing pressure on the program and researchers. With regard to the South-South component, the study concludes that the modality is under-conceptualized, lacks clarity of purpose and has failed to generate sustainable collaboration within the SSA region. The implications of these findings for NSRP programming, the NUFU program in particular, are that historical asymmetries remain firmly entrenched; without a radical reconstitution of the economic and political relations between Northern and Southern states, the most powerful international actors, be they states, private entities or multilateral agencies, will continue to dominate and determine knowledge production capacities and outputs. The study concludes by suggesting opportunities for NSRP programs to augment their support of Southern universities and by reflecting on how ongoing changes in current geo-political configurations could open new spaces for alternative development trajectories.

Keywords: Higher Education
Comparative and International Education
Advisor: Hayhoe, Ruth
A Comparative Study of the Shifting Nature of International Non-governmental Organization Global Education Programming in Canada and the United Kingdom

International development non-governmental organizations (INGOs) in the United Kingdom and Canada have demonstrated a distinct withdrawal from education programming towards campaigns and fundraising. This study explores how the nature of INGO global education programming has shifted over time. The purpose of this research is to gain a better understanding of a) the place of INGO-produced global education within the context of international development and the field of global education, and b) what type of role (if any) INGOs have to play in future global education programming. The shifts in INGO global education over time are identified through a comparative historical analysis of the socio-political and funding conditions affecting INGO-produced global education programming in Canada and the UK including the embedded case studies of two sister organizations, Save the Children UK and Save the Children Canada. This study looks broadly at the fifty year history of INGO global education, then focuses on the current experiences of two INGOs that are representative of conditions of INGO dependency within their country contexts. A conceptual framework based on the work on the educational typologies of Askew and Carnell (1998) and the ethical positionings of Barnett and Weiss (2008) is used to analyze, evaluate, explore, and describe the global education programming mechanisms prioritized by INGOs. The trend of INGO global education programming as fundraising campaigns lacks the commitment to relationship building, and the acquisition of the knowledge, skills, and attitudes that are important for developing informed and capable constituencies who would understand systemic inequalities. This begs the question as to whether INGOs are satisfied with the short-term, socially regulatory outcome of fundraising when they have the potential to facilitate the dialogical, equitable relationships that can increase the possibilities for social transformation.

Keywords: Global Education
Citizen Engagement
Advisor: Mundy, Karen
Diffeologies, Differential Spaces, and Symplectic Geometry

Diffeological and differential spaces are generalisations of smooth structures on manifolds. We show that the “intersection” of these two categories is isomorphic to Frölicher spaces, another generalisation of smooth structures. We then give examples of such spaces, as well as examples of diffeological and differential spaces that do not fall into this category. We apply the theory of diffeological spaces to differential forms on a geometric quotient of a compact Lie group. We show that the subcomplex of basic forms is isomorphic to the complex of diffeological forms on the geometric quotient. We apply this to symplectic quotients coming from a regular value of the momentum map, and show that diffeological forms on this quotient are isomorphic as a complex to Sjamaar differential forms. We also compare diffeological forms to those on orbifolds, and show that they are isomorphic complexes as well. We apply the theory of differential spaces to subcartesian spaces equipped with families of vector fields. We use this theory to show that smooth stratified spaces form a full subcategory of subcartesian spaces equipped with families of vector fields. We give families of vector fields that induce the orbit-type stratifications induced by a Lie group action, as well as the orbit-type stratifications induced by a Hamiltonian group action.

Keywords: diffeology
differential spaces
symplectic geometry
Lie groups
Hamiltonian group actions
subcartesian spaces
Advisor: Karshon, Yael
Development of Methods for Retrospective Ultrasound Transmit Focusing

Single frame ultrasound B-mode image quality is largely governed by the ability to focus the ultrasound beam over a range in depths both in transmission and reception. By developing a comprehensive understanding of acoustic wave propagation two signal processing methods were identified for solving the transmission problem. We made use of both the impulse response using the classical point spread function (PSF) and the spatial sensitivity function (SSF) which describes the spatial distribution at a particular time. Using the angular spectrum method, an accurate analytical model was developed for the field distribution arising from a finite geometry, apodized and focused, plane piston transducer. While there is a thorough understanding of the radiated field arising from uniformly excited plane piston transducers, the focused equivalent (i.e., one that allows a continuous change in phase over the plane piston surface) is incomplete and assumes the Fresnel approximation. Our model addresses the effects of diffraction and evanescent waves without the use of the Fresnel approximation and is applicable at all near- and far-field locations in a lossless medium. The model was analyzed to identify new insights into wave propagation and compared with the Fresnel approximation and the spherically-focused, concave transducer. The piston transducer model was then extended to an attenuating and dispersive medium. After analysing existing models of power-law frequency dependent attenuation, a causal, spherical wave Green’s function was derived from the Navier-Stokes equation for a classical viscous medium. Modifications to the angular spectrum method were presented and used to analyze the radiated field of a focused, planar piston transducer. Finally, after presenting our signal processing strategy for improving imaging spatial resolution through minimization of the SSF, two signal processing methods were derived and analysed in simulation: a deconvolution technique to remove the effects of the ultrasound excitation wave and suppress additive noise from the received ultrasound signal, and a retrospective transmit focusing method that changed the response from a predefined transmit focus to an arbitrary transmit focal depth. Proof-of-concept simulations were presented using a variable number of scatterers and compared with the traditional matched filtering and envelope detection technique.

Keywords: ultrasound
retrospective transmit focusing
wave propagation
attenuation
dispersion
apodized
focused
circular plane piston transducer
Advisor: Cobbold, Richard
Oblivious and Non-oblivious Local Search for Combinatorial Optimization

Standard local search algorithms for combinatorial optimization problems repeatedly apply small changes to a current solution to improve the problem's given objective function. In contrast, non-oblivious local search algorithms are guided by an auxiliary potential function, which is distinct from the problem's objective. In this thesis, we compare the standard and non-oblivious approaches for a variety of problems, and derive new, improved non-oblivious local search algorithms for several problems in the area of constrained linear and monotone submodular maximization. First, we give a new, randomized approximation algorithm for maximizing a monotone submodular function subject to a matroid constraint. Our algorithm's approximation ratio matches both the known hardness of approximation bounds for the problem and the performance of the recent ``continuous greedy'' algorithm. Unlike the continuous greedy algorithm, our algorithm is straightforward and combinatorial. In the case that the monotone submodular function is a coverage function, we can obtain a further simplified, deterministic algorithm with improved running time. Moving beyond the case of single matroid constraints, we then consider general classes of set systems that capture problems that can be approximated well. While previous such classes have focused primarily on greedy algorithms, we give a new class that captures problems amenable to optimization by local search algorithms. We show that several combinatorial optimization problems can be placed in this class, and give a non-oblivious local search algorithm that delivers improved approximations for a variety of specific problems. In contrast, we show that standard local search algorithms give no improvement over known approximation results for these problems, even when allowed to search larger neighborhoods than their non-oblivious counterparts. Finally, we expand on these results by considering standard local search algorithms for constraint satisfaction problems. We develop conditions under which the approximation ratio of standard local search remains limited even for super-polynomial or exponential local neighborhoods. In the special case of MaxCut, we further show that a variety of techniques including random or greedy initialization, large neighborhoods, and best-improvement pivot rules cannot improve the approximation performance of standard local search.

Keywords: Approximation Algorithms
Local Search
Submodular Maximization
Independence Systems
Advisor: Borodin, Allan
Design of High Performance Organic Light Emitting Diodes

Organic light emitting diodes (OLEDs) are being commercialized in display applications, and will be potentially in lighting applications in the near future. This thesis is about the design of high performance OLEDs, which includes both the electrical and optical design of OLEDs. In particular, the following work is included in this thesis: i) Energy level alignment and charge injection at metal/organic interfaces have been systematically studied. ii) Transition metal oxide anodes have been developed to inject sufficient holes into the OLEDs due to their high work function. The oxide anodes have also been used to systematically study the transport properties in organic semiconductors. iii) Highly simplified OLED devices with unprecedentedly high efficiency have been realized using both fluorescent and phosphorescent emitters. The high performance was enabled by using a high work function metal oxide anode and a hole transport material with very a deep highest occupied molecular orbital (HOMO). iv) An optical model has been developed to describe the optical electric field across the OLED device. By using the model, a high performance flexible OLED using metal anode was designed and realized.

Keywords: organic light emitting diodes
organic electronics
Advisor: Lu, Zhenghong
Improving Posing and Ranking of Molecular Docking

Molecular docking is a computational tool commonly applied in drug discovery projects and fundamental biological studies of protein-ligand interactions. Traditionally, molecular docking is used to address one of three following questions: (i) given a ligand molecule and a protein receptor, predict the binding mode (pose) of the ligand within the context of a receptor, (ii) screen a collection of small-molecules against a receptor and rank ligands by their likelihood of being active, and (iii) given a ligand molecule and a target receptor, predict the binding affinity of the two. Here, we focus on the first two questions, namely ranking and pose prediction. Currently, state-of-the-art docking algorithms predict poses within 2A of the native pose in a rate lower than ∼60% and in many cases, below 40%. In ranking, their ability to identify active ligands is inconsistent and generally suffers from high false-positive rate. In this thesis we present novel algorithms to enhance the ability of molecular docking to address these two questions. These algorithms do not substitute traditional docking but rather being applied on top of them to provide synergistic effect. Our algorithms improve pose predictions by 0.5-1.0A and ranking order for 23% of the targets in gold-standard benchmarks. As importantly, the algorithms improve the consistence of the posing and ranking predictions over diverse sets of targets and screening libraries. In addition to the posing and ranking, we present the pharmacophore concept. A pharmacophore is an ensemble of physiochemical descriptors associated with a biological target that elucidates common interaction patterns of ligands with that target. We introduce a novel pharmacophore inference algorithm and demonstrate its utilization in molecular docking. This thesis is outlined as follow. First we introduce the molecular docking approach for pose prediction and ranking. Second, we discuss the pharmacophore concept and present algorithms for pharmacophore inference. Third, we demonstrate the utilization of pharmacophores for pose prediction by re-scoring candidate poses generated by docking algorithms. Finally, we present algorithms to improve ranking by reducing bias in scoring functions employed by docking algorithms.

Keywords: Docking
Molecular Modeling
Pharmacophore
Advisor: Lilien, Ryan
The Statistical Learning Of Musical Expectancy

This project investigated the statistical learning of musical expectancy. As a secondary goal, the effects of the perceptual properties of tone set familiarity (Western vs. Bohlen-Pierce) and textural complexity (melody vs. harmony) on the robustness of that learning process were assessed. A series of five experiments was conducted, varying in terms of these perceptual properties, the grammatical structure used to generate musical sequences, and the methods used to measure musical expectancy. Results indicated that expectancies can indeed be developed following statistical learning, particularly for materials composed from familiar tone sets. Moreover, some expectancy effects were observed in the absence of the ability to successfully discriminate between grammatical and ungrammatical items. The effect of these results on our current understanding of expectancy formation is discussed, as is the appropriateness of the behavioural methods used in this research.

Keywords: music cognition
statistical learning
priming
expectancy
memory
Advisor: Schmuckler, Mark
Biology Inspired Nano-materials: Superhydrophobic Surfaces

In this research, a low-cost template-based process has been developed to structure the surfaces of polymeric materials rendering them superhydrophobic. This biology-inspired approach was developed using results from the first part of this thesis: the first known detailed study of superhydrophobic aspen leaf surfaces. Aspen leaves, similar to lotus leaves, possess a dual-scale hierarchical surface structure consisting of micro-scale papillae covered by nano-scale wax crystals, and this surface structure was used as a blueprint in the structuring of templates. These distinctive surface features coupled with a hydrophobic surface chemistry is responsible for these leaves’ extreme non-wetting property. Non-wetting is further augmented by the unique high aspect ratio aspen leafstalk geometry. The slender leafstalks offer very little resistance to twisting and bending, which results in significant leaf movement in the slightest breeze, facilitating water droplet roll-off. The structured template surfaces, produced by sand blasting and chemical etching of electrodeposited nanocrystalline nickel sheets, resemble the negative of the superhydrophobic aspen leaf surfaces. Re-usable templates were subsequently employed in a hot embossing technique where they were pressed against softened polymers (polyethylene, polypropylene and polytetrafluoroethylene) thereby transferring their surface structures. The resulting pressed polymer surfaces exhibited features very similar to aspen leaf surfaces. This process increased the water contact angle for all pressed polymers to values above 150 degrees. Additionally, after pressing the water roll-off angle for all polymer surfaces dropped below 5 degrees. The effects of water surfactant concentration, water drop size and temperature on the wetting characteristics of the structured polymers were studied to indicate in which applications these functional surfaces could be most beneficial. Coupling this attractive superhydrophobic surface property with mechanical motion (shaking, bending, or vibrating) could result in superhydrophobic surfaces with superior non-wetting properties suitable for a wide range of applications.

Keywords: Nano-materials
Superhydrophobic
Polymer Structuring
Electrodeposition
Advisor: Erb, Uwe
MRI in the Prediction and Diagnosis of Pediatric-onset Multiple Sclerosis: Insights from Children with Incident CNS Demyelination

An acute demyelinating syndrome (ADS) in a child may be a monophasic illness or may represent the incident attack of multiple sclerosis (MS) – an inflammatory demyelinating neurodegenerative disorder affecting the brain, spinal cord and optic nerves. The central objective of this dissertation was to identify MRI parameters present at ADS that predict MS diagnosis. A scoring tool was first created containing 14 parameters identified from the literature and demonstrating substantial inter-rater agreement (Cohen’s kappa values ≥0.6). Children aged <16 years were enrolled at incident ADS and are currently followed for five years at 23 Canadian centers. Standardized MRI scans were acquired at onset and serially. MS was defined based on the occurrence of a second demyelinating attack or MRI evidence of new lesions in accordance with McDonald criteria for dissemination in time. Multivariable Cox proportional hazards regression models were used to identify MRI parameters that predicted MS diagnosis. Over 1100 MRI scans in 284 children with ADS were evaluated. To date, 57(20%) children have been diagnosed with MS. For those that developed MS, the median (IQR) time from incident attack to diagnosis was 6.2 (4.7-11.1) months. The presence of ≥1 T1-hypointense lesion (HR 20.6, 95% CI 5.5-78.0) and ≥1 T2 periventricular lesion (3.3, 1.3-8.8) were associated with an increased likelihood for MS diagnosis (sensitivity 84%, specificity 93%, PPV 76%, NPV 96%). The predictive parameters were validated in an independent Dutch cohort of 45 children with ADS (n=15, 33% MS): sensitivity 93%, specificity 87%, PPV 78%, NPV 96%. Finally, it was determined that the 2010 McDonald criteria are applicable for diagnosis of pediatric-onset MS diagnosis in older children with non-ADEM presentations. The work embodied herein emphasizes the value of MRI in predicting MS diagnosis in children with incident ADS. Early identification of children with MS is important for planning clinical care and will be valuable in future pediatric MS treatment trials.

Keywords: multiple sclerosis
pediatric
magnetic resonance imaging
diagnosis
prediction
demyelination
central nervous system
Advisor: Banwell, Brenda
Mms1 & Mms22 Mediate Genome Stability in Saccharomyces cerevisiae

Mms1 and Mms22 are important mediators of genome stability in Saccharomyces cerevisiae. Deletion mutants of both genes display decreased viability in the presence of a number of known DNA damaging agents as well as agents that perturb DNA replication. Here I present a detailed analysis of Mms1 and Mms22 function in stabilizing DNA replication forks. I find that mms1∆ and mms22∆ strains accumulate spontaneous DNA damage and have an increased rate of mutation during a normal cell cycle. Additionally, treatment with genotoxic agents causes defects in induced recombination as well as inhibiting the ability of cells to efficiently recover from DNA damage. Genetic interaction data support a model where Mms1 and Mms22 function with components of the replication fork. Accordingly I observed that the enrichment of key replication fork proteins at regions proximal to replication origins is decreased in mms1∆ and mms22∆ cells during replication stress. Furthermore, I monitored DNA replication in wild-type and mms1∆ strains and found that mms1∆ strains exhibit irregular fork progression under conditions of replication stress. I therefore concluded that Mms1 and Mms22 function at replication forks. Lastly, I uncovered that Mms1 is regulated by Rtt101-dependent ubiquitin-mediated proteolysis. Mms1 degradation is likely necessary for its function as overexpression of Mms1 results in decreased cell viability both during a normal cell cycle, and during treatment with DNA damaging agents. I found that Mms1 and Mms22 operate at sites of DNA replication to promote the stability of the genome, especially under conditions of DNA damage and replication fork stress.

Keywords: Saccharomyces cerevisiae
DNA
Replication
Repair
Mms1
Mms22
Genome stability
Advisor: Brown, Grant