VictorJuiz/thesis huggingface dataset:
Teaching Science for Social Justice: An Examination of Elementary Preservice Teachers' Beliefs

This qualitative study examines the beliefs and belief changes of eleven elementary preservice teachers about teaching science for social justice. Using constructivist grounded theory, it forwards a new theory of belief change about teaching science for social justice. The theory posits that three teaching and learning conditions may facilitate belief change: preservice teachers need to recognize (1) the relationship between science and society; (2) the relationship between individuals and society; and (3) the importance of taking action on socioscientific issues. This research responds to calls by critical scholars of teacher education who contend that beliefs in relation to equity, diversity, and multiculturalism need to be explored. They have found that many preservice teachers hold beliefs that are antithetical to social justice tenets. Since beliefs are generally considered to be precursors to actions, identifying and promoting change in beliefs are important to teaching science for social justice. Such a move may lead to the advancement of curricular and pedagogical efforts to promote the academic participation and success in elementary science of Aboriginal and racialized minority students. The study was undertaken in a year-long science methods course taught by the researcher. It was centered on the preservice teachers – their beliefs, their belief changes, and the course pedagogies that they identified as crucial to their changes. However, the course was based on the researcher-instructor’s review of the scholarly literature on science education, teacher education, and social justice. It utilized a critical – cultural theoretical framework, and was aligned to the three dimensions of critical nature of science, critical knowledge and pedagogy, and sociopolitical action. Findings indicate that, at the beginning of the year, preservice teachers held two types of beliefs (liberal and critical) and, by the end of the course, they experienced three kinds of shifts in beliefs (minimal, substantial, and refined). The shifts in beliefs were attributed by preservice teachers to specific pedagogies. Yet their initial beliefs also served as filters to the pedagogies, consequently impacting their degrees of belief change. Therefore, this study reveals elements of unpredictability when engaging in teaching science for social justice.

Keywords: science education
beliefs
elementary education
urban education
Advisor: Goldstein, Tara
Collaborative Research Partnerships for Knowledge Mobilization

This study examines the elements of collaborative research partnerships (CRPs) between university researchers and other organizations or individuals in the education sector whose mandate is to conduct and disseminate research for service delivery. Studying these partnerships for knowledge mobilization(KMb)includes understanding the roles partners take on; the tensions or facilitators they face when bringing research into practice; the structures to maintain the partnership; and the knowledge mobilization activities. Phase 1 takes an in-depth look at one partnership using key informant interviews and document analysis, while phase 2 utilizes a survey between four overarching university-community organization partnerships across Canada. Findings suggest that although difficult, when research producers and users work together, capacity is built at the organizational level to view research evidence as an important part of the organizational service delivery, with small impacts on individual knowledge development; that partnerships remain informal in their practice; that the mechanisms by which partners use to communicate within the partnership and the frequency of communication helps to build relationships between partners; and the ideal type of CRP, where they ought to always be an equal endeavour, is overstated in the literature. Not all useful partnerships are exact equal contributions from research producers and their user-based partners. Implications include that researchers gain access to practice expertise and insights into practice-based research rather than engaging in only theoretical research while community partners gain access to greater capacity for understanding and using research through exchanges with academics.

Keywords: Collaboration
Research partnerships
Research utilization
Knowledge mobilization
Advisor: Campbell, Carol
Digital Microfluidics for Multidimensional Biology

Digital microfluidics (DMF) has emerged in the past decade as a novel microfluidic paradigm. As a liquid handling technology, DMF facilitates the electrostatic manipulation of discrete nano- and micro- litre droplets across open electrode arrays providing the advantages of single sample addressability, automation, and parallelization. This thesis presents DMF advances toward improved functionality and compatibility for automated miniaturized cell culture in two and three dimensions. Through the development and integration of surface patterning techniques we demonstrate a virtual microwell method for high precision on-device reagent dispensing in one and two plate DMF geometries. These methods are shown to be compatible with two-dimensional culture of immortalized cell lines on ITO, primary cells on coated surfaces, and for co-culture assays. We further extrapolate this method for the formation of microgels on-demand where form micro scale hydrogel structures through passive dispensing in a wide array of geometries. With this system we interrogate three-dimensional cell culture models, specifically for the recapitulation of kidney epthelialization and the analysis of functional cardiac microgels.

Keywords: Digital microfluidics
Microfluidics
Biology
Cell culture
3D cell culture
hydrogel
Advisor: Wheeler, Aaron
Self-assembly Drives the Control of the SPOP Cullin–Ring Ligase

The covalent modification of proteins with a suite of molecular tags, a process termed post-translational modification, is a powerful means to enhance the proteomic complexity of an organism far beyond that which is directly encoded by its genome. A particularly widespread form of modification involves the conjugation of the protein ubiquitin to specified substrates, which serves to regulate numerous cellular processes. The mechanism of ubiquitin conjugation, known as ubiquitylation, requires E3 ubiquitin ligases that specify and recruit substrate proteins for ubiquitin conjugation. Recent insights into the mechanisms of ubiquitylation demonstrate that E3 ligases can possess active regulatory properties beyond those of a simple assembly scaffold. This thesis describes the dimeric structure of the E3 ligase adaptor protein SPOP in complex with the N-terminal domain of Cul3 at 2.4 Å resolution. Here, it is demonstrated that SPOP forms large oligomers that can form heteromeric species with the closely related paralog SPOPL. In combination, SPOP and SPOPL form a molecular rheostat that can fine-tune E3 ubiquitin ligase activity by affecting the oligomeric state of the E3 complex. These results reveal a mechanism through which adaptor protein self-assembly may provide a graded level of regulation of the SPOP/Cul3 E3 ligase toward its multiple protein substrates.

Keywords: Ubiquitin
Cullin
Self-assembly
Oligomer
E3 Ligase
Advisor: Privé, Gilbert G.
Early Versus Delayed Cholecystectomy for Acute Calculous Cholecystitis

Introduction: Despite evidence in favour of cholecystectomy early during first presenting admission for most patients with acute calculous cholecystitis, variation in the timing of cholecystectomy remains evident worldwide. This dissertation characterizes the extent of variation within a large regional healthcare system, as well as addresses gaps in our current understanding of the clinical consequences and costs associated with early versus delayed cholecystectomy for acute cholecystitis. Methods: A population-based retrospective cohort of patients admitted emergently with acute cholecystitis was identified from administrative databases for the province of Ontario, Canada. First, the extent of variation across hospitals in the performance of early cholecystectomy (within 7 days of emergency department presentation) was characterized. Second, among patients discharged without cholecystectomy following index admission, the risk of recurrent gallstone symptoms over time was quantified. Third, operative outcomes of early cholecystectomy were compared to those of delayed cholecystectomy. Finally, a cost-utility analysis compared healthcare costs and quality-adjusted life-year gains associated with three management strategies for acute cholecystitis: early cholecystectomy, delayed cholecystectomy and watchful waiting, where cholecystectomy is performed urgently if recurrent gallstone symptoms arise. Results: The rate of early cholecystectomy varied widely across hospitals in Ontario (median rate 51%, interquartile range 25-71%), even after adjusting for patient characteristics (median odds ratio 3.7). Among patients discharged without cholecystectomy following an index cholecystitis admission, the probability of a gallstone-related emergency department visit or hospital admission was 19% by 12 weeks following discharge. Early cholecystectomy was associated with a lower risk of major bile duct injury (0.28%vs.0.53%, RR=0.53, 95%CI 0.31–0.90, p=0.025). No significant differences were observed in terms of open cholecystectomy (15%vs.14%, RR=1.07, 95%CI 0.99–1.16, p=0.10) or in conversion among laparoscopic cases (11%vs.10%, RR=1.02, 95%CI 0.93–1.13, p=0.68). Early cholecystectomy was on average less costly ($6,905 per person) and more effective (4.20 QALYs per person) than delayed cholecystectomy ($8,511; 4.18 QALYs per person) or watchful waiting ($7,274; 3.99 QALYs per person). Conclusions: Early cholecystectomy offers a benefit over delayed cholecystectomy in terms of major bile duct injury, mitigates the risk of recurrent symptoms, and is associated with the greatest QALY gains at the least cost.

Keywords: acute cholecystitis
cholecystectomy
Advisor: Nathens, Avery B.
Structural, Genetic and Physiological Analysis of the Juxtamembrane Region of Drosophila neuronal-Synaptobrevin

Synaptic transmission requires the fusion of neurotransmitter containing vesicles with the neuron's plasma membrane in a temporally restrictive manner. In Drosophila, this challenge is accomplished in part by the SNARE protein neuronal-Synaptobrevin (n-Syb). The juxtamembrane region of this molecule, linking the cytosolic SNARE motif and transmembrane region, is hypothesized to play a functional role in facilitating membrane fusion. This short, 10 amino acid, segment contains numerous charged residues and one conserved tryptophan residue. Its short rigid structure may be important in transducing force during SNARE complex assembly. Tryptophan residues, common in membrane proteins, are often observed at the membrane-water interface. It was hypothesized that this conserved tryptophan residue was important for anchoring and positioning n-Syb in the membrane. Proteins produced with tryptophan mutated were tested for anchoring and stability in a membrane model using NMR spectroscopy. Experiments testing depth of insertion using exposure to oxygen, a paramagnetic species, and exchange with deuterium demonstrated that tryptophan anchored n-Syb in the membrane. To test a potential functional role for the juxtamembrane region of n-Syb in synaptic transmission, a reverse genetic approach was employed. Wild-type and mutant P-element clones were made using the genomic sequence of n-syb including the endogenous promoter. n-Syb was found to be expressed, integrate and orient correctly in the membrane of Drosophila S2 cells. Transgenic Drosophila, produced via P-element transformation, were also found to produce transgenic protein. Transgenic expression of wild-type n-syb was found to restore an n-syb hypomorphic mutant from severe motor impairment and limited lifespan to wild-type levels. Synaptic transmission was assessed in 3rd instar larval preparations of mutant and wild-type transgenics. Mutation of the tryptophan residue and insertion of a short flexible linker were both found to inhibit synaptic transmission, while insertion of a long flexible linker was not.

Keywords: neuronal-Synaptobrevin
SNARE protein
Juxtamembrane region
Synaptic transmission
Advisor: Stewart, Bryan
Planetary Dynamo Models: Generation Mechanisms and the Influence of Boundary Conditions

The Earth's magnetic field is generated in its fluid outer core through dynamo action. In this process, convection and differential rotation of an electrically conducting fluid maintain the magnetic field against its ohmic decay. Using numerical models, we can investigate planetary dynamo processes and the importance of various core properties on the dynamo. In this thesis, I use numerical dynamo models in Earth-like geometry in order to understand the influence of inner core electrical conductivity and the choice of thermal and velocity boundary conditions on the resulting magnetic field. I demonstrate how an electrically conducting inner core can reduce the frequency of reversals and produce axial-dipolar dominated fields in our models. I also demonstrate that a strong planetary magnetic field intensity does not imply that the dynamo operates in the strong field regime as is usually presumed. Through a scaling law analysis, I find that irrespective of the choice of thermal or velocity boundary conditions, the available power determines the magnetic and velocity field characteristics like the field strength, polarity and morphology. Also, whether a dynamo model is in a dipolar, transitional or multipolar regime is dependent on the force balance in the model. I demonstrate that the Lorentz force is balanced by the Coriolis force in the dipolar dynamo regime models resulting in magnetostrophically balanced dynamos whereas the Lorentz force is balanced by the Inertial force (and not the Coriolis force) in the multipolar dynamo regime models resulting in a non-magnetostrophically balanced dynamo. The generation mechanism differs between the regimes and depends on the velocity boundary conditions. The zonal flows of the stress-free models are stronger than in the no-slip models, and bistability is more prominent when stress-free boundary conditions are used. A single scaling law may be feasible for all the models, but there does appear to be some variation for models with different thermal and velocity boundary conditions. The results presented in this thesis are not only applicable to the geodynamo, but will also aid in understanding the dynamos of other planets and exoplanets.

Keywords: Planetary Dynamo
Numerical Model
Boundary Conditions
Inner Core Conductivity
Scaling Laws
Generation Mechanism
Advisor: Stanley, Sabine
Exotic Phases In Geometrically Frustrated Quantum Magnets

Quantum magnetic materials provide pathways to exotic spin-disordered phases. We study two broad classes of quantum spin systems and their ground states. The first class is that of spin-dimer systems, which form valence-bond-solid states. In such systems, competition between interactions among the dimers can lead to interesting magnetization behaviour. We explain the magnetization of Ba3Cr2O8 as a Bose-Einstein condensate of spin-carrying excitations. Furthermore, we investigate possible dimerized and nearby magnetically ordered states in the Shastry-Sutherland compound (CuCl)LaNb2O7. The second class of spin systems feature geometric frustration, which may stabilize spin-liquid states without any order or particular dimerization. We argue the proximity of the face-centred-cubic double perovskite La2LiMoO6 to such a phase, to explain its lack of long-range order. We argue for the coexistence of such a state, along with spiral magnetic order, to explain the anomalous thermodynamic measurements in the spin-density-wave phase of powder samples of Volborthite, a distorted kagome-lattice spin system. Finally, we study spin liquid phases that have spin correlations consistent with those found from inelastic neutron scattering of the disordered kagome-lattice material Herbertsmithite. We predict electron spin resonance absorption lineshapes associated with these phases.

Keywords: Physics
Condensed Matter
Quantum Magnetism
Spin Liquids
Valence Bond Solid
Advisor: Kim, Yong Baek
The (Co)isoperimetric Problem in (Random) Polyhedra

We consider some aspects of the global geometry of cellular complexes. Motivated by techniques in graph theory, we develop combinatorial versions of isoperimetric and Poincare inequalities, and use them to derive various geometric and topological estimates. This has a progression of three major topics: 1. We define isoperimetric inequalities for normed chain complexes. In the graph case, these quantities boil down to various notions of graph expansion. We also develop some randomized algorithms which provide (in expectation) solutions to these isoperimetric problems. 2. We use these isoperimetric inequalities to derive topological and geometric estimates for certain models of random simplicial complexes. These models are generalizations of the well-known models of random graphs. 3. Using these random complexes as examples, we show that there are simplicial complexes which cannot be embedded into Euclidean space while faithfully preserving the areas of minimal surfaces.

Keywords: Geometry
Combinatorics
Advisor: Guth, Larry
Population Genetics and Speciation in Outcrossing Species in the Nematode Genus Caenorhabditis

In Caenorhabditis nematodes, the androdioecious, self-fertilizing reproductive strategy has evolved relatively recently from gonochoristic, outcrossing ancestors. Transitions in mating system impact how genes are vertically transmitted between generations and horizontally between populations through gene flow. To date, species-wide studies have targeted selfing species, and we have limited understanding about how population genetic processes have shaped the genome structure and evolutionary history of outcrossing species of Caenorhabditis. To fill this gap, I investigate patterns of genetic variation and population genetic processes focusing on two outcrossing species in the genus, C. brenneri and C. remanei, using a survey of nucleotide polymorphisms in a multipopulation, multilocus context. I discover extensive genetic diversity in Caenorhabditis brenneri, termed hyperdiversity, giving this species the highest known levels of nucleotide polymorphism for any multicellular eukaryote. Genetic crosses between populations, extensive intra-locus recombination, and evidence of weak selection on codon usage all suggest that this is due to a large effective population size in the species and not an artifact of cryptic species divergence. I demonstrate that C. remanei also is characterised by high genetic variation globally, albeit not as extreme as in C. brenneri, and within each local population. Despite geographic barriers, considerable gene flow occurs between inter-continental locations. While exploring genetic diversity in C. remanei, I discovered C. sp. 23, a new, gonochoristic species reproductively isolated and highly divergent from it. Subsequently, taking advantage of this newly discovered species pair, I explore the patterns of postzygotic reproductive isolation between C. remanei and C. sp. 23. I find evidence of partial F1 hybrid inviability, strong F1 hybrid male sterility (Haldane’s rule) and strong F2 hybrid breakdown between the two. The findings from this thesis, especially the notion of hyperdiversity, can be taken advantage of to answer key questions on testing limits of natural selection, of evolution of genome complexity as well as identifying and characterising functional, non-coding regulatory elements. Discovery of a new species pair in Caenorhabditis helps establish an emerging age of speciation genetics in the worm.

Keywords: population genetics
Caenorhabditis
speciation
genetic variation
Advisor: Cutter, Asher
Solving MAXSAT by Decoupling Optimization and Satisfaction

Many problems that arise in the real world are difficult to solve partly because they present computational challenges. Many of these challenging problems are optimization problems. In the real world we are generally interested not just in solutions but in the cost or benefit of these solutions according to different metrics. Hence, finding optimal solutions is often highly desirable and sometimes even necessary. The most effective computational approach for solving such problems is to first model them in a mathematical or logical language, and then solve them by applying a suitable algorithm. This thesis is concerned with developing practical algorithms to solve optimization problems modeled in a particular logical language, MAXSAT. MAXSAT is a generalization of the famous Satisfiability (SAT) problem, that associates finite costs with falsifying various desired conditions where these conditions are expressed as propositional clauses. Optimization problems expressed in MAXSAT typically have two interacting components: the logical relationships between the variables expressed by the clauses, and the optimization component involving minimizing the falsified clauses. The interaction between these components greatly contributes to the difficulty of solving MAXSAT. The main contribution of the thesis is a new hybrid approach, MaxHS, for solving MAXSAT. Our hybrid approach attempts to decouple these two components so that each can be solved with a different technology. In particular, we develop a hybrid solver that exploits two sophisticated technologies with divergent strengths: SAT for solving the logical component, and Integer Programming (IP) solvers for solving the optimization component. MaxHS automatically and incrementally splits the MAXSAT problem into two parts that are given to the SAT and IP solvers, which work together in a complementary way to find a MAXSAT solution. The thesis investigates several improvements to the MaxHS approach and provides empirical analysis of its behaviour in practise. The result is a new solver, MaxHS, that is shown to be the most robust existing solver for MAXSAT.

Keywords: Combinatorial optimization
Propositional logic
Maximum satisfiability
Weighted constraints
Integer programming
Satisfiability
Advisor: Bacchus, Fahiem
Appliction-driven Memory System Design on FPGAs

Moore's Law has helped Field Programmable Gate Arrays (FPGAs) scale continuously in speed, capacity and energy efficiency, allowing the integration of ever-larger systems into a single FPGA chip. This brings challenges to the productivity of developers in leveraging the sea of FPGA resources. Higher level of design abstractions and programming models are needed to improve the design productivity, which in turn require memory architectural supports on FPGAs. While previous efforts focus on computation-centric applications, we take a bandwidth-centric approach in designing memory systems. In particular, we investigate the scheduling, buffered switching and searching problems, which are common to a wide range of FPGA applications. Despite that the bandwidth problem has been extensively studied for general-purpose computing and application specific integrated circuit (ASIC) designs, the proposed techniques are often not applicable to FPGAs. In order to achieve optimized design implementations, designers need to take into consideration both the underlying FPGA physical characteristics as well as the requirements from applications. We therefore extract design requirements from four driving applications for the selected problems, and address them by exploiting the physical architectures and available resources of FPGAs. Towards solving the selected problems, we manage to advance state-of-the-art with a scheduling algorithm, a switch organization and a cache analytical model. These lead to performance improvements, resource savings and feasibilities of new approaches for well-known problems.

Keywords: FPGA
Memory System
Muti-port Memory Controller
Switch Fabric
Cache Churn Rate
Flash
XML
Quality-of-Service
Bandwidth Guarantee
Crosspoint Queued Switch
Zipf's Law
Online Video
Advisor: Zhu, Jianwen