VictorJuiz/thesis huggingface dataset:
Student Learning Heterogeneity in School Mathematics

The phrase "opportunities to learn" (OTL) is most commonly interpreted in institutional, or inter-individual, terms but it can also be viewed as a cognitive, or intra-individual, phenomenon. How student learning heterogeneity (LH) - learning differences manifested when children's understanding is later assessed - is understood varies by OTL interpretation. In this study, I argue that the cognitive underpinning of learning disability, learning difficulty, typical achievement, and gifted achievement in mathematics is not well understood in part because of the ambiguity of LH assumptions in previous studies. Data from 104,315 Ontario students who had responded to provincially-mandated mathematics tests in grades 3, 6, and 9 dataset were analyzed using latent trait analysis (LTM) and latent class analysis (LCA). The tests were constructed to distinguish four achievement levels per grade and, either five curriculum strands (grades 3 and 6), three strands (grade 9 applied) or four strands (grade 9 academic). Best-fitting LTM models reflected 3- or 4-factors (grade 9 applied and grades 3, 6, 9 academic, respectively). Best-fitting LCA solutions reflected 4- or 5-classes (grade 3, 6 and grade 9 applied, academic, respectively). There were differences in relative proportions of students who were distributed across levels and classes. Moreover, grade 9 models were more complex than the reported four achievement levels. To explore intrinsic modeled results further, latent factors were plotted against latent classes. Implications of institutional versus cognitive interpretations are discussed.

Keywords: latent variable analysis
mathematics
large-scale assesment
learning heterogeneity
Advisor: Childs, Ruth A.
"A Stepping-stone to do Something Else": Exploring why Jamaican Student Teachers Enter and Complete Teacher Education

The extensive educational reforms currently being implemented in Jamaica, in addition to my personal curiosity as a teacher educator, provide the rationale for this research. A better awareness and understanding of who enrols to learn to teach may be critical to the viability and success of the current reforms taking place in the Jamaican education system, and teacher education in particular. This study explores why Jamaican student teachers, who were not aspiring to learn to be teachers or teach, entered and completed a three-year teacher education programme. The study was guided by two essential research questions: (i) What accounts for Jamaican students, who indicate that teacher education and teaching are not their educational or occupational aspirations, entering and completing teacher education? (ii) What do these Jamaican students experience within the teacher education program that contributes to their belief that such a program is of benefit to their educational and occupational aspirations? Postcolonial theory (Ashcroft, Griffith & Tiffen, 1989) and theory of occupational choice (Ginzberg, 1963, 1972) serve as analytical frameworks to assist in better understanding the Jamaican student teacher experience. Qualitative methodology provided the means to including the essential “voices” of eight Jamaican student teachers; and, grounded theory the means to collecting and analysing what they had to say about entering and completing teacher education. The findings raise the notion of “youthfulness”, and how this may influence aspirations and decisions in an economic and academic environment of limited options and opportunities. They suggest that teacher education may serve as a “stepping-stone” to more desirable educational or occupational goals. The findings also reveal what these student teachers believed were significant aspects of the teacher education experience, and how this experience may contribute to their future educational or occupational plans and aspirations. Finally, this study supports the movement to reform teacher education in Jamaica; however, not at the expense of reducing the opportunities for higher education within the wider Jamaican populace. Suggestions are presented regarding possible reforms to secondary and post-secondary education in general; therefore, reforms which may support or enhance existing teacher education programmes.

Keywords: Teacher Education
Student Teachers
Caribbean Studies
Advisor: Kosnik, Clare
Current Limitations in Computer-assisted Surgery of Femoral Shaft Fractures and the use of Intraoperative CT to improve Characterization of Fracture Malalignment

Femoral shaft fractures are commonly encountered in orthopaedics and are typically treated using intramedullary (IM) nailing under fluoroscopic guidance. Inaccuracies in the location of the entry point of the nail and the alignment of the reduced fracture are not uncommon during this procedure. This can greatly increase the risk of iatrogenic fractures, malunions and, potentially, secondary degenerative joint disease. Fluoroscopy-based computer-assisted navigation workflows have been developed but are, as yet, not widely used. As such, there is a need to investigate the performance of these systems as well as the possibility of using newer imaging methods to enhance the reduction accuracy. This body of work investigated the impact of off-angle fluoroscopic images on the accuracy and precision of the selection of the entry points used in IM nailing and found that, while images were considered to be clinically acceptable, they resulted in large deviations in the selection of the entry point. Although higher precision was achieved with navigation, it did not improve the accuracy. This work extended the investigation of off-angle images by investigating the impact of the variation in the landmarks used by current navigation methods on quantification of femoral anteversion. The observed landmark variations were propagated through the calculation of femoral anteversion and yielded errors exceeding current clinical tolerances. As an alternative to fluoroscopy, this work developed two, semi-automated algorithms to quantify femoral shaft fracture alignment in six degrees of freedom (6DOF) based on a single, intraoperative cone-beam CT scan. Both algorithms were able to accurately quantify malalignment in all 6DOF with high repeatability and limited user interaction over a range of complex femoral shaft fractures, even in cases with severe comminution. The time requirements for the utilization of these algorithms were reasonable with respect to the time required for current, fluoroscopy-based navigation. Therefore, both of these algorithms would provide an efficient, robust and accurate alternative for the quantification of malalignment in 6DOF. Such an accurate and robust quantification of malalignment, when paired with the high precision tracking in current navigation systems, may enable the improvement of reduction accuracy in the treatment of complex femoral shaft fractures.

Keywords: computer-assisted surgery
femoral shaft fracture
orthopaedics
Advisor: Whyne, Cari
Schemitsch, Emil H.
The Syntax and Semantics of Modification in Inuktitut: Adjectives and Adverbs in a Polysynthetic Language

This thesis explores the properties of adjectives and adverbs in Inuit (Eskimo-Aleut), with focus on the Inuktitut dialect group. While the literature on Eskimoan languages has claimed that they lack these categories, I present syntactic evidence for two classes of adjectives, one verb-like and another strictly attributive, as well as a class of adverbs. These categories are then employed to diagnose more general properties of the language including headedness, word-formation, adjunct licensing, and semantic composition. In the first half of Chapter 2 I demonstrate that verb-like adjectives can be differentiated from verbs insofar as only the former are compatible with a particular copular construction involving modals. Similarly, verb-like adjectives can combine with a negative marker that is incompatible with genuine verbs. This contrast is further corroborated by an inflectional distinction between verb-like adjectives and verbs in the Siglitun dialect. A second class of strictly-attributive adjectives is argued for on the basis of stacking, variable order, optionality, and compositionality. The second half of the chapter examines semantic restrictions on membership in the strictly-attributive class whereby only adjectives with subsective and privative denotations are attested. These restrictions are explained by the proposal that Inuit lacks a rule of Predicate Modification, with the result that only adjectives with semantic types capable of composing with nouns via Functional Application can compose directly with nominals. Furthermore, to explain why this restriction does not extend to verb-like adjectives it is proposed that when these modify nominals, they are adjoined DP appositives and compose via Potts’s (2005) rule of Conventional Implicature Application. In Chapter 3 I argue for a class of adverbs, presenting evidence including degree modification, variable ordering, speaker-oriented meanings, and the ability to modify additional categories. Finally, data from adverb ordering is used to compare syntactically oriented and semantically oriented approaches to adjunct licensing and verbal-complex formation. I present arguments in favour of a right-headed analysis of Inuit in which the relative position of adverbs inside polysynthetic verbal-complexes is primarily determined by semantics, supporting Ernst (2002), contra cartographic approaches such as Cinque (1999).

Keywords: Inuktitut
Adjectives
Adverbs
Lexical Categories
Modification
Polysynthesis
Inuit
Adjuncts
Word-formation
Advisor: Johns, Alana
Behaviour of Shear-critical Reinforced Concrete Beams Retrofitted with Externally Applied Fibre-reinforced Polymers

Ageing infrastructure that is shear deficient and may be at risk of brittle collapse, particularly in seismically active regions, can be economically strengthened using externally bonded fibre-reinforced polymers (FRP). Although many studies have been conducted on small-scale specimens subject to monotonic loading, little experimental data exists for large-scale specimens and those tested under reversed cyclic loading to simulate a seismic event. An experimental study of large-scale (400 mm x 650 mm) beam specimens strengthened in shear with FRP was conducted to examine the effects of reversed cyclic loading and to quantify material shear strength contributions. Testing showed that FRP retrofits were highly effective at improving shear performance and were not adversely affected by reversed cyclic loading prior to the occurrence of flexural yielding. The shear resistance attributed to concrete was found to remain relatively consistent with reversed cyclic loading prior to flexural yielding, after which point concrete strength decay was apparent. The loss of concrete shear resistance directly influenced the rate of FRP straining and the achievable ductility. An analytical model using the Modified Compression Field Theory (MCFT) was developed for externally bonded FRP reinforcement to describe the experimental behaviour and to evaluate the accuracy of current FRP design methods. Failures were accurately modelled when appropriate FRP strain limits were used for the ultimate strength and for the stress transfer capacity across the shear crack. Proposed FRP strain limits were developed considering the strain distribution along the crack plane. In addition, improved strain limits incorporate the effect of rupture failure due to stress concentrations in the FRP wrapped around the beam corners. The proposed FRP formulations offer improved accuracy over the current FRP design methods (CSA S6-06 and ACI 440.2R-08), which suggest a broadly applied maximum strain limit of 0.004 mm/mm, which was determined to be overly conservative for FRP rupture failures.

Keywords: beam
cyclic load
debonding
ductility
fibre-reinforced polymer
FRP
MCFT
modified compression field theory
rehabilitation
reinforced concrete
retrofit
seismic
shear
strengthening
Advisor: Sheikh, Shamim A.
Soil Organic Matter Composition Impacts its Degradability and Association with Soil Minerals

Soil organic matter (OM) is a complex mixture of compounds, mainly derived from plants and microbes at various states of decay. It is part of the global carbon cycle and is important for maintaining soil quality. OM protection is mainly attributed to its association with minerals. However, clay minerals preferentially sorb specific OM structures, and clay sorption sites become saturated as OM concentrations increase. Therefore, it is important to examine how OM structures influence their association with soil minerals, and to characterize other protection mechanisms. Several techniques, which provide complementary information, were combined to investigate OM composition: Biomarker (lignin phenol, cutin-OH acid, and lipid) analysis, using gas chromatography/mass spectrometry; solid-state 13C nuclear magnetic resonance (NMR) spectroscopy; and an emerging method, solution-state 1H NMR spectroscopy. OM composition of sand-, silt-, clay-size, and light fractions of Canadian soils were compared. It was found that microbial-derived and aliphatic structures accumulated in clay-size fractions, and lignin phenols in silt-size fractions may be protected from further oxidation. Therefore, OM protection through association with minerals may be structure-specific. OM in soils amended with maize leaves, stems, and roots from a biodegradation study were also examined. Over time, lignin phenol composition, and oxidation; and aliphatic structure contribution changed less in soils amended with leaves compared to soils amended with stems and roots. Compared to soils amended with leaves and stems, amendment with roots may have promoted the more efficient formation of microbial-derived OM. Therefore, plant chemistry influenced soil OM turnover. Synthetic OM-clay complexes and soil mineral fractions were used to investigate lignin protection from chemical oxidation. Coating with dodecanoic acid protected lignin from chemical oxidation, and overlying vegetation determined the relative resistance of lignin phenols in clay-size fractions from chemical oxidation. Therefore, additional protection from chemical oxidation may be attributed to OM composition and interactions between OM structures sorbed to clay minerals. Overall, these studies suggest that while association with minerals is important, OM turnover is also influenced by vegetation, and protection through association with clay minerals was modified by OM structure composition. As well, OM-OM interaction is a potential mechanism that protects soil OM from degradation.

Keywords: Soil organic matter
lignin
particle size fractions
density fractions
humic substances
CuO oxidation
lipids
nuclear magnetic resonance
mass spectrometry
grassland soil
microbial-derived peptides
clay-size fraction
light density fraction
microbial-derived organic matter
plant-derived organic matter
solid-state 13C NMR
solution-state 1H NMR
clay
montmorillonite
sodium chlorite
sorption
maize transformation
lignin phenols
gas chromatography/mass spectrometry
Zea mays
corn
Advisor: Simpson, Myrna J.
Machine Learning Approaches to Refining Post-translational Modification Predictions and Protein Identifications from Tandem Mass Spectrometry

Tandem mass spectrometry (MS/MS) is the dominant approach for large-scale peptide sequencing in high-throughput proteomic profiling studies. The computational analysis of MS/MS spectra involves the identification of peptides from experimental spectra, especially those with post-translational modifications (PTMs), as well as the inference of protein composition based on the putative identified peptides. In this thesis, we tackled two major challenges associated with an MS/MS analysis: 1) the refinement of PTM predictions from MS/MS spectra and 2) the inference of protein composition based on peptide predictions. We proposed two PTM prediction refinement algorithms, PTMClust and its Bayesian nonparametric extension \emph{i}PTMClust, and a protein identification algorithm, pro-HAP, that is based on a novel two-layer hierarchical clustering approach that leverages prior knowledge about protein function. Individually, we show that our two PTM refinement algorithms outperform the state-of-the-art algorithms and our protein identification algorithm performs at par with the state of the art. Collectively, as a demonstration of our end-to-end MS/MS computational analysis of a human chromatin protein complex study, we show that our analysis pipeline can find high confidence putative novel protein complex members. Moreover, it can provide valuable insights into the formation and regulation of protein complexes by detailing the specificity of different PTMs for the members in each complex.

Keywords: Machine Learning
Unsupervised Learning
Clustering
Mass Spectrometry
Post-translational Modification Refinement
Protein Identification
Nonparameteric Bayesian method
Hierarchical clustering
Advisor: Frey, Brendan J.
Socio-environmental Determinants of Cardiovascular Diseases

Cardiovascular diseases (CVDs) are the leading cause of death and disability around the world. The purpose of this thesis is to investigate the impact of socio-environmental determinants of CVDs at the neighbourhood scale in order to inform actionable interventions, which may lead to large-scale reductions in preventable CVDs. Drawing on 2411 surveys carried out in Toronto, Canada, this thesis employs multilevel models to estimate the magnitude of socio-environmental influences on the risk of CVD while adjusting for individual-level risk factors. To advance current research methodology, strategies and innovations were developed to 1) improve the characterization of neighbourhoods by empirically testing a full range of socio-environmental influences; 2) account for non-residential exposures by including a combined analysis of work and home contexts; 3) account for variations in the duration of exposure through the use of time-weighted models; 4) deal with problem of spatial data aggregation by developing and testing a novel method of neighbourhood zone design, and 5) account for the spatial scales of different socio-environmental determinants by modeling at multiple scales. The thesis demonstrated that land use decisions are inextricably public health decisions. It found that living in neighbourhoods with inadequate access to food stores and areas for physical activity, burdened by violent crimes and fast food restaurants, and over-dependent on automobiles (leading to air pollution), with a high level of noise may significantly increase the risk of CVDs, over and above individual-level risks. The thesis also found that working in neighbourhoods that are socio-economically disadvantaged or have high-traffic may significantly increase CVD risk. The thesis developed and demonstrated novel methods to reduce the measurement error of neighbourhood exposures through 1) the use of “amoeba buffers” to improve neighbourhood zone design to better reflect participants’ local neighbourhoods and 2) the use of duration of exposure weights to adjust for individual differences in the time spent across different contexts. Finally, it found that the significance of socio-environmental factors depends on the scale of data aggregation; thus, investigation of multiple scales may be required to identify the relevant scale that matches the specific contextual factor in future research.

Keywords: Medical Geography
Cardiovascular Diseases
Multilevel Analysis
Planning
Social Determinants of Health
Environmental Determinants of Health
Geography
Health
Neighbourhoods
Public Health
Advisor: Walks, R. Alan
Flat Virtual Pure Tangles

Virtual knot theory, introduced by Kauffman, is a generalization of classical knot theory of interest because its finite-type invariant theory is potentially a topological interpretation of Etingof and Kazhdan's theory of quantization of Lie bi-algebras. Classical knots inject into virtual knots}, and flat virtual knots is the quotient of virtual knots which equates the real positive and negative crossings, and in this sense is complementary to classical knot theory within virtual knot theory. We classify flat virtual tangles with no closed components and give bases for its ``infinitesimal'' algebras. The classification of the former can be used as an invariant on virtual tangles with no closed components and virtual braids. In a subsequent paper, we will show that the infinitesimal algebras are the target spaces of any universal finite-type invariants on the respective variants of the flat virtual tangles.

Keywords: virtual knot
flat virtual knot
finite-type invariants
R-matrix
quantum invariant
immersed curves
Advisor: Bar-Natan, Dror
Functional Characterization of Amphiphysin in Drosophila melanogaster

Amphiphysin (Amph) is a multi-domain protein that has been implicated in synaptic vesicle (SV) endocytosis. In vertebrates, Amph1 associates with SVs and binds to known endocytic proteins, such as dynamin and clathrin. Overexpression of the vertebrate Amph1 SH3 domain is sufficient to inhibit SV endocytosis in the lamprey synapse. However, these in vitro and overexpression studies may not reflect Amph function in vivo. To investigate Amph function in vivo, I used Drosophila melanogaster as a model organism. I discovered that Drosophila Amph was broadly expressed throughout all developmental stages and was also highly expressed in specialized membranes such as the postsynaptic membrane at the larval neuromuscular junction and the t-tubule membranes of muscles. amph mutants were viable and had normal synaptic transmission, results that were inconsistent with a role for Amph in SV endocytosis. However, amph mutants had impaired locomotion, which may reflect a defect in the t-tubule network, a membrane system that is specialized to couple muscle membrane excitation to muscle contraction. To further explore this idea, I undertook a structure-function approach to ask if different Amph functional domains could rescue the t-tubule and locomotory defects observed in amph mutants. Partial rescue was observed for most constructs, suggesting that Amph function was dependent on more than one domain. To further elucidate how Amph functions at the t-tubule network, I used different in vitro methods to investigate novel protein partners for Amph. A GST pull-down approach identified actin as a potential Amph partner, consistent with studies in yeast. However, I could not confirm a direct interaction between Amph and actin in Drosophila. Another candidate partner was the actin-nucleating protein, Wiskott Aldrich Syndrome Protein, WASP. Although WASP and Amph could be coimmunoprecipitated in vitro, WASP was not expressed at the t-tubule membrane, and Wasp mutants had normal t-tubule morphology. Clearly, Amph is essential for normal t-tubule morphology and future work is needed to further define the function of Amph at the t-tubule network.

Keywords: Amphiphysin
Endocytosis
T-tubules
Muscle
Advisor: Boulianne, Gabrielle