VictorJuiz/thesis huggingface dataset:
Current Limitations in Computer-assisted Surgery of Femoral Shaft Fractures and the use of Intraoperative CT to improve Characterization of Fracture Malalignment
Keywords: computer-assisted surgery
femoral shaft fracture
orthopaedics

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.
The Syntax and Semantics of Modification in Inuktitut: Adjectives and Adverbs in a Polysynthetic Language
Keywords: Inuktitut
Adjectives
Adverbs
Lexical Categories
Modification
Polysynthesis
Inuit
Adjuncts
Word-formation

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).
Behaviour of Shear-critical Reinforced Concrete Beams Retrofitted with Externally Applied Fibre-reinforced Polymers
Keywords: beam
cyclic load
debonding
ductility
fibre-reinforced polymer
FRP
MCFT
modified compression field theory
rehabilitation
reinforced concrete
retrofit
seismic
shear
strengthening

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.
Soil Organic Matter Composition Impacts its Degradability and Association with Soil Minerals
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

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.
Machine Learning Approaches to Refining Post-translational Modification Predictions and Protein Identifications from Tandem Mass Spectrometry
Keywords: Machine Learning
Unsupervised Learning
Clustering
Mass Spectrometry
Post-translational Modification Refinement
Protein Identification
Nonparameteric Bayesian method
Hierarchical clustering

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.
Socio-environmental Determinants of Cardiovascular Diseases
Keywords: Medical Geography
Cardiovascular Diseases
Multilevel Analysis
Planning
Social Determinants of Health
Environmental Determinants of Health
Geography
Health
Neighbourhoods
Public Health

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.
Flat Virtual Pure Tangles
Keywords: virtual knot
flat virtual knot
finite-type invariants
R-matrix
quantum invariant
immersed curves

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.
Functional Characterization of Amphiphysin in Drosophila melanogaster
Keywords: Amphiphysin
Endocytosis
T-tubules
Muscle

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.
Angiogenesis in Patches and Injectable Biomaterials for Cardiac Repair
Keywords: angiogenesis
cardiac tissue engineering
biomaterials

Treatment of cardiac diseases involves transplantation of donor hearts, since the damaged heart has limited self-regeneration potential. An alternative treatment option has emerged as engineered cardiac tissues, grown in vitro by cultivation of cardiac cells on biomaterials, have comparable properties to native myocardium and can be implanted for cardiac repair. Major current limitations are a viable cell source and adequate vascularization to support cell survival. In this thesis, two proangiogenic biomaterials, a scaffold and a hydrogel, were developed to achieve vascularization in vitro and in vivo for cardiac repair. Scaffold patches are suitable for repairing congestive heart failure or congenital malformations, while injectable biomaterials allow minimally-invasive treatment post-myocardial infarction (MI). In the first aim, a collagen scaffold with covalently immobilized vascular endothelial growth factor (VEGF) was developed, and improved cell mobilization, survival and proliferation when used for free wall repair in adult rats. This increased angiogenesis, which aided in retaining the biomaterial size to allow tissue growth. In the second aim, a collagen-chitosan hydrogel with encapsulated thymosin β4 (Tβ4) was developed to 1) recruit cells from the heart epicardium for repair post-MI in vivo, and 2) guide capillary outgrowths from arteries and veins to form oriented capillary structure for in vitro cardiac tissue engineering. Results showed that the encapsulation of Tβ4 into collagen-chitosan hydrogels led to cell outgrowths from rat or mouse cardiac explants in vitro. A portion of the recruited cells were CD31-positive endothelial cells (ECs) that formed tubes. The hydrogel was injected in vivo to increase vascularization and number of cardiomyocytes within the infarct area post-MI, which improved left ventricular wall thickness. Tβ4-hydrogel also promoted the outgrowth of capillaries from vascular explants that followed the direction of the hydrogel-coated grooves of a micropatterned polydimethylsiloxane (PDMS) substrate. These capillary outgrowths eventually formed a vascular bed for engineering vascularized cardiac tissues. This thesis presents two bioinstructive biomaterials with sustained and localized delivery of angiogenic molecules to be used for in situ cardiac repair based on improved vascularization. The use of cell-free bioactive materials overcomes limitations of cell isolation and expansion as required for cell therapies or implantation of engineered tissues.
Dropped Foot Impairment Post Stroke: Gait Deviations and the Immediate Effects of Ankle-foot Orthotics and Functional Electrical Stimulation
Keywords: Gait
Stroke
Dropped foot
Ankle-foot orthotic
Functional electrical stimulation

Individuals with stroke often demonstrate impaired ankle-foot function, commonly termed dropped foot that affects their ability to walk safely at home and within their community. While interventions are available to improve gait function, they have inconsistency demonstrated positive effects due to the lack of evidence-based practice guidelines and a limited understanding of the mechanisms leading to dropped foot. The aim of this dissertation was to 1) determine the relationship between dropped foot gait deviations and impaired sensorimotor control, 2) compare gait biomechanics between stroke survivors with and without dropped foot impairment, and 3) evaluate the immediate effects of an ankle-foot orthotic (AFO) and functional electrical stimulation (FES) device among stroke survivors with dropped foot impairment. Our evaluation combined standardized clinical measures of ankle-foot function (i.e. sensorimotor control, strength, spasticity and range of motion) and gait analysis using advanced laboratory techniques (i.e. electromyography and electrical goniometers) to quantify mechanisms of dropped foot impairment. Fifty-five stroke survivors completed the assessment prior to discharge from inpatient rehabilitation. Individuals with poor generation of isometric dorsiflexor force and reduced passive ankle range of motion were likely to demonstrate greater plantarflexion in swing and limited stance phase ankle joint excursion, respectively. Results from the gait analysis revealed a delayed onset and reduced activation time of the ankle dorsiflexors, and decreased co-activation time in the stance phase as possible mechanisms leading to dropped foot. A detailed case series was performed with four stroke survivors with dropped foot currently using an AFO. Application of an AFO immediately improved peak dorsiflexion in the swing phase and limited ankle range of motion during stance. When walking with the FES device, individuals with moderate dorsiflexor muscle weakness improved their ankle position at initial contact and increased peak dorsiflexion during stance, while no significant changes were observed among individuals with greater impairment. Overall, the results highlighted individual differences in response to interventions aimed at improving dropped foot gait deviations. These findings contribute to a greater understanding of gait dysfunction post stroke, and may lead to the development of a more effective clinical assessment and intervention strategies to improve dropped foot impairment.