VictorJuiz/thesis huggingface dataset:
Adaptive and Robust Radiation Therapy Optimization for Lung Cancer

A previous approach to robust intensity-modulated radiation therapy (IMRT) treatment planning for moving tumours in the lung involves solving a single planning problem before treatment and using the resulting solution in all of the subsequent treatment sessions. In this thesis, we develop two adaptive robust IMRT optimization approaches for lung cancer, which involve using information gathered in prior treatment sessions to guide the reoptimization of the treatment for the next session. The first method is based on updating an estimate of the uncertain effect, while the second is based on additionally updating the dose requirements to account for prior errors in dose. We present computational results using real patient data for both methods and an asymptotic analysis for the first method. Through these results, we show that both methods lead to improvements in the final dose distribution over the traditional robust approach, but differ greatly in their daily dose performance.

Keywords: robust optimization
adaptive radiation therapy
intensity-modulated radiation therapy
Advisor: Chan, Timothy
Examining the Nature of Epistasis between wupA and for Incomplete Dominance at wupA and epistatic Interactions with for Alleles give Rise to a Gradient Effect in Foraging Behaviour

Foraging behaviour in Drosophila melanogaster larvae is influenced by natural allelic variation in the foraging (for) gene that encodes a cyclic GMP – dependent protein Kinase (PKG), such that rovers (forR) traverse greater distances while foraging than sitters (fors). Foraging behaviour is also influenced by natural allelic variation in the wings up A (wupA) gene that encodes the Troponin-I protein (TnI). Specifically, wupAlow allele suppresses the dominance of the forR allele, turning rovers into sitters. The dominance of the natural wupA alleles and their interactions with allelic combinations in for has not been characterized. I conducted various crosses and found that wupA alleles exhibit incomplete dominance. More importantly, I found that allelic combinations of wupA and for gave rise to a range in larval foraging behaviour. In this study, I propose that this gradient effect in foraging behaviour is due to variation in levels of PKG activity and TnI phosphorylation potential.

Keywords: Foraging behaviour
Drosophila Melanogaster
wings up A gene
foraging gene
Incomplete dominance
PKG
Troponin I
Advisor: Fitzpatrick, Mark
Desulphurization of Ferronickel Alloy using a Waste Material from Alumina Production

Red mud is a waste product of alumina production and has an adverse effect on environment. About 90 million tonnes of red mud are produced annually throughout the world and little is recycled for useful applications. The world nickel reserves consist of approximately 30% sulphide ores and 70% oxide ores. Despite the relative abundance of oxide ores, 55% of nickel and nickel alloys produced today are derived from sulphide ores. However, with the production of nickel and its alloys from low-grade oxide ores becoming increasingly important, a major concern is high sulphur level in the resultant alloy. For this reason, desulphurization of the ferronickel becomes an important consideration. In the present study, experiments were conducted to determine if red mud could be used as a major ingredient of custom designed fluxes for the desulphurization of ferronickel alloy. Factors investigated included desulphurization rates, contact angle measurements and flux-refractory interactions.

Keywords: desulphurization
ferronickel
red mud
recycling
sustainability
refractory materials
Advisor: McLean, Alexander
Reliability Models for Linear Assets

Linear assets are among the largest and most important engineered systems; their reliability is of the utmost importance. This thesis presents an overview of the reliability estimation methods used for the various types of linear assets, both observation- and statistically-based. While observation-based reliability monitoring and estimation methods are necessarily particular to a certain type of asset, statistically-based methods developed for one type can potentially inform those used for another. Therefore, this thesis looks to point out commonalities in the methods for the statistical evaluation of the reliability of various types of linear assets, develop and extend reliability models and methods with this knowledge, and suggest how maintenance strategies may be improved. To help illustrate and test the models described in this paper a case study was conducted with a utility operator; this thesis shows the modelling results from the study, and demonstrates the model’s use in a maintenance decision model.

Keywords: Reliability
Maintenance
Reliability Modelling
Linear Assets
Pipelines
Survival Analysis
Advisor: Jardine, Andrew K. S.
Performance of Support Systems Subjected to Dynamic Loads at Two Underground Nickel Mines

The consequences of mine seismicity can be mitigated by installing support systems capable of absorbing the energy generated by seismic events. Recent work has focused on the testing of individual support or reinforcement units under laboratory impact loads; this, however, does not render itself to easy extrapolation to field conditions. Hence, this thesis focuses on improving the understanding of the performance of support systems in real-world applications through passive monitoring of past rockburst events. 14 years of rockburst history were collected from Coleman Mine and Copper Cliff Mine, two of Vale’s underground (nickel) operations in Sudbury Ontario. Statistical analysis, principal component analysis (PCA) and partial least square projection (PLS) were utilized to find relation between collected parameters and performance capacity. This thesis discusses the adequacy of various support systems and investigates the validity of perceived support performance as compared to the actual performance based on analyses of field data.

Keywords: Vale
Support System Performance
Dynamic Loading
Coleman Mine
Copper Cliff Mine
Mining
Underground Support
Advisor: Hadjigeorgiou, John
Development of a Slab-on-Girder Wood-concrete Composite Highway Bridge

This thesis examines the development of a superstructure for a slab-on-girder wood-concrete composite highway bridge. Wood-concrete composite bridges have existed since the 1930's. Historically, they have been limited to spans of less than 10 m. Renewed research interest over the past two decades has shown great potential for longer span capabilities. Through composite action and suitable detailing, improvements in strength, stiffness, and durability can be achieved versus conventional wood bridges. The bridge makes use of a slender ultra-high performance fibre-reinforced concrete (UHPFRC) deck made partially-composite in longitudinal bending with glued-laminated wood girders. Longitudinal external unbonded post-tensioning is utilized to increase span capabilities. Prefabrication using double-T modules minimizes the need for cast-in-place concrete on-site. Durability is realized through the highly impermeable deck slab that protects the girders from moisture. Results show that the system can span up to 30 m while achieving span-to-depth ratios equivalent or better than competing slab-on-girder bridges.

Keywords: bridge
composite
wood
concrete
wood-concrete composites
composite bridges
slab-on-girder bridges
post-tensioned bridges
ultra-high performance fibre-reinforced concrete
glued-laminated timber
glulam
highway bridge
WCC
TCC
timber-concrete composites
advanced materials
short span bridges
unbonded post-tensioning
external post-tensioning
double-T
match-casting
bridge design
bridge engineering
laminated wood
Advisor: Gauvreau, Douglas Paul
The Info-immersive Modalities of Film Documentarian and Inventor Roman Kroitor

In this thesis, it is argued that Canadian film documentarian and inventor Roman Kroitor’s lifework is structured by simultaneous appeals to the realist and reflexive capacities of film and animation. It is shown that the diverse periods in Kroitor’s lifework (including documentary film production at the National Film Board of Canada; co-invention and development of the large-format film apparatus, IMAX; and software design for computer animation in stereoscopic 3D) are united by a general interest in facilitating immersive audience experiences with documentary information and evidentiary entertainment. Against those who have conceptualized cinema as functioning like a frame or a window, this thesis analyzes Kroitor’s diverse work in relation to Gene Youngblood’s conception of “expanded cinema” (1970). It is argued that Kroitor’s efforts in film and invention constitute modalities that actively eschew the architectonic limits that typically characterize the cinematic experience.

Keywords: Roman Kroitor
Immersion
Expanded Cinema
IMAX
National Film Board
Stereoscopy
Animation
Canada
Advisor: Dilevko, Juris B.
Triple Fortification of Salt with Vitamin A, Self-emulsifying Drug Delivery System, Iron, and Iodine

Triple fortification of salt with vitamin A, iron, and iodine has been investigated in the past to reduce micronutrient deficiencies in the developing world. The objective is to develop integrated nutrient delivery technology by microencapsulating a self-emulsifying drug delivery system (SEDDS) made of surfactants and a bioactive compound, retinyl palmitate. The SEDDS is used to enhance absorption of the vitamin A through food systems and to achieve targeted release of the active ingredient. Encapsulating vitamin A was difficult when using the spray dryer and the enteric coating, Aquacoat®. Losses of the micronutrient after a three month storage period ranged from 50-99% at both 25°C/20% RH and 45°C/60% RH. The result of a matrix encapsulation and poor coating formation contributed to the high losses. Further investigation of coating systems with the aim of stabilizing all three samples for a six month storage period such as using other encapsulating methods is recommended.

Keywords: Vitamin A
Microemulsion
Self-emulsifying drug delivery system
Spray drying
Microencapsulation
Bioavailability
Advisor: Diosady, Levente L.
Perceptions of Emergency Department Team Members on the Implementation of Clinical Decision Units

Objectives: CDUs have been implemented to address ED wait times. The objectives of this study were to investigate ED team members’ perceptions on the implementation of CDUs as well as the impact of CDUs on the delivery of emergency care. Methods: A case study design and change theories found in the literature were used to investigate the implementation of CDUs in four hospitals. Semi-structured interviews with ED team members led to the creation of themes for analysis. Results: Analysis demonstrated that patient flow, work processes and communication contribute to the type of CDU set-up, whether it is a co-located or virtual CDU. The sustainability of CDUs relies on communication and a common vision in the fulfillment of purposes and goals. Conclusions: This study contributes to the understanding of the implementation of CDUs. The application of change frameworks assists with the identification of key success factors for implementing and sustaining change.

Keywords: Clinical Decision Units
Emergency Department
Perceptions of Emergency Department Team Members
CDU Implementation
Advisor: Lemieux-Charles, Louise
Disrupting the Non-specific Interactions between DNA and the Escherichia coli Transcriptional Repressor NikR

The Escherichia coli transcription factor NikR is responsible for nickel-mediated repression of the nik operon. The crystal structure of NikR in complex with its operator sequence provided insight into the mechanistic details of nickel-activated NikR-DNA complex formation. The crystal structure revealed that the α3 helix and its preceding loop (residues 63-79) in two of the metal-binding domains—which become structurally ordered after high-affinity nickel binding—make non-specific contacts with the DNA phosphodiester backbone. The proposed mechanism of NikR binding to DNA suggests that the non-specific interactions between the DNA phosphodiester backbone and the positively-charged residues Lys64 and Arg65 anchor NikR to the DNA, thereby allowing the protein to initiate a one-dimensional search for its recognition sequence. The DNA-binding studies presented here strongly support an important role for Lys64 and Arg65 in NikR-DNA complex formation which is in agreement with the proposed model of NikR binding to DNA.

Keywords: NikR
nickel
transcription factor
transcriptional repressor
Advisor: Zamble, Deborah
Thermally Conductive Polymer Composites for Electronic Packaging Applications

Advancements in the semiconductor industry have lead to the miniaturization of components and increased power densities, resulting in thermal management issues. In response to this shift, finding multifunctional materials with excellent thermal conductivity and tailored electrical properties are becoming increasingly important. For this research thesis, three different studies were conducted to develop and characterize thermally conductive polymer composites. In the first study, a PPS matrix was combined with different types of carbon-based fillers to determine the effects of filler’s size, shape, and orientation on thermal conductivity. In the second study, effects of adding ceramic- and carbon- based fillers on the tailored thermal and electrical properties of composites were investigated. Lastly, the possibility of improving the thermal conductivity by introducing and aligning polymer fibers in the composites was investigated. The composites were characterized with respect to their physical, thermal, and electrical properties to propose possibilities of application in the electronic packaging industries.

Keywords: Composites
Electronic Packaging
Thermal Conductivity
Electrical Conductivity
Nano
heat sinks
Advisor: Naguib, Hani E.
Dawson, Francis P.
Ecological Interface Design for a Water Monitoring Decision Aid

In joint human-automation systems, operators must often supervise the automation and adapt their reliance on it based on judgments of its context-specific reliability. For this to occur, operators should trust the automation appropriately. In the design of a water monitoring decision aid’s display, Ecological Interface Design was used to satisfy design guidelines for supporting appropriate trust. Design focused upon a visualization that made the aid’s use of the Dempster-Shafer theory directly perceptible. The display was evaluated using a signal detection theory-based approach that measured reliance on automation. Results indicated that the ecological display yielded less appropriate reliance and poorer performance than a conventional display for a highly reliable decision aid. However, the experimental task prevented participants from adapting to the aid’s context-specific reliabilities, reducing the validity of the findings. A subsequent study is proposed to further study the effects of ecological displays on automation reliance.

Keywords: human factors
interface design
Advisor: Jamieson, Gregory Allan
Differences in Performance and Herbivory Along a Latitudinal Gradient for Common Burdock (Arctium minus)

Plant populations near the northern limits of their geographic distribution may experience different biotic pressures than southern populations. For instance, if herbivores are scarce in northern populations, performance of their host plants may benefit. In this study, I looked at populations of burdock (Arctium minus) along an 815 km latitudinal gradient from the northern range limit to more southern populations. I found that plant height, stem diameter, and number of seeds all increased on approaching the northern limit. In addition, I also found significant decreases in herbivory by generalist and specialist leaf and seed predators, even though northern plants invested less in physical and possibly chemical defenses. In an experiment in which seeds were planted in different soils, marginal soil initially produced smaller plants, but subsequently larger plants than soil from southern populations. These results indicate northern populations experience relaxed pressure from natural enemies and may benefit as a result.

Keywords: Range margin, herbivory, arctium minus, burdock, latitudinal gradient, soil feedback, physical defense
Advisor: Kotanen, Peter M.
Validation of de novo Bioinformatic Predictions of Arabidopsis thaliana Cis-regulatory Elements using in planta GUS Expression Assays

The study of cis-regulatory elements (CREs) will allow for increased understanding of regulation and lead to insight regarding the mechanisms governing growth, development, health, and disease. The aim of this study was to characterize the de novo in silico predictions of Arabidopsis CREs. Eight synthetic and 30 native promoter-constructs containing an eGFP/GUS reporter protein were generated for cold, genotoxic, heat, osmotic, and salt stress; the circadian clock; ABA signaling; root and epidermis tissue. Constructs were stably transformed into A. thaliana Col-0 and the effects of the CREs were evaluated by in planta stress or tissue assays using GUS expression levels. Results reveal a novel genotoxic element that specifically directs GUS expression in rosette leaves during genotoxic stress. Results also look promising for novel epidermis and root-specific elements. Results of these assays validate the de novo prediction pipeline's ability to identify novel and known CREs related to abiotic stress.

Keywords: cis-regulatory elements
bioinformatics
GUS
cold stress
enhancer
silencer
insulator
local control regions (LCRs)
MARs/SARs
in planta
evening element
circadian rhythm
arabidopsis
genotoxic
bleomycin
mitomycin c
heat stress
stem epidermis
root
abscisic acid (ABA)
osmotic stress
salt stress
synthetic constructs
expression assays
transcription factor binding sites
CaMV35S
columbia-0
Advisor: Provart, Nicholas
Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) for the Study of Noncovalent Complexes

Mass spectrometry has become an important tool for analysis of protein complexes. This study utilizes electrospray ionization (ESI) coupled to a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) to analyze noncovalent complexes in the gas phase. Binding of cucurbit[7]uril (CB7) to intact bovine insulin and the B-chain of insulin was investigated. Competition experiments involving the B-chain and a mutant B-chain were performed to probe the solution-phase binding site. Electron capture dissociation (ECD) of CB7 complexed to intact insulin and to the B-chain, produced a series of peptidic fragments of insulin in complex with CB7. Analysis of these fragments allowed the determination of the apparent gas-phase binding site, which appears different than the proposed solution-phase binding-site. These studies thus suggest that CB7 migrates when the complex is transferred from solution to gas phase. The results of this study caution against using ECD-MS as a stand-alone structural probe of solutionphase binding.

Keywords: Mass Spectrometry
noncovalent
Electron capture dissociation
Advisor: Jockusch, Rebecca A.
Association Between Early Follow-up with a Nephrologist and Death in Survivors of Acute Kidney Injury

Background: Survivors of severe acute kidney injury remain at high risk of death well-after apparent recovery from the initial event. Methods: We conducted a cohort study of hospitalized adults in Ontario from 1996 to 2008 with acute kidney injury who received temporary dialysis and survived for 90 days following discharge independent from dialysis. The exposure was nephrology follow-up. We used propensity scores to match individuals with early nephrology follow-up to those without. The primary outcome was time to mortality. Results : We identified 3877 patients with acute kidney injury who met the eligibility criteria. A total of 1583 patients had nephrology follow. The incidence of all-cause mortality was lower in those with early nephrology follow-up as compared to those without early follow-up (8.4 vs. 10.6 per 100 person-years, HR 0.76 (95% CI 0.62-0.93)). Conclusions: Nephrology follow-up after hospitalization with acute kidney injury and temporary dialysis was associated with improved survival.

Keywords: acute kidney injury
Advisor: Etchells, Edward
Pursuing Enterprise Risk Management: A Local Roadmap for Canadian Health Care Leaders

An in-depth analysis of organizational risk management in health care, and in particular the concepts of Enterprise Risk Management (ERM), has identified a five part model that can be used by Canadian health care leaders as an evidence supported approach to successful organizational risk management. The Model for Organizational Risk Management has been developed as a basis for linking the components of an ERM framework into a Canadian health organization in order to overcome the barriers that commonly disrupt strategic risk management. The Model addresses how an ERM framework can fit within an existing health organization by building off of and enhancing existing processes and resources in order to ensure familiarity, acceptance, and sustainability of the risk management program. By approaching the Model in a stepwise fashion (based on individual organizational context) health care leaders are provided with a roadmap from which to advance their own organizational risk management program.

Keywords: ERM
Risk Management
Organizational Risk
Health Care
Corporate Risk
Clinical Risk
Planning
Mitigation
Decision Support
Enterprise Risk
Health Care Management
Risk Assessment
Risk Program
Liability
Risk Model
Knowledge Transfer
Canadian Health Care
Public Health Care
Enterprise Risk Management
Advisor: Cockerill, Rhonda
Church, John
Clinical and Spatiotemporal Aspects of Gait: A Secondary Analysis of the Walking Characteristics of Subjects with Sub-acute Incomplete Spinal Cord Injury

Objective: To describe the walking characteristics of a sample of ambulatory subjects with sub-acute incomplete spinal cord injury (iSCI). Methods: 52 subjects were included in a secondary analysis of clinical and spatiotemporal measures of walking. The study sample was described as a whole and subsequently divided into subgroups on the basis of 3 clinical factors (etiology, severity, and neurological level of injury) and 4 gait factors (gait aid, velocity, symmetry, and variability). Results: Clinical and spatiotemporal parameters were highly variable across the study population. Sub–groups with unique gait features were best identified by velocity and variability. Conclusions: Spatiotemporal measures of walking provide augmented description of walking in the sub-acute iSCI population. Sub-grouping by gait factors warrants further investigation with respect to their ability to act as predictors and modifiers of treatment effect.

Keywords: spinal cord injury
walking
sub-acute
spatiotemporal
Advisor: Verrier, Molly