title: Biosynthetic gene clusters guide rational antibiotic discovery from Actinomycetes

contributor:
Wright, Gerard
Biochemistry and Biomedical Sciences

subject:
Antibiotics
Infectious Disease
Actinomycetes
Natural Products
Biosynthetic gene cluster
Genome mining
Autolysin
ClpP

abstract:
As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a pre-antibiotic era urgently requires the discovery of novel antibiotics. Actinomycetes, a family of bacteria commonly isolated from soil, are a proven source of clinically useful antibiotics. However, easily identifiable metabolites have been exhausted and the rediscovery of common antibiotics thwarts searches for rarer molecules. Sequencing of actinomycete genomes reveals that they contain far more biosynthetic gene clusters with the potential to encode antibiotics than whose products can be readily observed in the laboratory. The work presented in this thesis revolves around developing approaches to mine these previously inaccessible metabolites as a source of new antibiotics.
	First, I describe how inactivation of biosynthetic gene clusters for common antibiotics can uncover rare antibiotics otherwise masked in these strains. By applying CRISPR-Cas9 to knockout genes encoding nuisance antibiotics, I develop a simple strategy to reveal the hidden biosynthetic potential of actinomycete strains that can be used to discover rare or novel antibiotics.

	Second, I describe the use of the evolutionary history of biosynthetic gene clusters to prioritize divergent members of an antibiotic family, the glycopeptide antibiotics, that are likely to possess new biological activities. Using these predictions, I uncover a novel functional class of glycopeptide antibiotics that blocks the action of autolysins, essential peptidoglycan hydrolases required for remodelling the cell wall during growth.

	Finally, I apply target-directed genome mining, which makes use of target duplication as a predicted resistance mechanism within an antibiotic’s biosynthetic gene cluster. Using this approach, I discover the association of a family of gene clusters with the housekeeping protease ClpP and characterize the produced metabolite’s effect on ClpP function.

These three research projects mine previously inaccessible chemical matter from a proven source of antibiotics, actinomycetes. The techniques and antibiotics described are required now more than ever to develop life-saving antibiotics capable of combatting multidrug-resistant pathogens.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Antibiotics are essential for treating life-threatening infections, but the rise of antibiotic resistance renders them ineffective. To treat these drug-resistant infections, new antibiotics that work in new ways are required. A family of bacteria commonly isolated from soil called Actinomycetes produce most antibiotics we use today, but it has become increasingly difficult to find new antibiotics from this source. My work describes three techniques that can be applied to actinomycetes to help overcome the challenges associated with antibiotic discovery. Specifically, these techniques guide discovery efforts by making use of regions in actinomycete genomes called biosynthetic gene clusters that often encode antibiotics. In doing so, I describe ways to uncover rare antibiotics from actinomycete strains that produce common and uninteresting antibiotics, use antibiotic family trees to discover antibiotics that work in new ways, and apply antibiotic resistance to identify biosynthetic gene clusters likely to act on a certain bacterial target.


title: Evaluation of the Prevalence and Transmission of Asymptomatic Clostridioides Difficile Carriage in the Hamilton In-patient Setting Using Multi-level Modelling

contributor:
Mertz, Dominik
Health Research Methodology

subject:
Clostridioides difficile
C. difficile infection
C. difficile

abstract:
Background: C. difficile is one of the primary infectious causes of morbidity and mortality in Canada. Colonized patients can pose a risk to others as a factor in the transmission and development of hospital-associated C. difficile infections. Despite immense efforts and resources invested in the reduction in C. difficile transmission within Canada and Hamilton Health Sciences – further reduction in these rates are unlikely, and novel screening strategies are imperative in this field of study.

Methods: This project was a retrospective cohort study of adult in-patients admitted to either The Juravinski, Hamilton General, or St. Joseph’s Healthcare Hamilton Hospitals from January to April 2018 and September 2018 to August 2019. MSRA/VRE swabs were collected during admission or through universal point prevalence screening and subsequently tested for colonization.

Results: From the 1056 patients in the data sample, 72 were colonized with asymptomatic C. difficile resulting in a prevalence rate of 6.81%. In-patient point prevalence screening strategies identified more carriers than admission swabs alone  (p < 0.001). Risk factors for colonization on admission were being female (OR 2.66, 95% CI 1.02-8.33) and previous CDI (OR 4.76, 95% CI 1.49 – 13.86). During hospitalization, risk factors for colonization were previous CDI (OR 4.75 95% CI 2.14-9.94) and recent hospitalization within the last 12 months (OR 2.35, 95% CI 1.30-4.42). The multi-level Cox PH model identified those with a recent hospitalization (OR 2.21, 95% CI 1.32 – 3.73) and those with previous CDI (OR 2.40, 1.34 – 4.30) were twice as likely to develop asymptomatic C. difficile colonization throughout hospitalization.

Conclusion: The addition of universal point prevalence screening in addition to admission screening helped identify more than double the amount of carriers in the population. Moreover, a previous hospitalization, previous CDI, and being female may indicate patients at the highest risk of colonization.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: C. difficile infection (CDI) is a severe infectious disease. Patients with asymptomatic C. difficile present a risk to others as they can contribute to the spread and development of hospital-associated CDI. We are currently unsure of the proportion of adult in-patients colonized with asymptomatic C. difficile. Identifying these carriers early on in their hospital stay is imperative to reduce CDI rates in health care settings. Our study objectives were to determine the best screening strategies to identify asymptomatic carriers, identify risk factors for carriage, and understand the transition from asymptomatic C. difficile to symptomatic CDI. We demonstrated that being female, being recently hospitalized or previously having CDI may increase a patient's risk of being an asymptomatic carrier. Also, timely screening throughout a hospital stay in addition to admission screening helped identify more colonized in-patients. Lastly, we determined that 1 in 5 carriers would go on to develop symptomatic CDI infection.


title: A novel approach to thin film deposition and rare-earth incorporation for silicon integrated photonics

contributor:
Mascher, Peter
Bradley, Jonathan
Engineering Physics

subject:
rare-earth
terbium
hybrid sputtering
silicon
silicon oxide
germanium oxide
silicon photonics

abstract: In this thesis, group IV material oxides for silicon photonics applications were deposited using novel deposition techniques. Erbium and terbium doped silicon oxide thin films were deposited through a novel hybrid radio frequency (RF) magnetron sputtering source in an electron cyclotron resonance (ECR)-plasma enhanced chemical vapour deposition (PECVD) reactor chamber. This approach contrasts with traditional doping methods which use metal-organic precursors to introduce rare-earth dopant species into the host matrix. The effects of sputtering power applied to the rare-earth target and system plasma pressure on the thin film properties were investigated. It was found that the sputtering power strongly influences the rare-earth incorporation, and a wide range of control over the doping level can be achieved. The effect of sputtering power on the refractive index, stoichiometry, and film density were also investigated. Doped thin films deposited with this technique showed low as-deposited hydrogen concentrations. In the case of terbium doped silicon oxide (SiOx), photoluminescence (PL) studies were conducted finding bright emission due to 5D4 → 7F5 transitions visible with the naked eye in films annealed above 1150 °C. Further investigation found that silicon nanostructures formed at the high annealing temperatures and were likely sensitizing the Tb3+ ions. These results demonstrate that hybrid sputtering in ECR-PECVD can be an effective tool for integrating optically active rare-earth dopants into silicon-based thin films. Using alternating current (AC) plasma assisted reactive magnetron sputtering (PARMS), low optical loss germanium oxide (GeO2) thin films were also produced. The films were fabricated at low temperature and high deposition rates of 6–38 nm/min on silicon and thermally oxidized silicon substrates. Prism coupling measurements demonstrated losses of 0.1 dB/cm at wavelengths ranging from 638 to 980 nm attributed to good uniformity and low surface roughness demonstrated through atomic force microscopy (AFM) measurements. The thin films materials developed here are highly promising for their applications in silicon photonics devices, including light sources and amplifiers.

abstract: Thesis

abstract: Candidate in Philosophy


title: Mismatch Negativity and General Anesthesia

contributor:
Connolly, John
Service, Elisabet
Goldreich, Daniel
Neuroscience

subject:
Consciousness
Event-related potentials
Auditory processing
General anesthesia

abstract: In order to further explore the nature of anesthesia-induced unconsciousness and its relationship to nociception, investigators attempted to determine whether mismatch negativity could be detected during general anesthesia and surgery.  An auditory odd-ball paradigm designed to elicit mismatch negativity was presented to ten patients during general anesthesia and surgery.   Five of the ten also underwent testing in the awake state prior to surgery.  Multiple EEG recordings were obtained in each patient and each condition using the BioSemi ActiveTwo  64 EEG electrode  system.  The anesthetic regime required only that 0.7 MAC of an inhaled agent was administered.  Several methods of analysis were utilized to determine whether an MMN response could be identified:  visual inspection of ERP waveforms, targeted t-tests, cluster permutation tests, and multivariate pattern analysis.  Whereas deviant-related negativity was readily detected in the awake state,  deviant-related negativity was not detected during surgery and general anesthesia.   Results demonstrate that essential components of the MMN response are abolished during typically conducted general anesthesia even with significant surgical stimulation.  These results are consistent with previous research on ERPs and anesthesia.  Results cast doubt on the possibility of sensory memory related to intraoperative events.

abstract: Thesis

abstract: Master of Science (MSc)


title: Exercise Instruction for Older Adults: Embodied Education and (In/Ex)clusive Physical Cultures

contributor:
Griffin, Meridith
Health and Aging

subject:
Exercise Instruction
Physical Cultures
Educational Gerontology
Fitness Instruction
Physical Activity and Aging
Institutional Ethnography
Grounded Theory
Social Gerontology

abstract: The intent of this thesis was to better understand the educative role of group exercise instructors, and how this role is approached when working with older exercisers. Data were collected using textual analysis, observations of instructors’ teachings in group exercise classes, semi-structured interviews with instructors and older exercisers, and go-alongs with older exercisers. This thesis is comprised of four papers (three journal articles and one book chapter). The first paper reports findings from a scoping review and elucidates that the educative role of exercise instructors is vital but under researched. Paper 2, a book chapter, reports findings from a qualitative content analysis of eight curricula used to train and certify fitness instructors in Canada and the United States. This paper proposes strategically employing compassionate ageism to meet older exercisers’ needs without (re)producing social inequalities in response to finding that the curricula conceive the older body as different from the healthy, supposedly ideal standard. Paper 3, an Institutional Ethnography, provides evidence for some of the ways employers and the aforementioned curricula influence how instructors teach. Paper 3 reports that multi-level teaching may not be enough to foster inclusivity, thus suggesting a greater need for stratification by ability rather than age. Additionally, findings outline some ableist teaching practices, which some instructors resisted by drawing on their competence to employ teaching methods respecting exercisers’ agency. Finally, Paper 4 introduces a substantive, grounded theory of age capital, which builds on Bourdieu’s theorizations of cultural capital, as well as Mauss’ habitus and body techniques. Age capital is defined as possessing a gerontological embodied competence, or cognitive and embodied knowledge of the socio-cultural practices throughout one’s life course. Collectively, this thesis provides several recommendations for teaching group exercise in a manner that fosters more inclusive classes for older adults.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The key goals of this research were to understand how fitness instructors’ training might influence how instructors teach in their group exercise classes, learn how and what fitness instructors teach, and identify how instructors’ teaching is (or should be) different with older exercisers. I found that fitness instructors are important to group exercise classes, as they bring people together and teach people how to exercise safely. It is also especially important that instructors have special training to work with older people, but there is a lack of consistency in the training of exercise instructors and instructors received mixed messages about ageism in their training. This could reinforce the idea that older persons lose abilities as they age and result in a one-size fits all way of teaching that fails to include older exercisers’ diverse abilities. This research suggests ways instructors can be better trained to relate to older exercisers.


title: "They Will Have to Protect Themselves": African American Resistance to Racialized Violence in the Southern United States

contributor:
Balcom, Karen
History

subject:
African American History
American History
Digital History

abstract:
Black men and women were the victims of verbal abuse, neglect, intimidation, rape, physical assault, lynching, and other manifestations of violence in both the late antebellum and postemancipation South. This dissertation reconstructs how the newly freed black population experienced racialized violence during the transition from slavery to freedom and in the decades immediately following emancipation. By analyzing primary source collections that chronicle the transitional period between slavery and freedom, it is possible to frame resistance to racialized violence as part of a continuum. The struggle to combat racialized violence, I argue, was conditioned by the experiences of black men and women during slavery. This dissertation, then, highlights the continuities that existed in a period of apparent discontinuity.
To reconstruct the experiences of black men and women, this dissertation also reconceptualizes how we think about violence and resistance. There is a tendency among scholars who study racialized violence to equate violence with the use of physical force. This dissertation, however, defines violence as the use of physical force or power, threatened or actual, that either results in or has a high likelihood of resulting in injury, death, psychological harm, maldevelopment, or deprivation. By adopting a definition of violence that is broader than those used in most existing studies of racialized violence, it becomes possible to understand the long-term, psychological, and developmental impact of racialized violence on black men and women. Resistance, similarly, must be understood in broader terms to include acts that are not explicitly recognized as resistance by those involved, but that informed observers might perceivably recognize as thwarting an attempt at subjugation. The reality is that overt resistance was dangerous for African Americans, and so many turned towards clandestine methods of resistance to voice their opposition.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: This dissertation examines how black men and women experienced racialized violence during the transition from slavery to freedom and in the decades immediately following emancipation. The struggle to combat racialized violence, I argue, was conditioned by the experiences of black men and women during slavery. By adopting and transforming resistance techniques developed to oppose slavery, the newly freed black population found ways to contest subjugation. To reconstruct the experiences of black men and women, this dissertation also reconceptualizes how we think about violence and resistance. It moves beyond the equation of violence with physical force, and instead recognizes that acts of violence can result from an imbalance of power. Resistance, similarly, should be understood in broader terms to include acts that are not explicitly recognized as resistance by those involved, but that informed observers might reasonably perceive as thwarting attempts at subjugation.


title: Integrated Battery Charger Topologies for Traction Inverters in Electrified Vehicles

contributor:
Emadi, Ali
Electrical and Computer Engineering

abstract:
Electric vehicles today include several power electronics modules which are critical
to their operation. The traction inverter converts direct current from the battery
pack into alternating current suitable for powering the electric motor, allowing the
vehicle to drive. When the vehicle is parked, the onboard charger enables conversion
of alternating current from a standard outlet to direct current suitable for charging
the battery pack. The traction inverter and onboard charger typically represent the
majority of the power electronics cost, weight and volume in an electric vehicle. The
temporal exclusivity and functional similarities of the inverter and charger present
a basis for investigating how they may be combined into a single system which can
achieve both functions. To that end, a novel approach to developing integrated traction
inverter and battery charging systems, along with subsequent implementations, is
considered.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Materials Preparation and Characterization of the Quasi-Two Dimensional Triangular Rare-Earth Magnets Ba6Yb2Ti4O17 and ErMgGaO4

contributor:
Gaulin, Bruce
Physics and Astronomy

subject:
Marerial Synthesis
Magnetic Materials
Neutron Scattering
X-Ray Diffraction
Magnetism

abstract:
Within in this work, I present the successful synthesis of Ba6Yb2Ti4O17 in a powder
form. To the best of my knowledge, this is the first instance in which this
has been achieved. I also show that single crystal synthesis experiments using
the floating zone synthesis (FZS) technique have yet to produce single crystals.
The magnetic characterization of Ba6Yb2Ti4O17 powder is also presented. DC
susceptibility measurements reveal no spin freezing or ordering down to 0.5K and
inverse susceptibility shows antiferromagnetic coupling between spins. A cold neutron
scattering experiment was performed at low temperatures with and without
an applied magnetic field on Ba6Yb2Ti4O17 powder. This experiment shows the
possibility of spinon-like excitations with a band width of approximately 0.3meV,
but this is inconclusive due to the signal to noise ratio. The powder averaged
g-tensor for Ba6Yb2Ti4O17 was also experimentally estimated to be approximately
2.4. Further work required to complete this study is also discussed.
Synthesis of phase pure ErMgGaO4 has yet to be reported in the literature.
Here, I show that small amounts of phase pure polycrystalline ErMgGaO4 can
be produced using the FZS technique. Through using FZS, 0.85g of phase pure
ErMgGaO4 powder was produced and supplemented using 1.26g of ErMgGaO4
powder containing approximately 1% Er3Ga5O12 magnetic impurity. To estimate
the effect of this magnetic impurity on the magnetic signatures exhibited
by ErMgGaO4, DC susceptibility measurements were performed between 0.5K
and 50K. The magnetic impurity in such small quantity was shown to have negligible
effect on the bulk ErMgGaO4 magnetic features. Cold neutron scattering
conducted on this material revealed a spinon excitation continuum similar to the
one observed in YbMgGaO4.[1] Also present at low temperatures was a diffuse
elastic magnetic feature that was used to estimate an order parameter for the material.
Analysis of this diffuse feature also revealed a Warren line shape, indicative
of two dimensional correlations within the Er3+ triangular planes. Analysis of the
spinon excitation continuum revealed a gapless spinon continuum overall. Results
presented for both Ba6Yb2Ti4O17 and ErMgGaO4 will be discussed and compared
to neutron scattering experiments performed on YbMgGaO4

abstract: Thesis

abstract: Master of Science (MSc)


title: Stability of Perovskite Solar Cells

contributor:
GU, XU
Materials Science and Engineering

abstract:
Organic−inorganic hybrid perovskite solar cells (PSC) have been widely considered as a promising candidate for the next generation of photovoltaics (PV). The power conversion efficiency of a single junction PSC has achieved a maximum of 25.5% within only one decade, rivaling traditional PV technologies. While PSCs inspired a new era for photovoltaic development, they exhibited severe instability problems, thereby impeding their commercialization. Thus, the main projects in this thesis are to improve stability of PSCs.
  To enhance the intrinsic stability of PSC, a hydrophobic five-membered ring cation is introduced to replace the unstable protype methyl-ammonium (MA) cation. In Chapter 2, the crystal structure of the new perovskite material, (C4H8NH2)PbI3 (PyPbI3) is determined and illustrated by single crystal X-ray diffraction. UV absorption spectra, steady state photoluminescence and XRD results show it is a promising alternative to hybrid organic–inorganic perovskites due to its good water resistance and suitable bandgap.
  The MA-based perovskites are unstable at high temperature or under moisture attack. To overcome this barrier, both thermal stability and water resistance of PyPbI3 are investigated in Chapter 3. It presents not only prolonged moisture resistance up to 4 months in ambient conditions and a favorable bandgap of 1.80 eV, as determined by P-XRD and UV absorption, but also excellent thermal stability, as verified via the in situ thermal XRD technique.
  The phase stability of PyPbI3 is investigated in Chapter 4. The hybrid perovskite was synthesized successfully via a simple drop casting method. It presents not only excellent phase stability, but also low trap-state density, as confirmed via XRD and space-charge-limited currents measurements. The results indicate that Py-based perovskite is environmentally stable.
  The commonly employed formamidinium (FA)-containing PSCs exhibit a severe phase instability problem. Here in Chapter 5, both phase stability and energy efficiency of FA-based PSCs are improved by treating the perovskite surface with pyrrolidinium hydroiodide (PyI) salts, resulting in a 1D perovskite structure (PyPbI3), stacked on the original 3D perovskite. By employing in situ XRD measurements, we revealed that the temperature-dependent phase transition activation barrier was enhanced after forming the 1D/3D structure, resulting in a prolonged transition time by 30−40-fold. From the first-principle calculations, we found the thermodynamic energy difference between two phases reduced from −0.16 to −0.04 eV after the stacking of 1D PyPbI3, offering additional lifetime improvement. Moreover, the champion 1D/3D bilayer PSC exhibits a boosted power conversion efficiency of 19.62%, versus 18.21% of the control. Such 1D/3D bilayer structure may be employed in PSCs to enhance their phase stability and photovoltaic performance.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Association between Long-Term Care Resident Characteristics and Transfers to the Emergency Department: A Population-level Retrospective Cohort Study

title: Long-Term Care Resident Transfer to the Emergency Department

contributor:
Costa, Andrew
Health Research Methodology

subject:
Long-term Care
Older Adults
Emergency Department
Retrospective Cohort Study

abstract:
Introduction: Long term care (LTC) residents require complete or extensive support, including 24-hour nursing and personal care. LTC residents contribute a greater number of emergency department (ED) visits when compared to community-dwelling older adults. Little is known about which resident-level characteristics at admission are predictive of LTC resident transfer to the ED. The objective of this thesis was to identify which admission characteristics are associated with ED transfers in Ontario, Canada.
Methodology: I conducted a population-level retrospective cohort study using the Resident Assessment Instrument Minimum Data Set Version 2.0 (RAI-MDS). The cohort included 56,433 LTC resident admission assessments from January 1, 2017, to December 31, 2018. Logistic regression and 10-fold cross-validation were used to identify adjusted associations between characteristics routinely collected during LTC admission assessment and ED transfers. Model performance was assessed using the area under the receiver operating characteristics curve (AUC). Outcomes of interest included any ED use, potentially preventable, and low acuity ED transfers.
Results: A recent change in medical orders, previous ED visitation, female sex, the presence of an indwelling catheter, and the need for oxygen therapy were informative predictors for any, potentially preventable, and low acuity ED transfers. Deterioration in cognitive status and change in behavior was influential to any ED transfers only. Urinary tract infections, pneumonia, indictors of delirium, and change in mood are unique to potentially preventable ED transfers, and antibiotic resistance is unique to low acuity ED transfers. Similar discrimination was reached for any ED use (AUC = 0.630), potentially preventable transfers (AUC = 0.659), and low acuity transfers (AUC = 0.645).
Conclusion: The factors associated with ED transfers may be modifiable, and closer attention to these factors may help reduce ED transfers. Although the discriminability of the models was poor, advanced knowledge of informative characteristics can support upstream decision-making for clinicians. Future studies are required to validate these findings, derive risk scales, and demonstrate the utility of this model in health service planning.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Long term care (LTC) provides residents with 24-hour nursing and personal care. When the care or clinical needs of the resident cannot be met in the LTC facility, they may be transferred to the Emergency Department (ED). However, the ED’s are poorly situated to manage the distinct needs of older adults, given the sole focus on medical acuity rather than geriatric complexity. Unwarranted ED transfers are burdensome for LTC residents and increase their risk for adverse health events, such as nosocomial infections, delirium, and injuries. Understanding characteristics associated with ED transfers can help identify which residents may be at a risk of an ED transfer. The objective of this thesis was to identify which LTC resident characteristics at admission are associated with ED transfers in Ontario, Canada. A recent change in medical orders, previous ED visitation, female sex, the presence of an indwelling catheter, and the need for oxygen therapy were informative predictors for ED transfers.


title: An Interpretation of Biological Development

contributor:
Arthur, Richard
Philosophy

abstract: The research programs and practices used to address biological problems are often grounded in the way one interprets biological organisms.  There is a practical motive to explain organismic development in terms of genes and the environments in which genes are expressed.  This interpretation presupposes that organisms are simply gene environments.  In this way, genes either control the outcome of development or contain information that specifies particular outcomes.  In either case, development is basically a problem to be resolved through an increased understanding of genes and the ways genes are expressed.  This interpretation fails to adequately explain the process by which complex form is generated.  Therefore, there are grounds for rejecting it.  An approach centred around the whole organism directs attention towards its many constituents and requires that one take seriously the role of multiple organismic elements in order to adequately explain development.

abstract: Thesis

abstract: Master of Philosophy (MA)


title: The Nernst-Planck-Poisson Reactive Transport Model for Concrete Carbonation and Chloride Diffusion in Carbonated and Non-carbonated Concrete

contributor:
Razaqpur, A. Ghani
Civil Engineering

subject:
Chloride
Concrete durability
Carbonation
Nernst-Planck-Poisson model
Reactive transport
Combined carbonation and chloride
Finite element
NPP
Diffusion
Electromigration
Fick’s law
Ionic activity

abstract: The intrusion of chlorides and carbon dioxide into a reinforced concrete (RC) structure can initiate corrosion of the reinforcing steel, which, due to its expansive nature, can damage the structure and adversely affects its serviceability and safety. Corrosion will initiate if at the steel surface the concrete free chloride concentration exceeds a defined limit, or its pH falls below a critical level. Hence, determination of the time to reaching these critical limits is key to the assessment of RC structures durability and service life. Due to the ionic nature of the chlorides and  the bicarbonate anion (HCO3-) formed by the CO2 in the multi-ionic pore solution, the transport of both species is driven by Fickian diffusion combined with  electromigration and ionic activity, which can be mathematically expressed  by the Nernst-Planck-Poisson (NPP) equations. For a complete representation of the phenomenon, however, the NPP equations must be supplemented by the relevant chemical equilibrium equations to ensure chemical balance among the various species within the concrete pore solution. The combination of NPP with the chemical equilibrium equations is often termed the NPP reactive transport model. In this study, such a model is developed, coded into the MATLAB platform, validated by available experimental data, and applied to analyze the time-dependent concrete carbonation and the movement of chlorides in carbonated and non-carbonated concrete. The results of these analyses can be used to predict the time to corrosion initiation. The transient one-dimensional governing equations of NPP are numerically solved using the Galerkin’s finite element formulation in space and the backward (implicit) Euler scheme in the time domain. The associated system of chemical equilibrium equations accounts for the key homogeneous and heterogeneous chemical reactions that take place in the concrete during carbonation and chlorides transport. At each stage of the analysis, the effects of these reactions on the changes in the pore solution chemical composition, pH, cement chloride binding capacity, concrete porosity, and the hydrated cement solids volumetric ratio are determined. The study demonstrates that given accurate input data, the presently developed NPP reactive transport model can accurately simulate the complex transport processes of chlorides and CO2 in concrete as a reactive porous medium, and the ensuing physical and chemical changes that occur due to the reaction of these species with the pore solution and the other cement hydration products.  This conclusion is supported by the good agreement between results of the current analyses with the corresponding available experimental data from physical tests involving carbonation, and chloride diffusion in non-carbonated and carbonated concrete.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Electrically conductive hollow fiber membrane development: addressing the scalability challenges and performance limits of conductive membrane fabrication

contributor:
Latulippe, David
de Lannoy, Charles
Chemical Engineering

subject:
Electrically conductive membranes
Hollow fiber membranes
Carbon nanotube coatings
Crossflow deposition

abstract: Electrically conductive membranes (ECMs) are of significant research interest for their ability to mitigate fouling, enhance separation capacity, and induce electrochemical degradation of contaminants. Most ECM development has been in flat sheet format suitable for laboratory studies; in industrial applications, formats such as hollow fiber (HF) are preferred for their high packing density. While ECMs in HF format are emerging in research, these techniques typically employ the same methods proven for flat sheet, often involving direct deposition of conductive material onto a support membrane with no further investigation into how the deposition process affects ECM properties. This is a significant challenge for long (~1 m) HF membranes where coating uniformity is essential to ensure consistent performance. The goal of this project was to fabricate conductive HF membranes, ensuring uniform performance along the fiber. In this work, we have developed a “crossflow deposition” technique to deposit a uniform layer of single walled/ double walled carbon nanotubes (SW/DWCNTs) onto the interior surface of commercial polyether sulfone HF membranes. In a design-of-experiments model, feed pressure and crossflow velocity were shown to directly impact composite membrane conductivity and permeability. The highest permeability (~2900 LMH/bar) and conductivity (~670 S/m) were both achieved at the high pressure (0.2 bar) and high crossflow velocity (1.06 cm/s) condition. An inverse relationship was identified between conductivity and permeability for 29 different HF membranes coated under various flow and particle loading conditions. Similar trends were evident in ECM literature when comparing 80 membranes across 38 papers, covering various conductive materials, separation types, configurations, and applications. Metallic-based ECMs outperformed graphitic nanomaterial or conductive polymer-based ECMs with conductivities three orders of magnitude higher. This review also revealed a wide variation in performance testing with 35 unique pollutants in 63 total tests, indicating a need for standardization to accurately compare ECMs and a need for testing with more realistic feed sources. Finally, electrochemical degradation of methyl orange using the CNT-coated HF membranes was evaluated in batch and continuous removal experiments. Although no significant MO removal was detected in either configuration, these modules can be used for further optimization in terms of targeted conductivity, contact time, and electrochemical parameters such as applied voltage. This work highlights the existence of a conductivity/ permeability trade-off in ECM development and how manipulation of flow parameters during deposition can impact this trade-off in HF membrane development.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Membrane separation technologies are a common purification strategy in many fields due to their simplicity and low energy requirements. Membranes operate by rejecting particles from feed water based on their chemical or physical properties such as size or charge. Long-term membrane operations are limited by fouling, incurring large operating costs for frequent cleaning cycles and downtime. Furthermore, traditional membrane separations only physically remove particles, presenting a risk for contaminant re-introduction into the environment. Electrically conductive membranes are an emerging strategy for addressing these concerns due to their demonstrated antifouling, enhanced selectivity, and redox capabilities. To date, these membranes have almost exclusively been developed as flat sheets with limited research into other membrane formats. Hollow fiber membranes resemble thin tubes ~1 mm in diameter and up to ~1 m in length where filtration occurs through the tubular wall of the fiber; the small diameter allows for hundreds of fibers to pack into an individual module, thus maximizing throughput. In this thesis, several issues with hollow fiber conductive membrane fabrication are addressed to ensure consistent performance along the length of the fiber. A key trade-off between membrane surface conductivity and throughput was found to exist universally in the conductive membrane field. This knowledge can be used to select fabrication methods and parameters to target certain performance ranges.


title: Internalizing and Externalizing Problems in Children with ASD, ADHD, and OCD: Identifying Behavioural Profiles Within and Across Diagnostic Categories

title: Behavioural Profiles Within and Across ASD, ADHD, and OCD

contributor:
Georgiades, Stelios
Hall, Geoffrey
Neuroscience

subject:
internalizing behaviours
externalizing behaviours
behavioural phenotypes
Autism
ASD
ADHD
OCD
neurodevelopmental disorders

abstract: Updated: Current version includes the name of Supervisor, and Co-supervisor. Error corrected in preliminary pages.

abstract:
Background: Emerging evidence suggests that there is both within-disorder heterogeneity and across-disorder overlap in the clinical presentation of children with ASD, ADHD, and OCD. Two prevalent dimensional phenotypes in children with these NDDs that warrant close attention, and are suitable for cross-disorder investigation, are internalizing and externalizing problems.
Objectives: The current study uses a data-driven, diagnosis-agnostic approach to identify homogenous clusters that describe behavioural profiles of internalizing and externalizing problems within and across ASD, ADHD, and OCD.
Methods: Data on 1565 children (M = 10.76 years) were drawn from the Province of Ontario Neurodevelopmental Disorder (POND) Network. Non-hierarchical clustering approaches were used to empirically derive, distinct behavioural profiles of internalizing and externalizing problems indexed by the Child Behavior Checklist (CBCL). Empirically derived groups were characterized using measures of adaptive functioning indexed by the Adaptive Behaviour Assessment (ABAS-II), and interpreted in relation to original diagnoses.
Results: Cluster analyses identified four distinct behavioural profiles that cut across all diagnostic groups: High Internalizing Externalizing (HIE; 15%), High Externalizing (HE; 21%), Low Internalizing Externalizing (LIE; 38%), and Low Externalizing (LE; 26%). Derived clusters had variable levels of adaptive behaviours and reflected different behavioural profiles than the ones defined by the original diagnostic category groups of ASD, ADHD, and OCD.
Conclusion: Data-driven, diagnosis-agnostic approaches can inform our understanding of the between and within phenotypic heterogeneity seen in ASD, ADHD, and OCD. Empirical ways of classifying children with homogeneous behavioural profiles may complement existing diagnostic models in our efforts to develop cross-disorder, more personalized interventions for children with neurodevelopmental disorders.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: ASD, ADHD, and OCD are heterogenous neurodevelopmental disorders (NDDs) with some overlapping clinical characteristics and etiological factors. Internalizing and externalizing behavioural problems persist across these three NDDs, and in this study, are used to identify unique behavioural profiles. Study findings reveal four groups with distinct behavioural profiles of internalizing and externalizing problems that are not identified by the original diagnostic groups. This empirical way of classifying children with similar behavioural profiles can be used in combination with diagnostic labels to enhance transdiagnostic interventions that can be tailored to each child’s needs.


title: Biomechanical and Medical Imaging Investigation of the Effects of Bicycling on the Knee Using Computational Methods

title: EFFECTS OF BICYCLING ON THE KNEE: A COMPUTATIONAL STUDY

contributor:
Maly, Monica R
Rehabilitation Science

subject:
Knee
Osteoarthritis
Biomechanics
Magnetic Resonance Imaging
Machine Learning
Bicycling
Deep Learning

abstract:
Knee osteoarthritis (OA) is a global problem that causes joint pain and decreased mobility and quality of life. Knee OA costs the Canadian economy billions of dollars.  Cartilage and bone are both implicated in knee OA pathogenesis.  Obesity is a major risk factor for knee OA.  Physical activity decreases pain and improves quality of life in those with knee OA.  Nonetheless, we have limited biomechanical evidence to create concrete recommendations for prescription of aerobic exercise that improves clinical outcomes without exacerbating pain or worsening joint structures in knee OA.  We have a limited understanding of how cartilage of the OA knee responds to physical activity, and the role of bone shape on the response.

This thesis fills four identified gaps in the literature.  First, Chapter 2 used a fully-crossed random assignment study design where 40 healthy participants completed 18 bicycling positions to define novel equations for setting bicycle saddle position based on minimum or maximum knee flexion angle.  This work is important because the current gold-standard of setting bicycle saddle position for mitigating injury focuses on a desired knee flexion angle; yet no easy methods exist.  Second, Chapter 3 used the same dataset to identify how joint kinematics affect tibiofemoral and patellofemoral joint forces during bicycling.  This work showed joint forces are least sensitive to the gold standard bicycle-fit parameter, minimum knee flexion angle; instead, minimum hip flexion angle was the most important.  Third, Chapter 4 describes and validates a multi-stage convolutional neural network framework for efficiently segmenting cartilage and bone from magnetic resonance imaging data.  The algorithm produced state-of-the-art predictions on the commonly tested Osteoarthritis Initiative dataset in an average of 1.5 mins per knee.  These methods will be crucial for improving experimental and epidemiologic studies of cartilage and bone.  Fourth, Chapter 5 combines statistical shape models of the tibia and femur, joint forces estimated at the knee, and statistical parametric mapping to explore continuously over the cartilage surface how cartilage deforms after walking and bicycling.  This study showed for the first time that the acute response of cartilage in women with symptomatic knee OA is dependent on bone shape and knee joint forces.

The bicycle-fit related studies provide the first comprehensive insights into how lower limb joint kinematics affect knee joint forces and provide novel equations to use this knowledge to easily set bicycle saddle position in the clinic, bicycle shop, or at home.  The image analysis chapter describes an image segmentation framework that excels when applied to the knee.  The final chapter integrates biomechanical measures with statistical shape models using custom data processing pipelines that yielded new insights and that hold great potential for evoking novel and specific findings about knee OA pathophysiology at the intersection of bone, cartilage, and mechanics.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Hardware Assertions for Mitigating Single-Event Upsets in FPGAs

contributor:
Nicolici, Nicola
Electrical and Computer Engineering

subject:
single-event upsets
reliability
Boolean satisfiability
fault tolerance
FPGA

abstract:
The memory cells used in modern field programmable gate arrays (FPGAs) are highly
susceptible to single event upsets (SEUs). The typical mitigation strategy in the industry is some form of hardware redundancy in the form of duplication with comparison (DWC) or triple modular redundancy (TMR). While this strategy is highly effective in masking out the effect of faults, it incurs a large hardware cost. In this thesis, we explore a different approach to hardware redundancy. The core idea of our approach is to exploit the conflict-driven clause learning (CDCL) mechanism in modern Boolean satisfiability (SAT) solvers to provide us with
invariants which can be realized as hardware checkers. Furthermore, we develop the algorithms required to select a subset of these invariants to be included as part of a checker circuit. This checker circuit then augments the original FPGA design. We find which look-up table (LUT) memory cells are sensitive to bitflips, then we automatically generate a checker circuit consisting of hardware invariants targeted towards those faults. We aim to reach 100% coverage of sensitizable faults. After extensive experimentation, we conclude that this approach is not competitive with DWC with respect to hardware area. However, we demonstrate that many bitflips will have reduced a detection latency compared to DWC.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Comparison of Structure, Properties and Wear Performance of Coatings Applied by HiPIMS and CAE PVD Deposition Methods During the Machining of Difficult-to-Machine Alloys

contributor:
Veldhuis, Stephen
Mechanical Engineering

subject:
Machining
Physical Vapor Deposition
High Power Impulse Magnetron Sputtering
Inconel
Stainless Steel
Coating

abstract:
High Power Impulse Magnetron Sputtering (HiPIMS) comes as a new and promising PVD method for the development of high-performance coatings for cutting applications. This technique utilizes high energy and ionization which can produce a denser and stronger ceramic in comparison to traditional deposition techniques. Important coating characteristics that arise from this method such as enhanced hardness, adhesion, and less defects, can be applied when machining hard-to-cut materials. In this study, investigation of tool life and wear mechanisms, mechanical and physical properties of AlTiN coatings deposited on carbide tools by HiPIMS and Cathodic Arc Evaporation (CAE) were analyzed when machining Inconel 718 and Stainless Steel 304. Experimental turning tests were performed to evaluate tool life, and the wear mechanisms were analyzed by optical and scanning electron microscopy. Nanohardness, scratch test, fracture toughness and other methods were carried out to evaluate the coating properties. Impedance experiments were performed to determine the coating porosity and resistance to corrosion.
The results showed that HiPIMS coating presented higher hardness, toughness to fracture and adhesion to the substrate in comparison to CAE coatings. The HiPIMS coated tool substantially improved tool life when machining Inconel. The dominant wear mechanism found was abrasion, which is induced by the presence of hard carbides. The main wear patterns observed were flank, notch, and crater wear. The tool performance of HiPIMS was found to have enhanced mechanical properties, lower porosity, and form a larger amount of tribo-oxides when machining, in comparison to CAE.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Improvements on an Adhesiometer Design That Imitates High Stress/Temperature Conditions Typical of Machining

contributor:
Veldhuis, Stephen C.
Mechanical Engineering

subject: Adhesiometer

subject: tribometer

subject: friction

subject: 1045

subject: ti64

abstract:
The objective of this work was to develop a new method for establishing the coefficient of friction for the machining conditions found on the rake face of a cutting tool. Critical aspects include the high pressures and high temperatures in the cutting zone. Using the base of an existing High-load High Temperature tribometer an adaptation referred to as a double-sided pin was implemented. The objectives were two-fold to improve the repeatability of the measurements and reduce the setup time by simplifying the alignment problems experienced on the previously used system.
The concept of the new setup is to press a double-end spherical pin made of the tool material between two flat surfaces made of workpiece material and rotating it using a string connected to a slider module. The normal load applied, the friction force needed to rotate the pin together with the temperature provided by a welder are then gathered and with the measurements of the imprints the coefficient of friction under specific loads can be established.
This work also studied the impact on the tests of pin radius and roughness of the pin surface in order to stablish the measurement limitations and conditions for a successful test.
Roughness of the pin had a significant impact on coefficient of friction results. Pins with roughness values around Ra = 0.5 demonstrated half the values of coefficient of friction than pins with Ra = 0.05. This was due the wear and the penetration of the pin into the workpiece sample material. The increase in pin dimensions facilitated testing on softer materials like AISI 1045. It was found to avoid seizure conditions but could not achieve pressures typical of machining difficult to cut materials like Ti-6Al-4V. The increase in pin size also helped in developing an understanding of how to measure the temperature at the contact zone between the pin and disk. Final testing showed a system repeatability of 8% was achieved with setup time reduced by approximately five times.

abstract: Thesis

abstract: Master of Science in Mechanical Engineering (MSME)


title: The Development and Application of In Situ NMR Methods for Lithium-Ion Batteries

contributor:
Goward, Gillian R.
Chemistry and Chemical Biology

subject:
In Situ NMR
Solid-State NMR
Magic-Angle Spinning
Silicon

abstract:
This body of work is tackling some of the challenges in the field of lithium-ion
batteries (LIBs) for electric vehicles through in situ nuclear magnetic resonance
(NMR). In situ NMR allows for the simultaneous monitoring of both liquid and
solid components (electrolyte, cathode, anode, separator) and provides timely
data acquisition making it a great method to extract real-time information
about structural changes, degradation products and failure mechanisms in
batteries.
A combined in situ 7Li NMR and ex situ 29Si magic-angle spinning (MAS)
NMR study on silicon and silicon monoxide was used to compare structural
differences in these anode materials using a custom-made in situ cell. Some
key differences between the two materials were obtained, highlighting the
importance of in situ NMR to be used for identifying phases, which are not
present under ex situ conditions. In addition, fast charging of silicon anodes was
investigated to gain a better understanding of their performance at high current
rates. Magnetic resonance imaging was also implemented to localize lithium
metal deposition under these conditions, which was made possible by a unique
in situ parallel-plate resonator setup. Finally, the successful development of a
novel in situ MAS NMR technique is introduced, which for the first time allows
for an in situ analysis of a LIB under MAS. This strategy paves the way toward
acquisition of valuable in situ data on the formation and transformations of
metastable states within the active materials of both electrodes; data that is
difficult to obtain from static in situ NMR experiments alone.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Polymer-grafted Cellulose Nanocrystals and their Incorporation into Latex-based Pressure Sensitive Adhesives

contributor:
Cranston, Emily
Hoare, Todd
Chemical Engineering

subject:
Cellulose nanocrystals
Polymer-grafting
Emulsion polymerization
Pressure sensitive adhesives
SI-ATRP
latex nanocomposites

abstract:
This thesis investigates the effect of reaction media on the efficiency of grafting hydrophobic polymers from cellulose nanocrystals (CNCs) via surface-initiated atom transfer radical polymerization (SI-ATRP), with the goal of producing highly-modified CNCs for incorporation into latex-based pressure sensitive adhesives (PSAs). A latex is a dispersion of polymer particles in water made by emulsion polymerization; latexes are commonly used in paints, coatings, elastomers, inks/toners, household products, cosmetics, and adhesives. However, latex-based PSAs often underperform compared to their organic solvent-polymerized counterparts due to a lack of cohesive strength in the cast latex films. The environmental benefit of using latex-based PSAs synthesized in water is significant, but the development of strategies to improve their performance are required.
CNCs are hydrophilic rod-shaped nanoparticles with high mechanical strength. Adding CNCs to latex-based PSAs has been shown to improve both adhesive (i.e., tack and peel strength) and cohesive (i.e., shear strength) properties and offers a degree of sustainability because CNCs are derived from natural cellulose sources such as wood pulp. However, their hydrophilicity, particularly relative to the hydrophobic polymers used in PSAs, has constrained CNCs to the continuous (i.e., water) phase of the latex. To improve CNC compatibility with the dispersed (i.e., polymer) phase and improve their distribution in cast latex films, hydrophobic polymers can be grafted from CNCs. However, CNCs with a high polymer graft density are required to ensure their compatibility with monomers/polymers during latex synthesis.
To begin, grafting poly(butyl acrylate) (PBA) from CNCs using SI-ATRP in polar dimethylformamide (DMF) versus non-polar toluene was directly compared. The enhanced colloidal stability of initiator-modified CNCs in DMF led to improved accessibility to surface initiator groups during polymer grafting. As such, PBA-grafted CNCs produced in DMF had up to 30 times more grafted polymer chains than PBA-grafted CNCs produced in toluene.  The PBA-grafted CNCs produced in DMF showed high contact angles when cast in a film and formed stable suspensions in toluene. This work highlights that optimizing CNC colloidal stability in a given solvent prior to polymer grafting is a more crucial consideration than solvent–polymer compatibility in the context of obtaining high graft densities and thus hydrophobic CNCs via SI-ATRP.
The improved polymer grafting method in DMF was then used to produce PBA and poly(methyl methacrylate) (PMMA)-grafted CNCs at two polymer chain lengths. Polymer grafted CNCs were incorporated in situ during a seeded semi-batch emulsion polymerization to produce PBA latex nanocomposite PSAs. Viscosity measurements revealed significant differences between latexes prepared with CNCs versus polymer-grafted CNCs, with the lower viscosities of the latter suggesting their incorporation inside the polymer particles. When CNCs with short polymer grafts were introduced into PSAs at 1 wt. % loading, they exhibited comparable tack and improved peel strength compared to unmodified CNCs (and all properties improved relative to the base latex without any CNCs). This is attributed to their improved distribution throughout the PSA, the enhanced wettability of the substrate with the CNC containing latex, and the increased polymer chain mobility achieved based on the low molecular weight of the grafts. CNCs with long polymer grafts aggregated in the latex and did not improve PSA properties. PMMA-grafted CNCs slightly outperformed PBA-grafted CNCs likely due to the higher glass transition temperature of PMMA. These results provide insight into future optimization of more sustainable latex-based PSA formulations as well as new commercial CNC-latex products, where the presence of low molecular weight grafts on CNC surfaces could improve polymer mobility and tack and peel strength.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: When the adhesives used in tapes, labels or sticky notes are produced using water-based reactions, they normally underperform compared to conventional adhesives produced using toxic solvents. To improve such water-based adhesives, adding nanocellulose (tiny particles derived from wood pulp) during synthesis has been shown to be an asset. Nanocellulose can be chemically modified to improve its compatibility with adhesive ingredients, and thus change the role of nanocellulose during adhesive manufacturing. In this thesis, modified nanocelluloses were added to water-based adhesives to evaluate their effect on performance (i.e., strength and stickiness). It was found that the reaction conditions during nanocellulose modification were crucial for obtaining highly modified particles that are compatible with adhesive ingredients. This work aims to provide insight for future production of less environmentally taxing adhesives made in water and expand the use of nanocellulose in new commercial products.


title: Community-Based, Slow-Stream Rehabilitation, Hospital-To-Home Transition Program for Older Adults

contributor:
Dal Bello-Haas, Vanina
Rehabilitation Science

subject:
Older Adult
Slow-Stream Rehabilitation
Community-Based
Hospital-to-Home Transition
Program Evaluation

abstract:
Current models of hospital-to-home transitions for older adults do not typically include a rehabilitation perspective, which led to the endeavor of this thesis. Chapter 2 (Paper 1) is a scoping review that summarized current literature related to slow-stream rehabilitation (SSR) for older adults. Chapter 3 (Paper 2) was a descriptive prospective cohort study that examined frequency, intensity, type and time (FITT) parameters for cardiovascular and resistance exercises completed by older adult participants in a community-based, SSR, hospital-to-home transition program; and to compare FITT parameters of completed exercises to established guidelines. Chapter 4 (Paper 3) was a qualitative study that examined perspectives of those working in or referring to the community-based, SSR, hospital-to-home transition program to identify factors that act as barriers or facilitators to successful implementation and function of an enhanced, community-based, SSR, hospital-to-home transition program.
The scoping review found that SSR programs in single payer healthcare systems improved physical and functional outcomes, decreased hospital readmission and institutionalization for older adults with complex healthcare needs. SSR programs were multidisciplinary, ranged in program and session length, and only took place in institutional settings. The prospective cohort study found that older adults with complex healthcare needs participating in a community-based, SSR, hospital-to-home transition program were able to meet many of the cardiovascular and resistance frequency, intensity, and time (FIT) guideline parameters for community-dwelling older adults. Exercise interventions should be tailored to older adult needs and preferences, at the appropriate FIT to allow for functional gains. The qualitative study found the current program’s services e.g., rehabilitation, education, and nursing care were of benefit. Most of the stated barriers were at a macro or meso level and were out of the study participants’ control, while all the facilitators were at a micro level.
Community-based, SSR, hospital-to-home transition programs can serve as a holistic model of care that address identified gaps in the literature.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract:
Hospital-to-home transition care models do not often include a rehabilitation ‘lens’ which led to this thesis. Chapter 2 was a scoping review of slow-stream rehabilitation (SSR) for older adults; Chapter 3 looked at exercises older adults completed during an SSR hospital-to-home program; and, Chapter 4 studied facilitators and barriers to enhancing a current community-based, SSR, hospital-to-home program.
These studies found: 1) SSR programs in healthcare systems like Canada were geared towards older adults with many health problems, only took place in hospital or long-term care settings, and were of benefit; 2) Older adults participating in a SSR hospital-to-home program should exercise at the appropriate intensity, time and frequency to see gains in function; 3) The current program’s services e.g., rehabilitation, education, and nursing care were beneficial, but barriers to enhancing the program were out of the participants’ control.
Community-based, SSR, hospital-to-home transition models of care that include rehabilitation are very important for older adults.


title: Convergence of neurodevelopmental disorder risk genes on common signaling pathways

contributor:
Singh, Karun
Biochemistry and Biomedical Sciences

subject: Neurodevelopmental disorders

subject: BioID

subject: 15q13.3

subject: DISC1

subject: NRG1

subject: OTUD7A

subject: Dendritic spines

abstract: Neurodevelopmental disorders (NDDs) are a heterogeneous set of disorders that are characterized by early disruptions to brain development and include autism spectrum disorder (ASD), attention deficit/hyperactivity disorder (ADHD), developmental delay (DD), intellectual disability (ID), epilepsy and schizophrenia (SZ). Although thousands of genetic risk variants have been identified, there is a lack of understanding of how they impact cellular and molecular mechanisms that underlie the clinical presentation and heterogeneity of NDDs. To investigate this, we used a combination of cellular, molecular, bioinformatic and omics methods to study NDD-associated molecular pathways in distinct neuronal populations. First, we studied the interaction between the high-confidence SZ risk genes DISC1 and NRG1-ErbB4 in cortical inhibitory neurons and found that NRG1-ErbB4 functions through DISC1 to regulate dendrite growth and excitatory synapses onto inhibitory neurons. Next, we studied the 15q13.3 microdeletion, a recurrent copy number variation (CNV) that is associated with multiple NDDs. Using a heterozygous mouse model [Df(h15q13)/+] and human sequencing data we identified OTUD7A (encoding a deubiquitinase) as an important gene driving neurodevelopmental phenotypes in the 15q13.3 microdeletion syndrome. Due to the paucity of literature on the function of OTUD7A in the brain, we used a proximity-labeling approach (BioID2) to elucidate the OTUD7A protein interaction network (PIN) in cortical neurons, and to examine how patient mutations affect the OTUD7A PIN. We found that the OTUD7A PIN was enriched for postsynaptic and axon initial segment proteins, and that distinct patient mutations have shared and distinct effects on the OTUD7A PIN. Further, we identified the interaction of OTUD7A with a high-confidence bipolar risk gene ANK3, which encodes AnkyrinG. We identified decreased levels of AnkyrinG in Df(h15q13)/+ neurons, and synaptic phenotypes were rescued by increasing AnkyrinG levels or targeting the Wnt pathway. Future investigation should include examination of the role of OTUD7A deubiquitinase activity in neural development.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: Neurodevelopmental disorders result from disruptions to early brain development and include autism spectrum disorder (ASD), developmental delay (DD), epilepsy, and schizophrenia (SZ). These disorders affect more than 3% of children worldwide and can have a significant impact on an individual’s quality of life, including an increased risk of death in some cases. There is currently a lack of understanding of how these disorders develop and how to effectively treat them. Neurodevelopmental disorders are thought to arise from alterations in the connections between brain cells (neurons) and one of the major risk factors for these disorders is having certain variations in regions of the genome (DNA sequences), with more than 1000 of these risk variants having been identified so far. In this thesis, we analyzed how genetic risk factors interact in neurons to regulate neural connectivity. We discovered that risk variants found in individuals with different disorders actually work together to regulate similar processes important for neural connectivity, which suggests that distinct disorders may share a common underlying cause. Additionally, we established the importance of a new ASD risk gene and discovered that it interacts with other known risk genes to regulate neural connectivity. This thesis provides new insights into the  processes in the brain that lead to neurodevelopmental disorders and has implications for future development of effective therapies for individuals affected by these disorders.


title: Experiences of Caregivers of Older Persons with Delirium Superimposed on Dementia in Acute Care Hospitals: An Interpretive Description Study

contributor:
Ploeg, Jenny
Nursing

subject:
nursing
delirium superimposed on dementia
caregivers

abstract:
Background: Delirium superimposed on dementia (DSD) is a highly prevalent, yet difficult to recognize problem in hospitals. Delirium is a disturbance in cognition often seen in persons aged 65 and older. DSD occurs when a person living with dementia (PLWD) also develops delirium. DSD is a highly distressing experience for caregivers.
Aims: This study aims to explore the experiences of caregivers of older persons with DSD in acute care hospitals; their role in the detection and management of DSD; and the type of support they require during this experience. The knowledge generated from this study can be used to identify strategies to assist caregivers during their experience, and to improve the early detection and management of DSD, with the aim to improve health outcomes for both the hospitalized older person with DSD and the caregiver.
Methods: Thorne’s interpretive description method was used. In-person, semi-structured interviews were conducted with nine caregivers of older persons with DSD who were hospitalized in four medicine units. Interviews were transcribed and thematic analysis was conducted.
Results: The following themes related to caregivers’ experiences were identified: (a) caregivers found DSD to be an overwhelming experience, (b) caregivers were concerned about the quality of care that the older person received, (c) caregivers’ experiences were influenced by the nature of their relationship with the health care team, and (d) caregivers can play an important role in the detection and management of DSD.
Conclusion: Findings provide guidance in increasing support and building collaborative relationships between caregivers and the health care team. Recommendations on delivering caregiver-centred care to caregivers of older persons with DSD are outlined.

abstract: Thesis

abstract: Master of Science in Nursing (MSN)


title: Contaminants of Emerging Concern in Groundwater Polluted by Historic Landfills: Leachate Survey and Stream Impact Assessment

contributor:
Smith, James
Roy, James
Earth and Environmental Sciences

subject:
contaminant hydrogeology
groundwater-surface water interaction
contaminants of emerging concern

abstract: Many types of contaminants of emerging concern (CECs), including per- and poly-fluoroalkyl substances (PFAS), have been found in leachate of operating municipal landfills. However, information on CECs in leachate of historic landfills (≥3 decades since closure, often lacking engineered liners or leachate collection systems) and the related risk posed from groundwater plumes discharging to nearby aquatic ecosystems is limited. In this study, 48 samples of leachate-impacted groundwater were collected from 20 historic landfills in Ontario, Canada. The CECs measured included artificial sweeteners (ASs), PFAS, organophosphate esters (OPE), pharmaceuticals, bisphenols, sulfamic acid, perchlorate, and substituted phenols. Several landfills, including ones closed in the 1960s, had total PFAS concentrations similar to those previously measured at modern landfills, with a maximum observed here of 12.7 μg/L. Notably elevated concentrations of several OPE, cotinine, and bisphenols A and S were found at many 30-60 year-old landfills. There was little indication of declining concentrations with landfill age, suggesting historic landfills can be long-term sources of CECs to groundwater. A full-year field study was performed on a 0.5-km reach of an urban stream receiving contaminated groundwater from nearby historic landfills. Elevated concentrations of ammonium, the AS saccharin, an indicator of old landfill leachate, and CECs (e.g., maximum total PFAS of 31 μg/L) in the shallow discharging groundwater were relatively stable across the seasons but were spatially restricted by hyporheic exchange and discharge of other groundwater. This indicates a patchy but long-term exposure for endobenthic organisms, which are rarely monitored. Stream water concentrations were more dilute, but increased markedly across the landfill stretch, and showed signs of increases in winter and after rain/snowmelt events. These findings provide guidance on which CECs may require monitoring at historic landfill sites and suggest how landfill monitoring programs could be improved to fully capture the risk to receiving water bodies.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Historic landfills are a known source of groundwater contamination. This study investigated whether these landfills contain new groups of chemicals, called contaminants of emerging concern (CECs), which are suspected to pose serious environmental and human health risks. This study found many CECs at high concentrations in most of the 20 historic landfill sites investigated, even those closed up to 60 years. A full-year investigation at one historic landfill site showed that organisms living in the sediments of a nearby stream are exposed to high concentrations all year long. Concentrations in the stream increased as it flowed past the landfill, and may be higher in winter and after rains, times monitoring is rarely done. The elevated concentrations of harmful contaminants in this water are potentially threatening the stream ecosystem. Operators of historic sites should consider testing for CECs and ensure that monitoring strategies accurately evaluate the risk posed to the environment.


title: Molecular Mechanisms of Allosteric Inhibition in Cylic-Nucleotide Dependent Protein Kinases

title: Allosteric Inhibition in Protein Kinases

contributor:
Melacini, Giuseppe
Biochemistry and Biomedical Sciences

subject:
Allostery
Protein-Ligand Interactions
Cell Signalling
Kinase Inhibition
Protein Dynamics
Cyclic Nucleotides
NMR Spectroscopy
Ensemble Allosteric Model

abstract: Allosteric inhibition of kinases provides high selectivity and potency due to lower evolutionary pressure in conserving allosteric vs. orthosteric sites. The former are regions distinct from the kinase active site, yet, when perturbed through allosteric effectors, induce conformational and/or dynamical changes that in turn modulate kinase function. Protein kinases involved in cyclic nucleotide signalling are important targets for allosteric inhibition due to their association with diseases, from infections to Cushing’s syndrome. This dissertation specifically focuses on elucidating the molecular mechanism of allosteric inhibition in the cAMP-dependent protein kinase (PKA) and the Plasmodium falciparum cGMP-dependent protein kinase (PfPKG), which are targets for a generalized tumor predisposition commonly referred to as Carney Complex and for malaria, respectively.  In chapters 2 and 3, we focus on the agonism-antagonism switch (i.e. allosteric pluripotency) observed as the phosphorothioate analog of cAMP, Rp-cAMPS (Rp), binds to PKA. Utilizing Nuclear Magnetic Resonance (NMR), Molecular Dynamics (MD) simulations and Ensemble Allosteric Model (EAM), we determined that two highly homologous cAMP-binding domains respond differently to Rp, giving rise to a conformational ensemble that includes excited inhibition-competent states. The free energy difference between this state and the ground inhibition-incompetent state is tuned to be similar to the effective free energy of association of the regulatory (R) and catalytic (C) subunits, leading to allosteric pluripotency depending on conditions that perturb the R:C affinity. The general significance of these results is a re-definition of the concept of allosteric target to include not only the isolated allosteric receptor, but also its metabolic and proteomic sub-cellular environment. In chapter 4, we utilize a mutant that silences allosteric pluripotency to reveal that the agonism-antagonism switch of PKA not only arises from the mixed response of tandem domains, but also from the mixed response of allosteric regions within a single domain that mediates interactions with Rp. In chapter 5, the allosteric inhibition of PfPKG associated with malaria is induced through base-modified cGMP-analogs and the underlying inhibitory mechanism is determined. We show that, when bound to a PfPKG antagonist, the regulatory domain of PfPKG samples a mixed intermediate state distinct from the native inhibitory and active conformations. This mixed state stabilizes key cGMP-binding regions, while perturbing the regions critical for activation, and therefore it provides an avenue to preserve high affinity, while promoting significant inhibition. Overall, in this thesis, previously elusive mechanisms of allosteric inhibition were elucidated through the combination of NMR, MD, and EAM methods. Through this integrated approach, we have unveiled an emerging theme of inhibitory ‘mixed’ states, either within a single domain or between domains, which offer a simple but effective explanation for functional allostery in kinases.

abstract: Thesis

abstract: Candidate in Philosophy


title: DESIGN, ANALYSIS, AND REPORTING OF PILOT STUDIES IN HIV

contributor:
Mbuagbaw, Lawrence
Health Research Methodology

subject:
Pilot Study
Feasibility Study
HIV
AIDS
Key populations

abstract:
Pilot studies, a subset of feasibility studies, are essential in determining the feasibility of a larger study. This is especially true when targeting populations that are difficult to recruit, such as people with HIV. Designing high quality pilot studies can help limit waste by informing researchers how to proceed.

We conducted a meta-epidemiological review of pilot studies in the HIV literature published until November 25, 2020 using Medline, Embase and Cochrane Controlled Register of Trials (CENTRAL). We extracted bibliometric information, including the region and income of the country where the study was conducted, study design, using the pilot label, source of funding, nature of intervention, whether feasibility was the primary objective, progression criteria, protocol registration and sample size estimation. We used descriptive analysis to evaluate how pilot studies are designed and conducted, the outcomes assessed and how are they defined.

Our search retrieved 10,597 studies, of which 248 were included in our final review. The number of pilot studies has increased with time, with 25, 55, and 44 HIV studies published in 2018, 2019, and 2020, respectively. We found that 128 studies (70.39%) used the pilot or feasibility labels in their title, however 20.31% used these titles interchangeably. 5 studies in this review included progression criteria, all of which were published in 2020. Sample size estimation was only found in 59 studies (23.9%).

Pilot studies in the HIV literature are mislabeled. Sample size estimations are seldom included, and progression criteria are used. Formal guidance on the design and reporting of pilot studies in the HIV literature is necessary.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Pilot studies are important in evaluating whether planned larger studies can be conducted. They are particularly useful in the field of HIV where participants may be hard to identify and recruit. However, there are few instructions on how pilot studies in HIV should be designed. We searched the literature to see the current state of HIV pilot studies, including how they are designed, and their findings reported. We found that pilot studies are becoming more popular in the HIV field. However, there were gaps in how these studies are designed and reported. Studies were often mislabeled as pilots when they were not, the pilot study criteria were applied inconsistently and the outcomes that were evaluated were often poorly defined and their information poorly presented. Pilot studies in HIV can be reported better.


title: Costs and Benefits of Shared Mobility in a Suburban Context:  The Impact of Powertrain Technology

contributor:
Razavi, Saiedeh
Mohamed, Moataz
Civil Engineering

subject:
suburban mobility
shared mobility
fleet composition
cost evaluation

abstract:
Emerging technologies and business models have contributed to the improvement of transportation systems and services towards a more sustainable approach to mobility. Shared mobility has become widespread as a viable solution to the increasing demand for transportation. Many cities worldwide have implemented shared mobility service and demonstrated that it could offer numerous environmental and operational benefits. However, their implementation in rural and suburban areas that feature lower population density and dispersed travel demand is not receiving the same attention.
This research considers four suburban communities to evaluate the operation of a fleet of shared mobility as a potential substitute for the currently fix-route public transportation services.
 For each area, four scenarios were defined to consider different powertrain technologies. These scenarios include the Internal Combustion Engine, Battery Electric, and two Autonomous Electric Vehicles scenarios. While assessing the efficiency of the fleet composition system, four vehicle sizes are considered. Further, an optimized routing solution for serving the known travel demand is utilized to calculate the total cost of fleet ownership, which accounts for the purchase price, energy consumption, CO2, and driver labour costs.
The results highlight potential benefits of adopting a fleet of shared Autonomous Electric Vehicles for the case studies and show approximately 67-68% and 69-70% savings compared to a shared fleet of conventional and Battery Electric vehicles, respectively, mainly due to the omission of the driver costs. In the absence of operationally safe Autonomous Electric Vehicles, the more conservative scenario of employing a fleet of shared Autonomous Electric Vehicles with the presence of safety attendants could result in 6-8% and 13-14% savings compared to a shared fleet of conventional and Battery Electric vehicles. Nevertheless, the results indicate low utilization rates for the fleet attributed to the inconsistency in demand throughout the day. The results provided in this research can inform policymakers and service providers and be used for further evaluations of such transportation services.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: In pursuit of more equitable, sustainable, and connected transportation services in rural and suburban areas, this research investigates the quantitative benefits and costs of operating a ride-sharing service for four suburban areas located in Hamilton, Ontario. The study considers and compares several options in vehicle sizes and technologies to provide a better ground of knowledge for service providers and policymakers.


title: A Family Affair: Examining Canadian English-language News Media Portrayals of Muslim Families in the Post-9/11 Era

title: A Family Affair

contributor:
Chakraborty, Chandrima
English and Cultural Studies

subject: Muslim, Masculinity, Femininity, Multiculturalism, Race, Racism, Gender, Violence, Terror, 9/11, Canada, Heteronormativity, Orientalism, Settler-Colonialism, Family, Civility, Whiteness, News Media, Racialized, Immigration, Gender-Based Violence, Domestic Violence, Fathers, Mothers, Citizenship

abstract: This dissertation intervenes in debates in Media Studies, Gender and Sexuality Studies, Canadian Immigration Studies, and Critical Race Studies to explore how shifting news media and political representations of Muslim families reflect the complexities of what it means to be Canadian beyond holding citizenship. In the post-9/11 era, the Muslim family has re-emerged in Canadian English-language news media and Canadian political debates as a site of inherent violence. Drawing on orientalist narratives of the Muslim family, news media and political conversations tend to frame these homes as being headed by patriarchal fathers and oppressed mothers, and children seeking to break from families and traditions, yet always holding the potential to become violent themselves. Even though Canada identifies as a multicultural nation, Muslim families are often presented in media as undeserving of the rights of Canadian citizenship, and even deserving of state violence. While news media play a key role in reproducing orientalist framings of Muslim families, news media can also take the government to task when it comes to the violation of immigrant and racialized Canadians’ rights as citizens. Some news media coverage counter orientalist narratives by producing “positive” representations of Muslim families, however, these “positive” representations frequently frame Muslims who are worthy of the rights of citizenship as adhering to heteronormative family dynamics, productive citizenship, and normative Western gender roles and kinship formations. These “positive” portrayals produce varying representations of Muslim families, but such framings can also labour in the way of reifying Canada’s multicultural ideals and Canada’s idea of itself as “civilized.” Drawing on the news media coverage of the family of Maher Arar, the Khadrs, and the Shafias, I argue that such representations still produce the norms of the settler-colonial Canadian nation, where some racialized bodies, in this case Muslim families, can be granted the rights of Canadian citizenship if they are able to proximate normative Canadian kinship formations.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)

abstract: In the wake of 9/11, many Canadian English-language news media have framed Muslim men as violent and Muslim women as oppressed. This dissertation analyzes the shifting Canadian news media portrayals of the Muslim family. Muslim homes in Canada are often portrayed as spaces for the perpetuation of violence that threatens the Canadian nation. Simultaneously, news media also portray some Muslim homes as spaces of purportedly “good” Canadian citizens, if these Muslim families are able to conform to Canadian “values.” I examine how Canadian news media mobilize heteronormativity, middle-class status, productive citizenship, among others, to portray some Muslims as ascribing to Canadian values, and therefore worthy of the rights of citizenship. Drawing on the news media coverage of the cases of Maher Arar and Monia Mazigh, Ahmed and Omar Khadr and Maha Elsamnah, and Mohammed Shafia, Rona Mohammed, and Tooba Yahya, I analyze how Muslims who are viewed as not assimilating to Western ideals of family are deemed as undeserving of the rights of citizenship, and, in addition, may even deserve violence.


title: Spreading of a two-dimensional granular analogue of a liquid puddle: Predicting structure through a “granular capillary length”

contributor:
Dalnoki-Veress, Kari
Physics and Astronomy

abstract:
When granular materials accumulate at a surface (i.e. salt being poured on a table)
they will typically form a conical pile with a measurable angle of repose. Conversely,
liquids will reach a critical height, proportional to their capillary length, and spread
out across a surface. The focus of this thesis is an experiment in which adhesive
monodisperse oil droplets, in a two-dimensional con figuration, spread more similarly
to a liquid than a granular material. In a two-dimensional system, the oil droplets
accumulate at a linear barrier as opposed to a surface. Oil droplets are created in a
chamber  filled with an aqueous solution of sodium dodecyl sulfate, a surfactant, and
accumulate at a barrier, forming an aggregate. The angle of the chamber, concentration
of surfactant, and size of the droplets can be modified which in turn impacts the
effect of gravity and adhesion acting on the aggregate. By modifying these forces,
the steady-state height of the aggregate can be controlled. A parameter, we call the
"granular capillary length" is de fined, which describes the height of the aggregate
through a balance of gravity and adhesion. The "granular capillary length" provides
an analogy to the capillary length in liquids where the height of a puddle is determined
through a balance between gravity and interfacial tension.

abstract: Thesis

abstract: Master of Science (MSc)


title: Development of a Cloud-Based Dual-Objective Nonlinear Programming Model for Irrigation Water Allocation

contributor:
Baetz, Brian
Li, Zoe
Civil Engineering

subject:
Uncertainty
Optimization model
Irrigation
Cloud model
Water resource
Agriculture management

abstract: Irrigation water allocation is essential to the management of agricultural water use in irrigation districts. Many irrigation optimization models were proposed from previous studies to provide decision support for water managers. In order to capture the complex nonlinear relationships and meet different water demands, more advanced multi-objective nonlinear programming models were developed in the past decade. However, it is still a challenging task to address varies uncertainties associated with irrigation optimization. Fuzzy programming, interval programming, and chance-constrained programming can be used to quantify uncertainties in simplified formats, but none of them can represent complex uncertainty in a composite format. In this thesis, a cloud-based dual objective nonlinear programming (CDONP) model is developed by implementing a cloud modeling method in an irrigation model to address the uncertainties of reference evapotranspiration (ET0) and surface water availability (SWA). The cloud modeling method is used to generate 2,000 data samples from historical data. The results show that the generated samples are consistent with historical data. Optimized allocation schemes are provided, and the performance of the CDONP model are discussed. This is the first Canadian study that used the cloud modeling method in irrigation water allocation. This method provides a solution to quantify composite uncertainties based on limited data, which represents a unique contribution to irrigation water allocation modeling. This study provides valuable decision support for agriculture management to improve water use efficiency.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Sociocultural Dimensions to Improve Uptake of Midwifery Care in Morocco:  A Scoping Review

contributor:
McNiven, Patricia
Global Health

subject: Midwifery, Morocco, Global Health

abstract: Despite improvements in health care services there are poor perinatal outcomes in the rural and remote regions of Morocco.  A national plan was adopted as part of a WHO, UNICEF and UNFPA initiative to reduce maternal and neonatal deaths in underserviced regions.  Strengthening the profession of midwifery was identified as a key component of the initiative.  In 2008, a Moroccan framework for midwifery education, regulation and funding was established.  There is evidence that funded midwifery care is not being accessed by women in rural regions.  A scoping review was undertaken to examine the social barriers.  The review was conducted using the Arksey and O’Malley’s 2005 framework for scoping reviews.  The research stages included 1) identifying the research question; 2) identifying the relevant studies; 3) study selection; 4) charting the data; 5) collating, summarizing and reporting the results.  The aim was to identify how the socio-cultural context can impede the uptake of midwifery care and thus impact maternal and neonatal outcomes.  Language barriers, cultural differences and gender inequality were identified as key barriers that impact the acceptability of midwifery care in Morocco.

abstract: Thesis

abstract: Master of Science (MSc)


title: Use of Radar Estimated Precipitation for Flood Forecasting

contributor:
Coulibaly, Paulin
Earth and Environmental Sciences

subject:
Flood Forecasting
Weather Radar
Hydrological models
Deterministic forecast
radar‐gauge merging
WKR C‐band radar
NEXRAD Radar
Hydrology
Z-R relationship
Flood mapping
Radar QPEs
FEWS

abstract: Flooding is one of the deadliest natural hazards in the world. Forecasting floods in advance can significantly reduce the socio-economic impacts. An accurate and reliable flood forecasting system is heavily dependent on the input precipitation data. Real-time, spatially, and temporally continuous Radar Quantitative Precipitation Estimates (QPEs) is useful precipitation information source. This research aims to investigate the efficacy of American and Canadian weather radar QPEs on hydrological model calibration and validation for flood forecasting in urban and semi-urban watersheds in Canada. A comprehensive review was conducted on the weather Radar network and its’ hydrological applications, challenges, and potential future research in Canada. First, radar QPEs were evaluated to verify the reliability and accuracy as precipitation input for hydrometeorological models. Then, the radar-gauge merging techniques were assessed to select the best method for urban flood forecasting applications. After that, merged Radar QPEs were used as precipitation input for the hydrological models to assess the impact of radar QPEs on hydrological model calibration and validation. Finally, a framework was developed by integrating hydrological and hydraulic models to produce flood forecasts and inundation maps in urbanized watersheds. Results indicated that dual-polarized radar QPEs could be effectively used as a source of precipitation input to hydrological models. The radar-gauge merging enhances both the accuracy and reliability of Radar QPEs, and therefore, the accuracy of streamflow simulation is also improved. Since flood forecasting agencies usually use hydrological models calibrated and validated using gauge data, it is recommended to use bias-corrected Radar QPEs to run existing hydrological models to simulate streamflow to produce flood extent maps. The hydrological and hydraulic models could be integrated into one framework using bias-corrected Radar QPEs to develop a successful flood forecasting system.

abstract: Thesis

abstract: Doctor of Science  (PhD)

abstract: Floods are common and increasing deadly natural hazards in the world. Predicting floods in advance using Flood Early Warning System (FEWS) can facilitate flood mitigation. Radar Quantitative Precipitation Estimates (QPEs) can provide real-time, spatially, and temporally continuous precipitation data. This research focuses on bias-correcting and evaluating radar QPEs for hydrologic forecasting. The corrected QPE are applied into a framework connecting hydrological and hydraulic models for operational flood forecasting in urban watersheds in Canada. The key contributions include:  (1) Dual-polarized radar QPEs is a useful precipitation input to calibrate, validate and run hydrological models; (2) Radar-gauge merging enhance accuracy and reliability of radar QPEs; (3) Floods could be more accurately predicted by integrating hydrological and hydraulic models in one framework using bias-corrected Radar QPEs; and (4) Gauge-calibrated hydrological models can be run effectively using the bias-corrected radar QPEs. This research will benefit future applications of real-time radar QPEs in operational FEWS.


title: Interrogating Data-integrity from Archaeological Surface Surveys Using Spatial Statistics and Geospatial Analysis: A Case Study from Stelida, Naxos

contributor:
Boyce, Joseph
Carter, Tristan
Earth and Environmental Sciences

subject:
Spatial Analysis
Pedestrian Surveys
Lithics
Predictive Mapping
Empirical Bayesian Kriging
UAV survey
Structure from Motion
Erosion Mapping
RUSLE

abstract: The implementation and application of Geographic Information Systems (GIS) and spatial analyses have become standard practice in many archaeological projects.  In this study, we demonstrate how GIS can play a crucial role in the study of taphonomy, i.e., understanding the processes that underpinned the creation of archaeological deposits, in this case the distribution of artifacts across an archeological site. The Stelida Naxos Archeological Project (SNAP) is focused on the exploration of a Paleolithic-Mesolithic stone tool quarry site located on the island of Naxos, Greece. An extensive pedestrian survey was conducted during the 2013 and 2014 archeological field seasons. An abundance of lithic material was collected across the surface, with some diagnostic pieces dating to more than 250 Kya. Spatial statistical analysis (Empirical Bayesian Kriging) was conducted on the survey data to generate predictive distribution maps for the site. This study then determined the contextual integrity of the surface artifact distributions through a study of geomorphic processes. A digital surface model (DSM) of the site was produced using Unmanned Aerial Vehicle (UAV) aerial photography and Structure from Motion (SfM) terrain modeling. The DSM employed to develop a Revised Universal Soil Loss Equation (RUSLE) model and hydrological flow models. The model results provide important insights into the site geomorphological processes and allow categorization of the diagnostic surface material locations based on their contextual integrity. The GIS analysis demonstrates that the surface artifact distribution has been significantly altered by post-depositional geomorphic processes, resulting in an overall low contextual integrity of surface artifacts. Conversely, the study identified a few areas with high contextual integrity, loci that represent prime locations for excavation. The results from this study will not only be used to inform and guide further development of the archeological project (as well as representing significant new data in its own right), but also contributes to current debates in survey archaeology, and in mapping and prospection more generally. This project demonstrates the benefit of using spatial analysis as a tool for planning of pedestrian surveys and for predictive mapping of artifact distributions prior to archaeological excavations.

abstract: Thesis

abstract: Master of Science (MSc)


title: Advanced Torque Ripple Reduction Methods in Switched Reluctance Motor Drives

contributor:
Emadi, Ali
Electrical and Computer Engineering

subject:
switched reluctance machine
torque ripple
torque control
torque sharing function

abstract:
This thesis presents advanced torque control methods for torque ripple reduction and performance improvement in switched reluctance motor (SRM) drives.
A new offline torque sharing function (TSF) method is proposed for torque ripple reduction in SRMs. The proposed TSF achieves lower current tracking error by establishing a new current reference generation strategy. The phase current reference is first derived from the torque command using offline calculations and also from the phase current response that is obtained from the dynamic model of the SRM. Then, an optimization problem is formulated to shape the current reference for the objective of minimizing the torque ripple and copper losses, while maintaining the required average output torque at the given operating speed. The dynamic simulation of the SRM model is also utilized in the optimization problem.
A new online TSF method is proposed for torque ripple reduction in SRMs. The proposed TSF takes the current dynamics and induced electromotive force into account by establishing a new online current profile generation technique. First, a primary phase current reference derived from the torque reference is applied to the SRM. Then, the decaying phase current after the turn-off angle is sampled, and it is used to update the current reference. A new online optimization strategy is performed to shape the current reference during the operation of the machine. Owing to the proposed current profile generation technique, the optimization process is decoupled to independently minimize the torque ripple by optimizing the turn-on angle and minimizing copper losses by optimizing the turn-off angle.
Compared to the conventional TSFs and existing optimization-based TSFs, the proposed two TSFs achieve accurate torque control, improved torque-speed capability, reduced torque ripple, and better current tracking performance. All the proposed TSF methods are validated by both simulations and experiments on a 3-phase, 12/8 SRM.

abstract: Dissertation

abstract: Doctor of Philosophy (PhD)