title: Factors that influence heparin levels in patients with venous thromboembolism treated with subcutaneous weight-adjusted unfractionated heparin and low-molecular weight heparin, and whether heparin levels are associated with bleeding and recurrent venous thromboembolic events

contributor:
Kearon, Clive
Health Research Methodology

subject:
heparin
anti-Xa levels
venous thromboembolism
bleeding
outcomes
regression

abstract:
1.	Abstract
1.1.	Background It is uncertain whether 1) patient’s characteristics (e.g., age, weight, height, and sex) influence anti-Xa heparin levels (hereafter referred to as "heparin levels"), or 2) if heparin levels influence recurrent venous thromboembolism (VTE) or bleeding events, in patients with acute VTE treated with weight-adjusted therapeutic-dose subcutaneous (SC) unfractionated heparin (UFH) or SC low-molecular weight heparin (LMWH). To determine if either association exist, we analyzed data from the Fixed-Dose Heparin (FIDO) study, in which patients were randomized to either SC UFH or SC LMWH, each given in fixed weight-adjusted doses and overlapped with 3 month of warfarin therapy for treatment of acute VTE.
1.2.	Methods During the original study, 708 patients were asked to participate in a sub-study that would measure peak heparin levels while they were treated with heparin. 408 patients provided blood samples and met the eligibility criteria for the analyses in this thesis. Linear regression was used to examine the influence of patients’ baseline characteristics (e.g., age, weight, height, body mass index [BMI], sex) on heparin levels. The influence of other factors (e.g., type of heparin [UFH or LMWH]) on heparin levels was also assessed. Logistic regression was used to examine the association of heparin levels with the outcomes of 1) recurrent VTE during 3 months of follow up, and 2) bleeding events in the first 10 days of follow up.
1.3.	Results:  Mean heparin levels were 0.695 in patients treated with UFH, 0.698 in those treated with dalteparin and 1.034 in those treated with enoxaparin (p<0.001; R2=0.08 for variability accounted for by type of heparin). In a univariable analysis, heparin levels increase by 0.04 IU/ml (95% CI 0.02-0.07; p=0.001; R2=0.03) for every 10-kg increment in weight, by 0.02 IU/ml (95% CI 0.01-0.03; p<0.001; R2=0.04) for each unit of BMI, and by 0.03 IU/ml (95% CI 0.01-0.05; p=0.001; R2=0.03) for every 10 mol/l increment in creatinine. In a multivariable analysis, weight, BMI, and creatinine still influenced heparin levels, after adjusting for type of heparin and timing of blood sample withdrawal. Although heparin levels increased with weight, the magnitude was not large enough to suggest altering the current weight-based dosing method for LMWH. Other baseline factors such as age, height, type of VTE, creatinine clearance and hospitalization status did not influence heparin levels in patients treated with UFH or LMWH. In a univariable analysis, when heparin levels were treated as a continuous variable, higher heparin levels were associated with a lower risk of recurrent VTE at 90-days in patients treated with LMWH (OR 0.04, 95% CI 0.003-0.550, for each 1.0 IU/ml increase in heparin levels), but not in patients treated with UFH (OR 1.46, 95% CI 0.37-5.58, for each 1.0 IU/ml increase in heparin levels). In addition, higher heparin levels were associated with a higher risk of bleeding at 10-days in patients treated with UFH (OR 3.32, 95% CI 1.30-8.46 for each 1 IU/ml increase in heparin levels) but not in patients treated with LMWH (OR 3.77, 95% CI 0.42-33.92, for each 1.0 IU/ml increase in heparin levels). In a multivariable analysis, the association of heparin levels with VTE at 90-days in patients receiving LMWH (lower VTE events) and with bleeding events at 10-days in patients receiving UFH (higher bleeding events) persisted after adjusting for antiplatelet use at baseline and diagnosis of cancer at baseline. When heparin levels were treated as a dichotomous variable (subtherapeutic vs. non-subtherapeutic levels and supratherapeutic vs. non-supratherapeutic levels), the proportion of patient with recurrent VTE was significantly higher in patients with subtherapeutic levels compared with non-subtherapeutic levels in patients receiving LMWH (8.6% vs. 1.3%, p = 0.01).  No significant difference was found in the proportion of patients with subtherapeutic levels and non-subtherapeutic levels in patients receiving UFH (0% vs. 3.4%, χ2=0.15, p= 0.70). The test of interaction supported the decision to analyze LMWH and UFH groups separately (p=0.02). Finally, the proportion of patient with bleeding was higher in patients with supratherapeutic compared with non-supratherapeutic heparin levels (6.5% vs. 1.5%, χ2=7.65, p=0.01). The test of interaction did not support the decision to analyze LMWH and UFH groups separately (p=0.13).
1.4.	Conclusions Although it was possible to identify factors that were associated with heparin levels in patients who had been treated with weight-adjusted UFH or LMWH, none of these associations were strong enough to suggest that variables other than weight should influence SC heparin dosing. Subtherapeutic heparin levels were associated with a higher risk of recurrent VTE in patients treated with LWMH but not UFH, and supratherapeutic heparin levels were associated with a higher risk of bleeding in patients treated with UFH but not LMWH. Indirectly, these findings suggest that adjusting UFH or LMWH dose in response to heparin levels might improve clinical outcomes.

abstract: Thesis

abstract: Master of Science (MSc)


title: Lattice-based Robust Distributed Coding Scheme for Correlated Sources

contributor:
Dumitrescu, Sorina
Chen, Jun
Electrical and Computer Engineering

subject:
Distributed source coding
lattice quantization
high resolution analysis

abstract: In this thesis we propose two lattice-based robust distributed source coding systems, one for two correlated sources and the other for three correlated sources. We provide a detailed performance analysis under the high resolution assumption. It is shown that, in a certain asymptotic regime, our scheme for two correlated sources achieves the information-theoretic limit of quadratic multiple description coding (MDC) when the lattice dimension goes to infinity, whereas a variant of the random coding scheme by Chen and Berger with Gaussian codes is 0.5 bits away from this limit. Our analysis also shows that, under the same asymptotic regime, when the lattice dimension goes to infinity, the proposed scheme for three correlated sources is very close to the theoretical bound for the symmetric quadratic Gaussian MDC problem with single description and all three descriptions decoders.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: SANCTUARY REGIONS AND THE STRUGGLE FOR BELONGING AND RECOGNITION AMONG UNDOCUMENTED IMMIGRANTS IN THE UNITED STATES

contributor: Political Science - International Relations

abstract: This thesis argues that local governments and institutions across the state of California that offer various forms of sanctuaries to undocumented immigrants create what I call ‘sanctuary regions’.  These regions create a ‘safe zone’ for undocumented immigrants and facilitate their ability to make claims for human rights.  This dissertation also argues that these regions create an important form of resistance to federal state authority in terms of immigration and the management of borders – something that is typically attributed to state power in the study of International Relations (IR).  Through the analysis of sanctuary movements across the state of California, interviews with local organizers and undocumented immigrants; and the analysis of stories published and written by undocumented immigrants, I make three major conclusions.  One, sanctuary policies that provide greater protection to undocumented immigrants facilitate the path for them to acquire rights, access services and perform acts of citizenship. Second, the regional dynamic of these sanctuary regions makes them more powerful in contesting state authority on deportation and immigration policy.  Finally, citizenship is performed by undocumented immigrants in these regions based on their sense of belonging and contributions to the communities within sanctuary regions.  Through my analysis, this dissertation also theorizes the potential for non-state-based citizenship and the conditions which allow certain individuals to access human rights and citizen rights by advocating to local governments and institutions.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Intelligent State-of-Charge and State-of-Health Estimation Framework for Li-ion Batteries in Electrified Vehicles using Deep Learning Techniques

contributor:
Emadi, Ali
Electrical and Computer Engineering

subject:
Energy Management Systems
Deep Learning
Li-ion Batteries
Neural Networks
State-of-Charge
Machine Learning
State-of-Health

abstract:
The accurate and reliable estimation of the State-of-Charge (SOC) and State-of-Health (SOH) of Li-ion batteries is paramount to the safe and reliable operation of any electrified vehicle. Not only is accuracy and reliability necessary, but these estimation techniques must also be practical and intelligent since their use in real world applications can include noisy input signals, varying ambient conditions and incomplete or partial sequences of measured battery data. To that end, a novel framework, utilizing deep learning techniques, is considered whereby battery modelling and state estimation are performed in a single unified step.

For SOC estimation, two different deep learning techniques are used with experimental data. These include a Recurrent Neural Network with Long Short-Term Memory (LSTM-RNN) and a Deep Feedforward Neural Network (DNN); each one possessing its own set of advantages. The LSTM-RNN achieves a Mean Absolute Error (MAE) of 0.57% over a fixed ambient temperature and a MAE of 1.61% over a dataset with ambient temperatures increasing from 10°C to 25°C. The DNN algorithm, on the other hand, achieves a MAE of 1.10% over a 25°C dataset while, at -20°C, a MAE of 2.17% is obtained.

A Convolutional Neural Network (CNN), which has the advantage of shared weights, is used with randomized battery usage data to map raw battery measurements directly to an estimated SOH value. Using this strategy, average errors of below 1% are obtained when using fixed reference charge profiles. To further increase the practicality of this algorithm, the CNN is trained and validated over partial reference charge curves. SOH is estimated with a partial reference profile with the SOC ranging from 60% to 95% and achieves a MAE of 0.81%. A smaller SOC range is then used where the partial charge profile spans a SOC of 85% to 95% and a MAE of 1.60% is obtained.

Finally, a fused convolutional recurrent neural network (CNN-RNN) is used to perform combined SOC and SOH estimation over constant charge profiles.  This is performed by feeding the estimated SOH from the CNN into a LSTM-RNN, which, in turn, estimates SOC with a MAE of less than 0.5% over the lifetime of the battery.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: COORDINATION OF DISTRIBUTED MPC SYSTEMS THROUGH DYNAMIC REAL-TIME OPTIMIZATION WITH CLOSED-LOOP PREDICTION

contributor:
Swartz, Christopher L.E.
Chemical Engineering

subject:
optimization
MPC
coordination
closed-loop prediction

abstract:
A dynamic real-time optimization (DRTO) formulation with closed-loop prediction is used to coordinate distributed model predictive controllers (MPCs) by rigorously predicting the interaction between the distributed MPCs and full plant response in the DRTO formulation. This results a multi-level optimization problem and that is solved by replacing the MPC quadratic programming subproblems by their equivalent Karush-Kuhn-Tucker (KKT) first-order optimality conditions to yield a single-level mathematical program with complementarity constraints (MPCC). The proposed formulation is able to perform both target tracking and economic optimization with significant performance improvement over decentralized control, and similar performance to centralized MPC.  A linear dynamic case study illustrates the performance of the proposed strategy for coordination of distributed MPCs for different levels of plant interaction,.  The method is thereafter applied to a nonlinear integrated plant with recycle, where its performance in both set-point target tracking and economic optimization is demonstrated.

Subsequently, this study presents two techniques for approximation of the closed-loop prediction within the DRTO formulation -  a hybrid closed-loop formulation and an input clipping formulation. The hybrid formulation generates closed-loop predictions for a limited number of time intervals along the DRTO prediction horizon, followed by an open-loop optimal control formulation extended to rest of the horizon. The input clipping formulation utilizes an unconstrained MPC optimization formulation for each distributed MPC, coupled with the application of an input saturation mechanism. The performance of the approximation techniques is evaluated through application to case studies based on linear and nonlinear dynamic plant models respectively.  The approximation techniques are demonstrated to be more computationally efficient than than the rigorous counterpart without significant loss in performance.

The performance of the proposed DRTO formulation can be further improved by the introduction of nonlinearity. The nonlinear dynamic plant model is firstly introduced in the DRTO formulation while maintaining the linear formulation for the distributed MPCs. The performance of resulting formulation is demonstrated and compared against the linear counterpart. The nonlinear MPC formulation is then included in both lower-level control implementation and DRTO formulation. By reformulating the Lagrangian of the nonlinear MPC optimization subproblems, the nonlinear MPC formulation is successfully implemented in the DRTO formulation. The performance of such DRTO formulation is further improved and shown using a nonlinear case study.

The conclusion of this study is summarized and the potential directions of this research such as large-scale applications, variation of MPC implementations, and robust model-based control are outlined and explained in the end.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Wet Oxidation Performance of Type 310S Stainless Steel

contributor:
Kish, Joseph
Botton, Gianluigi
Materials Science and Engineering

subject:
High-Temperature
Wet Oxidation
Stainless Steel

abstract: High-temperature wet oxidation resistance of Type 310S stainless steel arises from the formation of a thin, adherent and compact external Cr2O3 scale that is more protective compared with the other oxides. Stability of the Cr2O3 scale is often at risk in the presence of water vapour at higher temperatures, which promotes the loss of oxidized Cr to volatilization. Continuous volatilization of the Cr2O3 scale accelerates the rate of oxidation and increases the risk of non-protective Fe-rich oxide formation that immensely contributes to the oxide thickening (breakaway oxidation). In this study, the possibility of surrogating high-pressure supercritical water with an ambient pressure air-10% H2O mixture is studied at temperatures associated with the predicted coolant outlet conditions in the current GEN IV design concepts. Factors influencing structure and composition of the Cr2O3 scale during wet oxidation are then examined in the wet environments. An increase in the total gas pressure, water vapour partial pressure and temperature is shown to accelerate the Fe-rich oxide formation by increasing the rate of oxidized Cr loss. A more complete physical description of the oxidation kinetics in terms of the evolution of the oxide scale structure and composition at the various exposure conditions is also reported. Presence of small amount of Mn in the alloy is shown herein to be beneficial as it assists the formation of a MnCr2O4 layer on top of the Cr2O3 scale, which serves to reduce the volatilization rate. It is shown however that the MnCr2O4 layer itself is only temporary protective and becomes prone to volatilization (loss of oxidized Cr) at relatively high temperatures, pressures and exposure times. The formation of a MnCr2O4 cap is therefore, only a temporary solution for delaying the onset of accelerated Fe-rich oxide formation. Addition of Si is proposed to be a more promising way of controlling the onset of the Fe-rich oxide formation. Increase in the Si content to ~6 wt.% results in the formation of a continuous SiO2 barrier layer under the Cr2O3 scale as well as Cr-rich silicide intermetallic phases in the starting microstructure that serve as effective Cr reservoirs in helping to maintain the structure and composition of the compact protective Cr2O3 scale despite the continued loss of oxidized Cr to volatilization.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The effects of total gas pressure, water vapour partial pressure, temperature and minor alloying elements (Mn and Si in particular) on the wet oxidation performance of Type 310S stainless steel were examined within the context of the stability of the protective chromia (Cr2O3) scale formed. Focus was placed on examining factors that influence the onset of accelerated linear oxidation associated with the Fe-rich oxide formation and oxide thickening. Links between changes in structure and composition of the protective Cr2O3 scale and breakaway oxidation as exhibited in water vapour-containing environments are made using advanced electron microscopy techniques. Si addition up to ~6 wt.% assists the formation of a continuous silica (SiO2) barrier layer under the Cr2O3 scale as well as Cr-rich silicide intermetallic phases that act as reservoirs to supply for the oxidized Cr lost to volatilization. Si addition is proposed to be a promising way of prohibiting Fe-rich oxide formation albeit modifications to the morphology of the silicide intermetallic phases are required.


title: INVESTIGATING MECHANISMS OF PEPTIDE INDUCED IMMUNE MODULATION OF MURINE MODELS OF ALLERGIC AIRWAYS DISEASE

title: IMMUNE MODULATION OF ALLERGIC RESPONSES

contributor: Medical Sciences (Molecular Virology and Immunology Program)

subject: Peptide immunotherapy, immune modulation, Th2, Treg, allergy, asthma, bystander tolerance.

abstract:
Asthma is defined as reversible airflow obstruction and an estimated 1-in-3 Canadians will be diagnosed over their lifetime. Many clinical phenotypes of asthma exist, but allergic asthma is the most common presentation. Despite effective therapies, approximately 65% of Canadian asthmatics have poorly controlled disease. Thus, there remains pressing need to develop disease modifying therapies.
Allergen-specific immunotherapy (SIT) is a disease-modifying therapy for allergic disease that consists of repeatedly administering doses of allergen, to an allergic individual; over 100 years of clinical use, SIT has been demonstrated to reduce symptoms of disease both during and after cessation of therapy. Widespread clinical uptake of SIT has been limited by the risk of developing anaphylaxis as a response to therapy. Peptide immunotherapy is a derivation of SIT, that attempts to retain the disease-modifying benefits, while lessening the risk of anaphylaxis, by treating subjects with allergen-derived T-cell peptide epitopes. Peptide immunotherapy has been demonstrated to reduce symptoms of allergic disease in treated subjects; however, it remains unknown how administration of a single (or several) T-cell epitopes can modulate immune responses to entire complex allergens. Additionally, how genetic diversity in peptide epitope presentation effects the development of immune tolerance is unknown. In this thesis, we sought to characterize these mechanisms of peptide immunotherapy; the hypothesis was, “The induction of immunosuppression by peptide immunotherapy involves the infectious spread of tolerance beyond the treatment epitope, and is dependent upon treatment peptide dose and affinity to MHC”.
Through the definition of these mechanistic traits we hoped to expedite and inform the design of future peptide based therapeutics. The studies presented within this thesis examine the
topic of immune modulation of allergic disease in mouse models, and have focused upon broadly pertinent characteristics of immune modulation, such as the number, dose and affinity of immunomodulatory epitopes.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: Asthma is a disease of the airways that can cause difficulties in breathing. In some people, asthma develops because their immune system reacts in an uncontrolled manner to common environmental proteins, called allergens. Whole allergen immunotherapy is a treatment for asthma, where asthmatic people are injected with doses of allergen until their immune system no longer responds to (or ‘tolerates’) the allergen. In some people, injection of allergen can lead to a life-threatening immune response known as ‘anaphylaxis’. Peptide-immunotherapy is a form of whole allergen immunotherapy where people are given small fragments of the allergen (a ‘peptide’) rather than the whole allergen. The benefit of peptide immunotherapy is that the treatment peptides are too small to cause anaphylaxis, but remain large enough to teach the immune system. In this thesis, we examined how treatment with small peptides teaches the immune system to tolerate the larger and more complex whole allergen.


title: MULTIPHASE POWER ELECTRONIC CONVERTERS FOR ELECTRIC VEHICLE MACHINE DRIVE SYSTEMS

contributor:
Schofield, Nigel
Electrical and Computer Engineering

subject:
Electric Vehicle
Power Electronics
Multiphase
Voltage Source Inverter
DC-link Capacitor
Thermal Study

abstract:
The past few decades have seen a rapid sales increase and technological development of electric vehicles (EVs). As the key part of the electrical powertrain systems, the traction machine drive systems in modern EVs are composed of voltage source inverters (VSI) and electric machines. In this thesis, multiphase VSIs are studied and designed to achieve volume reductions when compared with existing 3-phase benchmark VSIs.
Different existing switching strategies for arbitrary phase number multiphase VSIs are investigated resulting in an understanding of best practice and a newly proposed switching strategy. Thus, the first contribution of this thesis is switching strategies that support subsequent investigations and experimental validation.
DC-link capacitor and heat sink are two bulkiest components in VSIs and hence it is more efficient to decrease their volumes to achieve the compactness improvement. The investigation methodology and procedure for arbitrary phase number VSI DC-link capacitor requirements, i.e. capacitance and RMS current ratings, are firstly developed. Increased phase number decreases the DC-link capacitor requirements and hence the VSI volume significantly. Throughout this analysis, the connected multiphase machine is considered appropriately, though no electric machine design is described in the thesis. While other authors have studied DC-link current ripple, this thesis qualifies and quantifies the system benefits. This is the second contribution.
Multiphase VSIs thermal models are built and their respective thermal performances studied and evaluated against a reference 3-phase benchmark VSI. The power loss deviation among different semiconductor dies is lower or even eliminated in the multiphase VSIs. Furthermore, the multiphase integrated design VSIs have a significant heat sink volume reduction when compared to the 3-phase benchmark VSI. This study and concluding benefits are the third contribution. Finally, comparative test validations are made on an experimental set-up designed to illustrate the benefits of a 9-phase against a reference 3-phase system. Here, the test hardware and implementation are carefully designed to representatively illustrate performance benefits.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Affect of the Political

title: On the Politics and Psychology of Internalizing the International

subject: affect, emotion, thumos, international relations theory, political theory, sovereignty

abstract: This thesis investigates the historical relationship between understandings of human emotion, and how they manifest in our understanding of the political. Specifically, this thesis returns to the presentation of individual political psychology in ancient Greece (Thucydides, Aristotle), the 17th and 18th centuries (Hobbes, Rousseau, Kant), and the 20th century (Schmitt, Fukuyama, Lebow) to illuminate how these understandings have shaped our idea of Sovereignty as an idea, institution, and practice. By turning to the rich history in political thought on emotion and affect, this thesis demonstrates a consistent and prolonged constitutive relationship between presentations of individual political psychology and international political order. This thesis also rehabilitates the full scope of affective insights into political phenomena— by turning to literature on rhetoric and aesthetics—in order to open up new space to critique common understandings of Sovereignty. Moreover, given that the institution and concept of Sovereignty is central to research in the disciplines of International Relations and Political Theory, this thesis also argues for a much-needed closure of intellectual space between these two branches of Political Science. In short, this thesis demonstrates the centrality of the politics of affect and the divergent and disparate pictures of individual political psychology that are taken for granted in defenses and critiques of the concept of Sovereignty.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Correlating Self-Consolidating Concrete mixture composition to its rheological properties

contributor:
Chidiac, Samir
Civil Engineering

subject: SCC, SCC mixture composition, Workability, Rheology, Rheological properties

abstract:
Self-Consolidating concrete (SCC), a highly flowable concrete, is gaining wide acceptance in the concrete industries due to a higher productivity, lower energy consumption, improved working environment and increase quality. SCC is susceptible to segregation and therefore a balance between flow-ability and stability is required.  The absence of a comprehensive SCC mixture composition design guidelines merits investigating the effects of SCC mixture variables on the properties affecting its performance, namely flow and stability.

An experimental and analytical study were carried out to study the influence of 5 design variables, namely water to binder ratio (w/b), percent addition of silica fume (SF), percent addition of Ground Granulated Blast Furnace Slag (GGBFS), bulk volume of coarse aggregates and binder content, on the workability and rheology of SCC.  Workability measurements, specifically the slump flow, T50, L-Box and segregation column, and rheological properties, namely plastic viscosity, yield stress, and thixotropy were measured to evaluate SCC’s performance.  A revised modified Bingham model was proposed to adequately account for the linear and non-linear responses of the concrete flow. It postulates that the flow is divided into a linear and non-linear part.  The revised model is found to provide more consistent and precise estimate of the rheological properties.  Using regression analyses, yield stress and plastic viscosity models that account for the statistically significant variables were derived from experimental test data.  Yield stress is found to depend on the bulk volume fraction of the coarse aggregate, Silica Fume content, High Range Water Reducing Agent (HRWRA) and Viscosity Modifying Agent (VMA), and plastic viscosity on w/b, HRWRA and Average Paste Thickness (APT).

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Reconstruction results for first-order theories

contributor:
Hart, Bradd
Mathematics

subject:
logic
model theory
categorical logic
strong conceptual completeness
ultraproducts
ultracategory

abstract: In this thesis, we study problems related to the reconstruction (up to bi-interpretability) of first-order theories from various functorial invariants: automorphism groups, endomorphism monoids, (categories of) countable models, and (ultra)categories of models.

abstract: Thesis

abstract: Master of Science (MSc)


title: Focused flow during water infiltration into ethanol-contaminated unsaturated porous media

contributor:
Smith, James E.
Earth Sciences

subject: focused flow

subject: solute-induced capillarity-dependent focused flow

subject: SCIFF

subject: vadose zone

subject: infiltration

subject: ethanol

subject: unsaturated zone

subject: flow cell

subject: porous media

subject: rainulator

subject: constant flux

subject: tension infiltrometer

subject: constant head

subject: soil physics

subject: hydrology

subject: hydrogeology

abstract:
The increasing commercial and industrial use of ethanol, i.e., in biofuel and gasoline, has generated increased incidents of vadose zone contamination by way of ethanol spills and releases. This has increased the interest in better understanding infiltration behaviours of ethanol in unsaturated porous media and the multiphase interactions in the vadose zone. Solute-dependent capillarity-induced focused flow (SCIFF) is a vertical, highly focused flow infiltration behaviour first reported by Smith et al. (2011) in butanol-contaminated sands. Through the use of highly controlled laboratory experiments, this thesis research investigates focused flow (SCIFF) and related behaviours through water infiltration into ethanol-contaminated unsaturated sand.

Focused flow behaviours (SCIFF) were demonstrated through the infiltration of water into an ethanol-contaminated unsaturated sand using both constant flux and constant head methodologies. The observation of focused flow behaviours in ethanol-contaminated sand supported the primary hypothesis of this work. The secondary hypothesis was also supported, as focused flow behaviours were not observed, rather stable semicircular infiltration patterns were observed during ethanol infiltration into water-wet sand. Comparisons between constant flux and constant head application methods under similar flow rates and fluid volumes produced similar results. The zone of lower saturation, or the “halo effect” reported in previous literature, was strongly expressed during water infiltration in ethanol-contaminated sand. This halo effect is affected by the maximum (at 40% to 50%) of aqueous concentration of ethanol. This maximum enhances the zone of lower saturation and stabilizes the solute front. The SCIFF focused flow also overcame the effects of minor heterogeneities in the sand. However, additional laboratory and modelling work is required to further understand the extent of SCIFF behaviour.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Understanding the behaviour and interaction of water and contaminants in soils is important as environmental contamination and spills can have devastating environmental impacts. In recent decades, ethanol spills and accidental releases onto ground surface have increased as the commercial and industrial use of ethanol has increased. The goals of this work were to qualitatively visualize and quantify the unique nature of water infiltration into the ethanol-contaminated soil and understand the complex mechanisms behind water-ethanol interactions. This research showed that water infiltration creates an uncommon vertical, focused pattern when flowing into sand contaminated by ethanol. However, when ethanol is applied to standard water-wet sand, that behaviour is not observed. This work provided greater insight into the nature of ethanol-contaminated soils. These findings furthered the understanding needed to evaluate impacts that ethanol contamination can have on remedial efforts and the rate of migration of contaminants to groundwater.


title: Elucidating the Role of Senataxin During HSV-1 Infection

title: Elucidating the Role of Senataxin During Herpes Simplex Virus Type-1 Infection

contributor:
Miller, Matthew S.
Biochemistry and Biomedical Sciences

subject: HSV-1, Senataxin, R-loops

abstract: Unlike RNA viruses, which typically encode their own RNA-dependent RNA polymerases, DNA viruses typically utilize host RNA Polymerase II (RNAPII) to transcribe their genes. Therefore, host factors that interact with RNAPII often maintain important regulatory roles during DNA virus infections. Senataxin (SETX) is a ubiquitously expressed 303 kDa RNA:DNA helicase that associates with RNAPII. It is involved in the resolution of R-loops and plays a role during the DNA damage response. Mutations in SETX are implicated in the neurodegenerative diseases Type 2 Ataxia with Oculomotor Apraxia (AOA2) and juvenile Amyotrophic Lateral Sclerosis (ALS4). Recent work from our group has demonstrated that SETX also acts as an antagonist of the antiviral response during RNA virus infections. Infections, including those caused by Herpes Simplex Virus type I (HSV-1), have been identified as potential environmental triggers of neurodegenerative diseases. Therefore, we elected to study the role of SETX during DNA virus infections since, in addition to regulating host genes, it may also play a role in viral transcription and/or DNA replication. Our data suggests that SETX is involved in the regulation of viral gene expression, and that SETX facilitates DNA replication and contributes to viral biogenesis. SETX attenuates the antiviral response, and in mouse models of infection, is protective against HSV-1 disease pathogenesis. These studies have enhanced our understanding of the role played by SETX during viral infection and may shed light on the mechanism(s) through which SETX dysfunction results in neurodegenerative diseases.

abstract: Thesis

abstract: Master of Health Sciences (MSc)

abstract: DNA viruses utilize host proteins in gene expression, therefore, associated factors play roles during DNA virus infections. Senataxin (SETX) is a RNA:DNA helicase associated with these proteins. SETX mutations are implicated in the neurodegenerative diseases Type 2 Ataxia with Oculomotor Apraxia (AOA2) and juvenile Amyotrophic Lateral Sclerosis (ALS4). Recently, our group demonstrated SETX antagonizes antiviral responses to RNA virus infections. Infections, including those caused by Herpes Simplex Virus type I (HSV-1), are identified as potential triggers of neurodegenerative diseases. We elected to study the role of SETX during DNA virus infections. Our data suggests that SETX is involved in the regulation of viral gene expression, facilitates HSV-1 DNA replication, attenuates the antiviral response, and in mouse models of infection, is protective against HSV-1 disease pathogenesis. These studies enhance understanding of the role of SETX during viral infection and may shed light on the mechanism(s) of SETX role in neurodegenerative disease.


title: APPLICATIONS OF STATISTICAL LEARNING ALGORITHMS IN ELECTRON SPECTROSCOPY

title: TOWARDS CALIBRATION-INVARIANT SPECTROSCOPY USING DEEP LEARNING

contributor:
Botton, Gianluigi
Materials Science and Engineering

subject:
Spectroscopy
machine learning
statistical learning
neural networks
electron microscopy
electron energy loss spectroscopy

abstract:
Building on the recent advances in computer vision with convolutional neural networks, we have built SpectralNet, a spectroscopy-optimized convolutional neural network architecture capable of classifying spectra despite large temporal (i.e. translational, chemical, calibration) shifts. Present methods of measuring the local chemical environment of atoms at the nano-scale involve manual feature extraction and dimensionality reduction of the original signal such as: using the peak onset, the ratio of peaks, or the full-width half maximum of peaks. Convolutional neural networks like SpectralNet are able to automatically find parts of the spectra (i.e. features) of the spectra which maximally discriminate between the classes without requiring manual feature extraction. The advantage of such a process is to remove bias and qualitative interpretation in spectroscopy analysis which occurs during manual feature extraction. Because of this automated feature extraction process, this method of spectroscopy analysis is also immune to instrument calibration differences since it performs classification based on the shape of the spectra. Convolutional neural networks are an ideal statistical classifier for spectroscopy data (i.e. time-series data) due to its shared weighting scheme in neural network weights which is ideal for identifying local correlations between adjacent dimensions of the time-series data.
Over 2000 electron energy loss spectra were collected using a scanning transmission electron microscope of three oxidation states of Mn. SpectralNet was trained to learn the differences between them. We prove generalizability by training SpectralNet on electron energy loss spectroscopy data from one instrument, and test it on a variety of reference spectra found in the literature with perfect accuracy. We also test SpectralNet against a wide variety of high noise samples which a trained human spectroscopist would find incomprehensible. We also compare other neural network architectures used in the literature and determine that SpectralNet, a dense-layer free neural network, is immune to calibration differences whereas other styles of network are not.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Spectroscopy is the study of the interaction between photons or electrons and a material to determine what that material is made of. One advanced way to make accurate measurements down to the atomic scale is to use high energy electrons in a transmission electron microscope. Using this instrument, a special type of photograph can be taken of the material (a spectrograph or spectrum) which is detailed enough to identify which kinds of atoms are in the material. The spectrographs are very complicated to interpret and the human eye struggles to find patterns in noisy and low resolution data. Depending on which instrument that the spectrographs are taken on, the resulting spectrograph will also change which adds extra difficulty. In this study, advanced algorithms are used to identify which types of atoms can be identified in the noisy signal from the spectrograph regardless of which instrument is used. These algorithms (convolutional neural networks) are also used in self-driving cars for a similar task of identifying objects whereas in this study we use it for identifying atoms.


title: An Experimental Investigation of the Hardenabilities Tensile and Fracture Properties of Powdered Metal Steels

contributor:
Malakhov, Dmitri
Materials Science and Engineering

subject:
Powdered Metal
Hardenability
Sintering
Particle Sizes
Martensite
Jominy
Metal Matrix Composite
Pearlite
Porosity
Rockwell

abstract:
Powder metallurgy (PM) steel is produced by near net shape manufacturing, which is used to fabricate alloy steels for many purposes. Designing new powder metal steels that can form a significant fraction of martensite relies on hardenability calculations developed for wrought steels. These proven tools are built upon assumptions for wrought steels that do not hold true for PM steels. One assumption is that the alloying elements are homogenized throughout the material. In admixed powder blends that are industrially sintered this is not the case. Using prealloyed powder is a solution to this issue, yet it places restrictions on alloy design and compressibility. There are tools available to computationally optimize diffusion problems, yet the complexity during the sintering of PM steel is such that a robust model has yet been produced. It is intuitive that with smaller particles of Fe sintering time can be reduced. A direct experimental investigation linking Fe-powders’ sizes and hardenability on Fe-C-Cr-Mn-Mo-Ni PM steel was subject to microstructure analysis and mechanical properties (Jominy test) for comparative analysis.

Another assumption that is made for wrought steel is a consistent density of 7.87g/cm3. This is not the case for PM steel as the press and sinter method produces pores, decreasing the density. This directly affects the thermal conductivity and phase transformation of the steel. In an effort to understand how these differences affect Grossmann’s predictions of hardenability, a direct experimental investigation linking the density to hardenability was launched on prealloyed FL-4605 and FL-4605+2%Cu. Specifically the Jominy test was completed on a range of densities, as well as compared to software predictions.

The chemical variations in admixed and sintered PM steel produce a unique system where one TTT diagram cannot predict the entire final microstructure. PM steel such as this is observed in industry, and can be created through incorporating larger Fe-particles such that less alloying constituents have a chance to fully alloy these regions. Since the large particles will not have the chance to be alloyed, they will not have the ability to form martensite. Since the regions between large particles will be alloyed, martensite will form, creating a hard matrix surrounding softer particles. This structure is characteristic of a metal matrix composite (MMC), and therefore should be treated as such. There are methods of MMC design that involve numerical methods of predicting strength and toughness. These methods, along with experimental data (tensile and Charpy testing) of Fe-C-Cr-Mn-Mo-Ni PM steels with ranging volume fractions of pearlitic inclusions were compared.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: SYNTHESIS AND CHARACTERIZATION OF IRON OXIDE NANOPARTICLES FOR INCORPORATION INTO ORGANIC ELECTRONIC DEVICES

contributor:
Ayse, Turak
Engineering Physics

subject:
iron oxide
nanoparticles
structure
Raman
dispersion
magnetic

abstract:
Surface modification of electrodes becomes a powerful process to improve the performance
of organic electronic devices such as organic light emitting diodes (OLEDs)
and organic photovoltaic cells (OPVs), boosting their further commercialization. Effective
improvement can be achieved by introducing several types of nanoparticles
onto the electrodes. Magnetic fields also have influence in the organic electronics,
due to charge transport mechanisms of organic semiconducting materials. Therefore,
magnetic nanoparticles are of particular interest.

Magnetic γ-Fe2O3 nanoparticles have been produced using diblock copolymer reverse
micelles method. The processes were elucidated in detail by Raman spectroscopy
to reveal the iron oxide evolution. Compositional and structural information of individual
γ-Fe2O3 nanoparticles were also characterized thoroughly by transmission
electron microscopy (TEM) equipped with energy-dispersive X-ray spectroscopy (EDX)
and electron energy loss spectroscopy (EELS), while their magnetic properties of the
nanoparticles arrays were also evaluated by superconducting quantum interference
device (SQUID) magnetometer. The low temperature annealing process was developed
to facilitate the incorporation of γ-Fe2O3 nanoparticles in practical devices. Introducing
γ-Fe2O3 nanoparticles onto the anode of basic OPV devices showed a positive
effect on performance during the preliminary test.

By using several methods, dispersion of γ-Fe2O3 nanoparticles can be tuned, examined
by disLocate which is a comprehensive suite of tools for quantitative dispersion
analysis. Additionally, the size of the nanoparticles can be changed simply by changing
the loading ratio of FeCl3 below the maximum loading which was determined by
quantum mechanical mapping using atomic force microscopy (AFM-QNM). With
high control in terms of size and dispersion, the magnetic γ-Fe2O3 nanoparticles are
ready to be employed to study the surface modification and magnetic effect on organic
electronic devices.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Effect of Alloying Additions and Heat Treatment on Localized Corrosion Susceptibilities of AA7xxx Alloys Grain Refined with Al-5Ti-1B Master Aloy

contributor:
Kish, Joey
Shankar, Sumanth
Materials Science and Engineering

subject: Aluminum Corrosion

abstract:
The aim of this research was to identify the effect of alloying additions and heat treatment on the localized corrosion mechanisms of AA7xxx alloys that have been grain refined with an Al-5Ti-1B master alloy.  The major alloying elements, Zn (3.5 – 6.5 wt. %), Mg (1.5 – 2.5 wt.%), Cu (0 – 3 wt. %), and Ti (0.04 – 0.25 wt.%), were varied and ten AA7xxx aluminum alloys were cast, heat treated to the T4, T6, T79, T76, and T73 tempers, and studied extensively.
	Casting high integrity near net shaped AA7xxx components by introducing Ti and B into the melt to facilitate a non-dendritic microstructure produced a unique microstructure due to the phenomena of athermal nucleation, unconstrained growth, and solute field impingement. The three phenomena listed above create three microstructural regimes; dendritic area rich in Ti, interdendritic region lean in Ti, and grain boundary area rich in eutectic phases.
	The breakdown potential, Eb, in a detreated 0.5 M NaCl(aq) was determined for each alloy and heat treatment after 1 h at the open circuit potential.  The effect of alloying element composition and heat treatment on Eb was examined and an empirical expression was created.  It was determined that a semi-logarithmic relationship exists between Eb and the Zn/Cu weight ratio.  Zn and Cu have opposing effects on Eb, where, Zn-depletion from the solid solution into the strengthening precipitates increased the Eb while Cu-depletion decreased the same.  Cu-lean alloys have a continually increasing Eb from T4 to T6 and T7x temper conditions, while, Cu-rich alloys have no significant change in Eb with temper condition. The critical Zn/Cu weight ratio was determined to be approximately 5.
	Corrosion initiation mechanisms of a Cu-lean and Cu-rich alloy were studied using the dual beam FIB-SEM platform after 5 min of potentiostatic polarization in detreated 0.5 M NaCl(aq) at potentials of interest.  The initiation mechanism of the Cu-rich alloy (alloy 3) was determined to be dealloying of the S-phase (Al2CuMg) along the grain boundary leading to intergranular corrosion.  The surface of the Cu-lean alloy (alloy 6) after potentiostatic polarization above Eb showed three mechanisms of corrosion; corrosion domes, corrosion rings, and interdendritic corrosion.  Corrosion rings were identified as the initiation mechanism, corrosion domes were determined to be metastable sites and not a precursor to further corrosion, interdendritic corrosion was determined to be the propagation mechanism.  Interdendritic corrosion is the selective dissolution of the interdendritic region leaving the dendritic regime intact after immersion in a corrosive solution which is unique to these alloys grain refined with the Ti-B master alloy.  Corrosion domes were shown to cause an active-passive region in the potentiodynamic polarization curve.
	Modified EXCO experiments were used to study the propagation mechanism in each of the alloys at each temper.  All alloys and tempers were susceptible to interdendritic corrosion, however Cu-lean alloys showed less surface damage after 96 h of immersion in the modified EXCO solution.  Alloys with a Zn/Mg weight ratio < 2 were susceptible to intergranular corrosion in the T6 temper, however, in the T4 and T7x temper the primary mode of corrosion propagation is interdendritic corrosion.  Due to the bimodal distribution of the grain size, intergranular corrosion was only observed in the small grain areas.  The extent of attack was more severe in the small grain regions with intergranular corrosion present than areas without leading to the conclusion that intergranular corrosion is more detrimental than interdendritic corrosion.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Thermal stability of spray dried vaccine powders encapsulating enveloped and non-enveloped viral vectors

contributor:
Cranston, Emily
Chemical Engineering

subject:
vaccine
spray drying
chemical engineering
sugar

abstract:
This thesis work aims to improve the thermal stability of vesicular stomatitis virus (VSV) through spray drying and investigates differences in thermal stability in a matrix between enveloped and non-enveloped viral vectors.  The spray drying process was used to dry and encapsulate the VSV vector within the glassy amorphous phase of a matrix of carbohydrate excipients, which imparted increased thermal stability.  Viral activity was maintained when the powders were stored for 30 days at 37 °C, in contrast to the liquid control that lost all activity after 15 days.  The best excipients for enhancing thermal stability of VSV were trehalose and a 3:1 blend of trehalose and dextran.  Immunogenic response from the spray dried trehalose-VSV particles was detected through an in vivo study with Female BALB/c mice after storing the vaccine for 15 days at 37 °C.
Two enveloped viral vectors, VSV and influenza, and a non-enveloped viral vector, human type 5 adenoviral vector (AdHu5) were spray dried with the same formulations to observe how excipients enhance thermal stability and encapsulate the different groups of viruses.  The thermal stability of both enveloped viral vectors was enhanced the most when spray dried with trehalose or a 3:1 trehalose/dextran blend, and exhibited the greatest activity loss when spray dried with a mannitol/dextran blend, determined by in vitro TCID50 assays measuring GFP expression. Conversely, the best performing excipient formulation for the non-enveloped viral vector was a mannitol/dextran blend.  This led to the hypothesis that the encapsulation mechanism differs between the two groups of viruses.  The glass transition temperature (Tg) of the spray dried formulations (without virus) stored at 37 °C for 10 days was measured to infer the potential molecular mobility of the viral vector within the primarily amorphous matrix.  Formulations containing dextran exhibited the smallest depression in Tg after storage, indicating minimal increase in molecular mobility over time.  RNA leakage from aged spray dried powders containing VSV was quantified to investigate the encapsulation mechanism of enveloped viral vectors and followed a similar trend to the in vitro activity tests.  VSV with poor performing excipients yielded the least detectable RNA/pfu after three days of storage at 45°C, suggesting that the lipid envelopes ruptured and released viral RNA which denatured during storage.  This work demonstrates that the VSV vector can be thermally stabilized through spray drying but highlights that different carbohydrates interact differently with enveloped versus non-enveloped viral vectors, providing a guideline for future work with the advent of new vaccines.

abstract: Thesis

abstract: Master of Applied Science (MASc)

abstract: Most vaccines lose their activity when stored at room temperature and therefore are required to be stored at temperatures between 4 °C and -80°C to maintain vaccine potency.  The refrigeration required to meet these temperatures is costly and limits the distribution of vaccines to resource poor areas in the world where refrigeration technology is uncommon.  Spray drying, a process that rapidly dries a solution to form a dry powder, was used to trap vaccines within a sugar matrix to protect the vaccine from heat and structural changes that would otherwise deactivate it.  The spray dried powders demonstrated higher thermal stability than liquid samples, which decreases the need for refrigeration during transportation and storage.   Thermal stability trends for spray dried powders produced with various sugars and categories of viruses are presented.


title: Riesz Sequences and Frames of Exponentials associated with non-full rank lattices.

contributor:
Gabardo, Jean-Pierre
Mathematics and Statistics

abstract:
Let
   Rd be a measurable set of  nite positive measure (not necessarily bounded).
Let (cj)kj
=1 be a given collection of vectors in Rd, and let H be the dual lattice of a full
rank lattice K   Rd. For   2 Rd, let e  denote the exponential
e (x) := e2 ih ;xi; x 2 Rd:
It is known that, the collection
E( ) := fe  :   2  g;
where   = f(cj + h) 2 Rd : h 2 H; j 2 f1; :::; kgg; forms Riesz basis on
   Rd if the
domain
 is a k-tile domain and if, in addition, it satis es an extra arithmetic property,
called the admissibility condition. The theory of shift invariant spaces generated by the
full rank lattice K plays an important role to analyze and solve the above problem.
The main goal of this thesis is to study a variant of the problem above where the dual
lattice H is replaced by a non-full rank lattice in Rd. In particular, given an at most
countable index set J and a collection of vectors (cj)j2J   Rd, we examine the existence
of Riesz sequences, frames and Riesz bases of the form
E( ) := fe  :   2  g;
where   = f(cj +h) 2 Rd : h 2 H; j 2 Jg; on
   Rd as above, and H, a non-full rank
lattice in Rd. Our results are obtained using an extention of the theory of shift invariant
subspaces of L2(Rd), where the shifts are now generated by a non-full rank lattice in
Rd.

abstract: Thesis

abstract: Master of Science (MSc)


title: Molecular Insight into Cellulose Nanocrystals and their Interaction with Cellulosic Oligomers by All-Atom Simulation

title: Molecular simulation of cellulose surface interactions

contributor:
Xi, Li
Chemical Engineering

subject:
Cellulose Nanocrystals
CNC-polymer interaction
Potential of Mean Force

abstract: Cellulose nanocrystal (CNC) has found application in a variety of novel products due to its spectrum of properties. Notably, the CNC-polymer systems have seen numerous applications in special materials like Pickering emulsions, foams and gels etc. CNC interacts with different polymers to a different extent. These interactions include molecular level and bulk interactions. Subsequently, they modify the interfacial properties. Though vibrant, the CNC-polymer molecular interaction is still unclear. We took this void in our understanding as our motivation to explore these interactions. In this work, we tried to understand why CNC interacts differently with different polymers and what drives the adsorption of polymer on CNC. Our work can also help us to understand the configurations and origins of CNC-polymer system properties. The broad range of length and time scales covered by this physical process requires a multiscale simulation approach. In this thesis, we start with the all-atom molecular simulation and focus on the specific energetic interactions between CNC surfaces and unrealistically short polymer chains. In future work, we will build on this model and develop a multiscale modeling approach for capturing the full scope of CNC-polymer interaction, including the configuration and dynamics of realistic long polymer chains around CNCs. We propose that there are two driving forces for adsorption based on the free energy difference values obtained via PMF (potential of mean force) calculations done on eight systems with different physical components. Overall, we conclude that the balance between polymer's ability to form hydrogen bonds with the surface and their interactions with the bulk solvent control the adsorption and desorption phenomenon. A larger coarse-grained model developed from our simulations will help to understand these systems better. This presented work deals with the specific energy interactions and information which we will need for the systematic coarse-graining of these systems.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Towards optimizing the operation of microbial electrolysis cells for heavy metal removal

contributor:
Kim, Younggy
Civil Engineering

subject:
microbial electrolysis cells
bioelectrochemical system
heavy metal removal
wastewater

abstract:
Heavy metals are a growing environmental concern as they are unable to be
metabolized in the environment, leading to bioaccumulation in the food chain and
impacting human health. Treating heavy metals is difficult and expensive. Current
methods include precipitation (which generates sludge that is costly to dispose of) or
requires the use of a membrane, which fouls and requires regeneration.
Microbial electrolysis cells (MECs) represent an alternative for treating heavy
metal contaminated wastewater. Reactor components are cheap, and operation requires
only a small amount of electricity. The electrically active biofilm oxidizes organics in the
wastewater while transferring electrons first to the anode, then to the cathode, where
aqueous metals are reduced to a solid deposit, a mechanism called electrodeposition. Few
studies have been conducted to investigate the best operational conditions for heavy
metal removal in MECs. In this study, the effects of hydrodynamics, applied voltage, and
initial metal concentration on heavy metal removal mechanisms are investigated, and the
best operational practices are determined on a high level.
Mixing in the cathode chamber increased electrodeposition by 15%, decreased the
cathode potential by -0.06 V, and increased current generation between 10-30%.
Increasing the applied voltage from 0.6 V to 1.2 V increased electrodeposition by 22%.
With both mixing and higher voltage applied, 93.35% of cadmium was removed from the
catholyte in 24 hours. Although high voltage application maximized electrodeposition for
short-term treatment, long-term treatment indicated lower applied voltage resulted in
healthier MEC reactors, better overall metal recoveries, along with a more stable cathode
potential.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Exploring Airplane Boarding

contributor:
Lovric, Miroslav
Mathematics

subject: Math Simulations

abstract: The airline industry is crucial to economic growth and the number of passengers is expected to increase by approximately 250 million from 2017 to 2018.  IATA believes it is imperative to increase airline efficiency to maintain sustainability.  Passenger boarding is known to constitute 60% of airplane turnaround time, identifying this step as rate determining.  In this study, we investigate passenger boarding strategies utilized by airline companies and strategies simulated by existing literature.  We propose more efficient passenger boarding methods for the Airbus A320/ Boeing 737 and Airbus A380-800/ Boeing 777-300ER airline classes.  We use GNU Octave to construct a cellular automaton model that operates on the interaction of a 2-dimensional matrix, representing passenger attributes, and a 4-dimensional matrix, representing the cells of the airplane in consideration.  We consider row interferences, aisle interferences, luggage stow away time, and general passenger delays.  We find that boarding strategies which minimize passenger interferences are the most efficient for both airline classes.  Interestingly, some boarding strategies for the Airbus A320/ Boeing 737 are more efficient when boarding at 30 passengers/ min instead of 60 passengers/ min.  However, the Airbus A380-800/ Boeing 777-300ER shows slower boarding rates for any boarding frequency less than 60 passengers/ min, suggesting the size of the airplane layout determines sensitivity to boarding frequency.  With the Airbus A380-800/ Boeing 777-300ER having limited documentation, we define and propose new boarding strategies, OBFOIZ and OBFOISA, that improve on the passenger boarding times in the existing literature for this double-aisled airplane.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: The airline industry is crucial to economic growth and the number of passengers is increasing every year, reaching increases of 250 million.  In light of this, the International Air Transport Association believes it is imperative to increase airline efficiency.  Since airplanes generate revenue while they are in the air, we look to minimize the time they are on the tarmac, also known as airplane turnaround time.  Passenger boarding has shown to constitute 60% of airplane turnaround time, identifying this step as a bottleneck.  In this study, we investigate passenger boarding strategies utilized by airline companies and documented by existing literature.  We then propose more efficient passenger boarding methods for the Airbus A320/ Boeing 737 and Airbus A380-800/ Boeing 777-300ER airline classes.  With the Airbus A380-800/ Boeing 777-300ER having limited documentation, we define and propose new boarding strategies that improve the passenger boarding time.


title: Military-Age Males in U.S Counterinsurgency and Drone Warfare

contributor:
Beier, J. Marshall
Political Science

subject: International Relations, security studies, gender

abstract:
In 2012, The New York Times reported that the Obama Administration excluded all Military-Age Males from the collateral damage count in areas where the U.S engaged in drone warfare/ Though the Military-Age Male (MAM) category references the draft, the term is applied to all boys and men, including civilians, who are aged sixteen years and older. The Military-Aged Male category is not synonymous with 'combatant,' but marks boys and men for differentiated treatment in conflict zones, to the point where male bodies are used as a shorthand for 'combatant' when assessing the collateral damage count.

This dissertation seeks to answer an empirical puzzle. The U.S Army/Marine Corps Counter-Insurgency Field Manual (2006), a document which emerged from the American intervention in Iraq and Afghanistan, emphasizes that militants vie for the civilian population's support as a way to win the war against a stronger and better-resourced military force. These documents state that the United States cannot rely on military prowess alone and that, in fact, “non-military means are the most effective” way to win an irregular war against militant groups.

Both the Bush Jr. and Obama Administrations used the Military-Age Male category to structure military strategy, meaning that civilian protection was applied asymmetrically and that military violence was legitimized when directed against male civilians. These security practices would seemingly cause resentment from a large segment of the population and undermine the success of U.S foreign policy.

This dissertation documents the political ecosystem that legitimized violent military action against the  'Military-Age Male.' Specifically, I examine Military-Age Males under the Bush and Obama Administrations and illustrate how counterinsurgency and drone warfare became practices that were sustained by an elaborate bureaucracy that interpreted the battlespace—and combatant from civilian—by using assumptions about gender.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: Photon Absorptiometry in Three Component Systems; Bone Mineral at the Spine and in the Presence of a Hip Prosthesis

contributor:
Webber, C. E.
Physics

subject: photon absorptiometry bone prosthesis

abstract: The non-invasive measurement of the mass of bone is a clinically relevant problem. The bone is one component of a composite system. At the spine it may include fat, lean and bone mineral. At a hip prosthesis it may include soft tissue, bone mineral and metal. The measurement of the attenuation of photons of different energies can be used to determine the mass of one or all of the components of the composite system. The first system is currently measured using only two photon energies by assuming that it is a two component system. A model was developed which predicts the effect of the third component, fat, and was validated using phantom measurements. Typical parameters for the volume and spatial distribution of fat 𝘪𝘯 𝘷𝘪𝘷𝘰 were determined using CT scans. In combination with the model a median error of 8% is introduced by the third component. The feasibility of using a third energy to correct for the error was investigated. A model for the variance of the bone measurement normalized to emitted photon flux was developed. The optimal set of photon energies yielded a minimum value for the variance. However, this variance was excessively high, requiring a radiation dose 3000 times that for dual photon absortiometry. For the second system a triple photon absorptiometry technique was developed using the isotopes 203-Hg and 141-Ce. The technique was shown to be valid, but the variance was high due to cross-over of high energy photons in the detector and by scattering. In order to make measurements with a precision of 1%, counting times of 70 hours are required. Monte Carlo simulations were performed to determine the optimal geometry to reduce cross-over from scattering. However, cross-over cannot be reduced sufficiently with 203-Hg and 141-Ce. A three isotope source is required to make clinical bone measurements at a prosthesis.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Membrane-Mediated Conformation of Dynorphin A-(1-13)-Peptide as Studied by Nuclear Magnetic Resonance Spectroscopy, Circular Dichroism Spectropolarimetry, and Molecular Dynamics

contributor:
Epand, R. M.
Biochemistry

subject:
dynorphin
peptide
dichroism
magnetic resonance

abstract: The structural requirements for the binding of dynorphin to the kappa opioid receptor are of profound clinical interest in the search for a powerful non-addictive analgesic. These requirements are thought to be met by the membrane-mediated conformation of the opioid peptide dynorphin A-(1-13}, Tyr¹-Gly²-Gly³-Phe⁴-Leu⁵-Arg⁶-Arg⁷-Ile⁸-Arg⁹-Pro¹⁰-Lys¹¹-Leu¹²-Lys¹³. Schwyzer [𝘉𝘪𝘰𝘤𝘩𝘦𝘮𝘪𝘴𝘵𝘳𝘺 25: 4281-4286 (1986)] has proposed an essentially α-helical membrane-mediated conformation of the tridecapeptide. In the present study, the hydrophobic moment, the helix probability and a four -state secondary structure prediction were computed. They signified, in agreement with circular dichroism (CD) studies on phospholipid-bound dynorphin A-(1-13)-tridecapeptide, negligible helical content of the peptide. CD studies demonstrated that the aqueous-membraneous interphase can be mimicked by methanol. The 500 and 620 MHz ¹H nuclear magnetic resonance (NMR) spectra of dynorphin A-(1-13) in methanolic solution were sequence-specifically assigned with the aid of correlated spectroscopy (COSY), double-quantum filtered phase-sensitive COSY, relayed COSY (RELAY) and nuclear Overhauser enhancement spectroscopy (NOESY). 2-D CAMELSPIN/ROESY experiments indicated that at least the part of the molecule from Arg⁷ to Arg⁹ was in an extended or β-strand conformation, which was in line with deuterium exchange and temperature dependence studies of the amide protons. ¹³C_α spin-lattice relaxation rate constants indicated a non-rigid backbone conformation. Transferred nuclear Overhauser effect studies on aqueous systems containing dynorphin A-(1-13) in the presence of dimyristoyl-phosphatidylcholine bilayers indicated a folded conformation from Tyr¹ to Leu⁵. The findings were incorporated into a tentative molecular model, which also indicated a non-helical, non-extended conformation for the rest of the molecule in the presence of corresponding distance-restrained negative charges.

abstract: Thesis

abstract: Master of Science (MSc)


title: Short Synthetic DNA Oligomers and Their Interaction with Cisplatin

contributor:
Lock, C. J. L.
Neilson, T.
Chemistry

subject: DNA oligomers cisplatin

abstract:
The interaction between short oligodeoxynucleotides of specific sequence with cisplatin, cis-Pt(NH₃)₂Cl₂, has been examined under single stranded and duplexing conditions by ¹H nuclear magnetic resonance (NMR) spectroscopy. The oligonucleotides were synthesized by a modified phosphotriester technique adapting procedures initially used in oligoribonucleotide synthesis. The oligo sequences were designed to favour the intrastrand cis-Pt(NH₃)₂[d(-GpXₙpG-)-N7(l),N7(n+l)] crosslink, where X was up to three thymine units. Variable pH NMR was used to determine the site of platination on the oligomer. Variable temperature NMR was used to determine changes in base stacking and duplex formation resulting from oligomer platination.
In the short oligomers, the intrastrand cisplatin crosslink formed between terminal guanines resulted in the internal section of the sequence being bulged out of a normal stacking orientation. The chemical shifts of the guanine H-8 resonances indicated that platination caused one of the guanine bases to flip from the normal anti geometry into a more syn-like orientation. This was observed for the three oligomers examined (X=thymidine, n=1,2,3). Variable temperature NMR of exchangeable imino protons in the oligomers with larger loops (n=2,3), indicated that the loop region of the complex was a random coil and that water access to the loop was restricted.
i i i
Longer sequences were examined which contained the cis-Pt(NH₃)₂[d(GpXₙpG)-] complex as well as external nucleotide units, 3' and 5' to the platinated region. Platination disrupted intrastrand base stacking of nucleotides externally adjacent to the platinum complex.
Complementary and partially complementary sequences were examined under duplexing conditions. Stabilities, reflected in the Tₘ of the duplex, of fully complementary hexamer, heptamer and octamer oligomer mixtures were obtained by variable temperature NMR. Changes in duplex stability resulting from oligomer sequence and length along with the nature of the duplex to coil transition were discussed.
Imperfect duplexes, designed to mimic the loop structures formed in platinated oligomers, indicated that the duplex containing one extra core thymine formed a helix resembling the fully complementary hexamer duplex with the extra base stacked out of the helix. With the core of the duplex containing two thymine units and one opposing complementary adenine, both thymines stacked into the helix with the adenine oscillating between the two thymines. When the oligomer mixture contained two extra thymine units with no opposing complements, duplex formation was not observed. A comparison between the duplex to coil transition in normal and imperfect duplexes was discussed.
Similar duplex experiments were carried out using the platinated oligomer sequences. In each case examined, aggregation of the platinated strand, coupled with the oligomer sequences employed contributed to the failure of duplex formation.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: The Social Transmission of Food Preferences in Small Colonies of Norway Rats

title: Social Transmission of Food Preferences in Norway Rats

contributor:
Galef, B. G.
Psychology

subject:
food
norway
rats
social transmission

abstract: The present research investigates the social transmission of food preferences in small colonies of domestic rats. In Experiment 1, four demonstrator rats were poisoned for consumption of a particular flavored diet and placed in a floor enclosure with a choice between the averted diet and an alternative diet. These original demonstrators were replaced one by one each 24-hr over a period of 4 days with naive subjects. The original demonstrators effectively transmitted a preference for the alternative diet to the naive replacements, as these replacements exhibited a preference for the alternative diet for a period of 4 days following the departure of the final demonstrator. Employing essentially the same methodology as that used in Experiment 1, videotape analysis of the feeding behavior of subjects on the sixth day (zero original demonstrators, four naive replacements) of Experiment 2 revealed no significant difference in the food choices of the first, second, third and fourth replacement subjects, indicating that naive replacements became effective demonstrators following interaction with original demonstrators. Random placement of the food bowls each day during Experiment 3 revealed that the social transmission of food preferences from original demonstrators to naive replacements can persist in the absence of excretory cues around a particular feeding site. In Experiment 4, removal of demonstrators from the floor enclosure during periods in which foods were available there for replacement subjects to choose between revealed that naive observers could obtain sufficient information from demonstrators during non-consumption periods to guide their food choices. Observers in Experiment 4 exhibited a preference for their respective demonstrators' diets when presented a choice between their demonstrators' diet and an alternative diet in the absence of demonstrators. In the General Discussion, variables were discussed that might modify the strength of socially transmitted food preferences in rats and could be examined in future research using the present paradigm.

abstract: Thesis

abstract: Master of Science (MSc)


title: An Investigation of the Parameters of CCK-Induced Satiety

contributor:
Weingarten, H.P
Psychology

subject: satiety, kinetics,interaction, sham feeding, derivative, oropharyngeal stimulation

abstract:
Two major aspects of CCK-induced satiety were examined in the
food deprived sham-feeding rat: the kinetics of the inhibition of
feeding produced by CCK and the interaction of CCK-induced satiety with
oropharyngeal stimulation. Four results were presented regarding the
kinetics of the CCK satiety effect. First, CCk administered coincident
with the initiation of sham feeding inhibits feeding in a dose-related
manner. Second, the increased efficacy of the higher dose of CCK
delivered at the same time as sham feeding results from an increase in
the size of maximum suppression and an increase in the time of
suppression effected via a decreased latency to suppression. Third, CCk
delivered 15 minutes before sham feeding begins has no effect on
feeding. Fourth, the administration of a long-lasting derivative of CCK
15 minutes prior to the initiation of sham feeding can suppress intake.
Two results were presented regarding the role of oropharyngeal
stimulation in CCK-induced satiety. First, it was shown that
oropharyngeal stimulation enhances the satiety action of CCK. Second,
the amount and pattern of feeding inhibition produced by CCK are
equivalent regardless of whether the peptide is administered coincident
with, or some time after, the initiation of sham feeding. The
implications of these results for the therapeutic use of this peptide
and its role in producing satiety are discussed.

abstract: Thesis

abstract: Master of Arts (MA)


title: The Role of Macrophage Scavenger Receptor Class B, Type 1 (SR-BI) in the development of Atheroscelerosis in Apolipoprotein E Deficient Mice

contributor:
Trigatti, Bernardo L.
Biochemistry

subject: high density lipoprotein, cholesterol transport, atherosclerotic development

abstract:
The high density lipoprotein (HDL) receptor Scavenger Receptor, Class B, Type I (SRBI)
is a 509 amino acid integral membrane protein which has been shown to have an
important role in HDL-mediated reverse cholesterol transport. SR-BI has been shown to
mediate selective uptake of cholesterol, and also mediates efflux of cholesterol to HDL as
seen in in vitro cell culture studies. SR-BI is abundant in the liver and steroidogenic
tissues, and is also present in macrophages, which play an important role in the initial
stages of atherosclerotic development. SR-BI has been shown to be protective against
atherosclerosis by way of overexpression and knockout (KO) studies in murine
atherosclerosis models, including low density lipoprotein receptor (LDLR) knockout
mice, apolipoprotein E (ApoE) knockout mice, and human apolipoprotein B (ApoB)
transgenic mice. SR-BI/LDLR double knockout (dKO) mice show a 6-fold increase in
diet-induced atherosclerosis compared to LDLR single KO controls, and SR-BI/ApoE
dKO mice show severe coronary occlusion, myocardial infarction, and premature death
on a normal chow diet. In both, plasma total cholesterol levels are significantly elevated,
and associated with abnormally large HDL particles. The majority ofSR-BI's
atheroprotective effect has been shown to result from plasma cholesterol clearance by
way of selective uptake in the liver. Recently, Covey et al showed that elimination of SRBI
expression in macrophages of LDLR KO mice resulted in increased diet-induced
atherosclerosis. To see if SR-BI in macrophages contributes to the overall
atheroprotective effect of SR-BI in ApoE KO mice, presumably by mediating cellular
cholesterol efflux to HDL, selective deletion ofSR-BI was induced in bone marrow
derived cells of ApoE KO mice using bone marrow transplantation. Female ApoE -/recipient
mice were transplanted with either SR-BI +/+ ApoE -/-or SR-BI -/- ApoE -/bone
marrow from male donor mice, and fed a high fat diet for 12 weeks. This resulted in
significantly increased atherosclerosis in mice transplanted with SR-BI -/- ApoE -/-bone
marrow, with a concomitant decrease in cholesterol associated with HDL-sized
lipoproteins. No significant differences were seen in plasma total cholesterol levels or
levels of cholesterol associated with non-HDL lipoproteins. These data suggest that SRBI
in macrophages contributes to SR-BI's overall protective effect against
atherosclerosis, and also plays a role in the regulation ofHDL cholesterol, in ApoE
deficient mice.

abstract: Thesis

abstract: Master of Science (MSc)


title: SHC Functions in the Development and Transformation of the Mouse Mammary Gland

title: SHC Functions in the Mouse Mammary Gland

contributor:
Muller, W. J.
Biology

subject:
mouse
mammary gland
SHC

abstract: The adapter protein Shc is a ubiquitously expressed Src homology 2 (SH2) domain protein implicated in the transmission of activation signals to Ras. She proteins become phosphorylated on tyrosine in cells stimulated with a variety of growth factors and in v-𝘴𝘳𝘤 transformed cells and are able to transform fibroblasts and differentiate PC12 cells in a Ras-dependent fashion. To assess the transforming ability of Shc in the mouse mammary gland, I generated transgenic mice harbouring the p52ˢʰᶜ cDNA under the transcriptional control of the mouse mammary tumor virus long terminal repeat (MMTV LTR). While p52ˢʰᶜ expression was correlated with multiple enlarged terminal end buds in virgin mouse mammary glands, multiparous mice developed mammary hyperplasias and mammary carcinomas. The frequency, latency and focal nature with which these tumors arose suggests that additional events are necessary to induce malignant conversion of primary mammary epithelial cells. To directly test the role of Shc in established mammary tumor models, I have generated two strains of bigenic mice. When Shc was overexpressed with NDL 1-2, a constitutively activated form of the Neu receptor tyrosine kinase, latency of tumor onset was decreased over that of parental MMTV/NDL 1-2 mice. Polyomavirus middle T antigen (PyV MT) mutants with a functionally inactive Shc binding site (MT Y250F) are debilitated in mammary tumor formation compared to wild-type PyV MT transgenic animals. Concurrent overexpression of Shc with MT Y250F accelerated tumor kinetics and increased the propensity for metastasis to the lungs of bigenic animals.

abstract: Thesis

abstract: Master of Science (MSc)


title: Purification and Inhibition of Hydroxymethylglutaryl Coenzyme A Synthase

contributor:
Harrison, Paul
Chemistry

subject: synthase, purification, ethanol fractionation, irreversible

abstract:
Hydroxymethylglutaryl-CoA synthase (HMG-CoA synthase) catalyzes the
formation of HMG-CoA from acetyl-CoA and acetoacetyl-CoA. F-244 (1), a naturally
occurring J3-lactone isolated from Fusarium sp. ATCC 20788 and other species, is known
to be a potent and specific inhibitor ofHMG-CoA synthase isolated from rat liver.
1Ji,, HO,.,._.. .. , '• .. ,....13_.,., ;=(
0
14 0
0
(1) (2)
This thesis describes the 48 fold purification of HMG-CoA synthase from
bakers yeast in a three step procedure involving ethanol fractionation followed by
ammonium sulfate precipitation and then hydroxylapatite chromatography. This
procedure was found to be reproducible and yields a preparation of specific activity 0.14
units (j...tmolfmin)/mg in an overall yield of 8%.
In our study, F-244 was found to be a potent irreversible inhibitor of HMGCoA
synthase isolated from bakers yeast, with an IC50 value of 0.009 j...tM. This value is
almost identical to the inhibitory activity of F-244 on rat liver HMG-CoA synthase that
has been reported in the literature.
Tritium labeled F-244 was prepared, for the first time, by feeding methyl-[3H]methionine
to cultures of Fusarium sp. The [15, 16, 17, 18-3H] F-244 isolated had a
specific activity of 1.3 x 106 DPM/mg. This tritiated F-244 was then used as an affinity.label for HMG-CoA synthase. Attempts to isolate the enzyme-inhibitor complex were
unsuccessful due to the low level of radioactivity associated with the tritiated F-244.
HMG-CoA synthase was also shown to be inhibited in a time-dependent
irreversible manner by {±)-(3-butyrolactone (2). The rate of inactivation (~) was found to
be 0.4697 s-1 and the inhibition constant (K1) was found to be 9 mM. The inactivation was
found to be irreversible over several hours.

abstract: Thesis

abstract: Master of Science (MS)


title: “Dark Shades Don’t Sell”: Race, Gender, and Cosmetic Advertisements in the Mid-Twentieth Century United States

contributor:
Balcom, Karen
History

subject: race, gender, cosmetics, twentieth century, United States, feminism, hair, skin, racialization, racism, skin bleach, straightening

abstract: In this study I examine the two major cosmetic categories - products for skin and products for hair - aimed at frican American women and advertised within the black press between 1920 and 1960. Specifically, I examine the Chicago Defender, Afro-American, Plaindealer, and Ebony. My project analyzes the images and conceptions of blackness and beauty sold to women of colour by white-owned and black-owned cosmetics companies.  I explore the larger racial and social hierarchies these advertising images and messages maintained or destabilized. A central theme of this project has been tracing the differences in advertising messages and conceptions of beauty communicated by black-owned and white-owned companies. Many of the images and much of the advertising copy produced by black-owned cosmetic companies challenged hegemonic beauty ideals that venerated white beauty and sold white idealization as a norm. The black cosmetic industry, however, was dominated by white-owned companies. The dominant position of white-owned companies was linked to the advantages associated with whiteness, which allowed these companies to advertise with greater frequency throughout the forty-year period. White-owned and black-owned companies often pursued diverging advertising strategies and messaging about black beauty. An important finding of the project is that white-owned companies were more likely to use degrading language and stereotypes to describe black beauty in their advertisements. However, a company’s racial identity did not always determine advertising strategies or messaging about black beauty. An important concept that permeated the 1920s and 1930s was the strategy of racial uplift, which was promoted by several black-owned companies. This strategy tapered out by the1940s as new technologies like photography regularly depicted black women with dignity and accuracy. The 1940s and 1950s witnessed new advertising strategies including the appeal to glamour. This period also saw the introduction of Ebony magazine, which fundamentally altered advertising messages through their appeal to middle class sensibilities.

abstract: Thesis

abstract: Master of Arts (MA)

abstract: My project analyzes skin bleaching and hair straightening advertisements appearing in four black-owned periodicals between 1920-1960: Chicago Defender, Afro-American, Plaindealer, and Ebony. The main goal has been to document the advertising messages about blackness and beauty communicated to black women through the advertisements of black-owned and white-owned cosmetic companies. I explore the larger racial and social hierarchies these advertising images and messages maintained or destabilized. A major finding of this project has been that advertising messages usually, but not always, diverged along racial lines. White-owned companies were more likely to use denigrating language to describe black hair and skin, and more likely to measure the beauty of black women based on how closely they approximated whiteness. Black-owned companies tended to challenge this ideology. They used messages about racial uplift as part of this challenge.


title: FRAMING NATURE AND NATION: THE ENVIRONMENTAL CINEMA OF THE NATIONAL FILM BOARD, 1939-1974

contributor:
Egan, Michael
History

subject:
Film
Canadian cinema
Nature
Environment
NFB
Environmental History

abstract:
This project is about the visual ways people represent the nonhuman world, and the struggles over its meaning. It is the story of how the Canadian government used the National Film Board of Canada (NFB) to manufacture and sustain a national identity that was defined by its encounters with nature, and how those definitions morphed over time. The NFB was established in 1939 by the federal government. It was to be the eyes and ears of Canada, a way for Canadians to experience the nation. As a cultural institution supported by the state, the NFB is fertile ground for an examination of state discourses about nature. In particular, I analyze NFB films as vehicles for the Canadian government’s long-running nation-building project. Between 1939 and 1974, NFB filmmakers aligned their representations of nature with the views of the government. They imagined nature as a unifying symbol of national identity and as an object to be surveyed, rationalized and exploited by government institutions. Utilitarian narratives about natural resources and wilderness management served other ideological motives too. Specifically, NFB films about nature in the postwar period privileged a high modern way of seeing the environment.
This project also seeks to discern instances of ideological conflict between filmmakers and official “environmental” viewpoints, where government strategies are questioned, ridiculed or reformulated in the films themselves. Although the NFB is a product of state policy as well as an interpreter of it, it was also actively involved in producing grass-roots narratives about the environment. The NFB’s directive to “interpret Canada to Canadians” unwittingly created opportunities for independent filmmakers to share their own visions of nature that often diverged from the state. This project therefore investigates moments where filmmakers used the camera as an apparatus of reflection to challenge and subvert state modes of thinking.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)

abstract: The National Film Board of Canada (NFB) was established and financed by the federal government to be the “eyes of Canada.” It is therefore a valuable site in which to examine, among other things, how the state defined the limits and uses of nature. While NFB discourses about the environment often mirrored state ideology, they also reflected alternative voices and perspectives. Filmmakers made documentaries within the NFB production system that challenged, questioned, or even ridiculed state ideology. In other words, nature was not only imagined as a national resource to be exploited and controlled through technology and science, it was also envisioned as something to be appreciated for its ecological diversity and its wildness.


title: Investigation of the Role of Mate Choice in the Evolution of Menopause under Serial Monogamy

title: HUMAN MATE CHOICE AND THE EVOLUTION OF MENOPAUSE

contributor:
Singh, Rama
Biology

subject:
evolution
menopause
mate choice
serial monogamy

abstract:
Menopause, the cessation of reproductive capabilities before death, is a detrimental trait
for female fitness, yet persists in all human populations. Numerous hypotheses have been
published to describe how menopause has been maintained but failed to explain the origin and
genetic basis of this trait. In 2013, Morton et al. proposed an influence of the mate choice
behaviour, specifically a bias in mating ages that could allow for a trait, seemingly detrimental
to fitness, to become neutrally fixed in a population. The goal of our research, presented herein,
is to understand the role of the mating system, the sexual behaviour of a group, and especially
mate choice, on the origin and evolution of menopause under a serial monogamy scenario.
Analysis was conducted using an agent-based computational model that simulated
populations. The populations were generated according to specified demographic parameters
and reproduced according to a serial monogamy mating system. With the model, parameters
were investigated including population lifespan, fecundity, pairing eligibility, age of loss of
fecundity, and timing of decay in fecundity. Simulations revealed that, under certain
restrictions, menopause can neutrally evolve. When mate choice was restricted to a particular
age preference bias, menopause can appear with no diminishment of fitness. This novel mode
for the origin of menopause is inferred to result from the accumulation of deleterious mutations
in the female genome. By combining this ability of fertility-diminishing mutations to
accumulate with research into the genetic basis of menopause, we provide a system for the
evolution of menopause in a population of serial monogamy.

abstract: Thesis

abstract: Master of Science (MSc)

abstract: Despite decades of research into menopause, there remains no clear understanding of how this deleterious trait came to persist in the human population. It has been proposed that a bias in mate choice such that only younger females are chosen to mate can result in the accumulation of deleterious mutations, ultimately leading to menopause. We analyzed the evolution of menopause under a mating system of serial monogamy by a computational simulation. We came to three main conclusions. Firstly, under modern demographic parameters, menopause cannot evolve under serial monogamy. Secondly, in a population of shortened longevity, similar to chimpanzee, menopause neutrally appears at an age presently experienced by women. Finally, when mate choice is restricted such that only young females are eligible to mate within a system of serial monogamy, menopause can evolve. This means with the current mate choice shift towards older women, menopause can be postponed or even eliminated.


title: From Battle of the Bands to the Big Leagues: How do live music venues structure local music scenes?

contributor:
Fetner, Tina
Sociology

subject: music; culture; organization

abstract:
This dissertation examines the role of live music venues in structuring local music scenes, using the city of Hamilton as case study. To explore this, I first develop a categorization scheme to distinguish “types” of venues to which individual establishments cluster into on the basis of their organizational characteristics. These venues types allow for claims to
be made about the organizational structure of venues within the local scene. I then move forward to show that these venue types are better understood as organizational forms, by conducting a textual and visual analysis of the promotional data, which coincide with types of venue logics which inform promotional practices of each venue form. Finally, I
examine the role of venues in contributing to gender inequality in the music scene, by looking at the types of bands that are booked to play in each venue form, taken into account not only gender composition but also the artist configuration (solo/band). Taken together this dissertation highlights the importance of venues as part of the social organization of any music scene over and above the social dynamics of artists and audiences.

abstract: Thesis

abstract: Doctor of Philosophy (PhD)


title: THERMOPHILIC ANAEROBIC DIGESTION OF WASTEWATER SLUDGE

subject:
Anaerobic digestion
Thermophilic anaerobic digestion
Anaerobic digestion modelling
Autohydrolysis
Pretreatment
Hydrolysis

abstract: Sludge management is the highest operating cost in municipal wastewater treatment. Anaerobic digestion (AD) is used to stabilize the sludge and reduce biosolids generation. Hydrolysis kinetics limit the rate of anaerobic digestion and must be improved to increase the overall process rate. In this study a new sludge characterization analysis was used to evaluate hydrolysis in a lab-scale pretreatment process operated at 55℃, 65℃, and 75℃. The experimental results were used to develop a new AD mathematical model, the hydrolysis digestion model (HDM). The model developed is easier to use, as the number of processes and variables were reduced by half, in comparison to existing models. The model variables can be measured using standard sludge characterization analysis, and the hydrolysis reactions included the fermenting microorganism to more accurately model the two-phase hydrolysis model. Model simulations were found to be a good fit of the experimental results, accurately predicting the rate and extent of hydrolysis in the pretreatment digester.

abstract: Thesis

abstract: Master of Applied Science (MASc)


title: Aerobic Reductive "Activation" of 5-Nitro-2-Furaldehyde Semicarbazone by Rat Liver Xanthine Dehydrogenase

contributor:
McCalla, D. R.
Biochemistry

subject:
activation
rat
liver
xanthine dehydrogenase

abstract: 5-Nitrofurans are synthetic antibacterial agents. In general, nitrofurans have been shown to be toxic and mutagenic to cultured mammalian cells and carcinogenic in rodents. The possibility that human exposure to nitrofurans may be causing genetic damage or cancer has stimulated research directed towards elucidating the metabolism and mechanism of action of these compounds. A comprehensive understanding of the molecular basis of nitrofuran action may also be useful for comprehending the mechanism of action of other aryl and heterocyclic nitro compounds. It is known that enzymatic reduction of nitrofurans to reactive but uncharacterized metabolites that damage DNA constitutes an important "activation" step in both bacteria and hypoxic mammalian cells. However, since the known mammalian enzymes having nitroreductase activity are reported to be strongly inhibited by molecular oxygen, the relation of reductive activation to the DNA-damaging effects of nitrofurans in intact animals or in aerobic cultured cells is unclear. In rodents the liver is a major site of nitrofuran reduction in vivo. Net reduction of 5-nitro-2-furaldehyde semicarbazone (nitrofurazone) by rat liver homogenate was found to be relatively insensitive to oxygen when compared to net nitroreduction by milk xanthine oxidase. Intermediates generated in the aerobic nitroreduction bound tightly and probably covalently to protein. The nitroreductase in the rat liver preparation was identified as xanthine oxidoreductase by its apparent MW, substrate specificity and inhibition by allopurinol. Xanthine oxidoreductase is known to function in vivo as xanthine dehydrogenase (D form) which is converted to xanthine oxidase (0 form) during purification and storage. The 0 form is considered to be the major cytosolic nitroreductase and its activity is strongly inhibited by oxygen in vitro. Net nitroreduction by the D form has not been studied previously. In the rat liver preparation the bulk of the aerobic nitroreductase activity was associated with the D form of xanthine oxidoreductase during chromatography on CM cellulose, heat conversion of D form to 0 form and chemical interconversion of D form to 0 form and back to D form. Thus, net reduction of nitrofurazone by xanthine dehydrogenase is considerably less sensitive to inhibition by oxygen than is net nitroreduction by rat liver or milk xanthine oxidase. The ability of xanthine dehydrogenase to reduce nitrofurazone aerobically to highly reactive species in vitro suggests that this enzyme may play a role in a nitroreductive process which contributes to the mutagenic and carcinogenic action of nitrofurans and other nitroheterocyclic and nitroaromatic compounds in vivo. On the other hand, the nitroreductase activity of xanthine dehydrogenase in non-target tissues may, in some cases, decrease the amount of nitrocompound available in target tissues and hence play a "protective" role.

abstract: Thesis

abstract: Master of Science (MSc)


title: Studies on Insulin Receptor in Xenopus Laevis Oocytes

title: Studies on Insulin Receptor in X. Laevis Oocytes

contributor:
Andrews, D. W.
Ananthanarayanan, V. S.
Biochemistry

subject:
oocytes
insulin
xenopus laevis

abstract: The Xenopus laevis oocyte was examined as a model system for investigating insulin receptor function. The role of extracellular calcium on insulin-stimulated deoxyglucose uptake (ISDU) in the 𝘟𝘦𝘯𝘰𝘱𝘶𝘴 𝘭𝘢𝘦𝘷𝘪𝘴 oocyte was investigated. It was determined that removal of calcium from the medium did not alter the rate of ⁴⁵Ca²⁺ release from oocytes preloaded with ⁴⁵CaCl₂ In contrast to earlier reports using tissue explants and cultured cells, the insulin response in oocytes is not sensitive to a range of extracellular calcium concentrations from 1 μM to 10 mM. However, treatment of oocytes with 1 mM EGTA, in the absence of Ca²⁺, prior to, during or within 5 minutes of insulin addition resulted in a 2-4 fold inhibition of ISDU. To further investigate the event(s) in insulin signalling inhibited by EGTA, the number of receptors for insulin on the oocyte must be increased. To this end we have investigated the effects of the 5' and 3' untranslated regions as well as the coding region of mRNA on translational efficiency in reticulocyte lysate and oocytes. The results obtained in Xenopus oocytes are consistent with earlier cell-free data (Falcone and Andrews, 1991). We have demonstrated that replacing the cognate 5' UTR with the Xenopus beta globin 5' UTR appropriately linked to a consensus sequence for efficient translation initiation (ACCATGG) results in increased in translation in Xenopus oocytes. In vitro synthesized preprolactin transcript injected into oocytes was found to be functionally stable for several days (D. Andrews unpublished data). Stabilization of the preprolactin 3' transcript was localized to the UTR. Furthermore, inserting the preprolactin 3' UTR downstream of another coding region resulted in stabilization of the modified transcript. These results provided a basis for improving expression of cloned human insulin receptor in Xenopus oocytes. By optimizing the 5' and 3' UTR's of the insulin receptor clone we were successful in expressing high levels of insulin receptors in Xenopus oocytes. Effects of the coding region on translation were also investigated and we provide evidence that sequences in the coding region modulate translational efficiency.

abstract: Thesis

abstract: Master of Science (MSc)