VictorJuiz/thesis huggingface dataset:
Model Based Design of a Saccharomyces cerevisiae Platform Strain with Improved Tyrosine Production Capabilities

Large-scale production of plant secondary metabolites is of interest because of their application in production of many valuable products. Recent advances in the area of DNA recombinant technology has made it possible to produce these valuable compounds using microbial routes. The objective of this work was, to design a platform strain of Saccharomyces cerevisiae with improved intracellular tyrosine pools using computational modeling. This engineered yeast could be used as a host for producing important plant secondary metabolites on an industrial-scale. In this study, a combination of steady-state and dynamic modeling methods were used for strain design. Initial strain design was performed using steady-state modeling, and the predictions from steady-state modeling were prioritized for experimental validation using dynamic modeling. The final strategy proposed included deletion of PDC1, ZWF1, ARO10; over-expression of ALD6, and alleviation of tyrosine feedback resistance in shikimate pathway. Initial experiments for validation of this strategy showed promising results.

Keywords: Model based strain design
tyrosine
Saccharomyces cerevisiae
Advisor: Mahadevan, Radhakrishnan
Syk Inhibition Attenuates Airway Hyperresponsiveness in a Murine Model of Asthma and Exacerbation by Air Pollution

Airway hyperresponsiveness (AHR) is a cardinal feature of asthma that is aggravated by environmental air pollution (EAP). Splenocyte tyrosine kinase Syk has been associated with asthma pathogenesis. Therefore, we sought to investigate the effect of Syk inhibition on AHR and its exacerbation by EAP. For this purpose, we examined Syk protein expression in lung homogenates from three murine models of ovalbumin (OVA)-induced asthma expressing different pathophysiological features of the disease: airway inflammation, AHR and remodeling. Increased Syk expression was observed only in the chronic model of airway inflammation and remodeling. In vivo Syk inhibition attenuates AHR in this model, and further augmentation induced by EAP without affecting the underlying airway inflammation. We demonstrated, for the first time, that Syk inhibition effectively reverted AHR in an already established chronic model of asthma. These findings highlight the therapeutic potential of targeting Syk for the treatment of asthma and its exacerbations by EAP.

Keywords: asthma
airways hyperresponsiveness
Syk
pollution
Advisor: Chow, Chung-Wai
Scott, Jeremy A.
Maturation of Cervical Vertebrae in Patients with Complete Unilateral Cleft Lip and Palate

This retrospective cohort study of 336 lateral cephalometric radiographs from 62 children (34 males and 28 females) with non-syndromic complete unilateral cleft lip and palate from the Hospital for Sick Children and 50 non-cleft children (25 females and 25 males) from the Burlington Growth Centre. Cervical vertebral maturation stages at age 10, 12 and 14 were determined. The cervical vertebral maturation (CVM) was established using the 6-stage method described by Baccetti and coworkers. The reproducibility of classifying CVM stages was high, with an inter-rater reliability (ICC) with the standard (Baccetti et al, 2005) of 80% and intra-rater reliability of 85%. The Cervical vertebral maturation stage for both males and females with UCLP was significantly later than children without a cleft at age 10, 12 and 14. The results suggest that patients with UCLP show delayed skeletal maturation in comparison to non-cleft patients.

Keywords: Cleft Lip and Palate
Cervical vertebrae maturation
Advisor: Tompson, Bryan
Ross, Bruce
Lam, Ernest W.
The Influence of Ambiguous Identity on Person Perception: The Importance of Context

Biracial people are often stereotyped as cold and socially awkward. Two experiments assessed whether the racial context in which they are perceived influences the application of these stereotypes. Participants read about a Black/White student who chose or was assigned a White, Black or Black/White roommate. Roommate race was manipulated via photographs (Experiment 1), or written description (Experiment 2). When photos were provided, roommate race, not the relationship, influenced target evaluations. The biracial target with a White roommate was viewed the least positively and as least similar to participants, implying his minority status was highlighted by his roommate’s race. The written description produced only relationship effects. When the target chose his roommate he was evaluated as warmer, more competent and with more positive regard than when he was assigned a roommate. The results suggest that visual vs. narrative racial contexts produce divergent evaluations of biracial people.

Keywords: Multiracial
Discrimination
Context
Advisor: Chasteen, Alison L.
Investigation of the Maximum Shear Capacity of High-strength Reinforced Concrete Beams

In 2011, Roger Xu (UToronto) carried out an experimental study to investigate shear reinforcement ratios required to cause crushing of diagonal struts in high-strength reinforced concrete I-beams. Xu’s experimental results were found to be inconclusive due to detailing issues resulting in flange splitting and web blow-out. This thesis outlines an experimental test programme completed in Spring 2012 to mitigate the issues encountered by Xu. Through experimental observation, data acquisition, and numerical analysis, the test program described in this thesis is shown to overcome the aforementioned issues. The study is expanded upon with an additional test series of rectangular beams aimed to examine the applicability of the maximum shear capacity provision of the Canadian Standards Association (CSA) A23.3-04 design standard. Test data suggests that the 0.25fc'bwdv upper limit for shear reinforcement used in CSA A23.3-04 cannot be reliably attained when using high strength concrete.

Keywords: Reinforced
Concrete
Maximum
Shear
Beams
Advisor: Collins, Michael P.
Bentz, Evan
A Computational Study of Proton Uptake Pathways in Cytochrome c Oxidase

Cytochrome c oxidase (CcO), the terminal enzyme in the electron transport chain, couples proton pumping to the reduction of dioxygen into water. The coupling mechanism remains to be elucidated. Previous studies have identified several mutations within CcO's primary proton uptake pathway (the D-channel) that decouple proton pumping from redox activity. Here, I examine the molecular basis for decoupling in single and double mutants of highly conserved residues, D132 and N139, in order to gain insight into the coupling mechanism. In particular, I use molecular dynamics and free energy simulations of a new, unconstrained model of bacterial CcO embedded in a solvated lipid bilayer to investigate how such mutants affect functional hydration and ionic selectivity in the D-channel. Results support earlier mechanistic insights obtained in our laboratory from simplified molecular models and predict a new, testable hypothesis by which cations such as K+ may inhibit proton pumping in charged mutants of N139.

Keywords: cytochrome c oxidase
proton pumping
molecular simulations
computational biology
Advisor: Pomès, Régis
A Place Apart: The Harm of Solitary Confinement

This thesis examines the world of solitary confinement within the prison system. My research was inspired by Ashley Smith, a 19-year old segregated inmate who died in isolation while seven guards watched. This outrageous occurrence prompted me to question the practice of solitary confinement and a prison system in which such an event could occur. Studying the history of solitary confinement left me surprised to learn that it was originally intended as a therapeutic and merciful alternative to the punishments of the day. This revelation was one of a series of inversions that led me to conclude that solitary confinement is a world apart, not just physically, but also socially, temporally and legally. I have concluded that improving the lives of those segregated within our prisons requires the world of solitary confinement to become anchored within the broader legal and social context.

Keywords: prison
penitentiary
solitary confinement
isolation
torture
Advisor: Lemmens, Trudo
Hyaluronan-methylcellulose Hydrogels for Cell and Drug Delivery to the Injured Central Nervous System

Spinal cord injury and stroke are two devastating neurological events that lack effective clinical treatments. Recent neuroregenerative approaches involving the delivery of cells or drugs to the injured tissue have shown promise, but face critical challenges to clinical translation. Herein, hyaluronan-methylcellulose (HAMC) hydrogels were investigated as a versatile means of overcoming the challenges facing central nervous system cell and drug delivery. HAMC was shown to support the viability of encapsulated human umbilical tissue-derived cells, demonstrating utility as a scaffold for therapeutic cell delivery to the injured spinal cord. In a drug delivery context, release of the neuroregenerative drug cyclosporin A from the hydrogel was tunable over 2-28 days and the drug diffused to the stem cell niche in the brain and persisted for up to 24 days at a stable concentration when the HAMC-based system was implanted epi-cortically. HAMC is thus a promising tool for emerging neuroregenerative therapies.

Keywords: Drug Delivery
Cell Delivery
Hydrogel
Central Nervous System
Advisor: Shoichet, Molly
The Long-term Neurocognitive Development of Children Exposed to Above Manufacturer Recommended Doses of Diclectin In Utero

Nausea and vomiting of pregnancy (NVP) affects up to 90% of pregnancies. Diclectin (doxylamine/pyridoxine) is the only anti-emetic approved in Canada for NVP, at a maximum dose of 4 tablets/day. However, some women receive higher doses, up to 12 tablets/day. In this study we compared the neurocognitive development of children from four mother-child groups: (1) NVP and >4 tablets Diclectin, (2) NVP and ≤ 4 tablets Diclectin, (3) NVP and no treatment and (4) no NVP. Children received a full age-appropriate psychological assessment. All groups scored in the normal range for IQ and cognition tests. The Diclectin-exposed groups scored significantly higher on a small number of subtests, but none of the differences could be considered clinically significant. No dose-dependent effects were observed. Above manufacturer recommended doses of Diclectin do not appear to harm neurodevelopment and should be considered safe for the treatment of NVP.

Keywords: pharmacology
neuropharmacology
neurocognition
drug safety
Advisor: Gideon, Koren
The Double-edged Nature of Antigay Prejudice Confrontation: Confronting Antigay Prejudice is Effective but Comes at a Cost

Although confronting prejudice can be effective in reducing bias, it is potentially costly to confronters. Research on confronting racism or sexism has shown confronters from the targeted group are viewed more negatively than confronters who are not. It is unknown whether confronting antigay bias produces similar reactions, particularly since group membership is concealable. In my research, participants read two male profiles followed by a scripted conversation which included an antigay comment. Profiles varied in their depiction of the confronting individual’s sexual orientation, and conversations either included a confrontation or not. I found that confronting antigay bias is double-edged. On the positive side, confrontation increased awareness that prejudice occurred, and this awareness mediated the relation between confrontation viewing and participants’ own intention to confront. On the negative, individuals may be deterred from confronting antigay prejudice because confronters were perceived as more gay (a stigmatized identity), regardless of actual orientation.

Keywords: Prejudice
Confrontation
Homophobia
Antigay
Intergroup relations
Intervention
Sexual Orientation
Advisor: Chasteen, Alison L.
A Quotient-like Construction involving Elementary Submodels

This article is an investigation of a recently developed method of deriving a topology from a space and an elementary submodel containing it. We first define and give the basic properties of this construction, known as X/M. In the next section, we construct some examples and analyse the topological relationship between X and X/M. In the final section, we apply X/M to get novel results about Lindelof spaces, giving partial answers to a question of F.D. Tall and another question of Tall and M. Scheepers.

Keywords: Set Theory
Topology
Advisor: Tall, Franklin
An Energy Efficient FPGA Hardware Architecture for the Acceleration of OpenCV Object Detection

The use of Computer Vision in programmable mobile devices could lead to novel and creative applications. However, the computational demands of Computer Vision are ill-suited to low performance mobile processors. Also the evolving algorithms, due to active research in this fi eld, are ill-suited to dedicated digital circuits. This thesis proposes the inclusion of an FPGA co-processor in smartphones as a means of efficiently computing tasks such as Computer Vision. An open source object detection algorithm is run on a mobile device and implemented on an FPGA to motivate this proposal. Our hardware implementation presents a novel memory architecture and a SIMD processing style that achieves both high performance and energy efficiency. The FPGA implementation outperforms a mobile device by 59 times while being 13.5 times more energy efficient.

Keywords: FPGA
Computer Vision
Object Detection
OpenCV
Mobile
Advisor: Rose, Jonathan S.
Mandatory Disclosure and the CSA Proposed Legislation for Securitized Products

One of the main factors that spurred the 2008 financial crisis was the trading of securitized products without a clear understanding of the risks that those products bore. I argue that an appropriate regime of mandatory disclosure is the primary instrument regulators should refer to in order to correct the informational asymmetries that are present in the market for securities products. Subsequently, I take into consideration the CSA proposed legislation for the mandatory disclosure of securitized products and analyze its main components under the light of the principles of investor protection and market efficiency. I find that the new legislation should be welcome by market operators because it is a good balancing effort between the necessity to protect the investors and fostering the efficiency of the market.

Keywords: mandatory disclosure
securitized products
market for lemons
investor protection
Advisor: Anand, Anita
Quadrotor UAV Control for Vision-based Moving Target Tracking Task

The problem of stand-off tracking of a moving target using a quadrotor unmanned aerial vehicle (UAV) based on vision-sensing is investigated. A PID (Proportional-Integral-Derivative) controller is implemented for attitude stabilization of the quadrotor. An LQG-based (Linear-Quadratic-Gaussian) control law is designed and implemented for position control of the quadrotor for a moving target tracking task. A novel vision-based estimation algorithm is developed, enabling estimation of quadrotor’s position, altitude and yaw relative to the target based on limited information about the target. Two image processing algorithms are implemented and compared for the task of feature detection and feature tracking in a series of images. Image processing algorithms are integrated with quadrotor control and experiments are performed to validate proposed control and estimation approaches.

Keywords: Quadrotor control
UAV
Advisor: Liu, Hugh
Improving Extradition Procedure through Strengthening the Legal Status of an Individual and Transferring the Decision Making Right from the Executive to Judiciary Branch of Power

A special role amongst various efforts to combat transnational criminal activity belongs to extradition, which has transformed into a form of international cooperation and became an indispensable tool for ensuring criminal responsibility in any part of the world. However, for a long period of time, an individual in the process of extradition has been treated as a passive object of intergovernmental relations which have a significant political component. In this thesis, the claim is that treatment of an individual as a rights bearer and an active subject of legal relationships among other parties of the process, combined with transfer of final decision-making right from the executive to judiciary branch of power, is capable to enable application of the Rule of law principles to particular extradition cases, limit broad discretion of decision makers and minimize political component of extradition.

Keywords: Extradition
International legal personality of an individual
Rule of law
Advisor: Audrey, Macklin
Proteomic Profiling of the Planarian Schmidtea mediterranea and its Mucous Reveals Similarities with Human Secretions and those Predicted for Parasitic Flatworms

The freshwater planarian Schmidtea mediterranea has been used in research for over 100 years, and is an emerging stem cell model. Exteriorly, planarians are covered in mucous secretions of unknown composition. While the planarian genome has been sequenced, it remains mostly unannotated. The goal my master’s research was to annotate the planarian proteome and mucous sub-proteome. Using a proteogenomics approach, I elucidated the proteome and mucous subproteome via mass spectrometry together with an in silico translated transcript database. I identified 1604 proteins, which were annotated using the Swiss-Prot BLAST algorithm and Gene Ontology analysis. The S. mediterranea proteome is highly similar to that predicted for the trematode Schistosoma mansoni associated with schistosomiasis. Remarkably, orthologs of 119 planarian mucous proteins are present in human mucosal secretions and tear fluid. I suggest planarians have potential to be a model system for parasitic worms and diseases underlined by mucous aberrancies.

Keywords: Proteomics
Planarians
Stem Cells
Mass Spectrometry
Schistosomiasis
Mucous
Proteogenomics
Annotation
Advisor: Moran, Michael
International Commercial Arbitration and Technology Transfer Disputes

The thesis explores the concept of International Arbitration, an alternative to litigation. It argues the benefits and the inherent limitations parties are likely to face while resorting to this instrument to resolve Transfer of Technology and Intellectual Property related disputes. The paper further explains how Arbitrability limitations can be taken care of in relation to transfer of technology disputes. Emphasis is placed on the institutional role of the World Intellectual Property Organization’s Arbitration and Mediation Center as an appropriate arbitration forum to deal with complex technological and Intellectual Property related disputes.

Keywords: International Arbitration
Technology Transfer
Intellectual Property
Arbitrability
Advisor: Katz, Ariel
The Paradox of Women's Rights: Malaysia's Struggle Towards Legal And Religious Pluralism

Family is the foundation society. Women are the backbone of families even in fundamental patriarchal society like Malaysia. However, Malaysia’s system of religious accommodation results in different rights available to individuals based on the states diverse religious affiliation. Contemporary family issues are inadequately addressed in current Malaysian Family Law: one for the Muslims and one for the non-Muslims. Most cases highlighted inconsistencies when conversion to Islam affected the rights of women during breakdown of marriage. In permitting a path to accommodate diversity, and to reach a new engagement between the civil and the Shariah courts, it is necessary to appreciate Malaysia’s history, sentiment, constraints and strengths. This paper proposes that not only Malaysia has adequate strengths to provide a strong platform to address the conflict, but possesses the mechanisms to create a dynamic set of joint governance of Family Laws to enhance religious accommodation.

Keywords: Women's Rights
Legal Pluralism
Religious Pluralism
Civil Law
Islamic Law
Family Law
Conversion To Islam
Dual Legal System
Consent of Spouse
Custody of Children
Advisor: Fadel, Mohammad
Energy Consumption Tends of Multi-unit Residential Buildings in the City of Toronto

The purpose of this research is to determine the average energy intensity of multi-unit residential buildings (MURBs) in Toronto, and evaluate whether certain building characteristics influence energy intensity. This information is particularly important in the Toronto market. Relative to the city’s population, Toronto has an unusually high proportion of MURBs with more than half of residential dwellings in apartment buildings. Additionally, Toronto MURBs are significant consumers of energy and produce an estimated 1.3M tonnes of CO2e each year. The ultimate goal is to assess the most efficient building retrofit measures. Energy consumption data for Toronto MURBs were collected and weather normalized. Correlations between the energy data and the building characteristics were examined. Window characteristics and heating system type were found to have the most significant influence on energy intensity. Establishing energy consumption characteristics of MURBs is the first step towards improving the energy efficiency of Toronto’s MURBs stock.

Keywords: energy consumption
multi-unit residential
trends
correlation
Toronto
building science
MURBs
weather normalization
building retrofit
energy intensity
Advisor: Pressnail, Kim D.
Neural Circuitry in Obsessive Compulsive Disorder: an fMRI Study of the Effect of IV Citalopram

Background: Functional imaging studies have examined the neural circuitry of subjects with obsessive compulsive disorder (OCD), and the changes associated with oral treatment. However, the effect of intravenous (IV) serotonin reuptake inhibitors (SRIs) on neuronal activation has not been investigated in OCD subjects, even though IV SRIs have been shown to be more effective than oral pharmacotherapy. Methods: Six OCD and 6 control subjects underwent functional magnetic resonance imaging while receiving infusions of citalopram and placebo, in a randomized, crossover design. Results: Compared to controls, OCD subjects exhibited hyperactivation of the orbitofrontal cortex and anterior cingulate cortex while looking at symptom provoking pictures at baseline. However, after the citalopram infusion, patients displayed attenuations of these regions, which correlated with reductions in subjective anxiety ratings. Conclusion: The effects observed after the IV citalopram infusion are similar to modulations observed after prolonged oral pharmacotherapy trials, illustrating the benefits of IV SRIs.

Keywords: Obsessive Compulsive Disorder
Citalopram
fMRI
Intravenous
Orbitofrontal Cortex
Anterior Cingulate Cortex
Neuroimaging
SSRI
Symptom provocation
Advisor: Ravindran, Arun
Distal Enhancer – Gene Interactions at the Lmo2 locus in Mouse Erythroid cells

Distal regulatory elements (DREs) have been identified upstream of the hematopoietic regulator Lim domain only 2 (Lmo2) gene in the human and mouse genomes. In this thesis I have investigated how these elements regulate Lmo2 transcription in erythroid cells. My results show that strong chromatin-chromatin interactions exist between the DREs and the Lmo2 gene promoter in erythroid cells. These interactions are absent from kidney cells that do not express Lmo2. Within the distal chromatin interaction cluster encompassing three of the DREs increased DNase I sensitivity, presence of high levels of H3K4me1, and binding of multiple transcription factors, p300, cohesin (RAD21) and CTCF are observed. CTCF bound regions are located between the farthest DRE and the neighboring Caprin1 promoter suggesting that CTCF insulates Caprin1 from the DREs. Hence, my data suggests that these DREs function through a chromatin looping mechanism supported by cohesin associated with CTCF and transcription factor bound regions.

Keywords: Molecular Biology
Cell Biology
Advisor: Mitchell, Jennifer