VictorJuiz/thesis huggingface dataset:
Molecular Phylogenetics of the Neotropical Electric Knifefish Genus Gymnotus (Gymnotidae, Teleostei): Biogeography and Signal Evolution of the Trans-Andean Species

Gymnotus, the banded electric knifefish, is a diverse genus with a range that extends from Argentina to southern Mexico and includes species distributed both east (cis-Andean) and west (trans-Andean) of the Andes. Each Gymnotus species exhibits a distinctive electric organ discharge (EOD), used for communication and navigation. Here, I present a new molecular phylogenetic hypothesis for 35 Gymnotus species based on two mitochondrial (cyt b and 16S) and two nuclear genes (RAG2 and Zic1). I found that the trans-Andean species are distributed in four distinct lineages with varying amounts of divergence from their closest cis-Andean sister taxa. I suggest that not all trans-Andean species evolved as a result of the orogeny of the Andes. I evaluate EOD phase number evolution in Gymnotus and find a trend for reduced phase numbers in both cis- and trans-Andean regions. Finally, I suggest hypotheses to account for the patterns of EOD phase number diversification.

Keywords: Gymnotiformes
signal evolution
molecular phylogenetics
Neotropical fish
Advisor: Lovejoy, Nathan
Lung Clearance Index as a Marker of Ventilation Inhomogeneity in Early Childhood with Health and Disease

Rationale: Ventilation inhomogeneity (VI) may be an early sign of obstructive airway disease. The lung clearance index (LCI) has been suggested as a sensitive marker of VI, although it has not been well characterized in young children in health and in those with CF and asthma. Objective: To determine if LCI can detect VI in asymptomatic infants and preschool-age subjects with CF or wheeze/asthma compared to healthy controls. Methods: Sulphur hexafluoride (SF6) multiple breath washout (MBW) testing was completed in all subjects. Results: LCI was found to be dependent on age in a large healthy cohort. Accounting for age, LCI was significantly elevated in disease groups compared to healthy controls in early childhood, illustrating early presence of VI in wheezy infants and the progression of disease in CF. Furthermore, the effects of breathing pattern and the variability of MBW parameters showed positive associations with age and VI.

Keywords: Ventilation Inhomogeneity
Lung Clearance Index
Cystic Fibrosis
Asthma
Childhood
Lung development
Advisor: Post, Martin
Subbarao, Padmaja
Stable Boron Subphthalocyanines: A Structure Property Relationship and New Processes for Further Synthetic Study

A structure property relationship relating photostability with the axial and peripheral substituents of Boronsubphthalocyanine (BsubPc) derivatives has been outlined: peripherally halogenating BsubPc has been determined to be the best way to increase the photostability, while axial substituents are found to have little effect. A solid state photostability test using BsubPc doped polymer films has been developed and was used to form this structure property relationship. The polymer in which BsubPc is tested is found to have an effect on the photostability and should be further explored. In addition to the structure property relationship, processes to make new BsubPc precursors, HO-BsubPc and Br-BsubPc, have been developed in order to further expand the derivatives available for study.

Keywords: subphthalocyanine
light fastness
Advisor: Bender, Timothy
The Efficacy of New Zealand Aid: An Analysis and Critique of New Zealand's Aid Programme

New Zealand’s aid programme reflects many of the controversies surrounding foreign aid more generally. From issues relating to the influence of political considerations and the administration and evaluation of aid agencies, to the fragmentation of the global aid system and the volatility of aid, these issues compromise the efficacy of aid provided to developing countries. This paper analyses the evolution of New Zealand’s aid programme and critiques its current policy and administrative structure in the context of these current controversies, in order to highlight the ways in which New Zealand’s aid can be delivered more effectively. The paper concludes, among other things, that New Zealand’s change in focus to economic development, its close alignment of aid policy with foreign policy and the re-absorption of its semi-autonomous aid agency NZAID back into its Ministry of Foreign Affairs and Trade risks compromising the effectiveness of the aid that New Zealand provides.

Keywords: foreign aid
administration
New Zealand
development
institutions
aid effectiveness
aid program
policy
efficacy of aid
Advisor: Trebilcock, Michael
Involvement of Primary Care Providers in the Care of Hospitalized Patients

This study examined the potential impact on processes of care and patient outcomes upon exposure of supportive and concurrent care provided by primary care providers (PCPs) to their hospitalized patients. A secondary objective was to describe the PCPs who conduct these services, and the patients who receive them. There was a marked, observable trend that PCP visits to their hospitalized patients is on the decline (dropped 10% between 2003 and 2009). The patients who received in-hospital visits from their PCPs had more disease burden and were hospitalized longer than the control group. Patients who received and in-hospital visit from their PCP were more likely to receive home care services and PCP visits post-discharge [adjusted OR 1.20 (95% CI 1.12-1.28)]. They were also less likely to experience the composite outcome of death, hospital readmission, or emergency department visit [aOR 0.95 (95% CI 0.91-0.98)].

Keywords: Primary Care
Continuity of Care
Quality of Care
Health Services Utilization
Advisor: Bell, Chaim
Responding to the Global Injury Burden by Improving Access to Orthopaedic Medical Devices: A Qualitative Case Study of Orthopaedic Services in Uganda

The global burden of injury is severely underappreciated and disproportionately affects low-income countries. With timely, appropriate orthopaedic treatment disability and mortality can be prevented, yet appropriate health resources are seldom available. Without orthopaedic medical devices (OMDs), quality of orthopaedic care suffers and the burden of preventable injury is exacerbated. A qualitative case study of 45 key informant interviews was conducted in Uganda to explore accessibility of OMDs, such as plaster, external fixators and implants. Data analysis elicited four major themes as barriers preventing access to OMDs in Uganda: 1) Poor leadership in government and corruption; 2) inadequate human resources; 3) inefficient and insufficient health care infrastructure; and 4) high costs of OMDs and poverty. Potential solutions for improving access to orthopaedic care were categorized as policies prioritizing orthopaedic services, training more orthopaedic specialists and creating incentives for them to work in underserviced areas, and innovative strategies funding for orthopaedic services.

Keywords: Global Injury Burden
Access to Orthopaedic Medical Devices
Orthopaedic care in low-income countries
Corruption in health care
Advisor: Kohler, Jillian Clare
Howard, Andrew
Systems Development, Assembly and Testing, and Mission Operations for Nanosatellites in the CanX Program

The Canadian Advanced Nanospace eXperiment (CanX) program at the University of Toronto's Space Flight Laboratory provides rapid, cost effective access to space through the use of micro- and nanosatellites. The primary focus of this thesis is the development of the CanX-4/-5 nanosatellite mission, which is intended to demonstrate precise, autonomous formation flying. This involves the development of nominal and contingency operations, system budgets, and requirements to produce a complete system architecture. Also described is the assembly, integration, and testing of flight hardware for this mission. In addition, this thesis addresses the on-orbit operation of CanX-2 and CanX-6/NTS, as it relates to operations planning for CanX-4/-5. The ground station operations for these two nanosatellite missions are described, with particular focus on payload operations and contingencies resulting from on-orbit anomalies. This experience is then related to the development of the CanX-4/-5 ground station software architecture.

Keywords: nanosatellite
systems development
Advisor: Zee, Robert E.
A Qualitative Descriptive Study: Older Adults' Postoperative Pain Medication Usage After Total Knee Arthroplasty

Postoperative pain is a major concern to patients undergoing surgical procedures but little research has been conducted on pain management after hospital discharge for orthopaedic patients. Since pain medication is a key component of pain management, it is important to study medication usage from a patient’s perspective, for greater patient–health care provider concordance. A qualitative descriptive approach was taken to investigate the experience of 14 participants with managing pain at home immediately after total knee arthroplasty. Most participants limited their consumption and weaned themselves off prescription analgesics and used over-the-counter pain medications. The participants adapted their regimens in response to several factors and generally were content to self-manage their pain but required access to professional support. The study suggests that when developing postoperative pain management plans, health care providers may need to increase the time they spend addressing patients’ concerns and considering patients’ preferences.

Keywords: qualitative research
postoperative pain
Advisor: McCartney, Colin
Webster, Fiona
Study of Fluid-structure Interactions of Communication Antennas

Large structures exposed to the environment such as the collinear omni and large panel communication antennas in this research suffer damage from cyclic wind, rain, hail, ice load and impacts from birds and stones. Stresses from self-weight, ice loading and wind gusts will produce deformations of the structure that will lead to performance deterioration of the antenna. In order to avoid such a case, it is important to understand the static, dynamic and aerodynamic behavior of these structures and thus optimization can be achieved. In this research the current fluid-structure interaction methods are used to model, simulate and analyze these communication antennas in order to assess whether failure would occur under service loads. The FEA models developed are verified against analytical models and/or experiments. Different antenna configurations are compared based on their capacity to minimize vibration effects, stress-induced deformations and aerodynamic loading effects.

Keywords: fluid structure interactions
communication antennas
flow induced vibrations
structural analysis
Advisor: Zu, Jean W.
Navigating Textual Space in Print and Digital Interfaces: A Study of the Material and Cognitive Dimensions of Reading Systems

This research examines situated behaviours and perceptions around textual navigation as it is practiced in situ by professionals working in various domains. In its investigation of interactions between human cognition and mediating artifacts, this research relies heavily on the resources of cognitive ethnography, including both observation and in-depth interviews with participants. Relevant contributions from the fields of information studies, book history, digital humanities, and human-computer interaction are presented to further elucidate the findings of this study. The findings reveal several emergent, interrelated navigational strategies, such as the use of annotations as navigational aids, reliance on automated interface actions, and the navigational value of interface metaphors. In further addressing the practice of textual navigation, this research also describes the creation of a prototype interface reflecting the study’s findings. This research proposes new ways of conceptualizing textual navigation and designing interfaces that support emergent textual interaction.

Keywords: information systems design
reading media
annotations
navigation
interface design
human computer interaction
hypertext
interaction styles
prototyping
distributed cognition
documents
Advisor: Galey, Alan
'Artificial' Land and 'Natural' Disaster: Hazard and Vulnerability on Created Urban Land

During the nineteenth and early twentieth centuries, waterfront cities expanded over wetlands and shallow water by building land on which to build the city. Today, this artificial land is threatened by a range of environmental hazards. This increases the risk of natural disaster for people occupying the area. A framework for risk analysis using Geographic Information Systems (GIS) to create maps based on the formula: ‘Risk = Hazard + Vulnerability’ is proposed. This methodology is demonstrated in four case study cities - Toronto’s Ashbridges Bay (Port Lands), Boston’s Back Bay, New Orleans’ Lakefront and Montreal’s Point St. Charles (Technoparc) – to show that census tracts that are both socially and environmentally vulnerable ought to take precedence in disaster prevention and relief efforts. Created land is inherently more hazardous than the adjacent natural land and requires planning focused on targeting and responding to the documented hazards.

Keywords: artificial land
disaster
waterfront
GIS
urban
Toronto
New Orleans
Boston
Montreal
Advisor: Hess, Paul M.
Boyes, Don
Wolff, Jane
CYP2A6 and CYP2B6 Genetic Variation, and Tobacco Use Behaviours and Biomarkers in Alaska Natives

The impact of CYP2A6 and CYP2B6 genetic variation on nicotine metabolism, tobacco use behaviours, and nicotine biomarkers was investigated in a group of Alaska Natives (n = 400). CYP2A6 and CYP2B6 allele frequencies were unique and associations of CYP2A6 genotype and CYP2A6 activity (plasma and urine trans 3’-hydroxycotinine/cotinine (3HC/COT) ratios) were robust. Notably, this population possessed a more rapid rate of CYP2A6 activity (higher plasma 3HC/COT) when compared to CYP2A6 wild-type individuals in other ethnic groups (ANOVA P < 0.001). Also demonstrated was a significant difference in urine total nicotine equivalents by CYP2A6 activity median split (t-test P < 0.01), the first evidence of nicotine titration by CYP2A6 activity within a light smoking population. Overall, this population possessed a distinctive pattern of CYP2A6 and CYP2B6 variant frequencies and a faster rate of nicotine metabolism, which may in part explain higher levels of tobacco use prevalence and tobacco-related disease risk.

Keywords: Nicotine
Alaska Native
CYP2A6
CYP2B6
Genetic Variation
Pharmacogenetics
Smoking & Tobacco Use
Tobacco-Related Disease
Advisor: Tyndale, Rachel
Transient Receptor Potential Melastatin 7 Channels Regulate Neuronal Cytoskeletal Dynamics

Transient Receptor Potential ‘Melastatin’ 7 (TRPM7) is a ubiquitously expressed, non-selective divalent cation channel implicated in diverse cellular functions including actomyosin cytoskeletal remodeling, magnesium homeostasis, and anoxic neuronal death. The present study investigates the role of TRPM7 in modulating neuronal morphology and regulating neuronal cytoskeletal dynamics after anoxia. Overexpression of GFP-tagged TRPM7 in neuronal cultures caused a stunted morphology with fewer neurite branches than controls, suggesting that TRPM7 regulates the neuronal cytoskeleton during dendritic outgrowth. I have discovered that TRPM7 may regulate morphology via activation of cofilin-1 (an actin binding protein). I found that TRPM7-dependent cofilin activation during anoxia mediated neuronal death. Overall my work reveals a novel link between anoxia-induced TRPM7 activity and cofilin activation, which likely contributes to neurodegeneration after ischemia.

Keywords: biology
stroke
TRPM7
cytoskeleton
cofilin
neuron
Advisor: Aarts, Michelle
An Examination of Possible Maternal Effects due to Parasite and Density Stress on the Mealworm Beetle, Tenebrio molitor

Few empirical studies examine the influence that the maternal parasite environment can have on offspring fitness (maternal effects) in invertebrates. Several recent studies have found that mothers can adjust offspring phenotype to counter the negative effects of parasite infection. In this thesis I subjected the parental generation of the host species, Tenebrio molitor (Insecta: Coleoptera), to a high parasite, high density, or control treatment. Offspring were subsequently subjected to either the same stress, the alternate stress, or to the control, and fitness-related life history traits were measured in both generations. The results from this thesis do not support the hypothesis that T. molitor mothers influence offspring fitness in a positive way. Instead, maternal effects led to a reduction in offspring fitness under both types of stress. At least under some environmental conditions, females invest in their fitness at the expense of their offspring.

Keywords: Host-parasite interactions
Maternal effects
Life history trade-offs
Invertebrates
Tenebrio molitor
Advisor: Baker, Robert L.
"Young Women Growing Graciously": Considering Sport, Gender and Development in Diasporic Space

This thesis aims to expand our understanding of the relationship between gender, sport and development. Specifically, it asks 1) how a sport, gender and development program is conceptualized and deployed by members of a young Somali-Canadian women’s group in Toronto, Canada and 2) if female participation in sport is thought to contribute to new gender norms, roles and relationships within such a diaspora community. Working within a postcolonial/transnational feminist framework, the thesis utilizes focus group interviews and engages with issues of power, representation and knowledge production. The findings shed light on the influences that have both informed and constrained this particular community initiative, as well as the possibilities and limitations of using sport to negotiate new gender norms, roles and relationships within the Somali diaspora. In conclusion, several recommendations are made to researchers and practitioners invested in the burgeoning field of international sport for development.

Keywords: sport
community development
diaspora
gender norms
social change
postcolonial feminism
transnational feminism
Somali-Canadian
Toronto
Advisor: Kidd, Bruce
Donnelly, Peter
Hydrazine as a Nucleophilic Anchor in the Formation of Hemoglobin Bis-tetramers

Two alternative compounds have been prepared and studied, as alternatives to the benzyl amine in the preparation of hemoglobin bis-tetramers. The reactivity of these compounds towards the activated ester groups on trimesoyl tris(3,5-dibromosalicylate), and 3,5-dibromosalicylate benzyl ester has been studied, as well as their functionality in a range of acidic solutions. Initial rate kinetics was used to determine rate constants for hydrazinolysis, and hydrolysis of the two esters. The objective was to find a suitable functional group that would be less basic than the benzyl amine yet still exhibit good nucleophilicity in the preparation of hemoglobin bis-tetramers. Hydrolysis being the main side reaction limiting the yield, could be slowed down in an acidic solution, but the nucleophile used could not be protonated in the process. It has been found that the benzyl hydrazine was the most effective and able to react with cross-linked hemoglobin to give the most product.

Advisor: Kluger, Ronald
When Daughters become Caregivers to a Parent who has Suffered a Stroke: A Qualitative Exploration of how the Parent-to-child Relationship is Associated with Caregiver Well Being

Rationale: Many community-dwelling stroke survivors receive care from their family, often daughters. However, we lack in-depth information on the caregiver/care-recipient relationship and its impact on adult daughter caregivers (ADCs). Objective: To systematically review the caregiving literature and qualitatively explore the pre-and post-stroke parent-to-child relationship and its association with ADCs’ well being. Method: A qualitative descriptive methodology used in-depth interviews of 23 ADCs. Analyses generated themes. Findings: Four themes were revealed: 1) The pre-stroke ADC-to-parent relationship is associated with the decision to take on the caregiving role; 2) Changes in the parent-to-child relationship occur as a result of providing care; 3) Changes to an ADC’s relationships with others arises from providing care to a parent and 4) Changes to caregiver lifestyle, outlook and physical and emotional well being arise from caregiving. Conclusion: There is a need for interventions that focus on role strains and issues related to relationship loss.

Keywords: Rehabilitation Science
Caregiving
Advisor: Cameron, Jill
Utilizing Managerial Cash Flow Estimates for Applied Real Options Analysis

Real options analysis has been recommended to identify and quantify opportunities where managerial flexibility can influence worth. However, real options models in the literature have become increasingly sophisticated, and managers have cited their reluctance to use such models due to their level of complexity and lack of transparency. Presented in this thesis is a real options model that can be easily incorporated into the current project selection methodology of a firm; the model uses managerial cash flow estimates to price real options on tangible investment opportunities in a financially consistent manner. Next, to demonstrate the application of real options analysis in practice, five real options models, including the proposed model, are applied to value a medical device project. The models all price the real option differently, due to the differences in their underlying assumptions, but they all yield the same investment conclusion: the medical device project has value.

Keywords: Real Options
Project Valuation
Medical Device
NPV Analysis
Managerial Information
Advisor: Lawryshyn, Yuri Andrew
Parathyroid Hormone Regulates Osterix Promoter Activity In Vitro and Expression In Vivo

Osterix (Osx) is a transcription factor required for osteoblast differentiation and bone formation. We previously demonstrated that continuous parathyroid hormone (PTH) treatment inhibited Osx expression in murine calvaria and osteoblastic UMR106-01 cells through the regulation of two regions on the Osx promoter. Mutational analysis of transcription factor elements within these regions revealed two "Sp-sites" were vital for Osx promoter activity. Blockage of these Sp-sites with Mithramycin A demonstrated their importance for Osx expression. Osx bound to its own promoter at these sites, while PTH treatment inhibited this association. PTH regulation of Osx expression in vivo was investigated in mice by: daily injection of PTH for 3 days, continuous infusion of PTH from osmotic pumps for 14 days, or mice fed a calcium-deficient diet for 21 days. Osx expression was decreased by daily injection, while Osx expression was stimulated in mice receiving continuous PTH infusion and mice fed a calcium-deficient diet.

Keywords: Osterix
osteoblast
parathyroid hormone
gene regulation
Advisor: Mitchell, Jane A.