VictorJuiz/thesis huggingface dataset:
The Effectiveness of Modified Fat Breast Milk for the Treatment of Chyothorax in Infants Following Cardiothoracic Surgery

Background: Chylothorax occurs in ~4% of children undergoing cardiac surgery. Treatment requires transition to a medium chain triglyceride (MCT) based formula. Breast milk (EBM) is discontinued due to the presence of long chain triglycerides. Objective: To determine the effectiveness of a modified fat breast milk for the treatment of chylothorax. Methods: Infants with chylothorax were eligible. Treatment infants (n=8) received EBM that had been modified by removing the fat layer (centrifugation) from EBM and adding MCT and nutrients to provide 67 kcal/ml and 11 g/100 ml protein. Control infants (n=8) received MCT formula. Results: Volume of chest tube drainage was not different (p<0.40). Treatment infants experienced declines in mean weight (p<0.006), length (p<0.013) and head circumference (p<0.008) z-scores. Conclusion: Modified fat breast milk allowed for successful resolution of chylothorax. Strategies to address poor growth, however, need to be tested before clinical adoption of this novel treatment.

Keywords: Chylothorax
Breast Milk
Infant
Advisor: O'Connor, Deborah Louise
In Situ Mapping of Membranolytic Protein-membrane Interactions by Combined Attenuated Total Reflection Fourier-transform Infrared Spectroscopy-atomic Force Microscopy (ATR-FTIR-AFM)

A combined attenuated total reflection-Fourier-transform infrared spectroscopy (ATR-FTIR)-atomic force microscopy (AFM) platform was used to visualize and characterize membranolytic protein- and peptide-membrane interactions, allowing spectroscopic details to be correlated with structural features. Modifications to a previous combined platform permitted IR results for physiologically-relevant protein or peptide concentrations as well as provided nanometer-resolution height data for AFM. This combination provides greater insight than individual techniques alone. The interactions of hemolytic sticholysin proteins on a model red blood cell membrane showed evidence of conformational changes associated with a membrane-induced organization. In addition, the examination of a de novo cationic antimicrobial peptide on a model bacterial membrane showed that the peptide adopted a helical structure upon interaction with the membrane, and also provided evidence of membrane disruption and peptide aggregation. These results demonstrate that ATR-FTIR-AFM can be a powerful tool for understanding protein- and peptide-membrane interactions.

Keywords: atomic force microscopy
infrared spectroscopy
protein-membrane interactions
peptide-membrane interactions
sticholysin
cationic antimicrobial peptide
Advisor: Yip, Christopher M.
The Generation of Affinity Reagents Using High-throughput Phage Display and Building the Foundations of a Novel High-throughput Intrabody Pipeline

Phage display technology has emerged as the dominant approach in antibody engineering. Here I describe my work in developing a high-throughput method of reliably generating intracellular antibodies. In my first data chapter, I present the first known high-throughput pipeline for antibody-phage display libraries of synthetic diversity and I demonstrate how increasing the scale of both target production and library selection still results in the capture of antibodies to over 50% of targets. In my second data chapter, I present the construction and validation of a novel scFv-phage library that will serve as the first step in my proposed intrabody pipeline. Antibodies obtained from this library will be screened for functionality using a novel yeast-two-hybrid approach and have numerous downstream applications. This high-throughput pipeline is amenable to automation and can be scaled up to thousands of domains, resulting in the potential generation of many novel therapeutic reagents.

Keywords: phage display
high-throughput
intrabody
antibody
intrabodies
antibodies
Advisor: Sidhu, Sachdev
An "Obvious" Proposal - Using An Industry Sensitive Doctrine of Obviousness to Govern the Scope of Gene Patents After Association for Molecular Pathology v. USPTO

Currently there are approximately 20,000 valid gene patents in the United States. The debate regarding biotechnology and patent law has reached a pinnacle over the patentability of genes. Biotech is fighting a patentability war on two fronts. The Court of Appeals for the Federal Circuit cannot agree regarding the touchstone of patentability for genes; two branches of the Executive are at odds over whether gene sequences qualify under 35 U.S.C. §101. Recent U.S. Supreme Court and Federal Circuit jurisprudence also undermine the patentability of genes as obvious. This thesis argues that the patentable subject matter debate fails to adequately address the goals of patent policy in fostering innovation. Looking to Canadian and U.K. jurisprudence, it is possible to hone an approach to obviousness that addresses the ethical and research concerns in the patentable subject matter debate while fostering investment and patent protection for non-obvious biotech discoveries.

Keywords: Law, Patents, Biotechnology, Gene Patent, Obviousness, Patentable Subject Matter
Advisor: Katz, Ariel
Correlates of Calcium Supplement Use in Older Community-dwelling Ontario Women

Background: Older Canadian women are not meeting recommended calcium intake levels and therefore require calcium supplementation to maintain bone mass. Objective: To examine factors associated with calcium supplementation among older community-dwelling women, using the Health Belief Model (HBM) as a conceptual framework. Methods: Data previously collected from Ontario community-dwelling women aged 65 to 90 years (n=798) were analyzed. Multivariable logistic regression was utilized to determine HBM factors associated with calcium supplement use. Results: About half (54%) of women reported taking calcium supplements. Positive correlates of calcium supplementation included: perceived osteoporosis susceptibility, perceived calcium benefits, natural health product use, residing in Toronto and general osteoporosis management factors (discussion with a physician or pharmacist, osteoporosis screening, falls history and preventive health check-ups); a negative correlate included: use of etidronate therapy. Conclusion: Only half of older women were taking calcium supplements. Discussions with healthcare practitioners may help to improve recommended calcium intake levels.

Keywords: calcium
health belief model
Advisor: Cadarette, Suzanne M.
Evaluation of Pharmacotherapy for Common Medical Conditions in Pregnancy

Purpose Two new scales, CORECTS and PUQE-24 are introduced and validated, and the safety and effectiveness of Proctofoam-HC® in pregnancy is demonstrated. Method 315 of Motherisk NVP patients provided information on five clinical parameters as well as PUQE scores. 28 patients visiting a proctologist were graded for the severity of anal conditions by a proctologist before administering CORECTS. Pre and postnatal interviews were conducted with 204 pregnant women prescribed Proctofoam-HC®. Results Strong correlations were found between the following: PUQE-24 scores and parameters of well-being, hospitalization, and multivitamin intake; bleeding and pain components of CORECTS and the proctologist’s grade.There was no significant difference between mean birth weight of Proctofoam-HC® treated and comparison groups. There was a significant reduction in all symptoms of hemorrhoids. Conclusion PUQE-24 and CORECTS are the first validated scales used to assess the severity of NVP and hemorrhoids. Proctofoam-HC® is safe and effective for use in pregnancy.

Keywords: Pharmaceutical Sciences
Clinical Pharmacology
Pregnancy
Exposures
Advisor: Koren, Gideon
COI Barcoding of the Shorebirds: Rates of Evolution and the Identification of Species

This study assembles COI barcodes from 1814 specimens from the shorebird order, Charadriiformes and examines variation relative to time, rate of evolution and taxonomic level. In the suborder Scolopaci, 95% of sampled species were identified correctly. COI barcode variation within monotypic species was low (0-1% maximum distance) but showed a wide range within polytypic species (0-5%). Preliminary Charadrii results suggest similar trends but success is reduced in the third suborder, Lari. Rates of COI evolution are found to be lowest in the Lari and this leads to reduced species identification in recently radiated families: just 49% of the Laridae and 57% of the Stercoraridae are identified but 100% of the older Alcidae. In the faster Scolopaci, subspecies are at the limit of resolution with some well differentiated subspecies not distinguished by barcodes. The interplay of evolutionary rates, divergence dates and gene flow appears to determine COI barcode differentiation between taxa.

Keywords: DNA barcoding
Charadriiformes
substitution rate
mitochondrial DNA
shorebirds
white-headed gulls
Lari
Scolopaci
subspecies
COI
Advisor: Baker, Allan J.
Comparison of Schwann Cells Derived From Peripheral Nerve With Schwann Cells Differentiated From Skin-derived Precursors

Schwann cells are the glial cells of the peripheral nervous system. When transplanted into the injured central or peripheral nervous systems they promote repair. Traditionally Schwann cells have been isolated from the sciatic nerve, creating nerve-SC. An alternative Schwann cell source is from the differentiation of skin-derived precursors (SKPs), stem cells found in the skin, to Schwann cells (SKP-SC). SKP-SC have shown enhanced regenerative ability compared to nerve-SC. This study compares nerve-SC with SKP-SC at the functional and gene expression level to determine their degree of similarity and find their sources of variance. The functional ability of both Schwann cell types appeared similar. Their gene expression, as assessed by microarray, was similar but not identical. Genes that differed between nerve-SC and SKP-SC may represent differences important to regeneration. The similarity of SKP-SC to nerve-SC supports the use of SKP-SC for repair, and reasons for enhanced regeneration by SKP-SC are suggested.

Keywords: Skin-derived precursors
Schwann cells
skin
stem cells
Advisor: Miller, Freda
Dynamic Gd-DTPA Enhanced MRI as a Surrogate Marker of Angiogenesis in Tissue-engineered Rabbit Calvarial Constructs: A Pilot Study

Tissue engineering is limited by inability to create early and adequate blood supply. In-vivo DCE-MRI has imaged angiogenesis in soft tissues, yet has not been considered in hard tissues. Bilateral critical defects created in parietal bones of eighteen adult rabbits were left void, treated with haluronic acid acellular matrix (HA-ACM), or HA-ACM impregnated with vascular endothelial growth factor (VegF). DCE- MRI was acquired at weeks 1,2,3,6, and 12. Histologic analysis of HA-ACM treated defects demonstrated quantitatively greater immature bone formation, increased quantity and larger blood vessels compared to void. Statistically significant greater angiogenesis evidenced by quantitative perfusion on MRI supported histologic findings. DCE MRI is a novel means of imaging angiogenesis in grafted bone defects. DCE-MRI discerns physiologically important phases of angiogenesis: Initial vasoactive response, vessel network initiation, establishment, and pruning. DCE-MRI is adaptable to non-invasive study of candidate tissue engineered constructs and in evaluating scaffolds and treatments on angiogenesis.

Keywords: Angiogenesis
Tissue engineering
Bone regeneration
Calvarial
Rabbit
MRI
Dynamic MRI
Advisor: Cheng, Hai-Ling M.
Social Defeat Stress Causes a Switch in the Neural Systems Mediating Benzodiazepine Motivation

Benzodiazepines are widely abused by anxious individuals. Consequently, this thesis modeled anxiety in a mouse model in order to investigate benzodiazepine motivation within this sub-population. Using the Tube test of Social Dominance and the Resident/Intruder Paradigm I investigated whether animals identified as dominant or submissive/defeated would differentially display a preference for 0.25 mg/kg midazolam in a conditioned place preference paradigm. Consistent with my hypotheses, benzodiazepine preference was mediated by negative reinforcement as submissive but not dominant mice displayed a preference for midazolam. Furthermore, different neural systems mediated benzodiazepine preference dependent on the stress status of the animal (acute vs. chronic stress) such that, acutely stressed animals experienced benzodiazepine preference through a dopamine-independent pathway whereas chronically stressed animals experienced benzodiazepine preference through a dopamine-dependent pathway. Within chronically stressed mice, blockade of either D1 or D2 receptors attenuated benzodiazepine preference.

Keywords: Benzodiazepine Motivation
Social Defeat Stress
Conditioned Place preference
Tube Test of Social Dominance
Resident/Intruder Paragidm
Advisor: Kooy, Derek van der
A Learning-based Semi-autonomous Control Architecture for Robotic Exploration in Search and Rescue Environments

Semi-autonomous control schemes can address the limitations of both teleoperation and fully autonomous robotic control of rescue robots in disaster environments by allowing cooperation and task sharing between a human operator and a robot with respect to tasks such as navigation, exploration and victim identification. Herein, a unique hierarchical reinforcement learning (HRL) -based semi-autonomous control architecture is presented for rescue robots operating in unknown and cluttered urban search and rescue (USAR) environments. The aim of the controller is to allow a rescue robot to continuously learn from its own experiences in an environment in order to improve its overall performance in exploration of unknown disaster scenes. A new direction-based exploration technique and a rubble pile categorization technique are integrated into the control architecture for exploration of unknown rubble filled environments. Both simulations and physical experiments in USAR-like environments verify the robustness of the proposed control architecture.

Keywords: rescue robot
urban search and rescue
hierarchical reinforcement learning
semi-autonomous control
robot exploration
control architecture
Advisor: Nejat, Goldie
A Cost Analysis of Peripherally Inserted Central Catheter in Paediatrics

Introduction: Peripherally Inserted Central Catheters (PICCs) are commonly used in medium or long-term infusion therapy. This study aims to assess the costs associated with PICCs and its determinants. Methods: A retrospective cohort of patients with PICCs inserted at the Hospital for Sick Children between Jan.1, 2008 and Dec.31, 2008, were reviewed and followed until their PICCs were removed. Cost analysis, theoretical cost comparison with peripheral intravenous therapy (PIV), and multiple linear regressions were applied from the societal perspective. Findings: The average total cost is $2763.75/catheter/day, including inpatient ward cost. Age, male, ward, home care, catheter dwell days, and complications were found to be significant factors influencing the total cost. PICCs can become a cost saving device, compared to PIV, but is affected by several factors. Conclusion: Information gleaned from this study will inform decision makers maximizing the benefits of better resource allocation.

Keywords: cost analysis
PICC
Pediatrics
Advisor: Coyte, Peter C.
Constitutional Deradicalization of the Wagner Act Model:The Impact of B.C. Health Services and Fraser

For many years, workers petitioned the Supreme Court of Canada to intervene in labour relations to protect their collective bargaining rights. Finally, the Court answered the call, but the drastic changes made were not what workers expected. This thesis outlines the effect that the Court’s decision to intervene in labour relations had on the existing collective bargaining model. In making this determination, a historical analysis was done of the Court’s attitude towards using section 2(d) Freedom to Associate to protect collective bargaining, followed by a comparative analysis with United States jurisprudence to explain the effect of the Canadian decisions on the statutory provisions. The analysis revealed that the decisions had significantly weakened protections for workers’ rights, and provided the basis to conclude that the Supreme Court of Canada had used the Canadian Charter of Rights and Freedoms to deradicalize the existing collective bargaining model.

Keywords: Charter Section 2 (d) Freedom of Association
Collective Bargaining Rights
Labour Relations
Wagner Act Model
Supreme Court of Canada and Labour Law
Advisor: Langille, Brian A.
Product Tying Involving Intellectual Property: Pro or Anti-innovation Effects

This paper analyses the effects of tying arrangements involving IP rights on innovation. Tying, with its ability to temporarily exclude others from the potential benefits deriving from innovation, is pro-innovative by providing firms the incentive to allocate resources to realize newer and better products. However, when tying is used with or in place of IP rights to only help protect entry or growth into a market, it could discourage innovation. Market dominance, especially coupled with technological tying can create a barrier towards competition. It is shown that most pro-competitive effects of tying can also be seen as pro-innovatory as intense competition in the marketplace is shown to lead to innovation. In more competitive markets firms are pushed to innovate in order to maintain or improve their positioning for their products. The courts are faced with a difficult balancing judgment regarding product tying involving IP.

Keywords: product tying
intellectual property
competition law
innovation law
Advisor: Katz, Ariel
The Effects of Folic Acid Supplementation on Mammary Tumor Progression in the DMBA-carcinogen Animal Model

Folate intake in North America has drastically increased over the past decade due to folic acid fortification and widespread supplemental use. The role of folate in breast cancer is highly controversial and the effects of folic acid supplementation on breast cancer patients are currently unknown. An animal study was performed to determine the effects of folic acid supplementation on the progression of the mammary tumors in the DMBA-carcinogen model. Folic acid supplementation was associated with more rapid sentinel tumor progression and with higher sentinel tumor weight, volume, and area, although no clear dose-responsive relationship was observed. Folic acid supplementation was associated with an increased expression of proapoptotic protein PARP and decreased expression of proliferation protein PCNA. These data suggest that folic acid supplementation may promote the progression of established mammary tumors. Whether or not folic acid supplementation may adversely affect the outcome of patients with breast cancer warrants further studies.

Keywords: Breast Cancer
Folic Acid Supplementation
Advisor: Kim, Young-In
An Examination of the Free Hormone Hypothesis through Phylogenetic Comparison of Glucocorticoid and Corticosteroid-binding Globulin Levels Among the Vertebrates

The “Free Hormone Hypothesis” posits that only free, unbound hormone is biologically active and available to tissues. Conventional biomedical wisdom proposes that corticosteroid-binding globulin (CBG) normally binds 90-95% of blood glucocorticoid (GC), rendering it unavailable to tissues. Under chronic stress, GC levels greatly exceed binding capacity resulting in impaired bodily function and reduced fitness. However, under normal conditions in northern and southern flying squirrels, less than 10% of GC is bound, presenting a major challenge to the hypothesis. To assess the extent of variation in these properties among vertebrates, I compared all species (88) with known GC and CBG and levels. 92% conform reasonably to known convention. Flying squirrels appear as extreme species, as do New World monkeys, yet both groups evolved from ancestors that followed normal convention. I speculate as to how this state evolved and persisted through time.

Keywords: Glaucomys
evolution
HPA axis
stress physiology
field endocrinology
natural populations
receptors
Advisor: Boonstra, Rudy
Building a Better (Critical Democratic) Speech Culture: Feminist Blogs and Freedom of Speech

This thesis uses our lived experience of speech online to analyse the most common justification for freedom of speech: the "marketplace of ideas" metaphor. It opens with an account of a conversation in the feminist blogosphere that explicitly addressed the operation of social power in discussion. The lessons of that conversation is compared to accounts of the marketplace of ideas metaphor offered by theorists like Sunstein, Fiss, and Boyd White, as well as more internet-oriented theorists like Lessig, Benkler and Balkin. From that, and building on the insights of critics like Fraser and Mansbridge, the thesis argues that we ought to reject the "liberal-economic" paradigm of the function of speech and deliberation in a democracy, and proposes that we replace the "marketplace of ideas" metaphor with that of a "critical democratic culture." The thesis concludes by illustrating the usefulness of that new metaphor through the example of hate speech.

Keywords: internet
feminism
blogs
freedom of expression
deliberative theory
online discussion
Advisor: Nedelsky, Jennifer
Needs Assessment, Knowledge Translation and Barriers to Implementing EEG Monitoring Technology in Critical Care

Background: The neurological examination in critically ill patients is limited due to decreased level of consciousness and sedating medications. Electroencephalography (EEG) can be used to monitor brain injury; however, availability is limited. Methods: To determine the perceived need for EEG monitoring in the ICU and its current availability, we used rigorous methodology to develop and disseminate a survey to 199 Canadian critical care physicians. Results: Of 103 (52%) respondents (77% academic practice; 83% adult focus), 75% stated EEG monitoring should be a standard of care; yet, 75.5% were unable to obtain an EEG in an optimal timeframe. Technology under-use was exacerbated during non-standard working hours and greater in adult institutions. Perceived barriers to optimal care were lack of EEG technicians, physicians to interpret EEG and finances. Conclusion: Sub-optimal availability of EEG represents an important gap in the care of neurologically injured patients. Specific barriers represent targets for quality improvement.

Keywords: EEG
Critical Care
Knowledge Translation
Survey
Advisor: Fowler, Robert
The Impacts of Green Spaces on Temperature Variability

Parks located in urban areas are known to mitigate the Urban Heat Island. Their cooling effects are well established in the literature as studies have been performed in urbanized areas around the world. This particular study was aimed at assessing the nature of suburban parklands in the City of Toronto vs. urban (downtown) and rural (outside the Greater Toronto Area) settings. To do this, five study sites were chosen; three parks of varying sizes (large, medium and small) and two backyards. The main research objective was to quantify the cooling effects; among the sizes, within the surrounding neighbourhood and through the day. The metrics used in this study included Day to Day Temperature Variability, Diurnal Temperature Range, and Temperature Variation through Time. The results showed the importance of trees in providing shade and the lake breeze from Lake Ontario. A clear suburban signal from the metrics was found.

Keywords: Urban Heat Island
Parks
Advisor: Bill, Gough